library MatchmolDLL; (* checkmol/matchmol Norbert Haider, University of Vienna, 2003, 2004 norbert.haider@univie.ac.at Win32-DLL porting by: Alessandro Barozza PROCOS S.p.A www.procos.it - barozza@procos.it WHY? I needed substructure matching capability. I needed a dll for using with visual basic or VBA (MS-Access). I needed to pass the mol file as string (from a memo field in a database and not as a molfile on the disk) so... I've modified the original matchmol 1) line 1: subst. "program" with "library" 2) rem main routine 3) add "init_globals_DLL": this because the dll won't be unloaded between matches and memory for molecule must be instance only 1 time. This function is a modification of init_globals original function 4) add "yet_initialized" variable as boolean in global var section 4a) add "uses windows" 5) add "beep" procedure at the beginning because beep function in windows is different from standard pascal 6) add "mm_Init_mol" procedure 7) add "mm_Elab_mol" procedure 8) add "mm_SetCurrentMolAsQuery" procedure 9) add "mm_ReadInputLine" procedure 10) add "mm_SetMol" procedure 11) add "mm_getrings" 12) add "mm_getAtomRing" 12a)add "mm_Version" 13) subst all "writeln" with "mod_wrt_ln" because write and writeln function, in win32, cause a gpf error 14) subst "write" with "mod_wrt_noln" (see 13) 15) add at the beginning all overload functions for write substitution. Write & writeln now write on a string var (see 16) 16) add "gbl_str" in global var section 17) rem body of "mod_wrt_noln_mol" function (because of number format in write function not supported by overload functions. The original name of "mod_wrt_noln_mol" was "write_mol" but when "write" was substituded with mod. function also the name of functions containig "write" are modified 18) rem body of "mod_wrt_noln_needle_mol" function (see 17) 19) add export section (CASE SENSITIVE!!!) 20) substitute "bondtypes_OK" function with a modified version as suggested by prof. Haider in an e-mail to me. 21) modify version const from 0.2c to "W32DLL 0.2ca". COMPILE THE DLL!!! USE ALL OPTIMIZATION TO INCREASE SPEED!! Compile with fpc (Free Pascal, see http://www.freepascal.org) fpc MatchMolDLL.pas -S2 -Xs -OG -Or -O2u -Op1 -TWin32 In the original checkmol.pas package is suggested to use -Sd parameter but it is not compatible with overloading of functions. Use -S2 parameter. For molecule depicting I use pure-visualbasic code. I only use the checkmol capability for ring identification to find out and visualize double bonds in rings. (see the function mm_getatomring) The visual basic (or vba) declarations for functions in dll are: -------------------------------------------------------------------------------- Private Declare Sub mm_SetMol Lib "matchmolDLL.dll" (ByVal st As String) Private Declare Sub mm_SetCurrentMolAsQuery Lib "matchmolDLL.dll" () Private Declare Function mm_Match Lib "matchmolDLL.dll" (ByVal Exact As Boolean) As Long Private Declare Function mm_GetRings Lib "matchmolDLL.dll" () As Long Private Declare Function mm_GetAtomRing Lib "matchmolDLL.dll" (ByVal AtomNumber As Long) As Long Private Declare Sub mm_Version Lib "matchmolDLL.dll" (ByVal st As String) -------------------------------------------------------------------------------- The use is very simple: -------------------------------------------------------------------------------- Public Function MatchMol(Needle As String, Haystack As String, Optional ExactMatch As Boolean = False) As Boolean Static oldNeedle As String If oldNeedle <> Needle Then oldNeedle = Needle mm_SetMol Needle mm_SetCurrentMolAsQuery End If mm_SetMol Haystack If mm_Match(ExactMatch) <> 0 Then MatchMol = True End Function -------------------------------------------------------------------------------- The needle is not erased after matching so you can perform several matches without change the needle. When it changes it will be automaticly update in matchmol DLL. You can use this function also in a SQL query in MS-ACCESS. The DLL code is very stable and fast (on my pentium4 1400MHZ about 350 structures/sec were matched). -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- ORIGINAL CHECKMOL HEADER: This software is published under the terms of the GNU General Public License (GPL, see below). For a detailed description of this license, see http://www.gnu.org/copyleft/gpl.html If invoked as "checkmol", this program reads 2D and 3D molecular structure files in various formats (Tripos Alchemy "mol", Tripos SYBYL "mol2", MDL "mol") and describes the molecule either by its functional groups or by a set of descriptors useful for database pre-screening (number of rings, sp2-hybridized carbons, aromatic bonds, etc.). If invoked as "matchmol", the program reads two individual 2D or 3D molecular structure files in various formats (see above) and checks if the first molecule (the "needle") is a substructure of the second one (the "haystack"). "Haystack" can also be a MDL SD-file (containing multiple MOL files); if invoked with "-" as file argument, both "needle" and "haystack" are read as an SD-file from standard input, assuming the first entry in the SDF to be the "needle"; output: entry number + ":F" (false) or ":T" (true) Compile with fpc (Free Pascal, see http://www.freepascal.org), using the -Sd option (Delphi mode; IMPORTANT!) example for compilation and installation: fpc -Sd checkmol.pas as "root", do the following: cp checkmol /usr/local/bin cd /usr/local/bin ln checkmol matchmol Version history v0.1 extends "chkmol" utility (N. Haider, 2002), adds matching functionality; v0.1a minor bugfixes: stop ring search when max_rings is reached (function is_ringpath); fixed upper/lowercase of element symbol in MDL molfile output; added debug output for checkmol (-D option) v0.2 added functionality to switch ring search from SAR (set of all rings) to SSR (set of small rings; see below) if number of rings exceeds max_rings (1024), e.g. with Buckminster-fullerenes (thanks to E.-G. Schmid for a hint); added -r command-line option to force ring search into SSR mode; as SSR, we regard the set of all rings with max. 10 ring members, and in which no ring is completely contained in another one v0.2a fixed a bug in function is_ringpath which could cause SAR ring search to overlook a few rings (e.g., the six 8-membered rings in cubane) v0.2b fixed unequal treatment of needle and haystack structures with respect to aromaticity check (trusting input file vs. full check) v0.2c modified the changes of v0.2b so that they affect only "matchmol" mode; added quick_match function Credits: Rami Jbara (rami_jbara@hotmail.com) designed the 8-character functional group codes =============================================================================== DISCLAIMER This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, mod_wrt_noln to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. =============================================================================== *) uses SYSUTILS, WINDOWS; const version = 'W32DLL 0.2ca'; max_atoms = 1024; max_bonds = 1024; max_ringsize = 128; max_rings = 1024; max_fg = 256; TAB = #26; max_matchpath_length = 256; pmCheckMol = 1001; pmMatchMol = 1002; rs_sar = 2001; // ring search mode: SAR = set of all rings rs_ssr = 2002; // SSR = set of small rings // Definitions for functional groups: fg_cation = 001; fg_anion = 002; fg_carbonyl = 003; fg_aldehyde = 004; fg_ketone = 005; fg_thiocarbonyl = 006; fg_thioaldehyde = 007; fg_thioketone = 008; fg_imine = 009; fg_hydrazone = 010; fg_semicarbazone = 011; fg_thiosemicarbazone = 012; fg_oxime = 013; fg_oxime_ether = 014; fg_ketene = 015; fg_ketene_acetal_deriv = 016; fg_carbonyl_hydrate = 017; fg_hemiacetal = 018; fg_acetal = 019; fg_hemiaminal = 020; fg_aminal = 021; fg_thiohemiaminal = 022; fg_thioacetal = 023; fg_enamine = 024; fg_enol = 025; fg_enolether = 026; fg_hydroxy = 027; fg_alcohol = 028; fg_prim_alcohol = 029; fg_sec_alcohol = 030; fg_tert_alcohol = 031; fg_1_2_diol = 032; fg_1_2_aminoalcohol = 033; fg_phenol = 034; fg_1_2_diphenol = 035; fg_enediol = 036; fg_ether = 037; fg_dialkylether = 038; fg_alkylarylether = 039; fg_diarylether = 040; fg_thioether = 041; fg_disulfide = 042; fg_peroxide = 043; fg_hydroperoxide = 044; fg_hydrazine = 045; fg_hydroxylamine = 046; fg_amine = 047; fg_prim_amine = 048; fg_prim_aliph_amine = 049; fg_prim_arom_amine = 050; fg_sec_amine = 051; fg_sec_aliph_amine = 052; fg_sec_mixed_amine = 053; fg_sec_arom_amine = 054; fg_tert_amine = 055; fg_tert_aliph_amine = 056; fg_tert_mixed_amine = 057; fg_tert_arom_amine = 058; fg_quart_ammonium = 059; fg_n_oxide = 060; fg_halogen_deriv = 061; fg_alkyl_halide = 062; fg_alkyl_fluoride = 063; fg_alkyl_chloride = 064; fg_alkyl_bromide = 065; fg_alkyl_iodide = 066; fg_aryl_halide = 067; fg_aryl_fluoride = 068; fg_aryl_chloride = 069; fg_aryl_bromide = 070; fg_aryl_iodide = 071; fg_organometallic = 072; fg_organolithium = 073; fg_organomagnesium = 074; fg_carboxylic_acid_deriv = 075; fg_carboxylic_acid = 076; fg_carboxylic_acid_salt = 077; fg_carboxylic_acid_ester = 078; fg_lactone = 079; fg_carboxylic_acid_amide = 080; fg_carboxylic_acid_prim_amide = 081; fg_carboxylic_acid_sec_amide = 082; fg_carboxylic_acid_tert_amide = 083; fg_lactam = 084; fg_carboxylic_acid_hydrazide = 085; fg_carboxylic_acid_azide = 086; fg_hydroxamic_acid = 087; fg_carboxylic_acid_amidine = 088; fg_carboxylic_acid_amidrazone = 089; fg_nitrile = 090; fg_acyl_halide = 091; fg_acyl_fluoride = 092; fg_acyl_chloride = 093; fg_acyl_bromide = 094; fg_acyl_iodide = 095; fg_acyl_cyanide = 096; fg_imido_ester = 097; fg_imidoyl_halide = 098; fg_thiocarboxylic_acid_deriv = 099; fg_thiocarboxylic_acid = 100; fg_thiocarboxylic_acid_ester = 101; fg_thiolactone = 102; fg_thiocarboxylic_acid_amide = 103; fg_thiolactam = 104; fg_imido_thioester = 105; fg_oxohetarene = 106; fg_thioxohetarene = 107; fg_iminohetarene = 108; fg_orthocarboxylic_acid_deriv = 109; fg_carboxylic_acid_orthoester = 110; fg_carboxylic_acid_amide_acetal = 111; fg_carboxylic_acid_anhydride = 112; fg_carboxylic_acid_imide = 113; fg_carboxylic_acid_unsubst_imide = 114; fg_carboxylic_acid_subst_imide = 115; fg_co2_deriv = 116; fg_carbonic_acid_deriv = 117; fg_carbonic_acid_monoester = 118; fg_carbonic_acid_diester = 119; fg_carbonic_acid_ester_halide = 120; fg_thiocarbonic_acid_deriv = 121; fg_thiocarbonic_acid_monoester = 122; fg_thiocarbonic_acid_diester = 123; fg_thiocarbonic_acid_ester_halide = 124; fg_carbamic_acid_deriv = 125; fg_carbamic_acid = 126; fg_carbamic_acid_ester = 127; fg_carbamic_acid_halide = 128; fg_thiocarbamic_acid_deriv = 129; fg_thiocarbamic_acid = 130; fg_thiocarbamic_acid_ester = 131; fg_thiocarbamic_acid_halide = 132; fg_urea = 133; fg_isourea = 134; fg_thiourea = 135; fg_isothiourea = 136; fg_guanidine = 137; fg_semicarbazide = 138; fg_thiosemicarbazide = 139; fg_azide = 140; fg_azo_compound = 141; fg_diazonium_salt = 142; fg_isonitrile = 143; fg_cyanate = 144; fg_isocyanate = 145; fg_thiocyanate = 146; fg_isothiocyanate = 147; fg_carbodiimide = 148; fg_nitroso_compound = 149; fg_nitro_compound = 150; fg_nitrite = 151; fg_nitrate = 152; fg_sulfuric_acid_deriv = 153; fg_sulfuric_acid = 154; fg_sulfuric_acid_monoester = 155; fg_sulfuric_acid_diester = 156; fg_sulfuric_acid_amide_ester = 157; fg_sulfuric_acid_amide = 158; fg_sulfuric_acid_diamide = 159; fg_sulfuryl_halide = 160; fg_sulfonic_acid_deriv = 161; fg_sulfonic_acid = 162; fg_sulfonic_acid_ester = 163; fg_sulfonamide = 164; fg_sulfonyl_halide = 165; fg_sulfone = 166; fg_sulfoxide = 167; fg_sulfinic_acid_deriv = 168; fg_sulfinic_acid = 169; fg_sulfinic_acid_ester = 170; fg_sulfinic_acid_halide = 171; fg_sulfinic_acid_amide = 172; fg_sulfenic_acid_deriv = 173; fg_sulfenic_acid = 174; fg_sulfenic_acid_ester = 175; fg_sulfenic_acid_halide = 176; fg_sulfenic_acid_amide = 177; fg_thiol = 178; fg_alkylthiol = 179; fg_arylthiol = 180; fg_phosphoric_acid_deriv = 181; fg_phosphoric_acid = 182; fg_phosphoric_acid_ester = 183; fg_phosphoric_acid_halide = 184; fg_phosphoric_acid_amide = 185; fg_thiophosphoric_acid_deriv = 186; fg_thiophosphoric_acid = 187; fg_thiophosphoric_acid_ester = 188; fg_thiophosphoric_acid_halide = 189; fg_thiophosphoric_acid_amide = 190; fg_phosphonic_acid_deriv = 191; fg_phosphonic_acid = 192; fg_phosphonic_acid_ester = 193; fg_phosphine = 194; fg_phosphinoxide = 195; fg_boronic_acid_deriv = 196; fg_boronic_acid = 197; fg_boronic_acid_ester = 198; fg_alkene = 199; fg_alkyne = 200; fg_aromatic = 201; fg_heterocycle = 202; fg_alpha_aminoacid = 203; fg_alpha_hydroxyacid = 204; type str2 = string[2]; str3 = string[3]; str4 = string[4]; str5 = string[5]; str8 = string[8]; atom_rec = record element : str2; atype : str3; x : single; y : single; z : single; formal_charge : integer; real_charge : single; Hexp : smallint; // explicit H count Htot : smallint; // total H count neighbor_count : integer; ring_count : integer; arom : boolean; end; bond_rec = record a1 : integer; a2 : integer; btype : char; ring_count : integer; arom : boolean; end; ringpath_type = array[1..max_ringsize] of integer; matchpath_type = array[1..max_matchpath_length] of integer; atomlist = array[1..max_atoms] of atom_rec; bondlist = array[1..max_bonds] of bond_rec; ringlist = array[1..max_rings] of ringpath_type; neighbor_rec = array[1..8] of integer; fglist = array[1..max_fg] of boolean; molbuftype = array[1..(max_atoms+max_bonds+8192)] of string; matchmatrix = array[1..4,1..4] of boolean; molstat_rec = record n_QA, n_QB, n_chg : integer; // number of query atoms, query bonds, charges n_C1, n_C2, n_C : integer; // number of sp, sp2 hybridized, and total no. of carbons n_CHB1p, n_CHB2p, n_CHB3p, n_CHB4 : integer; // number of C atoms with at least 1, 2, 3 hetero bonds n_O2, n_O3 : integer; // number of sp2 and sp3 oxygens n_N1, n_N2, n_N3 : integer; // number of sp, sp2, and sp3 nitrogens n_S, n_SeTe : integer; // number of sulfur atoms and selenium or tellurium atoms n_F, n_Cl, n_Br, n_I : integer; // number of fluorine, chlorine, bromine, iodine atoms n_P, n_B : integer; // number of phosphorus and boron atoms n_Met, n_X : integer; // number of metal and hetero atoms n_b1, n_b2, n_b3, n_bar : integer; // number single, double, triple, and aromatic bonds n_C1O, n_C2O, n_CN, n_XY : integer; // number of C-O single bonds, C=O double bonds, CN bonds (any type), hetero/hetero bonds n_r3, n_r4, n_r5, n_r6, n_r7, n_r8 : integer; // number of 3-, 4-, 5-, 6-, 7-, and 8-membered rings n_r9, n_r10, n_r11, n_r12, n_r13p : integer; // number of 9-, 10-, 11-, 12-, and 13plus-membered rings n_rN, n_rN1, n_rN2, n_rN3p : integer; // number of rings containing N (any number), 1 N, 2 N, and 3 N or more n_rO, n_rO1, n_rO2p : integer; // number of rings containing O (any number), 1 O, and 2 O or more n_rS, n_rX, n_rAr : integer; // number of rings containing S (any number), any heteroatom (any number), number of aromatic rings end; var yet_initialized:boolean; gbl_str: string; progmode : integer; progname : string; i : integer; // general purpose index li : longint; opt_none : boolean; opt_verbose : boolean; opt_text : boolean; opt_text_de : boolean; opt_code : boolean; opt_bin : boolean; opt_bitstring : boolean; opt_stdin : boolean; opt_exact : boolean; opt_debug : boolean; opt_molout : boolean; opt_molstat : boolean; opt_molstat_X : boolean; opt_xmdlout : boolean; filetype : string; molfile : text; molfilename : string; ndl_molfilename : string; molname : string; ndl_molname : string; molcomment : string; n_atoms : integer; n_bonds : integer; n_rings : integer; // the number of rings we determined ourselves n_cmrings : integer; // the number of rings we read from a (CheckMol-tweaked) MDL molfile n_charges : integer; // number of charges n_heavyatoms : integer; n_heavybonds : integer; ndl_n_atoms : integer; ndl_n_bonds : integer; ndl_n_rings : integer; ndl_n_heavyatoms : integer; ndl_n_heavybonds : integer; cm_mdlmolfile : boolean; found_arominfo : boolean; found_querymol : boolean; atom : ^atomlist; bond : ^bondlist; ring : ^ringlist; ndl_atom : ^atomlist; ndl_bond : ^bondlist; ndl_ring : ^ringlist; matchresult : boolean; ndl_matchpath : matchpath_type; hst_matchpath : matchpath_type; fg : fglist; atomtype : str4; newatomtype : str3; molbuf : ^molbuftype; molbufindex : integer; mol_in_queue : boolean; mol_count : longint; molstat : molstat_rec; ndl_molstat : molstat_rec; ringsearch_mode : integer; max_vringsize : integer; // for SSR ring search // auxiliary functions & procedures {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} Function mod_IntToStr (I : Longint) : String; Var S : String; begin Str (I,S); mod_IntToStr:=S; end; Function mod_SingleToStr (I : Single) : String; Var S : String; begin Str (I:9:4,S); mod_SingleToStr:=S; end; procedure Mod_wrt_noln(i:single); begin gbl_str := gbl_str + mod_singletostr(i); end; procedure Mod_wrt_ln(i:integer); begin gbl_str := gbl_str + inttostr(i); end; procedure Mod_wrt_noln(st: string); begin gbl_str := gbl_str + st; end; procedure Mod_wrt_ln(st: string); begin Mod_wrt_noln (st); Mod_wrt_noln (#13); end; //Mod_wrt_noln(i,' ',atom^[i].element,' ',atom^[i].atype,' ',atom^[i].x:9:4,' ',atom^[i].y:9:4,' '); procedure Mod_wrt_noln(i:integer;st:string;ste:string;st2:string; stb:string;st3:string;i4:single;st4:string; i5:single;st5:string); begin Mod_wrt_noln (i); Mod_wrt_noln (st); Mod_wrt_noln (ste); Mod_wrt_noln (st2); Mod_wrt_noln (stb); Mod_wrt_noln (st3); Mod_wrt_noln (i4); Mod_wrt_noln (st4); Mod_wrt_noln (i5); Mod_wrt_noln (st5); end; //Mod_wrt_noln(i,' ',bond^[i].a1,' ',bond^[i].a2,' ',bond^[i].btype); procedure Mod_wrt_noln(i:integer;st:string;i2:integer;st2:string;i3:integer;st3:string;st4:string); begin Mod_wrt_noln (i); Mod_wrt_noln (st); Mod_wrt_noln (i2); Mod_wrt_noln (st2); Mod_wrt_noln (i3); Mod_wrt_noln (st3); Mod_wrt_noln (st4); end; procedure Mod_wrt_noln(st:string;i:integer;st2:string); begin Mod_wrt_noln (st); Mod_wrt_noln (i); Mod_wrt_noln (st2); end; procedure Mod_wrt_ln(st:string;i:integer;st2:string); begin Mod_wrt_noln (st); Mod_wrt_noln (i); Mod_wrt_noln (st2); Mod_wrt_noln (#13); end; procedure Mod_wrt_noln(i:integer;st:string); begin Mod_wrt_noln (i); Mod_wrt_noln (st); Mod_wrt_noln (#13); end; procedure Mod_wrt_noln(st:string;st2:string); begin Mod_wrt_noln (st); Mod_wrt_noln (st2); end; procedure Mod_wrt_ln(st: string; i:integer); begin Mod_wrt_noln (st); Mod_wrt_noln (i); Mod_wrt_noln (#13); end; procedure Mod_wrt_noln(st: string; i:integer); begin Mod_wrt_noln (st); Mod_wrt_noln (i); end; procedure Mod_wrt_ln(st: string; st2:string); begin Mod_wrt_noln (st); Mod_wrt_noln (st2); Mod_wrt_noln (#13); end; procedure Mod_wrt_ln(st: string; i:integer;st2: string; i2:integer;st3: string; i3:integer); begin Mod_wrt_noln (st); Mod_wrt_noln (i); Mod_wrt_noln (st2); Mod_wrt_noln (i2); Mod_wrt_noln (st3); Mod_wrt_noln (i3); Mod_wrt_noln (#13); end; {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} {****************************************************************************} Procedure Beep(); begin //beep(800,100); end; procedure init_globals; var i : integer; begin opt_verbose := false; opt_debug := false; opt_exact := false; opt_stdin := false; opt_text := false; opt_code := false; opt_bin := false; opt_bitstring := false; opt_molout := false; opt_molstat := false; opt_molstat_X := false; opt_xmdlout := false; cm_mdlmolfile := false; found_arominfo := false; found_querymol := false; ringsearch_mode := rs_sar; for i := 1 to max_fg do fg[i] := false; try getmem(molbuf,sizeof(molbuftype)); except on e:Eoutofmemory do begin mod_wrt_ln('Not enough memory'); halt(4); end; end; end; procedure init_molstat(var mstat:molstat_rec); begin with mstat do begin n_QA := 0; n_QB := 0; n_chg := 0; n_C1 := 0; n_C2 := 0; n_C := 0; n_CHB1p := 0; n_CHB2p := 0; n_CHB3p := 0; n_CHB4 := 0; n_O2 := 0; n_O3 := 0; n_N1 := 0; n_N2 := 0; n_N3 := 0; n_S := 0; n_SeTe := 0; n_F := 0; n_Cl := 0; n_Br := 0; n_I := 0; n_P := 0; n_B := 0; n_Met := 0; n_X := 0; n_b1 := 0; n_b2 := 0; n_b3 := 0; n_bar := 0; n_C1O := 0; n_C2O := 0; n_CN := 0; n_XY := 0; n_r3 := 0; n_r4 := 0; n_r5 := 0; n_r6 := 0; n_r7 := 0; n_r8 := 0; n_r9 := 0; n_r10 := 0; n_r11 := 0; n_r12 := 0; n_r13p := 0; n_rN := 0; n_rN1 := 0; n_rN2 := 0; n_rN3p := 0; n_rO := 0; n_rO1 := 0; n_rO2p := 0; n_rS := 0; n_rX := 0; n_rAr := 0; end; end; procedure debugoutput(dstr:string); begin if opt_debug then mod_wrt_ln(dstr); end; procedure left_trim(var trimstr:string); begin while (length(trimstr)>0) and ((trimstr[1]=' ') or (trimstr[1]=TAB)) do delete(trimstr,1,1); end; function left_int(var trimstr:string):integer; var numstr : string; auxstr : string; auxint, code : integer; begin numstr := '-+0123456789'; auxstr := ''; auxint := 0; while (length(trimstr)>0) and ((trimstr[1]=' ') or (trimstr[1]=TAB)) do delete(trimstr,1,1); while (length(trimstr)>0) and (pos(trimstr[1],numstr)>0) do begin auxstr := auxstr + trimstr[1]; delete(trimstr,1,1); end; val(auxstr,auxint,code); left_int := auxint; end; procedure show_usage; begin if progmode = pmMatchMol then begin mod_wrt_ln('matchmol version ',version); mod_wrt_ln('Usage: matchmol [options] '); mod_wrt_ln(' where and are the two molecules to compare'); mod_wrt_ln(' (supported formats: MDL *.mol, Alchemy *.mol, Sybyl *.mol2)'); mod_wrt_ln(' options can be:'); mod_wrt_ln(' -v verbose output'); mod_wrt_ln(' -x exact match'); mod_wrt_ln(' -r force SSR (set of small rings) ring search mode'); mod_wrt_ln(' -m mod_wrt_noln matching molecule as MDL molfile to standard output'); mod_wrt_ln(' (default output: record number + ":T" for hit or ":F" for miss'); end else begin mod_wrt_ln('checkmol version ',version); mod_wrt_ln('Usage: checkmol [options] '); mod_wrt_ln(' where options can be:'); mod_wrt_ln(' -v verbose output'); mod_wrt_ln(' and one of the following:'); mod_wrt_ln(' -e english text (common name of functional group; default)'); mod_wrt_ln(' -d german text (common name of functional group)'); mod_wrt_ln(' -c code (acronym-like code for functional group)'); mod_wrt_ln(' -b binary (a bitstring representing absence or presence of each group)'); mod_wrt_ln(' -s (the ASCII representation of the above bitstring, i.e. 0s and 1s)'); mod_wrt_ln(' -x print molecular statistics (number of various atom types, bond types, ring sizes, etc.)'); mod_wrt_ln(' -X same as above, listing all records (even if zero) as comma-separated list'); mod_wrt_ln(' -m mod_wrt_noln MDL molfile (with special encoding for aromatic atoms/bonds)'); mod_wrt_ln(' -r force SSR (set of small rings) ring search mode'); mod_wrt_ln(' options can be combined like -vc'); mod_wrt_ln(' specifies any file in the formats supported'); mod_wrt_ln(' (MDL *.mol, Alchemy *.mol, Sybyl *.mol2), the filename "-" (without quotes)'); mod_wrt_ln(' specifies standard input'); end; end; procedure parse_args; var p : integer; parstr : string; tmpstr : string; //is_option : boolean; l : integer; begin tmpstr := ''; opt_none := true; if progmode = pmCheckMol then begin for p := 1 to paramcount do begin parstr := paramstr(p); if p < paramcount then begin if (pos('-',parstr)=1) and (p < (paramcount)) then begin //is_option := true; tmpstr := paramstr(p); left_trim(tmpstr); l := 0; if pos('v',tmpstr) > 0 then inc(l); if pos('D',tmpstr) > 0 then inc(l); if pos('r',tmpstr) > 0 then inc(l); if (length(tmpstr) > (2 + l)) then begin show_usage; halt(1); end; opt_none := false; if pos('v',tmpstr)>0 then opt_verbose := true; if pos('D',tmpstr)>0 then opt_debug := true; if pos('e',tmpstr)>0 then opt_text := true else begin if pos('d',tmpstr)>0 then opt_text_de := true else begin if pos('c',tmpstr)>0 then opt_code := true else begin if pos('b',tmpstr)>0 then opt_bin := true else if pos('s',tmpstr)>0 then opt_bitstring := true; end; end; if pos('x',tmpstr)>0 then opt_molstat := true; if pos('r',tmpstr)>0 then ringsearch_mode := rs_ssr; if pos('X',tmpstr)>0 then begin opt_molstat := true; opt_molstat_X := true; //mod_wrt_ln('===================================='); end; if pos('m',tmpstr)>0 then begin opt_text := false; opt_text_de := false; opt_bin := false; opt_bitstring := false; opt_code := false; opt_molstat := false; opt_xmdlout := true; end; end; molfilename := tmpstr; end; end else begin if (pos('-',parstr)=1) then begin if length(parstr)>1 then begin show_usage; halt(1); end else begin opt_stdin := true; end; end else begin opt_stdin := false; molfilename := parstr; end; end; end; if (opt_text = false) and (opt_text_de = false) and (opt_code = false) and (opt_bin = false) and (opt_bitstring = false) and (opt_molstat = false) and (opt_molstat_X = false) and (opt_xmdlout = false) then opt_none := true; end; if progmode = pmMatchMol then begin ndl_molfilename := ''; molfilename := ''; for p := 1 to paramcount do begin parstr := paramstr(p); if p = 1 then begin if (pos('-',parstr)=1) then begin if pos('v',parstr)>1 then opt_verbose := true; if pos('D',parstr)>1 then opt_debug := true; if pos('x',parstr)>1 then opt_exact := true; if pos('m',parstr)>1 then opt_molout := true; if pos('r',parstr)>1 then ringsearch_mode := rs_ssr; if pos('h',parstr)>1 then begin show_usage; halt(0); end; end else ndl_molfilename := parstr; end; if p = (paramcount - 1) then begin if (pos('-',parstr)=0) then ndl_molfilename := parstr; end; if p = paramcount then begin if parstr <> '-' then molfilename := parstr else opt_stdin := true; end; end; end; // progmode = pmMatchMol end; // input-related functions & procedures function get_filetype(f:string):string; var rline : string; auxstr : string; i : integer; mdl1 : boolean; ri : integer; sepcount : integer; begin auxstr := 'unknown'; i := li; mdl1 := false; ri := li -1; sepcount := 0; while (ri < molbufindex) and (sepcount < 1) do begin inc(ri); rline := molbuf^[ri]; if (pos('$$$$',rline)>0) then inc(sepcount); if (i = li) and (copy(rline,7,5)='ATOMS') and (copy(rline,20,5)='BONDS') and (copy(rline,33,7)='CHARGES') then begin auxstr := 'alchemy'; end; if (i = li+3) // and (copy(rline,31,3)='999') and (copy(rline,35,5)='V2000') then mdl1 := true; if (i = li+1) and (copy(rline,3,6)='-ISIS-') then mdl1 := true; if (i = li+1) and (copy(rline,3,8)='WLViewer') then mdl1 := true; if (i = li+1) and (copy(rline,3,8)='CheckMol') then mdl1 := true; if (i = li+1) and (copy(rline,3,8)='CATALYST') then begin mdl1 := true; auxstr := 'mdl'; end; if (pos('M END',rline)=1) or mdl1 then begin //mod_wrt_ln('MDL format'); auxstr := 'mdl'; end; if pos('@MOLECULE',rline)>0 then begin auxstr := 'sybyl'; end; inc(i); end; get_filetype := auxstr; end; procedure zap_molecule; begin try if atom <> nil then freemem(atom,n_atoms*sizeof(atom_rec)); if bond <> nil then freemem(bond,n_bonds*sizeof(bond_rec)); if ring <> nil then freemem(ring,sizeof(ringlist)); except on e:Einvalidpointer do begin end; end; n_atoms := 0; n_bonds := 0; n_rings := 0; end; procedure zap_needle; begin try if ndl_atom <> nil then freemem(ndl_atom,ndl_n_atoms*sizeof(atom_rec)); if ndl_bond <> nil then freemem(ndl_bond,ndl_n_bonds*sizeof(bond_rec)); if ndl_ring <> nil then freemem(ndl_ring,sizeof(ringlist)); except on e:Einvalidpointer do begin end; end; ndl_n_atoms := 0; ndl_n_bonds := 0; ndl_n_rings := 0; end; function is_heavyatom(id:integer):boolean; var r : boolean; el : str2; begin r := true; el := atom^[id].element; if (el = 'H ') or (el = 'DU') or (el = 'LP') then r := false; is_heavyatom := r; end; function is_ndl_heavyatom(id:integer):boolean; var r : boolean; el : str2; begin r := true; el := ndl_atom^[id].element; if (el = 'H ') or (el = 'DU') or (el = 'LP') then r := false; is_ndl_heavyatom := r; end; function is_metal(id:integer):boolean; var r : boolean; el : str2; begin r := false; el := atom^[id].element; if (el = 'NA') or (el = 'K ') or (el = 'LI') or (el = 'MG') or (el = 'ZN') or (el = 'SN') or (el = 'PD') or (el = 'FE') or (el = 'AL') or (el = 'CU') or (el = 'CO') or (el = 'CR') or (el = 'HG') // etc. etc. then r := true; is_metal := r; end; function convert_type(oldtype : str4):str3; var i : integer; newtype : str3; begin newtype := copy(oldtype,1,3); for i := 1 to 3 do newtype[i] := upcase(newtype[i]); if newtype[1] = '~' then newtype := 'VAL'; If newtype[1] = '*' then newtype := 'STR'; convert_type := newtype; end; function convert_sybtype(oldtype : str5):str3; var newtype : str3; begin // NewType := Copy(OldType,1,3); // For i := 1 To 3 Do NewType[i] := UpCase(NewType[i]); // If NewType[1] = '~' Then NewType := 'VAL'; // If NewType[1] = '*' Then NewType := 'STR'; newtype := 'DU '; if oldtype = 'H ' then newtype := 'H '; if oldtype = 'C.ar ' then newtype := 'CAR'; if oldtype = 'C.2 ' then newtype := 'C2 '; if oldtype = 'C.3 ' then newtype := 'C3 '; if oldtype = 'C.1 ' then newtype := 'C1 '; if oldtype = 'O.2 ' then newtype := 'O2 '; if oldtype = 'O.3 ' then newtype := 'O3 '; if oldtype = 'O.co2' then newtype := 'O2 '; if oldtype = 'O.spc' then newtype := 'O3 '; if oldtype = 'O.t3p' then newtype := 'O3 '; if oldtype = 'N.1 ' then newtype := 'N1 '; if oldtype = 'N.2 ' then newtype := 'N2 '; if oldtype = 'N.3 ' then newtype := 'N3 '; if oldtype = 'N.pl3' then newtype := 'NPL'; if oldtype = 'N.4 ' then newtype := 'N3+'; if oldtype = 'N.am ' then newtype := 'NAM'; if oldtype = 'N.ar ' then newtype := 'NAR'; if oldtype = 'F ' then newtype := 'F '; if oldtype = 'Cl ' then newtype := 'CL '; if oldtype = 'Br ' then newtype := 'BR '; if oldtype = 'I ' then newtype := 'I '; if oldtype = 'Al ' then newtype := 'AL '; if oldtype = 'ANY ' then newtype := 'A '; if oldtype = 'Ca ' then newtype := 'CA '; if oldtype = 'Du ' then newtype := 'DU '; if oldtype = 'Du.C ' then newtype := 'DU '; if oldtype = 'H.spc' then newtype := 'H '; if oldtype = 'H.t3p' then newtype := 'H '; if oldtype = 'HAL ' then newtype := 'Cl '; if oldtype = 'HET ' then newtype := 'Q '; if oldtype = 'HEV ' then newtype := 'DU '; if oldtype = 'K ' then newtype := 'K '; if oldtype = 'Li ' then newtype := 'LI '; if oldtype = 'LP ' then newtype := 'LP '; if oldtype = 'Na ' then newtype := 'NA '; if oldtype = 'P.3 ' then newtype := 'P3 '; if oldtype = 'S.2 ' then newtype := 'S2 '; if oldtype = 'S.3 ' then newtype := 'S3 '; if oldtype = 'S.o ' then newtype := 'SO '; if oldtype = 'S.o2 ' then newtype := 'SO2'; if oldtype = 'Si ' then newtype := 'SI '; if oldtype = 'P.4 ' then newtype := 'P4 '; convert_sybtype := newtype; end; function convert_MDLtype(oldtype : str3):str3; var newtype : str3; begin // NewType := Copy(OldType,1,3); // For i := 1 To 3 Do NewType[i] := UpCase(NewType[i]); // If NewType[1] = '~' Then NewType := 'VAL'; // If NewType[1] = '*' Then NewType := 'STR'; newtype := 'DU '; if oldtype = 'H ' then newtype := 'H '; if oldtype = 'C ' then newtype := 'C3 '; if oldtype = 'O ' then newtype := 'O2 '; if oldtype = 'N ' then newtype := 'N3 '; if oldtype = 'F ' then newtype := 'F '; if oldtype = 'Cl ' then newtype := 'CL '; if oldtype = 'Br ' then newtype := 'BR '; if oldtype = 'I ' then newtype := 'I '; if oldtype = 'Al ' then newtype := 'AL '; if oldtype = 'ANY' then newtype := 'A '; if oldtype = 'Ca ' then newtype := 'CA '; if oldtype = 'Du ' then newtype := 'DU '; if oldtype = 'K ' then newtype := 'K '; if oldtype = 'Li ' then newtype := 'LI '; if oldtype = 'LP ' then newtype := 'LP '; if oldtype = 'Na ' then newtype := 'NA '; if oldtype = 'P ' then newtype := 'P3 '; if oldtype = 'S ' then newtype := 'S3 '; if oldtype = 'Si ' then newtype := 'SI '; if oldtype = 'P ' then newtype := 'P4 '; if oldtype = 'A ' then newtype := 'A '; if oldtype = 'Q ' then newtype := 'Q '; convert_MDLtype := NewType; end; function get_element(oldtype:str4):str2; var elemstr : string; begin if oldtype = 'H ' then elemstr := 'H '; if oldtype = 'CAR ' then elemstr := 'C '; if oldtype = 'C2 ' then elemstr := 'C '; if oldtype = 'C3 ' then elemstr := 'C '; if oldtype = 'C1 ' then elemstr := 'C '; if oldtype = 'O2 ' then elemstr := 'O '; if oldtype = 'O3 ' then elemstr := 'O '; if oldtype = 'O2 ' then elemstr := 'O '; if oldtype = 'O3 ' then elemstr := 'O '; if oldtype = 'O3 ' then elemstr := 'O '; if oldtype = 'N1 ' then elemstr := 'N '; if oldtype = 'N2 ' then elemstr := 'N '; if oldtype = 'N3 ' then elemstr := 'N '; if oldtype = 'NPL ' then elemstr := 'N '; if oldtype = 'N3+ ' then elemstr := 'N '; if oldtype = 'NAM ' then elemstr := 'N '; if oldtype = 'NAR ' then elemstr := 'N '; if oldtype = 'F ' then elemstr := 'F '; if oldtype = 'CL ' then elemstr := 'CL'; if oldtype = 'BR ' then elemstr := 'BR'; if oldtype = 'I ' then elemstr := 'I '; if oldtype = 'AL ' then elemstr := 'AL'; if oldtype = 'DU ' then elemstr := 'DU'; if oldtype = 'CA ' then elemstr := 'CA'; if oldtype = 'DU ' then elemstr := 'DU'; if oldtype = 'Cl ' then elemstr := 'CL'; if oldtype = 'K ' then elemstr := 'K '; if oldtype = 'LI ' then elemstr := 'LI'; if oldtype = 'LP ' then elemstr := 'LP'; if oldtype = 'NA ' then elemstr := 'NA'; if oldtype = 'P3 ' then elemstr := 'P '; if oldtype = 'S2 ' then elemstr := 'S '; if oldtype = 'S3 ' then elemstr := 'S '; if oldtype = 'SO ' then elemstr := 'S '; if oldtype = 'SO2 ' then elemstr := 'S '; if oldtype = 'SI ' then elemstr := 'SI'; if oldtype = 'P4 ' then elemstr := 'P '; if oldtype = 'A ' then elemstr := 'A '; if oldtype = 'Q ' then elemstr := 'Q '; get_element := elemstr; end; function get_sybelement(oldtype:str5):str2; var i : integer; elemstr : str2; begin if pos('.',oldtype)<2 then begin elemstr := copy(oldtype,1,2); end else begin elemstr := copy(oldtype,1,pos('.',oldtype)-1); if length(elemstr)<2 then elemstr := elemstr+' '; end; for i := 1 to 2 do elemstr[i] := upcase(elemstr[i]); get_sybelement := elemstr; end; function get_MDLelement(oldtype:str3):str2; var i : integer; elemstr : str2; begin elemstr := copy(oldtype,1,2); for i := 1 to 2 do elemstr[i] := upcase(elemstr[i]); if elemstr[1] = '~' then elemstr := '??'; If elemstr[1] = '*' then elemstr := '??'; get_MDLelement := elemstr; end; procedure read_molfile(mfilename:string); // reads ALCHEMY mol files var n, code : integer; rline, tmpstr : string; xstr, ystr, zstr, chgstr : string; xval, yval, zval, chgval : single; a1str, a2str, elemstr : string; a1val, a2val : integer; ri : integer; begin if n_atoms > 0 then zap_molecule; ri := li; rline := molbuf^[ri]; tmpstr := copy(rline,1,5); val(tmpstr,n_atoms,code); tmpstr := copy(rline,14,5); val(tmpstr,n_bonds,code); molname := copy(rline,42,length(rline)-42); try getmem(atom,n_atoms*sizeof(atom_rec)); getmem(bond,n_bonds*sizeof(bond_rec)); getmem(ring,sizeof(ringlist)); except on e:Eoutofmemory do begin mod_wrt_ln('Not enough memory'); halt(4); end; end; n_heavyatoms := 0; n_heavybonds := 0; for n := 1 to n_atoms do begin with atom^[n] do begin formal_charge := 0; real_charge := 0; Hexp := 0; Htot := 0; neighbor_count := 0; ring_count := 0; arom := FALSE; end; inc(ri); rline := molbuf^[ri]; atomtype := copy(rline,7,4); elemstr := get_element(atomtype); newatomtype := convert_type(atomtype); xstr := copy(rline,14,7); ystr := copy(rline,23,7); zstr := copy(rline,32,7); chgstr := copy(rline,43,7); val(xstr,xval,code); val(ystr,yval,code); val(zstr,zval,code); val(chgstr,chgval,code); with atom^[n] do begin element := elemstr; atype := newatomtype; x := xval; y := yval; z := zval; real_charge := chgval; end; if is_heavyatom(n) then inc(n_heavyatoms); end; for n := 1 to n_bonds do begin inc(ri); rline := molbuf^[ri]; a1str := copy(rline,9,3); a2str := copy(rline,15,3); val(a1str,a1val,code); if code <> 0 then beep; val(a2str,a2val,code); if code <> 0 then beep; with bond^[n] do begin a1 := a1val; a2 := a2val; btype := rline[20]; ring_count := 0; arom := false; end; if is_heavyatom(a1val) and is_heavyatom(a2val) then inc(n_heavybonds); end; fillchar(ring^,sizeof(ringlist),0); li := ri + 1; end; procedure read_mol2file(mfilename:string); // reads SYBYL mol2 files var n, code : integer; sybatomtype : string[5]; tmpstr, rline : string; xstr, ystr, zstr, chgstr : string; xval, yval, zval, chgval : single; a1str, a2str, elemstr : string; a1val, a2val : integer; ri : integer; begin if n_atoms > 0 then zap_molecule; rline := ''; ri := li -1; while (ri < molbufindex) and (pos('@MOLECULE',rline)=0) do begin inc(ri); rline := molbuf^[ri]; end; if ri < molbufindex then begin inc(ri); molname := molbuf^[ri]; end; if ri < molbufindex then begin inc(ri); rline := molbuf^[ri]; end; tmpstr := copy(rline,1,5); val(tmpstr,n_atoms,code); tmpstr := copy(rline,7,5); val(tmpstr,n_bonds,code); try getmem(atom,n_atoms*sizeof(atom_rec)); getmem(bond,n_bonds*sizeof(bond_rec)); getmem(ring,sizeof(ringlist)); except on e:Eoutofmemory do begin mod_wrt_ln('Not enough memory'); halt(4); end; end; n_heavyatoms := 0; n_heavybonds := 0; while ((ri < molbufindex) and (pos('@ATOM',rline)=0)) do begin inc(ri); rline := molbuf^[ri]; end; for n := 1 to n_atoms do begin with atom^[n] do begin formal_charge := 0; real_charge := 0; Hexp := 0; Htot := 0; neighbor_count := 0; ring_count := 0; arom := FALSE; end; if (ri < molbufindex) then begin inc(ri); rline := molbuf^[ri]; end; sybatomtype := copy(rline,48,5); elemstr := get_sybelement(sybatomtype); newatomtype := convert_sybtype(sybatomtype); xstr := copy(rline,18,9); ystr := copy(rline,28,9); zstr := copy(rline,38,9); chgstr := copy(rline,70,9); val(xstr,xval,code); val(ystr,yval,code); val(zstr,zval,code); val(chgstr,chgval,code); with atom^[n] do begin element := elemstr; atype := newatomtype; x := xval; y := yval; z := zval; real_charge := chgval; end; if is_heavyatom(n) then inc(n_heavyatoms); end; while ((ri < molbufindex) and (pos('@BOND',rline)=0)) do begin inc(ri); rline := molbuf^[ri]; end; for n := 1 to n_bonds do begin if (ri < molbufindex) then begin inc(ri); rline := molbuf^[ri]; end; a1str := copy(rline,9,3); a2str := copy(rline,14,3); val(a1str,a1val,code); if code <> 0 then mod_wrt_ln(rline, #7); val(a2str,a2val,code); if code <> 0 then mod_wrt_ln(rline,#7); with bond^[n] do begin a1 := a1val; a2 := a2val; if rline[19] = '1' then btype := 'S'; if rline[19] = '2' then btype := 'D'; if rline[19] = '3' then btype := 'T'; if rline[19] = 'a' then btype := 'A'; ring_count := 0; arom := false; end; if is_heavyatom(a1val) and is_heavyatom(a2val) then inc(n_heavybonds); end; fillchar(ring^,sizeof(ringlist),0); li := ri + 1; end; procedure read_charges(chgstring:string); var a_id, a_chg : integer; n_chrg : integer; // typical example: a molecule with 2 kations + 1 anion // M CHG 3 8 1 10 1 11 -1 begin if (pos('M CHG',chgstring)>0) then begin delete(chgstring,1,6); left_trim(chgstring); n_chrg := left_int(chgstring); //debug //if (n_chrg = 0) then mod_wrt_ln('strange... M CHG present, but no charges found'); while (length(chgstring) > 0) do begin a_id := left_int(chgstring); a_chg := left_int(chgstring); if (a_id <> 0) and (a_chg <> 0) then atom^[a_id].formal_charge := a_chg; end; end; end; procedure read_MDLmolfile(mfilename:string); // reads MDL mol files var n, code : integer; rline, tmpstr : string; xstr, ystr, zstr, chgstr : string; xval, yval, zval, chgval : single; a1str, a2str, elemstr : string; a1val, a2val : integer; ri : integer; sepcount : integer; begin if n_atoms > 0 then zap_molecule; cm_mdlmolfile := false; rline := ''; ri := li; molname := molbuf^[ri]; // line 1 if ri < molbufindex then inc(ri); // line 2 rline := molbuf^[ri]; if pos('CheckMol',rline)=3 then begin cm_mdlmolfile := true; found_arominfo := true; end; if ri < molbufindex then inc(ri); // line 3 rline := molbuf^[ri]; molcomment := rline; if ri < molbufindex then inc(ri); // line 4 rline := molbuf^[ri]; tmpstr := copy(rline,1,3); val(tmpstr,n_atoms,code); tmpstr := copy(rline,4,3); val(tmpstr,n_bonds,code); tmpstr := copy(rline,10,3); // if it is a CheckMol-tweaked molfile, this is the number of rings n_cmrings := 0; val(tmpstr,n_cmrings,code); if code <> 0 then n_cmrings := 0; try getmem(atom,n_atoms*sizeof(atom_rec)); getmem(bond,n_bonds*sizeof(bond_rec)); getmem(ring,sizeof(ringlist)); except on e:Eoutofmemory do begin mod_wrt_ln('Not enough memory'); close(molfile); halt(4); exit; end; end; n_heavyatoms := 0; n_heavybonds := 0; for n := 1 to n_atoms do begin with atom^[n] do begin formal_charge := 0; real_charge := 0; Hexp := 0; Htot := 0; neighbor_count := 0; ring_count := 0; arom := FALSE; end; inc(ri); rline := molbuf^[ri]; atomtype := copy(rline,32,3); elemstr := get_MDLelement(atomtype); newatomtype := convert_MDLtype(atomtype); xstr := copy(rline,2,9); ystr := copy(rline,12,9); zstr := copy(rline,22,9); chgstr := '0'; val(xstr,xval,code); val(ystr,yval,code); val(zstr,zval,code); val(chgstr,chgval,code); with atom^[n] do begin element := elemstr; if (elemstr = 'A ') or (elemstr = 'Q ') then found_querymol := true; atype := newatomtype; x := xval; y := yval; z := zval; real_charge := chgval; // read aromaticity flag from CheckMol-tweaked MDL molfile if (length(rline) > 37) and (rline[38] = '0') then begin arom := true; found_arominfo := true; end; end; if is_heavyatom(n) then inc(n_heavyatoms); end; for n := 1 to n_bonds do begin inc(ri); rline := molbuf^[ri]; a1str := copy(rline,1,3); a2str := copy(rline,4,3); val(a1str,a1val,code); if code <> 0 then beep; val(a2str,a2val,code); if code <> 0 then beep; with bond^[n] do begin a1 := a1val; a2 := a2val; if rline[9] = '1' then btype := 'S'; // single if rline[9] = '2' then btype := 'D'; // double if rline[9] = '3' then btype := 'T'; // triple if rline[9] = '4' then btype := 'A'; // aromatic if rline[9] = '5' then btype := 'l'; // single or double if rline[9] = '6' then btype := 's'; // single or aromatic if rline[9] = '7' then btype := 'd'; // double or aromatic if rline[9] = '8' then btype := 'a'; // any if pos(btype,'lsda') > 0 then found_querymol := true; arom := false; // read aromaticity flag from CheckMol-tweaked MDL molfile if (btype = 'A') or (rline[8] = '0') then begin arom := true; if (rline[8] = '0') then found_arominfo := true; end; ring_count := 0; end; if is_heavyatom(a1val) and is_heavyatom(a2val) then inc(n_heavybonds); end; sepcount := 0; while (ri < molbufindex) and (sepcount < 1) do begin inc(ri); rline := molbuf^[ri]; if (pos('M CHG',rline) > 0) then read_charges(rline); if (pos('$$$$',rline)>0) then begin inc(sepcount); if (molbufindex > (ri + 2)) then mol_in_queue := true; // we assume this is an SDF file end; end; fillchar(ring^,sizeof(ringlist),0); li := ri + 1; end; procedure lblank(cols:integer; var nstr:string); // inserts leading blanks up to a given number of total characters begin if length(nstr) >= cols then exit; while length(nstr) < cols do nstr := ' '+nstr; end; procedure mod_wrt_noln_MDLmolfile; var i : integer; tmpstr : string; wline : string; a_chg : integer; begin if length(molname)>80 then molname := copy(molname,1,80); mod_wrt_ln(molname); mod_wrt_ln(' CheckMol '); mod_wrt_ln(molcomment); wline := ''; tmpstr := ''; str(n_atoms:1,tmpstr); lblank(3,tmpstr); wline := wline+tmpstr; tmpstr := ''; // first 3 digits: number of atoms str(n_bonds:1,tmpstr); lblank(3,tmpstr); wline := wline+tmpstr; tmpstr := ''; // next 3 digits: number of bonds tmpstr := ' 0'; wline := wline + tmpstr; tmpstr := ''; // next 3 digits: number of atom lists (not used by us) str(n_rings:1,tmpstr); lblank(3,tmpstr); wline := wline+tmpstr; tmpstr := ''; // officially "obsolete", we use it for the number of rings wline := wline + ' 999 V2000'; mod_wrt_ln(wline); for i := 1 to n_atoms do begin wline := ''; str(atom^[i].X:1:4,tmpstr); lblank(10,tmpstr); wline := wline + tmpstr; str(atom^[i].Y:1:4,tmpstr); lblank(10,tmpstr); wline := wline + tmpstr; str(atom^[i].Z:1:4,tmpstr); lblank(10,tmpstr); wline := wline + tmpstr; tmpstr := atom^[i].element; tmpstr := lowercase(tmpstr); tmpstr[1] := upcase(tmpstr[1]); //wline := wline + ' '+atom^[i].element+' '; wline := wline + ' '+tmpstr+' '; wline := wline + ' 0'; // mass difference (isotopes) // now we code aromaticity into the old-style charge column (charges are now in the M CHG line) if atom^[i].arom then tmpstr := ' 00' else tmpstr := ' 0'; wline := wline + tmpstr; wline := wline + ' 0 0 0 0 0 0 0 0 0 0'; mod_wrt_ln(wline); end; for i := 1 to n_bonds do begin wline := ''; str(bond^[i].a1:1,tmpstr); lblank(3,tmpstr); wline := wline + tmpstr; str(bond^[i].a2:1,tmpstr); lblank(3,tmpstr); wline := wline + tmpstr; if bond^[i].btype = 'S' then tmpstr := ' 1'; if bond^[i].btype = 'D' then tmpstr := ' 2'; if bond^[i].btype = 'T' then tmpstr := ' 3'; if bond^[i].btype = 'A' then tmpstr := ' 4'; if bond^[i].btype = 'l' then tmpstr := ' 5'; if bond^[i].btype = 's' then tmpstr := ' 6'; if bond^[i].btype = 'd' then tmpstr := ' 7'; if bond^[i].btype = 'a' then tmpstr := ' 8'; // now encode our own aromaticity information if bond^[i].arom then tmpstr[2] := '0'; wline := wline + tmpstr+ ' 0 0 0 0'; mod_wrt_ln(wline); end; for i := 1 to n_atoms do begin a_chg := atom^[i].formal_charge; if a_chg <> 0 then begin wline := 'M CHG 1 '; str(i:1,tmpstr); lblank(3,tmpstr); wline := wline + tmpstr +' '; str(a_chg:1,tmpstr); lblank(3,tmpstr); wline := wline + tmpstr; mod_wrt_ln(wline); end; end; mod_wrt_ln('M END'); end; // chemical processing functions & procedures function nvalences(a_el:str2):integer; // preliminary version; should be extended to element/atomtype var res : integer; begin res := 1; if a_el = 'H ' then res := 1; if a_el = 'C ' then res := 4; if a_el = 'N ' then res := 3; if a_el = 'O ' then res := 2; if a_el = 'S ' then res := 2; if a_el = 'SE' then res := 2; if a_el = 'TE' then res := 2; if a_el = 'P ' then res := 3; if a_el = 'F ' then res := 1; if a_el = 'CL' then res := 1; if a_el = 'BR' then res := 1; if a_el = 'I ' then res := 1; if a_el = 'B ' then res := 3; if a_el = 'LI' then res := 1; if a_el = 'NA' then res := 1; if a_el = 'K ' then res := 1; if a_el = 'CA' then res := 2; if a_el = 'SR' then res := 2; if a_el = 'MG' then res := 2; if a_el = 'FE' then res := 3; if a_el = 'MN' then res := 2; if a_el = 'HG' then res := 2; if a_el = 'SI' then res := 4; if a_el = 'SN' then res := 4; if a_el = 'ZN' then res := 2; if a_el = 'CU' then res := 2; if a_el = 'A ' then res := 4; if a_el = 'Q ' then res := 4; nvalences := res; end; procedure count_neighbors; // counts heavy-atom neighbors and explicit hydrogens var i : integer; begin if (n_atoms < 1) or (n_bonds < 1) then exit; for i := 1 to n_bonds do begin if is_heavyatom(bond^[i].a1) then inc(atom^[(bond^[i].a2)].neighbor_count); if is_heavyatom(bond^[i].a2) then inc(atom^[(bond^[i].a1)].neighbor_count); if (atom^[(bond^[i].a1)].element = 'H ') then inc(atom^[(bond^[i].a2)].Hexp); if (atom^[(bond^[i].a2)].element = 'H ') then inc(atom^[(bond^[i].a1)].Hexp); end; end; function get_neighbors(id:integer):neighbor_rec; var i : integer; nb_tmp : neighbor_rec; nb_count : integer; begin fillchar(nb_tmp,sizeof(neighbor_rec),0); nb_count := 0; for i := 1 to n_bonds do begin if ((bond^[i].a1 = id) and (nb_count < 8)) and (is_heavyatom(bond^[i].a2)) then begin inc(nb_count); nb_tmp[nb_count] := bond^[i].a2; end; if ((bond^[i].a2 = id) and (nb_count < 8)) and (is_heavyatom(bond^[i].a1)) then begin inc(nb_count); nb_tmp[nb_count] := bond^[i].a1; end; end; get_neighbors := nb_tmp; // debug // if nb_count <> atom^[id].neighbor_count then // begin // mod_wrt_ln('Error! atom^[',id,'].neighborcount = ',atom^[id].neighbor_count,', nb_count = ',nb_count); // mod_wrt_ln; // end; // end debug end; function get_ndl_neighbors(id:integer):neighbor_rec; var i : integer; nb_tmp : neighbor_rec; nb_count : integer; begin fillchar(nb_tmp,sizeof(neighbor_rec),0); nb_count := 0; for i := 1 to ndl_n_bonds do begin if ((ndl_bond^[i].a1 = id) and (nb_count < 8)) and (is_ndl_heavyatom(ndl_bond^[i].a2)) then begin inc(nb_count); nb_tmp[nb_count] := ndl_bond^[i].a2; end; if ((ndl_bond^[i].a2 = id) and (nb_count < 8)) and (is_ndl_heavyatom(ndl_bond^[i].a1)) then begin inc(nb_count); nb_tmp[nb_count] := ndl_bond^[i].a1; end; end; get_ndl_neighbors := nb_tmp; // debug // if nb_count <> ndl_atom^[id].neighbor_count then // begin // mod_wrt_ln('Error! ndl_atom^[',id,'].neighborcount = ',ndl_atom^[id].neighbor_count,', nb_count = ',nb_count); // mod_wrt_ln; // end; // end debug end; function get_nextneighbors(id:integer;prev_id:integer):neighbor_rec; var i : integer; nb_tmp : neighbor_rec; nb_count : integer; begin // gets all neighbors except prev_id (usually the atom where we came from fillchar(nb_tmp,sizeof(neighbor_rec),0); nb_count := 0; for i := 1 to n_bonds do begin if ((bond^[i].a1 = id) and (bond^[i].a2 <> prev_id) and (nb_count < 8)) and (is_heavyatom(bond^[i].a2)) then begin inc(nb_count); nb_tmp[nb_count] := bond^[i].a2; end; if ((bond^[i].a2 = id) and (bond^[i].a1 <> prev_id) and (nb_count < 8)) and (is_heavyatom(bond^[i].a1)) then begin inc(nb_count); nb_tmp[nb_count] := bond^[i].a1; end; end; get_nextneighbors := nb_tmp; // debug // if nb_count <> atom^[id].neighbor_count then // begin // mod_wrt_ln('Error! atom^[',id,'].neighborcount = ',atom^[id].neighbor_count,', nb_count = ',nb_count); // mod_wrt_ln; // end; // end debug end; function get_ndl_nextneighbors(id:integer;prev_id:integer):neighbor_rec; var i : integer; nb_tmp : neighbor_rec; nb_count : integer; begin // gets all neighbors except prev_id (usually the atom where we came from fillchar(nb_tmp,sizeof(neighbor_rec),0); nb_count := 0; for i := 1 to ndl_n_bonds do begin if ((ndl_bond^[i].a1 = id) and (ndl_bond^[i].a2 <> prev_id) and (nb_count < 8)) and (is_ndl_heavyatom(ndl_bond^[i].a2)) then begin inc(nb_count); nb_tmp[nb_count] := ndl_bond^[i].a2; end; if ((ndl_bond^[i].a2 = id) and (ndl_bond^[i].a1 <> prev_id) and (nb_count < 8)) and (is_ndl_heavyatom(ndl_bond^[i].a1)) then begin inc(nb_count); nb_tmp[nb_count] := ndl_bond^[i].a1; end; end; get_ndl_nextneighbors := nb_tmp; // debug // if nb_count <> atom^[id].neighbor_count then // begin // mod_wrt_ln('Error! atom^[',id,'].neighborcount = ',atom^[id].neighbor_count,', nb_count = ',nb_count); // mod_wrt_ln; // end; // end debug end; function path_pos(id:integer;a_path:ringpath_type):integer; var i, pp : integer; begin pp := 0; for i := max_ringsize downto 1 do begin if (a_path[i] = id) then pp := i; end; path_pos := pp; end; function path_length(a_path:ringpath_type):integer; begin if a_path[max_ringsize] <> 0 then path_length := max_ringsize else begin path_length := path_pos(0,a_path)-1; end; end; function matchpath_pos(id:integer;a_path:matchpath_type):integer; var i, pp : integer; begin pp := 0; for i := max_matchpath_length downto 1 do begin if (a_path[i] = id) then pp := i; end; matchpath_pos := pp; end; function matchpath_length(a_path:matchpath_type):integer; begin if a_path[max_matchpath_length] <> 0 then matchpath_length := max_matchpath_length else begin matchpath_length := matchpath_pos(0,a_path)-1; end; end; function get_bond(ba1,ba2:integer):integer; var i, b_id : integer; begin b_id := 0; if n_bonds > 0 then begin for i := 1 to n_bonds do begin if ((bond^[i].a1 = ba1) and (bond^[i].a2 = ba2)) or ((bond^[i].a1 = ba2) and (bond^[i].a2 = ba1)) then b_id := i; end; end; get_bond := b_id; end; function get_ndl_bond(ba1,ba2:integer):integer; var i, b_id : integer; begin b_id := 0; if ndl_n_bonds > 0 then begin for i := 1 to ndl_n_bonds do begin if ((ndl_bond^[i].a1 = ba1) and (ndl_bond^[i].a2 = ba2)) or ((ndl_bond^[i].a1 = ba2) and (ndl_bond^[i].a2 = ba1)) then b_id := i; end; end; get_ndl_bond := b_id; end; procedure order_ringpath(var r_path:ringpath_type); // order should be: array starts with atom of lowest number, followed by neighbor atom with lower number var i, pl : integer; a_ref, a_left, a_right, a_tmp : integer; begin pl := path_length(r_path); if (pl < 3) then exit; a_ref := n_atoms; // start with highest possible value for an atom number for i := 1 to pl do begin if r_path[i] < a_ref then a_ref := r_path[i]; // find the minimum value ==> reference atom end; if a_ref < 1 then exit; // just to be sure if path_pos(a_ref,r_path) < pl then a_right := r_path[(path_pos(a_ref,r_path)+1)] else a_right := r_path[1]; if path_pos(a_ref,r_path) > 1 then a_left := r_path[(path_pos(a_ref,r_path)-1)] else a_left := r_path[pl]; if a_right = a_left then exit; // should never happen if a_right < a_left then begin // correct ring numbering direction, only shift of the reference atom to the left end required while path_pos(a_ref,r_path) > 1 do begin a_tmp := r_path[1]; for i := 1 to (pl - 1) do r_path[i] := r_path[(i+1)]; r_path[pl] := a_tmp; end; end else begin // wrong ring numbering direction, two steps required while path_pos(a_ref,r_path) < pl do begin // step one: create "mirrored" ring path with reference atom at right end a_tmp := r_path[pl]; for i := pl downto 2 do r_path[i] := r_path[(i-1)]; r_path[1] := a_tmp; end; for i := 1 to (pl div 2) do begin // one more mirroring a_tmp := r_path[i]; r_path[i] := r_path[(pl+1)-i]; r_path[(pl+1)-i] := a_tmp; end; end; end; function ringcompare(rp1,rp2:ringpath_type):integer; var i, j, rc, rs1, rs2 : integer; n_common, max_cra : integer; begin rc := 0; n_common := 0; rs1 := path_length(rp1); rs2 := path_length(rp2); if rs1 < rs2 then max_cra := rs1 else max_cra := rs2; for i := 1 to rs1 do for j := 1 to rs2 do if rp1[i] = rp2[j] then inc(n_common); if (rs1 = rs2) and (n_common = max_cra) then rc := 0 else begin if n_common = 0 then inc(rc,8); if n_common < max_cra then inc(rc,4) else begin if rs1 < rs2 then inc(rc,1) else inc(rc,2); end; end; ringcompare := rc; end; function rc_identical(rc_int:integer):boolean; begin if rc_int = 0 then rc_identical := true else rc_identical := false; end; function rc_1in2(rc_int:integer):boolean; begin if odd(rc_int) then rc_1in2 := true else rc_1in2 := false; end; function rc_2in1(rc_int:integer):boolean; begin rc_int := rc_int div 2; if odd(rc_int) then rc_2in1 := true else rc_2in1 := false; end; function rc_different(rc_int:integer):boolean; begin rc_int := rc_int div 4; if odd(rc_int) then rc_different := true else rc_different := false; end; function rc_independent(rc_int:integer):boolean; begin rc_int := rc_int div 8; if odd(rc_int) then rc_independent := true else rc_independent := false; end; function is_newring(n_path:ringpath_type):boolean; var i, j : integer; nr, same_ring : boolean; tmp_path : ringpath_type; rc_result : integer; begin nr := true; if n_rings > 0 then begin case ringsearch_mode of rs_sar : begin for i := 1 to n_rings do begin same_ring := true; for j := 1 to max_ringsize do if (ring^[i,j] <> n_path[j]) then same_ring := false; if same_ring then nr := false; end; end; rs_ssr : begin for i := 1 to n_rings do begin for j := 1 to max_ringsize do tmp_path[j] := ring^[i,j]; rc_result := ringcompare(n_path,tmp_path); if rc_identical(rc_result) then nr := false; if rc_1in2(rc_result) then begin // exchange existing ring by smaller one for j := 1 to max_ringsize do ring^[i,j] := n_path[j]; nr := false; debugoutput('replacing ring '+inttostr(i)+' by smaller one (ringsize: '+inttostr(path_length(n_path))+')'); end; if rc_2in1(rc_result) then begin // new ring contains existing one, but is larger ==> discard nr := false; end; end; end; end; // case end; is_newring := nr; end; procedure add_ring(n_path:ringpath_type); var i, pl : integer; a1, a2 : integer; begin pl := path_length(n_path); if pl < 1 then exit; if n_rings < max_rings then begin inc(n_rings); debugoutput('adding ring: '+inttostr(n_rings)); a2 := n_path[pl]; for i := 1 to pl do begin ring^[n_rings,i] := n_path[i]; inc(atom^[(n_path[i])].ring_count); a1 := n_path[i]; //inc(bond^[(get_bond(a1,a2))].ring_count); a2 := a1; end; end else debugoutput('max_rings exceeded!'); end; function is_ringpath(s_path:ringpath_type):boolean; var i, j : integer; nb : neighbor_rec; rp, new_atom : boolean; a_last, pl : integer; l_path : ringpath_type; begin rp := false; new_atom := false; fillchar(nb,sizeof(neighbor_rec),0); fillchar(l_path,sizeof(ringpath_type),0); pl := path_length(s_path); if pl < 1 then begin debugoutput('Oops! Got zero-length s_path!'); exit; end; for i := 1 to pl do begin l_path[i] := s_path[i]; end; // check if ring is already closed if (pl > 2) and (l_path[pl] = l_path[1]) then begin l_path[pl] := 0; // remove last entry (redundant!) order_ringpath(l_path); // debug // mod_wrt_noln('ordered: '); for j := 1 to pl do mod_wrt_noln(l_path[j],' '); mod_wrt_ln; // end debug if is_newring(l_path) then begin if (n_rings < max_rings) then add_ring(l_path) else begin debugoutput('maximum number of rings exceeded!'); is_ringpath := false; exit; end; end; rp := true; is_ringpath := true; exit; end; // any other case: ring is not (yet) closed a_last := l_path[pl]; nb := get_neighbors(a_last); if atom^[a_last].neighbor_count > 1 then begin if ((rp = false) and (n_rings < max_rings)) then // added in v0.2: check if max_rings is reached begin // if ring is not closed, continue searching for i := 1 to atom^[a_last].neighbor_count do begin new_atom := true; for j := 2 to pl do if nb[i] = l_path[j] then new_atom := false; // added in v0.1a: check if max_rings not yet reached // added in v0.2: limit ring size to max_vringsize instead of max_ringsize if (new_atom) and (pl < max_vringsize) and (n_rings < max_rings) then begin l_path[(pl+1)] := nb[i]; if (pl < max_ringsize-1) then l_path[pl+2] := 0; // just to be sure if is_ringpath(l_path) then rp := true; end; end; end; end; // else mod_wrt_ln('Atom ',a_last,' is a dead end!'); is_ringpath := rp; end; function is_ringbond(b_id:integer):boolean; var i : integer; ra1, ra2 : integer; nb : neighbor_rec; search_path : ringpath_type; rb : boolean; begin rb := false; ra1 := bond^[b_id].a1; ra2 := bond^[b_id].a2; fillchar(nb,sizeof(neighbor_rec),0); fillchar(search_path,sizeof(ringpath_type),0); nb := get_neighbors(ra2); if (atom^[ra2].neighbor_count > 1) and (atom^[ra1].neighbor_count > 1) then begin search_path[1] := ra1; search_path[2] := ra2; for i := 1 to atom^[ra2].neighbor_count do begin if (nb[i] <> ra1) and (is_heavyatom(nb[i])) then begin search_path[3] := nb[i]; if is_ringpath(search_path) then rb := true; end; end; end; is_ringbond := rb; end; procedure chk_ringbonds; var i : integer; a1rc, a2rc : integer; begin if n_bonds < 1 then exit; for i := 1 to n_bonds do begin a1rc := atom^[(bond^[i].a1)].ring_count; a2rc := atom^[(bond^[i].a2)].ring_count; if ((n_rings = 0) or ((a1rc < n_rings) and (a2rc < n_rings) )) then begin if is_ringbond(i) then begin //inc(bond^[i].ring_count); end; end; end; end; procedure update_ringcount; var i, j, a1, a2, b, pl : integer; begin if n_rings > 0 then begin for i := 1 to n_rings do begin pl := path_length(ring^[i]); a2 := ring^[i,pl]; for j := 1 to pl do begin a1 := ring^[i,j]; inc(atom^[a1].ring_count); b := get_bond(a1,a2); inc(bond^[b].ring_count); a2 := a1; end; end; end; end; function hetbond_count(a:integer):integer; var i : integer; nb : neighbor_rec; nb_el : str2; hbc : single; begin hbc := 0; if (a > 0) and (a <= n_atoms) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a); if atom^[a].neighbor_count > 0 then begin for i := 1 to atom^[a].neighbor_count do begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'A ') and (nb_el <> 'H ') and (nb_el <> 'LP') and (nb_el <> 'DU') then begin if (bond^[(get_bond(a,nb[i]))].btype = 'S') then hbc := hbc + 1; if (bond^[(get_bond(a,nb[i]))].btype = 'A') then hbc := hbc + 1.5; if (bond^[(get_bond(a,nb[i]))].btype = 'D') then hbc := hbc + 2; if (bond^[(get_bond(a,nb[i]))].btype = 'T') then hbc := hbc + 3; end; end; end; end; //debug //if (atom^[a].element = 'N ') then // begin // mod_wrt_ln('checking hetbond_count for N: hbc = ',hbc); // end; //end debug hetbond_count := round(hbc); end; function hetatom_count(a:integer):integer; var i : integer; nb : neighbor_rec; nb_el : str2; hac : integer; begin hac := 0; if (a > 0) and (a <= n_atoms) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a); if atom^[a].neighbor_count > 0 then begin for i := 1 to atom^[a].neighbor_count do begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') and (nb_el <> 'LP') and (nb_el <> 'DU') then inc(hac); end; end; end; hetatom_count := hac; end; function ndl_hetbond_count(a:integer):integer; var i : integer; nb : neighbor_rec; nb_el : str2; hbc : single; begin hbc := 0; if (a > 0) and (a <= n_atoms) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_ndl_neighbors(a); if ndl_atom^[a].neighbor_count > 0 then begin for i := 1 to ndl_atom^[a].neighbor_count do begin nb_el := ndl_atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') and (nb_el <> 'LP') and (nb_el <> 'DU') then begin if (ndl_bond^[(get_ndl_bond(a,nb[i]))].btype = 'S') then hbc := hbc + 1; if (ndl_bond^[(get_ndl_bond(a,nb[i]))].btype = 'A') then hbc := hbc + 1.5; if (ndl_bond^[(get_ndl_bond(a,nb[i]))].btype = 'D') then hbc := hbc + 2; if (ndl_bond^[(get_ndl_bond(a,nb[i]))].btype = 'T') then hbc := hbc + 3; end; end; end; end; ndl_hetbond_count := round(hbc); end; function ndl_hetatom_count(a:integer):integer; var i : integer; nb : neighbor_rec; nb_el : str2; hac : integer; begin hac := 0; if (a > 0) and (a <= ndl_n_atoms) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_ndl_neighbors(a); if ndl_atom^[a].neighbor_count > 0 then begin for i := 1 to ndl_atom^[a].neighbor_count do begin nb_el := ndl_atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'A ') and (nb_el <> 'H ') and (nb_el <> 'LP') and (nb_el <> 'DU') then inc(hac); end; end; end; ndl_hetatom_count := hac; end; function is_oxo_C(id:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and ((atom^[(nb[i])].element = 'O ') { or (atom^[(nb[i])].element = 'S ') or (atom^[(nb[i])].element = 'SE') } ) then // no N, amidines are different... r := true; end; end; is_oxo_C := r; end; function is_thioxo_C(id:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and ((atom^[(nb[i])].element = 'S ') or (atom^[(nb[i])].element = 'SE')) then // no N, amidines are different... r := true; end; end; is_thioxo_C := r; end; function is_imino_C(id:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and (atom^[(nb[i])].element = 'N ') then r := true; end; end; is_imino_C := r; end; function is_true_imino_C(id:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; nb_el : str2; a_n : integer; begin r := false; a_n := 0; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and (atom^[(nb[i])].element = 'N ') then a_n := nb[i]; end; if (a_n > 0) then begin r := true; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_n); for i := 1 to atom^[a_n].neighbor_count do begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') then r := false; end; end; end; is_true_imino_C := r; end; function is_exocyclic_imino_C(id,r_id:integer):boolean; var i,j : integer; r : boolean; nb : neighbor_rec; testring : ringpath_type; ring_size : integer; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[r_id,j] > 0 then testring[j] := ring^[r_id,j]; ring_size := path_length(testring); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and (atom^[(nb[i])].element = 'N ') then begin r := true; for j := 1 to ring_size do if nb[i] = ring^[r_id,j] then r := false; end; end; end; is_exocyclic_imino_C := r; end; function is_exocyclic_methylene_C(id,r_id:integer):boolean; var i,j : integer; r : boolean; nb : neighbor_rec; testring : ringpath_type; ring_size : integer; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[r_id,j] > 0 then testring[j] := ring^[r_id,j]; ring_size := path_length(testring); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and (atom^[(nb[i])].element = 'C ') then begin r := true; for j := 1 to ring_size do if nb[i] = ring^[r_id,j] then r := false; end; end; end; is_exocyclic_methylene_C := r; end; function is_hydroxy(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'O3 ') and (atom^[a_ref].neighbor_count = 1) then r := true; end; is_hydroxy := r; end; function is_sulfanyl(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'S3 ') and (atom^[a_ref].neighbor_count = 1) then r := true; end; is_sulfanyl := r; end; function is_amino(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if ((atom^[a_ref].atype = 'N3 ') or (atom^[a_ref].atype = 'N3+')) and (atom^[a_ref].neighbor_count = 1) then r := true; end; is_amino := r; end; function is_alkyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; nb_el : str2; het_count : integer; begin r := false; het_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') and (atom^[a_ref].atype = 'C3 ') and (atom^[a_ref].arom = false) then begin nb := get_neighbors(a_ref); for i := 1 to atom^[a_ref].neighbor_count do begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') and (nb_el <> 'DU') and (nb_el <> 'LP') then inc(het_count) end; if het_count <= 2 then r := true; // we consider (e.g.) alkoxyalkyl groups as alkyl end; is_alkyl := r; end; function is_true_alkyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; nb_el : str2; het_count : integer; begin r := false; het_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') and (atom^[a_ref].atype = 'C3 ') and (atom^[a_ref].arom = false) then begin nb := get_neighbors(a_ref); for i := 1 to atom^[a_ref].neighbor_count do begin if (nb[i] <> a_view) then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') and (nb_el <> 'DU') then inc(het_count) end; end; if het_count = 0 then r := true; // end; is_true_alkyl := r; end; function is_aryl(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') and (atom^[a_ref].element = 'C ') and (atom^[a_ref].arom = true) then r := true; is_aryl := r; end; function is_alkoxy(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'O3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if is_alkyl(a_ref,nb[i]) then r := true; end; end; end; end; is_alkoxy := r; end; function is_siloxy(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'O3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if (atom^[(nb[i])].element = 'SI') then r := true; end; end; end; end; is_siloxy := r; end; function is_true_alkoxy(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'O3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if is_true_alkyl(a_ref,nb[i]) then r := true; end; end; end; end; is_true_alkoxy := r; end; function is_aryloxy(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'O3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if is_aryl(a_ref,nb[i]) then r := true; end; end; end; end; is_aryloxy := r; end; function is_alkylsulfanyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'S3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if is_alkyl(a_ref,nb[i]) then r := true; end; end; end; end; is_alkylsulfanyl := r; end; function is_true_alkylsulfanyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'S3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if is_true_alkyl(a_ref,nb[i]) then r := true; end; end; end; end; is_true_alkylsulfanyl := r; end; function is_arylsulfanyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].atype = 'S3 ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if nb[i] <> a_view then begin if is_aryl(a_ref,nb[i]) then r := true; end; end; end; end; is_arylsulfanyl := r; end; function is_alkylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; alkyl_count : integer; begin r := false; alkyl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if is_alkyl(a_ref,nb[i]) then inc(alkyl_count); end; end; if alkyl_count = 1 then r := true end; end; is_alkylamino := r; end; function is_dialkylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; alkyl_count : integer; begin r := false; alkyl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if (nb[i] <> a_view) then begin if is_alkyl(a_ref,nb[i]) then inc(alkyl_count); end; end; if alkyl_count = 2 then r := true end; end; is_dialkylamino := r; end; function is_arylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; aryl_count : integer; begin r := false; aryl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if is_aryl(a_ref,nb[i]) then inc(aryl_count); end; end; if aryl_count = 1 then r := true end; end; is_arylamino := r; end; function is_diarylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; aryl_count : integer; begin r := false; aryl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if (nb[i] <> a_view) then begin if is_aryl(a_ref,nb[i]) then inc(aryl_count); end; end; if aryl_count = 2 then r := true end; end; is_diarylamino := r; end; function is_alkylarylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; alkyl_count : integer; aryl_count : integer; begin r := false; alkyl_count := 0; aryl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if (nb[i] <> a_view) then begin if is_alkyl(a_ref,nb[i]) then inc(alkyl_count); if is_aryl(a_ref,nb[i]) then inc(aryl_count); end; end; if (alkyl_count = 1) and (aryl_count = 1) then r := true end; end; is_alkylarylamino := r; end; function is_subst_amino(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (is_amino(a_view,a_ref)) or (is_alkylamino(a_view,a_ref)) or (is_arylamino(a_view,a_ref)) or (is_dialkylamino(a_view,a_ref)) or (is_alkylarylamino(a_view,a_ref)) or (is_diarylamino(a_view,a_ref)) then r := true; is_subst_amino := r; end; function is_true_alkylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; alkyl_count : integer; begin r := false; alkyl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if ((atom^[a_ref].atype = 'N3 ') or (atom^[a_ref].atype = 'N3+')) and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if is_true_alkyl(a_ref,nb[i]) then inc(alkyl_count); end; end; if alkyl_count = 1 then r := true end; end; is_true_alkylamino := r; end; function is_true_dialkylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; alkyl_count : integer; begin r := false; alkyl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if ((atom^[a_ref].atype = 'N3 ') or (atom^[a_ref].atype = 'N3+')) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if (nb[i] <> a_view) then begin if is_true_alkyl(a_ref,nb[i]) then inc(alkyl_count); end; end; if alkyl_count = 2 then r := true end; end; is_true_dialkylamino := r; end; function is_true_alkylarylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; alkyl_count : integer; aryl_count : integer; begin r := false; alkyl_count := 0; aryl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if ((atom^[a_ref].atype = 'N3 ') or (atom^[a_ref].atype = 'N3+')) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if (nb[i] <> a_view) then begin if is_true_alkyl(a_ref,nb[i]) then inc(alkyl_count); if is_aryl(a_ref,nb[i]) then inc(aryl_count); end; end; if (alkyl_count = 1) and (aryl_count = 1) then r := true end; end; is_true_alkylarylamino := r; end; function is_hydroxylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; oh_count : integer; begin r := false; oh_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if is_hydroxy(a_ref,nb[i]) then inc(oh_count); end; end; if (oh_count = 1) then r := true end; end; is_hydroxylamino := r; end; function is_nitro(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; o_count : integer; bond_count : integer; begin r := false; o_count := 0; bond_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if (nb[i] <> a_view) then begin if (atom^[(nb[i])].element = 'O ') then inc(o_count); if (bond^[get_bond(a_ref,nb[i])].btype = 'S') then inc(bond_count); if (bond^[get_bond(a_ref,nb[i])].btype = 'D') then inc(bond_count,2); end; end; if (o_count = 2) and (bond_count >= 3) then r := true end; end; is_nitro := r; end; function is_azido(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; bond_count : integer; n1, n2, n3 : integer; begin r := false; bond_count := 0; n1 := 0; n2 := 0; n3 := 0; if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 2) then begin n1 := a_ref; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(n1); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if (atom^[(nb[i])].element = 'N ') then begin n2 := nb[i]; if (bond^[get_bond(n1,n2)].btype = 'S') then inc(bond_count); if (bond^[get_bond(n1,n2)].btype = 'D') then inc(bond_count,2); if (bond^[get_bond(n1,n2)].btype = 'T') then inc(bond_count,3); end; end; end; if (n2 > 0) and (atom^[n2].neighbor_count = 2) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(n2); for i := 1 to 2 do begin if (nb[i] <> n1) then begin if (atom^[(nb[i])].element = 'N ') then begin n3 := nb[i]; if (bond^[get_bond(n2,n3)].btype = 'S') then inc(bond_count); if (bond^[get_bond(n2,n3)].btype = 'D') then inc(bond_count,2); if (bond^[get_bond(n2,n3)].btype = 'T') then inc(bond_count,3); end; end; end; end; if (n1 > 0) and (n2 > 0) and (n3 > 0) and (atom^[n3].neighbor_count = 1) and (bond_count > 3) then r := true end; end; is_azido := r; end; function is_diazonium(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; bond_count : integer; chg_count : integer; n1, n2 : integer; begin r := false; bond_count := 0; chg_count := 0; n1 := 0; n2 := 0; if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 2) then begin n1 := a_ref; chg_count := atom^[n1].formal_charge; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(n1); for i := 1 to 2 do begin if (nb[i] <> n1) then begin if (atom^[(nb[i])].element = 'N ') then begin n2 := nb[i]; chg_count := chg_count + atom^[n2].formal_charge; if (bond^[get_bond(n1,n2)].btype = 'S') then inc(bond_count); if (bond^[get_bond(n1,n2)].btype = 'D') then inc(bond_count,2); if (bond^[get_bond(n1,n2)].btype = 'T') then inc(bond_count,3); end; end; end; if (n1 > 0) and (n2 > 0) and (atom^[n2].neighbor_count = 1) and (bond_count >= 2) and (chg_count > 0) then r := true end; end; is_diazonium := r; end; function is_hydroximino_C(id:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; a_het : integer; begin r := false; a_het := 0; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and (atom^[(nb[i])].element = 'N ') and (hetbond_count(nb[i]) = 3) then a_het := nb[i];; end; if (a_het > 0) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_het); if (atom^[a_het].element = 'N ') and (atom^[a_het].neighbor_count > 0) then begin for i := 1 to atom^[a_het].neighbor_count do begin if is_hydroxy(a_het,nb[i]) then r := true; end; end; end; end; is_hydroximino_C := r; end; function is_hydrazono_C(id:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; a_het : integer; begin r := false; a_het := 0; fillchar(nb,sizeof(neighbor_rec),0); if (id < 1) or (id > n_atoms) then exit; nb := get_neighbors(id); if (atom^[id].element = 'C ') and (atom^[id].neighbor_count > 0) then begin for i := 1 to atom^[id].neighbor_count do begin if (bond^[get_bond(id,nb[i])].btype = 'D') and (atom^[(nb[i])].element = 'N ') { and (hetbond_count(nb[i]) = 3) } then a_het := nb[i];; end; if (a_het > 0) then begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_het); if (atom^[a_het].element = 'N ') and (atom^[a_het].neighbor_count > 0) then begin for i := 1 to atom^[a_het].neighbor_count do begin if (is_amino(a_het,nb[i])) or (is_alkylamino(a_het,nb[i])) or (is_alkylarylamino(a_het,nb[i])) or (is_arylamino(a_het,nb[i])) or (is_dialkylamino(a_het,nb[i])) or (is_diarylamino(a_het,nb[i])) then r := true; end; end; end; end; is_hydrazono_C := r; end; function is_alkoxycarbonyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_oxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if is_alkoxy(a_ref,nb[i]) then r := true; end; end; end; end; is_alkoxycarbonyl := r; end; function is_aryloxycarbonyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_oxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if is_aryloxy(a_ref,nb[i]) then r := true; end; end; end; end; is_aryloxycarbonyl := r; end; function is_carbamoyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_oxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then r := true; end; end; end; end; is_carbamoyl := r; end; function is_alkoxythiocarbonyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_thioxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if is_alkoxy(a_ref,nb[i]) then r := true; end; end; end; end; is_alkoxythiocarbonyl := r; end; function is_aryloxythiocarbonyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_thioxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if is_aryloxy(a_ref,nb[i]) then r := true; end; end; end; end; is_aryloxythiocarbonyl := r; end; function is_thiocarbamoyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_thioxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then r := true; end; end; end; end; is_thiocarbamoyl := r; end; function is_alkanoyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_oxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if (is_alkyl(a_ref,nb[i])) then r := true; end; end; end; end; is_alkanoyl := r; end; function is_aroyl(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (is_oxo_c(a_ref)) and (atom^[a_ref].neighbor_count = 3) then begin nb := get_neighbors(a_ref); for i := 1 to 3 do begin if nb[i] <> a_view then begin if (is_aryl(a_ref,nb[i])) then r := true; end; end; end; end; is_aroyl := r; end; function is_acyl(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (is_alkanoyl(a_view,a_ref)) or (is_aroyl(a_view,a_ref)) then r := true; is_acyl := r; end; function is_acylamino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; acyl_count : integer; begin r := false; acyl_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count = 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if is_acyl(a_ref,nb[i]) then inc(acyl_count); end; end; if acyl_count = 1 then r := true end; end; is_acylamino := r; end; function is_hydrazino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; nr_count : integer; begin r := false; nr_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count >= 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if (is_amino(a_ref,nb[i])) or (is_subst_amino(a_ref,nb[i])) then inc(nr_count); end; end; if (nr_count = 1) then r := true end; end; is_hydrazino := r; end; function is_subst_hydrazino(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; nr_count : integer; begin r := false; nr_count := 0; fillchar(nb,sizeof(neighbor_rec),0); if (is_heavyatom(a_view)) and (bond^[get_bond(a_view,a_ref)].btype = 'S') then begin if (atom^[a_ref].element = 'N ') and (atom^[a_ref].neighbor_count >= 2) then begin nb := get_neighbors(a_ref); for i := 1 to 2 do begin if (nb[i] <> a_view) then begin if (atom^[(nb[i])].element= 'N ') then inc(nr_count); end; end; if (nr_count = 1) then r := true end; end; is_subst_hydrazino := r; end; function is_cyano(a_view,a_ref:integer):boolean; var r : boolean; begin r := false; if (atom^[a_view].atype = 'C1 ') and (bond^[get_bond(a_view,a_ref)].btype = 'T') and (atom^[a_ref].atype = 'N1 ') and (atom^[a_ref].neighbor_count = 1) then r := true; is_cyano := r; end; function is_cyano_c(a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; //nb_el : str2; begin r := false; fillchar(nb,sizeof(neighbor_rec),0); if (atom^[a_ref].atype = 'C1 ') and (atom^[a_ref].neighbor_count > 0) then begin nb := get_neighbors(a_ref); for i := 1 to atom^[a_ref].neighbor_count do begin if (is_cyano(a_ref,nb[i])) then r := true; end; end; is_cyano_c := r; end; function is_nitrile(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; nb_el : str2; begin r := false; if is_cyano(a_view,a_ref) then begin if (atom^[a_view].neighbor_count = 1) and (atom^[a_view].formal_charge = 0) then r := true else // HCN is also a nitrile! begin nb := get_neighbors(a_view); for i := 1 to 2 do begin if nb[i] <> a_ref then begin nb_el := atom^[(nb[i])].element; if (nb_el = 'C ') or (nb_el = 'H ') then r := true; end; end; end; end; is_nitrile := r; end; function is_isonitrile(a_view,a_ref:integer):boolean; // only recognized with CN triple bond! var r : boolean; begin r := false; if (atom^[a_view].atype = 'C1 ') and (bond^[get_bond(a_view,a_ref)].btype = 'T') and (atom^[a_ref].atype = 'N1 ') and (atom^[a_ref].neighbor_count = 2) and (atom^[a_view].neighbor_count = 1) then r := true; is_isonitrile := r; end; function is_cyanate(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; if is_cyano(a_view,a_ref) then begin if (atom^[a_view].neighbor_count = 2) then begin nb := get_neighbors(a_view); for i := 1 to 2 do begin if nb[i] <> a_ref then begin if (is_alkoxy(a_view,nb[i])) or (is_aryloxy(a_view,nb[i])) then r := true; end; end; end; end; is_cyanate := r; end; function is_thiocyanate(a_view,a_ref:integer):boolean; var i : integer; r : boolean; nb : neighbor_rec; begin r := false; if is_cyano(a_view,a_ref) then begin if (atom^[a_view].neighbor_count = 2) then begin nb := get_neighbors(a_view); for i := 1 to 2 do begin if nb[i] <> a_ref then begin if (is_alkylsulfanyl(a_view,nb[i])) or (is_arylsulfanyl(a_view,nb[i])) then r := true; end; end; end; end; is_thiocyanate := r; end; procedure update_Htotal; var i, j, b_id : integer; nb : neighbor_rec; single_count, double_count, triple_count, arom_count : integer; total_bonds : integer; Htotal : integer; begin if n_atoms < 1 then exit; fillchar(nb,sizeof(neighbor_rec),0); for i := 1 to n_atoms do begin single_count := 0; double_count := 0; triple_count := 0; arom_count := 0; total_bonds := 0; Htotal := 0; nb := get_neighbors(i); if atom^[i].neighbor_count > 0 then begin // count single, double, triple, and aromatic bonds to all neighbor atoms for j := 1 to atom^[i].neighbor_count do begin b_id := get_bond(i,nb[j]); if b_id > 0 then begin if bond^[b_id].btype = 'S' then inc(single_count); if bond^[b_id].btype = 'D' then inc(double_count); if bond^[b_id].btype = 'T' then inc(triple_count); if bond^[b_id].btype = 'A' then inc(arom_count); end; end; total_bonds := single_count + 2*double_count + 3*triple_count + trunc(1.5*arom_count); // calculate number of total hydrogens per atom Htotal := nvalences(atom^[i].element) - total_bonds + atom^[i].formal_charge; if Htotal < 0 then Htotal := 0; // e.g., N in nitro group atom^[i].Htot := Htotal; end; end; end; procedure update_atypes; var i, j, b_id : integer; nb : neighbor_rec; single_count, double_count, triple_count, arom_count, acyl_count : integer; C_count, O_count : integer; total_bonds : integer; NdO_count : integer; NdC_count : integer; Htotal : integer; begin if n_atoms < 1 then exit; fillchar(nb,sizeof(neighbor_rec),0); for i := 1 to n_atoms do begin single_count := 0; double_count := 0; triple_count := 0; arom_count := 0; total_bonds := 0; acyl_count := 0; C_count := 0; O_count := 0; NdO_count := 0; NdC_count := 0; Htotal := 0; nb := get_neighbors(i); if atom^[i].neighbor_count > 0 then begin // count single, double, triple, and aromatic bonds to all neighbor atoms for j := 1 to atom^[i].neighbor_count do begin if (is_oxo_C(nb[j])) or (is_thioxo_C(nb[j])) then inc(acyl_count); if atom^[(nb[j])].element = 'C ' then inc(C_count); if atom^[(nb[j])].element = 'O ' then inc(O_count); b_id := get_bond(i,nb[j]); if b_id > 0 then begin if bond^[b_id].btype = 'S' then inc(single_count); if bond^[b_id].btype = 'D' then inc(double_count); if bond^[b_id].btype = 'T' then inc(triple_count); if bond^[b_id].btype = 'A' then inc(arom_count); if ((atom^[i].element = 'N ') and (atom^[(nb[j])].element = 'O ')) or ((atom^[i].element = 'O ') and (atom^[(nb[j])].element = 'N ')) then begin // check if it is an N-oxide drawn with a double bond ==> should be N3 if bond^[b_id].btype = 'D' then inc(NdO_count); end; if ((atom^[i].element = 'N ') and (atom^[(nb[j])].element = 'C ')) or ((atom^[i].element = 'C ') and (atom^[(nb[j])].element = 'N ')) then begin if bond^[b_id].btype = 'D' then inc(NdC_count); end; end; end; total_bonds := single_count + 2*double_count + 3*triple_count + trunc(1.5*arom_count); // calculate number of total hydrogens per atom Htotal := nvalences(atom^[i].element) - total_bonds + atom^[i].formal_charge; if Htotal < 0 then Htotal := 0; // e.g., N in nitro group atom^[i].Htot := Htotal; // refine atom types, based on bond types if atom^[i].element = 'C ' then begin if (arom_count > 1) then atom^[i].atype := 'CAR'; if (triple_count = 1) or (double_count = 2) then atom^[i].atype := 'C1 '; if (double_count = 1) then atom^[i].atype := 'C2 '; if (triple_count = 0) and (double_count = 0) and (arom_count < 2) then atom^[i].atype := 'C3 '; end; if atom^[i].element = 'O ' then begin if (double_count = 1) then atom^[i].atype := 'O2 '; if (double_count = 0) then atom^[i].atype := 'O3 '; end; if atom^[i].element = 'N ' then begin if total_bonds > 3 then begin if O_count = 0 then begin if (single_count > 3) or ((single_count = 2) and (double_count = 1) and (C_count >=2)) then atom^[i].formal_charge := 1; end else // could be an N-oxide -> should be found elsewhere begin // left empty, so far.... end; end; if (arom_count > 1) then atom^[i].atype := 'NAR'; if (triple_count = 1) or (double_count = 2) then atom^[i].atype := 'N1 '; if (double_count = 1) then begin if NdC_count > 0 then atom^[i].atype := 'N2 '; if (NdC_count = 0) and (NdO_count > 0) and (C_count >= 2) then atom^[i].atype := 'N3 '; // N-oxide is N3 except in hetarene etc. end; if (triple_count = 0) and (double_count = 0) then begin if (atom^[i].formal_charge = 0) then begin if (acyl_count = 0) then atom^[i].atype := 'N3 '; if (acyl_count > 0) then atom^[i].atype := 'NAM'; end; if (atom^[i].formal_charge = 1) then atom^[i].atype := 'N3+'; end; end; if atom^[i].element = 'P ' then begin if (single_count > 4) then atom^[i].atype := 'P4 '; if (single_count <= 4) and (double_count = 0) then atom^[i].atype := 'P3 '; if (double_count = 2) then atom^[i].atype := 'P3D'; end; if atom^[i].element = 'S ' then begin if (double_count = 1) and (single_count = 0) then atom^[i].atype := 'S2 '; if (double_count = 0) then atom^[i].atype := 'S3 '; if (double_count = 1) and (single_count > 0) then atom^[i].atype := 'SO '; if (double_count = 2) and (single_count > 0) then atom^[i].atype := 'SO2'; end; // further atom types should go here end; end; end; procedure chk_arom; var i, j, pi_count, ring_size : integer; testring : ringpath_type; a_ref, a_prev, a_next : integer; b_bk, b_fw : integer; bt_bk, bt_fw : char; conj_intr, ko : boolean; begin if n_rings < 1 then exit; for i := 1 to n_rings do begin fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[i,j] > 0 then testring[j] := ring^[i,j]; ring_size := path_length(testring); pi_count := 0; conj_intr := false; ko := false; a_prev := testring[ring_size]; for j := 1 to ring_size do begin a_ref := testring[j]; if (j < ring_size) then a_next := testring[(j+1)] else a_next := testring[1]; b_bk := get_bond(a_prev,a_ref); b_fw := get_bond(a_ref,a_next); bt_bk := bond^[b_bk].btype; bt_fw := bond^[b_fw].btype; if (bt_bk = 'S') and (bt_fw = 'S') then begin conj_intr := true; // first, assume the worst case (interrupted conjugation) // conjugation can be restored by hetero atoms if (atom^[a_ref].atype = 'O3 ') or (atom^[a_ref].atype = 'S3 ') or (atom^[a_ref].element = 'N ') or (atom^[a_ref].element = 'SE') then begin conj_intr := false; inc(pi_count,2); // lone pair adds for 2 pi electrons end; // conjugation can be restored by a formal charge at a methylene group if (atom^[a_ref].element = 'C ') and (atom^[a_ref].formal_charge <> 0) then begin conj_intr := false; pi_count := pi_count - atom^[a_ref].formal_charge; // neg. charge increases pi_count! end; // conjugation can be restored by carbonyl groups etc. if (is_oxo_C(a_ref)) or (is_thioxo_C(a_ref)) or (is_exocyclic_imino_C(a_ref,i)) then begin conj_intr := false; end; // conjugation can be restored by exocyclic C=C double bond, // adds 2 pi electrons to 5-membered rings, not to 7-membered rings if ((is_exocyclic_methylene_C(a_ref,i)) and odd(ring_size)) then begin conj_intr := false; if ((ring_size - 1) mod 4 = 0) then inc(pi_count,2); end; // if conjugation is still interrupted ==> knock-out if conj_intr then ko := true; end else begin // any other combination of bond types adds 1 pi electron inc(pi_count); end; // last command: a_prev := a_ref; // debug // mod_wrt_noln('current atom: ',a_ref,'; previous atom: ',a_prev,'; bond types: ',bt_bk,', ',bt_fw); // mod_wrt_noln(' pi_count: ',pi_count); // if conj_intr then mod_wrt_noln(' conj. interrupted') else mod_wrt_noln(' conj. uninterrupted'); // mod_wrt_ln; end; // for j := 1 to ring_size // now we can draw our conclusion if not ((ko) or (odd(pi_count))) then begin // apply Hueckel's rule if (abs(ring_size - pi_count) < 2) and ((pi_count - 2) mod 4 = 0) then begin // now mark _all_ bonds in the ring as aromatic a_prev := testring[ring_size]; for j := 1 to ring_size do begin a_ref := testring[j]; bond^[get_bond(a_prev,a_ref)].arom := true; a_prev := a_ref; // debug //mod_wrt_ln('aromatic ring found!'); // end debug end; end; end; end; // inner "for" loop // finally, mark all involved atoms as aromatic for i := 1 to n_bonds do begin if bond^[i].arom then begin atom^[(bond^[i].a1)].arom := true; atom^[(bond^[i].a2)].arom := true; end; end; end; procedure mod_wrt_noln_mol; var i, j : integer; testring : ringpath_type; ring_size : integer; aromatic : boolean; a_prev, a_ref : integer; begin {* if progmode = pmCheckMol then mod_wrt_ln('Molecule name: ',molname) else mod_wrt_ln('Molecule name (haystack): ',molname); mod_wrt_ln('atoms: ',n_atoms,' bonds: ',n_bonds,' rings: ',n_rings); if n_atoms < 1 then exit; if n_bonds < 1 then exit; for i := 1 to n_atoms do begin if i < 10 then mod_wrt_noln(' '); if i < 100 then mod_wrt_noln(' '); if i < 1000 then mod_wrt_noln(' '); mod_wrt_noln(i,' ',atom^[i].element,' ',atom^[i].atype,' ',atom^[i].x:9:4,' ',atom^[i].y:9:4,' '); mod_wrt_noln(atom^[i].z:9:4); mod_wrt_noln(' (',atom^[i].neighbor_count,' heavy-atom neighbors)'); if (atom^[i].formal_charge <> 0) then mod_wrt_noln(' charge: ',atom^[i].formal_charge); mod_wrt_ln; end; for i := 1 to n_bonds do begin if i < 10 then mod_wrt_noln(' '); if i < 100 then mod_wrt_noln(' '); if i < 1000 then mod_wrt_noln(' '); mod_wrt_noln(i,' ',bond^[i].a1,' ',bond^[i].a2,' ',bond^[i].btype); if bond^[i].ring_count > 0 then mod_wrt_noln(', contained in ',bond^[i].ring_count,' ring(s)'); if bond^[i].arom then mod_wrt_noln(' (aromatic) '); mod_wrt_ln; end; if n_rings > 0 then begin for i := 1 to n_rings do begin aromatic := true; fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[i,j] > 0 then testring[j] := ring^[i,j]; ring_size := path_length(testring); mod_wrt_noln('ring ',i,': '); a_prev := testring[ring_size]; for j := 1 to ring_size do begin mod_wrt_noln(testring[j],' '); a_ref := testring[j]; if (not bond^[get_bond(a_prev,a_ref)].arom) then aromatic := false; a_prev := a_ref; end; if aromatic then mod_wrt_noln(' (aromatic)'); mod_wrt_ln; end; end; *}end; procedure mod_wrt_noln_needle_mol; var i, j : integer; testring : ringpath_type; ring_size : integer; aromatic : boolean; a_prev, a_ref : integer; begin {* mod_wrt_ln('Molecule name (needle): ',ndl_molname); mod_wrt_ln('atoms: ',ndl_n_atoms,' bonds: ',ndl_n_bonds,' rings: ',ndl_n_rings); if ndl_n_atoms < 1 then exit; if ndl_n_bonds < 1 then exit; for i := 1 to ndl_n_atoms do begin if i < 10 then mod_wrt_noln(' '); if i < 100 then mod_wrt_noln(' '); if i < 1000 then mod_wrt_noln(' '); mod_wrt_noln(i,' ',ndl_atom^[i].element,' ',ndl_atom^[i].atype,' ',ndl_atom^[i].x:9:4,' ',atom^[i].y:9:4,' '); mod_wrt_noln(ndl_atom^[i].z:9:4); mod_wrt_noln(' (',ndl_atom^[i].neighbor_count,' heavy-atom neighbors)'); if (ndl_atom^[i].formal_charge <> 0) then mod_wrt_noln(' charge: ',ndl_atom^[i].formal_charge); mod_wrt_ln; end; for i := 1 to ndl_n_bonds do begin if i < 10 then mod_wrt_noln(' '); if i < 100 then mod_wrt_noln(' '); if i < 1000 then mod_wrt_noln(' '); mod_wrt_noln(i,' ',ndl_bond^[i].a1,' ',ndl_bond^[i].a2,' ',ndl_bond^[i].btype); if ndl_bond^[i].ring_count > 0 then mod_wrt_noln(', contained in ',ndl_bond^[i].ring_count,' ring(s)'); if ndl_bond^[i].arom then mod_wrt_noln(' (aromatic) '); mod_wrt_ln; end; if ndl_n_rings > 0 then begin for i := 1 to ndl_n_rings do begin aromatic := true; fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ndl_ring^[i,j] > 0 then testring[j] := ndl_ring^[i,j]; ring_size := path_length(testring); mod_wrt_noln('ring ',i,': '); a_prev := testring[ring_size]; for j := 1 to ring_size do begin mod_wrt_noln(testring[j],' '); a_ref := testring[j]; if (not ndl_bond^[get_bond(a_prev,a_ref)].arom) then aromatic := false; a_prev := a_ref; end; if aromatic then mod_wrt_noln(' (aromatic)'); mod_wrt_ln; end; end; *}end; procedure chk_so2_deriv(a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; het_count, o_count, or_count, hal_count, n_count, c_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); if atom^[a_ref].atype <>'SO2' then exit; nb := get_neighbors(a_ref); het_count := 0; o_count := 0; or_count := 0; hal_count := 0; n_count := 0; c_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') and (nb_el <> 'DU') and (nb_el <> 'LP') then inc(het_count); if nb_el = 'O ' then begin inc(o_count); if is_alkoxy(a_ref,nb[i]) or is_aryloxy(a_ref,nb[i]) then inc(or_count); end; if nb_el = 'N ' then inc(n_count); if nb_el = 'C ' then inc(c_count); if (nb_el = 'F ') or (nb_el = 'CL') or (nb_el = 'BR') or (nb_el = 'I ') then inc(hal_count); end; end; if het_count = 2 then // sulfuric acid derivative begin fg[fg_sulfuric_acid_deriv] := true; if (o_count = 2) then begin if (or_count = 0) then fg[fg_sulfuric_acid] := true; if (or_count = 1) then fg[fg_sulfuric_acid_monoester] := true; if (or_count = 2) then fg[fg_sulfuric_acid_diester] := true; end; if (o_count = 1) then begin if (or_count = 1) and (n_count = 1) then fg[fg_sulfuric_acid_amide_ester] := true; if (or_count = 0) and (n_count = 1) then fg[fg_sulfuric_acid_amide] := true; end; if (n_count = 2) then fg[fg_sulfuric_acid_diamide] := true; if (hal_count > 0) then fg[fg_sulfuryl_halide] := true; end; if (het_count = 1) and (c_count = 1) then // sulfonic acid derivative begin fg[fg_sulfonic_acid_deriv] := true; if (o_count = 1) and (or_count = 0) then fg[fg_sulfonic_acid] := true; if (o_count = 1) and (or_count = 1) then fg[fg_sulfonic_acid_ester] := true; if (n_count = 1) then fg[fg_sulfonamide] := true; if (hal_count = 1) then fg[fg_sulfonyl_halide] := true; end; if (het_count = 0) and (c_count = 2) then // sulfone begin fg[fg_sulfone] := true; end; end; procedure chk_p_deriv(a_ref:integer); var i : integer; nb : neighbor_rec; nb_el, dbl_het : str2; het_count, oh_count, or_count, hal_count, n_count, c_count : integer; begin if atom^[a_ref].element <>'P ' then exit; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); dbl_het := ''; het_count := 0; oh_count := 0; or_count := 0; hal_count := 0; n_count := 0; c_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'D' then begin dbl_het := atom^[(nb[i])].element; end; if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el = 'C ') then inc(c_count); if (is_hydroxy(a_ref,nb[i])) then inc(oh_count); if (is_alkoxy(a_ref,nb[i])) or (is_aryloxy(a_ref,nb[i])) then inc(or_count); if (nb_el = 'N ') then inc(n_count); if (nb_el = 'F ') or (nb_el = 'CL') or (nb_el = 'BR') or (nb_el = 'I ') then inc(hal_count); end; end; het_count := oh_count + or_count + hal_count + n_count; if (atom^[a_ref].atype = 'P3D') or (atom^[a_ref].atype = 'P4 ') then begin if (dbl_het = 'O ') then begin if (c_count = 0) then begin fg[fg_phosphoric_acid_deriv] := true; if (oh_count = 3) then fg[fg_phosphoric_acid] := true; if (or_count > 0) then fg[fg_phosphoric_acid_ester] := true; if (hal_count > 0) then fg[fg_phosphoric_acid_halide] := true; if (n_count > 0) then fg[fg_phosphoric_acid_amide] := true; end; if (c_count = 1) then begin fg[fg_phosphonic_acid_deriv] := true; if (oh_count = 2) then fg[fg_phosphonic_acid] := true; if (or_count > 0) then fg[fg_phosphonic_acid_ester] := true; //if (hal_count > 0) then fg[fg_phosphonic_acid_halide] := true; //if (n_count > 0) then fg[fg_phosphonic_acid_amide] := true; end; if (c_count = 3) then fg[fg_phosphinoxide] := true; end; if (dbl_het = 'S ') then begin if (c_count = 0) then begin fg[fg_thiophosphoric_acid_deriv] := true; if (oh_count = 3) then fg[fg_thiophosphoric_acid] := true; if (or_count > 0) then fg[fg_thiophosphoric_acid_ester] := true; if (hal_count > 0) then fg[fg_thiophosphoric_acid_halide] := true; if (n_count > 0) then fg[fg_thiophosphoric_acid_amide] := true; end; end; end; // if (atom^[a_ref].atype = 'P4 ') then fg[fg_phosphoric_acid_deriv] := true; if (atom^[a_ref].atype = 'P3D') then begin if (c_count = 3) and (het_count = 0) then fg[fg_phosphine] := true; if (c_count = 3) and (oh_count = 1) then fg[fg_phosphinoxide] := true; end; end; procedure chk_b_deriv(a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; het_count, oh_count, or_count, hal_count, n_count, c_count : integer; begin if atom^[a_ref].element <>'B ' then exit; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); het_count := 0; oh_count := 0; or_count := 0; hal_count := 0; n_count := 0; c_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el = 'C ') then inc(c_count) else if ((nb_el <>'H ') and (nb_el <>'LP')) then inc(het_count); if (is_hydroxy(a_ref,nb[i])) then inc(oh_count); if (is_alkoxy(a_ref,nb[i])) or (is_aryloxy(a_ref,nb[i])) then inc(oh_count); if (nb_el = 'N ') then inc(n_count); if (nb_el = 'F ') or (nb_el = 'CL') or (nb_el = 'BR') or (nb_el = 'I ') then inc(hal_count); end; end; // het_count := oh_count + or_count + hal_count + n_count; if (c_count = 1) and (het_count = 2) then begin fg[fg_boronic_acid_deriv] := true; if (oh_count = 2) then fg[fg_boronic_acid] := true; if (or_count > 0) then fg[fg_boronic_acid_ester] := true; end; end; procedure chk_ammon(a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; het_count, o_count, or_count, r_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); if (atom^[a_ref].atype <>'N3+') and (atom^[a_ref].formal_charge = 0) then exit; nb := get_neighbors(a_ref); het_count := 0; o_count := 0; or_count := 0; r_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') and (nb_el <> 'H ') and (nb_el <> 'DU') then begin inc(het_count); if (nb_el = 'O ') then begin inc(o_count); if atom^[(nb[i])].neighbor_count > 1 then inc(or_count); end; end; if (is_alkyl(a_ref,nb[i])) or (is_aryl(a_ref,nb[i])) then inc(r_count); end; if bond^[(get_bond(a_ref,nb[i]))].btype = 'D' then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') then begin inc(het_count,2); if (nb_el = 'O ') then begin inc(o_count,2); end; end; if nb_el = 'C ' then inc(r_count); end; if (het_count = 0) and (r_count = 4) then fg[fg_quart_ammonium] := true; if (het_count = 1) and (atom^[a_ref].neighbor_count >= 3) then begin if (o_count = 1) and (or_count = 0) then fg[fg_n_oxide] := true; // finds only aliphatic N-oxides! if ((((o_count = 1) and (or_count = 1)) or (o_count = 0)) and (atom^[a_ref].arom = true)) then fg[fg_quart_ammonium] := true; end; end; end; procedure swap_atoms(var a1,a2:integer); var a_tmp : integer; begin a_tmp := a1; a1 := a2; a2 := a_tmp; end; procedure orient_bond(var a1,a2:integer); var a1_el,a2_el : str2; begin a1_el := atom^[a1].element; a2_el := atom^[a2].element; if (a1_el = 'H ') or (a2_el = 'H ') then exit; if (a2_el = 'C ') and (a1_el <> 'C ') then swap_atoms(a1,a2); if (a2_el = a1_el) then begin if hetbond_count(a1) > hetbond_count(a2) then swap_atoms(a1,a2); end; if (a2_el <> 'C ') and (a1_el <> 'C ') and (a1_el <> a2_el) then begin if (a1_el = 'O ') or (a2_el = 'O ') then begin if (a1_el = 'O ') then swap_atoms(a1,a2); end; end; if (a2_el <> 'C ') and (a1_el <> 'C ') and (a1_el = a2_el) then begin if ((atom^[a2].neighbor_count - hetbond_count(a2)) > (atom^[a1].neighbor_count - hetbond_count(a1))) then swap_atoms(a1,a2); end; end; procedure chk_imine(a_ref,a_view:integer); var i : integer; nb : neighbor_rec; nb_el : str2; a_het : integer; a_c : integer; het_count, c_count : integer; begin het_count := 0; c_count := 0; if (atom^[a_view].neighbor_count = 1) then begin if (atom^[a_ref].arom = false) then fg[fg_imine] := true; end else begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); if atom^[a_view].neighbor_count > 1 then begin for i := 1 to atom^[a_view].neighbor_count do begin if (nb[i] <> a_ref) and (bond^[(get_bond(a_view,nb[i]))].btype = 'S' ) then begin nb_el := atom^[(nb[i])].element; if (nb_el = 'C ') then begin a_c := nb[i]; inc(c_count); end; if (nb_el = 'O ') or (nb_el = 'N ') then begin a_het := nb[i]; inc(het_count); end; end; end; if (c_count = 1) then begin if ((is_alkyl(a_view,a_c)) or (is_aryl(a_view,a_c))) and (atom^[a_ref].arom = false) then fg[fg_imine] := true; end; if (het_count) = 1 then begin nb_el := atom^[a_het].element; if (nb_el = 'O ') then begin if (is_hydroxy(a_view,a_het)) then fg[fg_oxime] := true; if (is_alkoxy(a_view,a_het)) or (is_aryloxy(a_view,a_het)) then fg[fg_oxime_ether] := true; end; if (nb_el = 'N ') then begin if (is_amino(a_view,a_het)) or (is_alkylamino(a_view,a_het)) or (is_dialkylamino(a_view,a_het)) or (is_alkylarylamino(a_view,a_het)) or (is_arylamino(a_view,a_het)) or (is_diarylamino(a_view,a_het)) then fg[fg_hydrazone] := true else begin // check for semicarbazone or thiosemicarbazone fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_het); if atom^[a_het].neighbor_count > 1 then begin for i := 1 to atom^[a_het].neighbor_count do begin if (nb[i] <> a_view) then begin if (is_carbamoyl(a_het,nb[i])) then fg[fg_semicarbazone] := true; if (is_thiocarbamoyl(a_het,nb[i])) then fg[fg_thiosemicarbazone] := true; end; end; end; end; end; end; end; end; end; procedure chk_carbonyl_deriv(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; c_count : integer; cn_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); c_count := 0; cn_count := 0; for i := 1 to atom^[a_view].neighbor_count do begin if bond^[(get_bond(a_view,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el = 'C ') then begin if (is_cyano_c(nb[i])) then begin inc(cn_count) end else begin inc(c_count); end; end; end; end; if is_oxo_c(a_view) then begin fg[fg_carbonyl] := true; if (c_count + cn_count < 2) then fg[fg_aldehyde] := true; if (c_count = 2) then begin if (atom^[a_view].arom) then fg[fg_oxohetarene] := true else fg[fg_ketone] := true; end; if (cn_count > 0) then fg[fg_acyl_cyanide] := true; end; if is_thioxo_c(a_view) then begin fg[fg_thiocarbonyl] := true; if (c_count < 2) then fg[fg_thioaldehyde] := true; if (c_count = 2) then begin if (atom^[a_view].arom) then fg[fg_thioxohetarene] := true else fg[fg_thioketone] := true; end; end; if is_imino_c(a_view) then begin chk_imine(a_view,a_ref); end; end; procedure chk_carboxyl_deriv(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; o_count, n_count, s_count : integer; a_o, a_n, a_s : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); o_count := 0; n_count := 0; s_count := 0; for i := 1 to atom^[a_view].neighbor_count do begin if bond^[(get_bond(a_view,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') then begin if nb_el = 'O ' then begin inc(o_count); a_o := nb[i]; end; if nb_el = 'N ' then begin inc(n_count); a_n := nb[i]; end; if nb_el = 'S ' then begin inc(s_count); a_s := nb[i]; end; end; end; end; if (is_oxo_c(a_view)) then begin if (o_count = 1) then begin // anhydride is checked somewhere else if (bond^[get_bond(a_view,a_o)].arom = false) then fg[fg_carboxylic_acid_deriv] := true; if (is_hydroxy(a_view,a_o)) then begin if (atom^[a_o].formal_charge = 0) then fg[fg_carboxylic_acid] := true; if (atom^[a_o].formal_charge = -1) then fg[fg_carboxylic_acid_salt] := true; end; if (is_alkoxy(a_view,a_o)) or (is_aryloxy(a_view,a_o)) then begin if (bond^[get_bond(a_view,a_o)].arom = false) then fg[fg_carboxylic_acid_ester] := true; if (bond^[get_bond(a_view,a_o)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_o)].arom = true) then //fg[fg_lactone_heteroarom] := true else fg[fg_lactone] := true; fg[fg_oxohetarene] := true else fg[fg_lactone] := true; end; end; end; if (n_count = 1) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then begin fg[fg_carboxylic_acid_deriv] := true; end else begin //fg[fg_lactam_heteroarom] := true; // catches also pyridazines, 1,2,3-triazines, etc. fg[fg_oxohetarene] := true; end; if (is_amino(a_view,a_n)) or ((atom^[a_n].atype = 'NAM') and (atom^[a_n].neighbor_count = 1) ) then begin fg[fg_carboxylic_acid_amide] := true; fg[fg_carboxylic_acid_prim_amide] := true; end; if (is_alkylamino(a_view,a_n)) or (is_arylamino(a_view,a_n)) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_amide] := true; if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_sec_amide] := true; if (bond^[get_bond(a_view,a_n)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_n)].arom = true) then //fg[fg_lactam_heteroarom] := true else fg[fg_oxohetarene] := true else fg[fg_lactam] := true; end; end; if (is_dialkylamino(a_view,a_n)) or (is_alkylarylamino(a_view,a_n)) or (is_diarylamino(a_view,a_n)) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_amide] := true; if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_tert_amide] := true; if (bond^[get_bond(a_view,a_n)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_n)].arom = true) then //fg[fg_lactam_heteroarom] := true else fg[fg_oxohetarene] := true else fg[fg_lactam] := true; end; end; if (is_hydroxylamino(a_view,a_n)) then begin fg[fg_hydroxamic_acid] := true; end; if (is_hydrazino(a_view,a_n)) then begin fg[fg_carboxylic_acid_hydrazide] := true; end; if (is_azido(a_view,a_n)) then begin fg[fg_carboxylic_acid_azide] := true; end; end; if (s_count = 1) then begin // anhydride is checked somewhere else if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_thiocarboxylic_acid_deriv] := true; if (is_sulfanyl(a_view,a_s)) then begin fg[fg_thiocarboxylic_acid] := true; end; if (is_alkylsulfanyl(a_view,a_s)) or (is_arylsulfanyl(a_view,a_s)) then begin if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_thiocarboxylic_acid_ester] := true; if (bond^[get_bond(a_view,a_s)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_s)].arom = true) then //fg[fg_thiolactone_heteroarom] := true else fg[fg_thiolactone] := true; fg[fg_oxohetarene] := true else fg[fg_thiolactone] := true; end; end; end; end; // end Oxo-C if (is_thioxo_c(a_view)) then begin // fg[fg_thiocarboxylic_acid_deriv] := true; if (o_count = 1) then begin // anhydride is checked somewhere else if (bond^[get_bond(a_view,a_o)].arom = false) then fg[fg_thiocarboxylic_acid_deriv] := true; if (is_hydroxy(a_view,a_o)) then begin fg[fg_carboxylic_acid] := true; end; if (is_alkoxy(a_view,a_o)) or (is_aryloxy(a_view,a_o)) then begin if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_thiocarboxylic_acid_ester] := true; if (bond^[get_bond(a_view,a_o)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_o)].arom = true) then //fg[fg_thiolactone_heteroarom] := true else fg[fg_thiolactone] := true; fg[fg_thioxohetarene] := true else fg[fg_thiolactone] := true; end; end; end; if (n_count = 1) then begin // debug // mod_wrt_ln('checking for N attached to C=S'); if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_thiocarboxylic_acid_deriv] := true else //fg[fg_thiolactam_heteroarom] := true; // catches also pyridazines, 1,2,3-triazines, etc. fg[fg_thioxohetarene] := true; // catches also pyridazines, 1,2,3-triazines, etc. if (is_amino(a_view,a_n)) then begin // mod_wrt_ln('==> amino'); fg[fg_thiocarboxylic_acid_amide] := true; // fg[fg_thiocarboxylic_acid_prim_amide] := true; end; if (is_alkylamino(a_view,a_n)) or (is_arylamino(a_view,a_n)) then begin // mod_wrt_ln('==> alkylamino or arylamino'); if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_thiocarboxylic_acid_amide] := true; //fg[fg_thiocarboxylic_acid_sec_amide] := true; if (bond^[get_bond(a_view,a_n)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_n)].arom = true) then //fg[fg_thiolactam_heteroarom] := true else fg[fg_thiolactam] := true; fg[fg_thioxohetarene] := true else fg[fg_thiolactam] := true; end; end; if (is_dialkylamino(a_view,a_n)) or (is_alkylarylamino(a_view,a_n)) or (is_diarylamino(a_view,a_n)) then begin // mod_wrt_ln('==> dialkylamino or diarylamino'); if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_thiocarboxylic_acid_amide] := true; //fg[fg_thiocarboxylic_acid_tert_amide] := true; if (bond^[get_bond(a_view,a_n)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_n)].arom = true) then //fg[fg_thiolactam_heteroarom] := true else fg[fg_thiolactam] := true; fg[fg_thioxohetarene] := true else fg[fg_thiolactam] := true; end; end; end; if (s_count = 1) then begin // anhydride is checked somewhere else if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_thiocarboxylic_acid_deriv] := true; if (is_sulfanyl(a_view,a_s)) then begin fg[fg_thiocarboxylic_acid] := true; end; if (is_alkylsulfanyl(a_view,a_s)) or (is_arylsulfanyl(a_view,a_s)) then begin if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_thiocarboxylic_acid_ester] := true; if (bond^[get_bond(a_view,a_s)].ring_count > 0) then begin if (bond^[get_bond(a_view,a_s)].arom = true) then //fg[fg_thiolactone_heteroarom] := true else fg[fg_thiolactone] := true; fg[fg_thioxohetarene] := true else fg[fg_thiolactone] := true; end; end; end; end; // end Thioxo-C if (is_true_imino_c(a_view)) then begin // debug //mod_wrt_ln('checking for imino'); //fg[fg_carboxylic_acid_deriv] := true; if (o_count = 1) then begin if (bond^[get_bond(a_view,a_o)].arom = false) then fg[fg_carboxylic_acid_deriv] := true; if (is_alkoxy(a_view,a_o)) or (is_aryloxy(a_view,a_o)) then begin if (bond^[get_bond(a_view,a_o)].arom = false) then fg[fg_imido_ester] := true; end; end; if (n_count = 1) and (bond^[get_bond(a_view,a_n)].arom = false) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_deriv] := true; if (is_amino(a_view,a_n)) or (is_subst_amino(a_view,a_n)) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_deriv] := true;fg[fg_carboxylic_acid_amidine] := true; end; if (is_hydrazino(a_view,a_n)) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_amidrazone] := true; end; end; if (n_count = 1) and (bond^[get_bond(a_view,a_n)].arom = true) then // catches also pyridazines, 1,2,3-triazines, etc. fg[fg_iminohetarene] := true; if (s_count = 1) then begin if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_carboxylic_acid_deriv] := true; if (is_alkylsulfanyl(a_view,a_s)) or (is_arylsulfanyl(a_view,a_s)) then begin if (bond^[get_bond(a_view,a_s)].arom = false) then fg[fg_imido_thioester] := true; end; end; end; if is_hydroximino_c(a_view) then begin if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_deriv] := true; if (o_count = 1) then begin if (is_hydroxy(a_view,a_o)) then begin fg[fg_hydroxamic_acid] := true; end; end; end; if is_hydrazono_c(a_view) then begin //debug //mod_wrt_ln('checking for hydrazono'); if (bond^[get_bond(a_view,a_n)].arom = false) then fg[fg_carboxylic_acid_deriv] := true; if (n_count = 1) then begin if (is_amino(a_view,a_n)) or (is_subst_amino(a_view,a_n)) then begin fg[fg_carboxylic_acid_amidrazone] := true; end; end; end; end; procedure chk_co2_sp2(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; o_count, or_count, n_count, nn_count, nnx_count, s_count, sr_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); o_count := 0; or_count := 0; n_count := 0; nn_count := 0; nnx_count := 0; s_count := 0; sr_count := 0; for i := 1 to atom^[a_view].neighbor_count do begin if bond^[(get_bond(a_view,nb[i]))].btype = 'S' then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') then begin if (nb_el = 'O ') then begin inc(o_count); if (is_alkoxy(a_view,nb[i])) or (is_aryloxy(a_view,nb[i])) then inc (or_count); end; if (nb_el = 'N ') then begin inc(n_count); if (is_hydrazino(a_view,nb[i])) then inc(nn_count); if (is_subst_hydrazino(a_view,nb[i])) then inc(nnx_count); // more general... end; if (nb_el = 'S ') then begin inc(s_count); if (is_alkylsulfanyl(a_view,nb[i])) or (is_arylsulfanyl(a_view,nb[i])) then inc (sr_count); end; end; end; end; if (is_oxo_c(a_view)) then begin if (o_count = 2) then begin fg[fg_carbonic_acid_deriv] := true; if (or_count = 1) then fg[fg_carbonic_acid_monoester] := true; if (or_count = 2) then fg[fg_carbonic_acid_diester] := true; end; if (o_count = 1) and (s_count = 1) then begin fg[fg_thiocarbonic_acid_deriv] := true; if (or_count + sr_count = 1) then fg[fg_thiocarbonic_acid_monoester] := true; if (or_count + sr_count = 2) then fg[fg_thiocarbonic_acid_diester] := true; end; if (s_count = 2) then begin fg[fg_thiocarbonic_acid_deriv] := true; if (sr_count = 1) then fg[fg_thiocarbonic_acid_monoester] := true; if (sr_count = 2) then fg[fg_thiocarbonic_acid_diester] := true; end; if (o_count = 1) and (n_count = 1) then begin fg[fg_carbamic_acid_deriv] := true; if (or_count = 0) then fg[fg_carbamic_acid] := true; if (or_count = 1) then fg[fg_carbamic_acid_ester] := true; end; if (s_count = 1) and (n_count = 1) then begin fg[fg_thiocarbamic_acid_deriv] := true; if (sr_count = 0) then fg[fg_thiocarbamic_acid] := true; if (sr_count = 1) then fg[fg_thiocarbamic_acid_ester] := true; end; if (n_count = 2) then begin if (nn_count = 1) then fg[fg_semicarbazide] := true else begin if (nnx_count = 0) then fg[fg_urea] := true; // excludes semicarbazones end; end; end; // end Oxo-C if (is_thioxo_c(a_view)) then begin if (o_count = 2) then begin fg[fg_thiocarbonic_acid_deriv] := true; if (or_count = 1) then fg[fg_thiocarbonic_acid_monoester] := true; if (or_count = 2) then fg[fg_thiocarbonic_acid_diester] := true; end; if (o_count = 1) and (s_count = 1) then begin fg[fg_thiocarbonic_acid_deriv] := true; if (or_count + sr_count = 1) then fg[fg_thiocarbonic_acid_monoester] := true; if (or_count + sr_count = 2) then fg[fg_thiocarbonic_acid_diester] := true; end; if (s_count = 2) then begin fg[fg_thiocarbonic_acid_deriv] := true; if (sr_count = 1) then fg[fg_thiocarbonic_acid_monoester] := true; if (sr_count = 2) then fg[fg_thiocarbonic_acid_diester] := true; end; if (o_count = 1) and (n_count = 1) then begin fg[fg_thiocarbamic_acid_deriv] := true; if (or_count = 0) then fg[fg_thiocarbamic_acid] := true; if (or_count = 1) then fg[fg_thiocarbamic_acid_ester] := true; end; if (s_count = 1) and (n_count = 1) then begin fg[fg_thiocarbamic_acid_deriv] := true; if (sr_count = 0) then fg[fg_thiocarbamic_acid] := true; if (sr_count = 1) then fg[fg_thiocarbamic_acid_ester] := true; end; if (n_count = 2) then begin if (nn_count = 1) then fg[fg_thiosemicarbazide] := true else begin if (nnx_count = 0) then fg[fg_thiourea] := true; // excludes thiosemicarbazones end; end; end; // end Thioxo-C if (is_true_imino_c(a_view)) and (bond^[get_bond(a_view,a_ref)].arom = false) then begin if (o_count = 1) and (n_count = 1) then begin fg[fg_isourea] := true; end; if (s_count = 1) and (n_count = 1) then begin fg[fg_isothiourea] := true; end; if (n_count = 2) then begin fg[fg_guanidine] := true; end; end; // end Imino-C end; procedure chk_co2_sp(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; nb_el : str2; o_count, n_count, s_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); o_count := 0; n_count := 0; s_count := 0; for i := 1 to atom^[a_view].neighbor_count do begin if bond^[(get_bond(a_view,nb[i]))].btype = 'D' then begin nb_el := atom^[(nb[i])].element; if (nb_el <> 'C ') then begin if (nb_el = 'O ') then begin inc(o_count); end; if (nb_el = 'N ') then begin inc(n_count); end; if (nb_el = 'S ') then begin inc(s_count); end; end; end; end; //if (o_count = 2) then fg[fg_carbon_dioxide] := true; //if (s_count = 2) then fg[fg_carbon_disulfide] := true; if (o_count = 1) and (n_count = 1) then fg[fg_isocyanate] := true; if (s_count = 1) and (n_count = 1) then fg[fg_isothiocyanate] := true; if (n_count = 2) then fg[fg_carbodiimide] := true; end; procedure chk_triple(a1,a2:integer); var a1_el, a2_el : str2; begin a1_el := atom^[a1].element; a2_el := atom^[a2].element; if (a1_el = 'C ') and (a2_el = 'C ') and (bond^[get_bond(a1,a2)].arom = false) then fg[fg_alkyne] := true; if (is_nitrile(a1,a2)) then fg[fg_nitrile] := true; if (is_isonitrile(a1,a2)) then fg[fg_isonitrile] := true; if (is_cyanate(a1,a2)) then fg[fg_cyanate] := true; if (is_thiocyanate(a1,a2)) then fg[fg_thiocyanate] := true; end; procedure chk_ccx(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; oh_count, or_count, n_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); oh_count := 0; or_count := 0; n_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin if (is_hydroxy(a_ref,nb[i])) then inc(oh_count); if (is_alkoxy(a_ref,nb[i])) or (is_aryloxy(a_ref,nb[i])) or (is_siloxy(a_ref,nb[i])) then inc(or_count); if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then inc(n_count); end; end; if (oh_count = 1) then fg[fg_enol] := true; if (or_count = 1) then fg[fg_enolether] := true; if (n_count = 1) then fg[fg_enamine] := true; end; procedure chk_xccx(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; oh_count, or_count, n_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); oh_count := 0; or_count := 0; n_count := 0; for i := 1 to atom^[a_view].neighbor_count do begin if bond^[(get_bond(a_view,nb[i]))].btype = 'S' then begin if (is_hydroxy(a_view,nb[i])) then inc(oh_count); if (is_alkoxy(a_view,nb[i])) or (is_aryloxy(a_view,nb[i])) or (is_siloxy(a_view,nb[i])) then inc(or_count); if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then inc(n_count); end; end; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin if (is_hydroxy(a_ref,nb[i])) then inc(oh_count); if (is_alkoxy(a_ref,nb[i])) or (is_aryloxy(a_ref,nb[i])) or (is_siloxy(a_ref,nb[i])) then inc(or_count); if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then inc(n_count); end; end; if (oh_count = 2) then fg[fg_enediol] := true; end; procedure chk_n_o_dbl(a1,a2:integer); var i : integer; nb : neighbor_rec; nb_el : str2; or_count, n_count, c_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a1); or_count := 0; n_count := 0; c_count := 0; for i := 1 to atom^[a1].neighbor_count do begin if (nb[i] <> a2) then begin nb_el := atom^[(nb[i])].element; if (nb_el = 'O ') then inc(or_count); if (nb_el = 'N ') then inc(n_count); if (nb_el = 'C ') then inc(c_count); // if (is_alkyl(a1,nb[i])) or (is_aryl(a1,nb[i])) then inc(c_count); end; end; if ((or_count + n_count + c_count) = 1) then // excludes nitro etc. begin if (or_count = 1) then fg[fg_nitrite] := true; if (c_count = 1) then fg[fg_nitroso_compound] := true; // if (n_count = 1) then fg[fg_nitrosamine] := true; // still missing end; if ((c_count > 1) and (or_count = 0) and (n_count = 0)) then begin fg[fg_n_oxide] := true; end; end; procedure chk_sulfoxide(a1,a2:integer); var i : integer; nb : neighbor_rec; nb_el : str2; o_count, c_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a1); o_count := 0; c_count := 0; for i := 1 to atom^[a1].neighbor_count do begin nb_el := atom^[(nb[i])].element; if (nb_el = 'O ') then inc(o_count); if (is_alkyl(a1,nb[i])) or (is_aryl(a1,nb[i])) then inc(c_count); end; if (o_count = 1) and (c_count = 2) then fg[fg_sulfoxide] := true; end; procedure chk_double(a1,a2:integer); var a1_el, a2_el : str2; begin a1_el := atom^[a1].element; a2_el := atom^[a2].element; if (a1_el = 'C ') and (a2_el <> 'C ') and (bond^[get_bond(a1,a2)].arom = false) then begin if (hetbond_count(a1) = 2) then begin chk_carbonyl_deriv(a1,a2); end; if (hetbond_count(a1) = 3) then begin chk_carboxyl_deriv(a1,a2); end; if (hetbond_count(a1) = 4) then begin if (atom^[a1].atype = 'C2 ') then chk_co2_sp2(a1,a2); if (atom^[a1].atype = 'C1 ') then chk_co2_sp(a1,a2); end; end; // end C=X if (atom^[a1].atype = 'C2 ') and (atom^[a2].atype = 'C2 ') and (bond^[get_bond(a1,a2)].arom = false) then begin if (hetbond_count(a1) = 0) and (hetbond_count(a2) = 2) then fg[fg_ketene_acetal_deriv] := true; if (hetbond_count(a1) = 0) and (hetbond_count(a2) = 1) then chk_ccx(a1,a2); if (hetbond_count(a1) = 1) and (hetbond_count(a2) = 1) then chk_xccx(a1,a2); if (hetbond_count(a1) = 0) and (hetbond_count(a2) = 0) and (atom^[a1].arom = false) and (atom^[a2].arom = false) then fg[fg_alkene] := true; end; if (a1_el = 'N ') and (a2_el = 'N ') and (hetbond_count(a1) = 2) and (hetbond_count(a2) = 2) and (bond^[get_bond(a1,a2)].arom = false) and (atom^[a1].neighbor_count = 2) and (atom^[a2].neighbor_count = 2) then fg[fg_azo_compound] := true; if (a1_el = 'N ') and (a2_el = 'O ') then chk_n_o_dbl(a1,a2); if (a1_el = 'S ') and (a2_el = 'O ') then chk_sulfoxide(a1,a2); end; procedure chk_c_hal(a1,a2:integer); var a2_el : str2; begin a2_el := atom^[a2].element; fg[fg_halogen_deriv] := true; if atom^[a1].arom then begin fg[fg_aryl_halide] := true; if (a2_el = 'F ') then fg[fg_aryl_fluoride] := true; if (a2_el = 'CL') then fg[fg_aryl_chloride] := true; if (a2_el = 'BR') then fg[fg_aryl_bromide] := true; if (a2_el = 'I ') then fg[fg_aryl_iodide] := true; end else begin if (atom^[a1].atype = 'C3 ') and (hetbond_count(a1) <= 2) then begin // alkyl halides fg[fg_alkyl_halide] := true; if (a2_el = 'F ') then fg[fg_alkyl_fluoride] := true; if (a2_el = 'CL') then fg[fg_alkyl_chloride] := true; if (a2_el = 'BR') then fg[fg_alkyl_bromide] := true; if (a2_el = 'I ') then fg[fg_alkyl_iodide] := true; end; if (atom^[a1].atype = 'C2 ') and (hetbond_count(a1) = 3) then begin // acyl halides and related compounds if (is_oxo_c(a1)) then begin fg[fg_acyl_halide] := true; if (a2_el = 'F ') then fg[fg_acyl_fluoride] := true; if (a2_el = 'CL') then fg[fg_acyl_chloride] := true; if (a2_el = 'BR') then fg[fg_acyl_bromide] := true; if (a2_el = 'I ') then fg[fg_acyl_iodide] := true; end; if (is_thioxo_c(a1)) then begin fg[fg_thiocarboxylic_acid_deriv] := true; end; if (is_imino_c(a1)) then begin fg[fg_imidoyl_halide] := true; end; end; if (atom^[a1].atype = 'C2 ') and (hetbond_count(a1) = 4) then begin // chloroformates etc. fg[fg_co2_deriv] := true; if (is_oxo_c(a1)) then begin fg[fg_carbonic_acid_deriv] := true; if (is_alkoxycarbonyl(a2,a1)) or (is_aryloxycarbonyl(a2,a1)) then fg[fg_carbonic_acid_ester_halide] := true; if (is_carbamoyl(a2,a1)) then begin fg[fg_carbamic_acid_deriv] := true; fg[fg_carbamic_acid_halide] := true; end; end; if (is_thioxo_c(a1)) then begin fg[fg_thiocarbonic_acid_deriv] := true; if (is_alkoxythiocarbonyl(a2,a1)) or (is_aryloxythiocarbonyl(a2,a1)) then fg[fg_thiocarbonic_acid_ester_halide] := true; if (is_thiocarbamoyl(a2,a1)) then begin fg[fg_thiocarbamic_acid_deriv] := true; fg[fg_thiocarbamic_acid_halide] := true; end; end; end; // still missing: polyhalogen compounds (-CX2H, -CX3) end; // end of non-aromatic halogen compounds end; procedure chk_c_o(a1,a2:integer); begin // ignore heteroaromatic rings (like furan, thiophene, etc.) if (bond^[get_bond(a1,a2)].arom = true) then exit; if (is_true_alkyl(a2,a1)) and (is_hydroxy(a1,a2)) then begin fg[fg_hydroxy] := true; fg[fg_alcohol] := true; if atom^[a1].neighbor_count <= 2 then fg[fg_prim_alcohol] := true; if atom^[a1].neighbor_count = 3 then fg[fg_sec_alcohol] := true; if atom^[a1].neighbor_count = 4 then fg[fg_tert_alcohol] := true; end; if (is_aryl(a2,a1)) and (is_hydroxy(a1,a2)) then begin fg[fg_hydroxy] := true; fg[fg_phenol] := true; // still missing: check for 1,2-diphenol end; if (is_true_alkyl(a2,a1)) and (is_true_alkoxy(a1,a2)) then begin fg[fg_ether] := true; fg[fg_dialkylether] := true; end; if ((is_true_alkyl(a2,a1)) and (is_aryloxy(a1,a2))) or ((is_aryl(a2,a1)) and (is_true_alkoxy(a1,a2))) then begin fg[fg_ether] := true; fg[fg_alkylarylether] := true; end; if (is_aryl(a2,a1)) and (is_aryloxy(a1,a2)) then begin fg[fg_ether] := true; fg[fg_diarylether] := true; end; end; procedure chk_c_s(a1,a2:integer); var i : integer; nb : neighbor_rec; nb_el : str2; o_count, oh_count, or_count, n_count, c_count, hal_count : integer; begin // ignore heteroaromatic rings (like furan, thiophene, etc.) if (bond^[get_bond(a1,a2)].arom = true) then exit; if (is_alkyl(a2,a1)) and (is_sulfanyl(a1,a2)) then begin fg[fg_thiol] := true; fg[fg_alkylthiol] := true; end; if (is_aryl(a2,a1)) and (is_sulfanyl(a1,a2)) then begin fg[fg_thiol] := true; fg[fg_arylthiol] := true; end; if (is_true_alkyl(a2,a1)) and (is_true_alkylsulfanyl(a1,a2)) then fg[fg_thioether] := true; if ((is_true_alkyl(a2,a1)) and (is_arylsulfanyl(a1,a2))) or ((is_aryl(a2,a1)) and (is_true_alkylsulfanyl(a1,a2))) then fg[fg_thioether] := true; if (is_aryl(a2,a1)) and (is_arylsulfanyl(a1,a2)) then fg[fg_thioether] := true; // check for sulfinic/sulfenic acid derivatives fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a2); o_count := 0; oh_count := 0; or_count := 0; n_count := 0; c_count := 0; hal_count := 0; for i := 1 to atom^[a2].neighbor_count do begin nb_el := atom^[(nb[i])].element; if (is_alkyl(a2,nb[i])) or (is_aryl(a2,nb[i])) then inc(c_count); if (is_hydroxy(a2,nb[i])) then inc(oh_count); if (is_alkoxy(a2,nb[i])) or (is_aryloxy(a2,nb[i])) then inc(or_count); if (is_amino(a2,nb[i])) or (is_subst_amino(a2,nb[i])) then inc(n_count); if (nb_el = 'F ') or (nb_el = 'CL') or (nb_el = 'BR') or (nb_el = 'I ') then inc(hal_count); if (nb_el = 'O ') then inc(o_count); end; if (c_count = 1) then begin if (atom^[a2].neighbor_count = 3) and ((o_count - (oh_count + or_count)) = 1) then // sulfinic acid & derivs begin fg[fg_sulfinic_acid_deriv] := true; if (oh_count = 1) then fg[fg_sulfinic_acid] := true; if (or_count = 1) then fg[fg_sulfinic_acid_ester] := true; if (hal_count = 1) then fg[fg_sulfinic_acid_halide] := true; if (n_count = 1) then fg[fg_sulfinic_acid_amide] := true; end; if (atom^[a2].neighbor_count = 2) and ((o_count - (oh_count + or_count)) = 0) then // sulfenic acid & derivs begin fg[fg_sulfenic_acid_deriv] := true; if (oh_count = 1) then fg[fg_sulfenic_acid] := true; if (or_count = 1) then fg[fg_sulfenic_acid_ester] := true; if (hal_count = 1) then fg[fg_sulfenic_acid_halide] := true; if (n_count = 1) then fg[fg_sulfenic_acid_amide] := true; end; end; end; procedure chk_c_n(a1,a2:integer); begin // ignore heteroaromatic rings (like furan, thiophene, pyrrol, etc.) if (atom^[a2].arom = true) then exit; if (is_true_alkyl(a2,a1)) and (is_amino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_prim_amine] := true; fg[fg_prim_aliph_amine] := true; end; if (is_aryl(a2,a1)) and (is_amino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_prim_amine] := true; fg[fg_prim_arom_amine] := true; end; if (is_true_alkyl(a2,a1)) and (is_true_alkylamino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_sec_amine] := true; fg[fg_sec_aliph_amine] := true; end; if (is_aryl(a2,a1)) and (is_true_alkylamino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_sec_amine] := true; fg[fg_sec_mixed_amine] := true; end; if (is_aryl(a2,a1)) and (is_arylamino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_sec_amine] := true; fg[fg_sec_arom_amine] := true; end; if (is_true_alkyl(a2,a1)) and (is_true_dialkylamino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_tert_amine] := true; fg[fg_tert_aliph_amine] := true; end; if ((is_true_alkyl(a2,a1)) and (is_diarylamino(a1,a2))) or ((is_aryl(a2,a1)) and (is_true_dialkylamino(a1,a2))) then begin fg[fg_amine] := true; fg[fg_tert_amine] := true; fg[fg_tert_mixed_amine] := true; end; if (is_aryl(a2,a1)) and (is_diarylamino(a1,a2)) then begin fg[fg_amine] := true; fg[fg_tert_amine] := true; fg[fg_tert_arom_amine] := true; end; if ((is_alkyl(a2,a1)) or (is_aryl(a2,a1))) and (is_hydroxylamino(a1,a2)) then fg[fg_hydroxylamine] := true; if ((is_alkyl(a2,a1)) or (is_aryl(a2,a1)) or (is_acyl(a2,a1))) and (is_hydrazino(a1,a2)) then fg[fg_hydrazine] := true; if ((is_alkyl(a2,a1)) or (is_aryl(a2,a1))) and (is_azido(a1,a2)) then fg[fg_azide] := true; if ((is_alkyl(a2,a1)) or (is_aryl(a2,a1))) and (is_diazonium(a1,a2)) then fg[fg_diazonium_salt] := true; if ((is_alkyl(a2,a1)) or (is_aryl(a2,a1))) and (is_nitro(a1,a2)) then fg[fg_nitro_compound] := true; end; procedure chk_c_c(a1,a2:integer); var i : integer; nb : neighbor_rec; oh_count, nhr_count : integer; begin // ignore aromatic rings if (atom^[a2].arom = true) then exit; //check for 1,2-diols and 1,2-aminoalcoholes if (atom^[a1].atype = 'C3 ') and (atom^[a2].atype = 'C3 ') then begin if (hetbond_count(a1) = 1) and (hetbond_count(a2) = 1) then begin oh_count := 0; nhr_count := 0; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a1); for i := 1 to atom^[a1].neighbor_count do begin if nb[i] <> a2 then begin if (is_hydroxy(a1,nb[i])) then inc(oh_count); if (is_amino(a1,nb[i])) or (is_alkylamino(a1,nb[i])) or (is_arylamino(a1,nb[i])) then inc(nhr_count); end; end; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a2); for i := 1 to atom^[a2].neighbor_count do begin if nb[i] <> a1 then begin if (is_hydroxy(a2,nb[i])) then inc(oh_count); if (is_amino(a2,nb[i])) or (is_alkylamino(a2,nb[i])) or (is_arylamino(a2,nb[i])) then inc(nhr_count); end; end; if oh_count = 2 then fg[fg_1_2_diol] := true; if (oh_count = 1) and (nhr_count = 1) then fg[fg_1_2_aminoalcohol] := true; end; end; // check for alpha-aminoacids and alpha-hydroxyacids if (atom^[a1].atype = 'C3 ') and (atom^[a2].atype = 'C2 ') then begin if (hetbond_count(a1) = 1) and (hetbond_count(a2) = 3) then begin oh_count := 0; nhr_count := 0; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a1); for i := 1 to atom^[a1].neighbor_count do begin if nb[i] <> a2 then begin if (is_hydroxy(a1,nb[i])) then inc(oh_count); if (is_amino(a1,nb[i])) or (is_alkylamino(a1,nb[i])) or (is_arylamino(a1,nb[i])) then inc(nhr_count); end; end; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a2); for i := 1 to atom^[a2].neighbor_count do begin if nb[i] <> a1 then begin if (is_hydroxy(a2,nb[i])) then inc(oh_count); end; end; if (oh_count = 2) and (is_oxo_C(a2)) then fg[fg_alpha_hydroxyacid] := true; if (oh_count = 1) and (nhr_count = 1) and (is_oxo_C(a2)) then fg[fg_alpha_aminoacid] := true; end; end; end; procedure chk_x_y_single(a_view,a_ref:integer); begin if (atom^[a_view].atype = 'O3 ') and (atom^[a_ref].atype = 'O3 ') then begin if (is_hydroxy(a_ref,a_view)) or (is_hydroxy(a_view,a_ref)) then fg[fg_hydroperoxide] := true; if ((is_alkoxy(a_ref,a_view)) or (is_aryloxy(a_ref,a_view)) or (is_siloxy(a_ref,a_view))) and ((is_alkoxy(a_view,a_ref)) or (is_aryloxy(a_view,a_ref)) or (is_siloxy(a_view,a_ref))) then fg[fg_peroxide] := true; end; // still missing: peracid if (atom^[a_view].atype = 'S3 ') and (atom^[a_ref].atype = 'S3 ') then begin if (atom^[a_view].neighbor_count = 2) and (atom^[a_ref].neighbor_count = 2) then fg[fg_disulfide] := true; end; if (atom^[a_view].element = 'N ') and (atom^[a_ref].element = 'N ') and (hetbond_count(a_view) = 1) and (hetbond_count(a_ref) = 1) then begin //if ((is_amino(a_ref,a_view)) or // (is_subst_amino(a_ref,a_view)) or // (is_acylamino(a_ref,a_view))) and // ((is_amino(a_view,a_ref)) or // (is_subst_amino(a_view,a_ref)) or // (is_acylamino(a_ref,a_view))) then if (bond^[get_bond(a_view,a_ref)].arom = false) then fg[fg_hydrazine] := true; end; if (atom^[a_view].element = 'N ') and (atom^[a_ref].atype = 'O3 ') then begin // bond is in "opposite" direction if ((is_alkoxy(a_view,a_ref)) or (is_aryloxy(a_view,a_ref))) and (is_nitro(a_ref,a_view)) then fg[fg_nitrate] := true; end; if (atom^[a_view].element = 'S ') and (atom^[a_ref].element = 'O ') then chk_sulfoxide(a_view,a_ref); end; procedure chk_single(a1,a2:integer); var a1_el, a2_el : str2; begin a1_el := atom^[a1].element; a2_el := atom^[a2].element; if (a1_el = 'C ') and ((a2_el = 'F ') or (a2_el = 'CL') or (a2_el = 'BR') or (a2_el = 'I ')) then chk_c_hal(a1,a2); if (a1_el = 'C ') and (a2_el = 'O ') then chk_c_o(a1,a2); if (a1_el = 'C ') and (a2_el = 'S ') then chk_c_s(a1,a2); if (a1_el = 'C ') and (a2_el = 'N ') then chk_c_n(a1,a2); if (a1_el = 'C ') and (is_metal(a2) and (is_cyano_c(a1) = false)) then begin fg[fg_organometallic] := true; if (a2_el = 'LI') then fg[fg_organolithium] := true; if (a2_el = 'MG') then fg[fg_organomagnesium] := true; end; if (a1_el = 'C ') and (a2_el = 'C ') then chk_c_c(a1,a2); if (a1_el <> 'C ') and (a2_el <> 'C ') then chk_x_y_single(a1,a2); end; procedure chk_carbonyl_deriv_sp3(a_ref:integer); var i : integer; nb : neighbor_rec; oh_count, or_count, n_count, sh_count, sr_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); oh_count := 0; or_count := 0; n_count := 0; sh_count := 0; sr_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if (is_hydroxy(a_ref,nb[i])) then inc(oh_count); if (is_alkoxy(a_ref,nb[i])) or (is_aryloxy(a_ref,nb[i])) then inc(or_count); if (is_sulfanyl(a_ref,nb[i])) then inc(sh_count); if (is_alkylsulfanyl(a_ref,nb[i])) or (is_arylsulfanyl(a_ref,nb[i])) then inc(sr_count); if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then inc(n_count); end; if (oh_count = 2) then fg[fg_carbonyl_hydrate] := true; if (oh_count = 1) and (or_count = 1) then fg[fg_hemiacetal] := true; if (or_count = 2) then fg[fg_acetal] := true; if ((oh_count = 1) or (or_count = 1)) and (n_count = 1) then fg[fg_hemiaminal] := true; if (n_count = 2) then fg[fg_aminal] := true; if ((sh_count = 1) or (sr_count = 1)) and (n_count = 1) then fg[fg_thiohemiaminal] := true; if (sr_count = 2) then fg[fg_thioacetal] := true; end; procedure chk_carboxyl_deriv_sp3(a_ref:integer); var i : integer; nb : neighbor_rec; or_count, n_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); or_count := 0; n_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if (is_alkoxy(a_ref,nb[i])) or (is_aryloxy(a_ref,nb[i])) or (is_siloxy(a_ref,nb[i])) then inc(or_count); if (atom^[(nb[i])].atype = 'N3 ') or (atom^[(nb[i])].atype = 'NAM') then inc(n_count); end; if (or_count + n_count > 1) then fg[fg_orthocarboxylic_acid_deriv] := true; if (or_count = 3) then fg[fg_carboxylic_acid_orthoester] := true; if (or_count = 2) and (n_count = 1) then fg[fg_carboxylic_acid_amide_acetal] := true; end; procedure chk_anhydride(a_ref:integer); var i : integer; nb : neighbor_rec; acyl_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); acyl_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if (is_acyl(a_ref,nb[i])) or (is_carbamoyl(a_ref,nb[i])) then inc(acyl_count); end; if (acyl_count = 2) and (atom^[a_ref].atype = 'O3 ') then begin fg[fg_carboxylic_acid_deriv] := true; fg[fg_carboxylic_acid_anhydride] := true; end; end; procedure chk_imide(a_ref:integer); var i : integer; nb : neighbor_rec; acyl_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); acyl_count := 0; for i := 1 to atom^[a_ref].neighbor_count do begin if (is_acyl(a_ref,nb[i])) or (is_carbamoyl(a_ref,nb[i])) then inc(acyl_count); end; if (acyl_count = 2) and (atom^[a_ref].element = 'N ') then begin fg[fg_carboxylic_acid_deriv] := true; fg[fg_carboxylic_acid_imide] := true; if (atom^[a_ref].neighbor_count = 2) then fg[fg_carboxylic_acid_unsubst_imide] := true; if (atom^[a_ref].neighbor_count = 3) then fg[fg_carboxylic_acid_subst_imide] := true; end; end; procedure chk_12diphenol(a_view,a_ref:integer); var i : integer; nb : neighbor_rec; oh_count : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_view); oh_count := 0; for i := 1 to atom^[a_view].neighbor_count do begin if bond^[(get_bond(a_view,nb[i]))].btype = 'S' then begin if (is_hydroxy(a_view,nb[i])) then inc(oh_count); end; end; fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); for i := 1 to atom^[a_ref].neighbor_count do begin if bond^[(get_bond(a_ref,nb[i]))].btype = 'S' then begin if (is_hydroxy(a_ref,nb[i])) then inc(oh_count); end; end; if (oh_count = 2) then fg[fg_1_2_diphenol] := true; end; procedure chk_arom_fg(a1,a2:integer); begin if (hetbond_count(a1) = 1) and (hetbond_count(a2) = 1) then chk_12diphenol(a1,a2); end; function is_arene(r_id:integer):boolean; var i,j : integer; r : boolean; testring : ringpath_type; ring_size : integer; a_prev, a_ref : integer; begin r := false; if (r_id < 1) or (r_id > n_rings) then begin is_arene := false; exit; end; fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[r_id,j] > 0 then testring[j] := ring^[r_id,j]; ring_size := path_length(testring); if (ring_size > 2) then begin r := true; a_prev := testring[ring_size]; for i := 1 to ring_size do begin a_ref := testring[i]; if (bond^[get_bond(a_prev,a_ref)].arom = false) then r := false; a_prev := a_ref; end; end; is_arene := r; end; function is_heterocycle(r_id:integer):boolean; var i,j : integer; r : boolean; testring : ringpath_type; ring_size : integer; a_ref : integer; begin r := false; if (r_id < 1) or (r_id > n_rings) then begin is_heterocycle := false; exit; end; fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[r_id,j] > 0 then testring[j] := ring^[r_id,j]; ring_size := path_length(testring); if (ring_size > 2) then begin for i := 1 to ring_size do begin a_ref := testring[i]; if (atom^[a_ref].element <> 'C ') then r := true; end; end; is_heterocycle := r; end; procedure chk_oxo_thioxo_imino_hetarene(r_id:integer); var i,j : integer; testring : ringpath_type; ring_size : integer; a_ref : integer; begin if (r_id < 1) or (r_id > n_rings) then exit; fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[r_id,j] > 0 then testring[j] := ring^[r_id,j]; ring_size := path_length(testring); if (is_arene(r_id)) and (odd(ring_size) = false) then begin for i := 1 to ring_size do begin a_ref := testring[i]; if (is_oxo_c(a_ref)) then fg[fg_oxohetarene] := true; if (is_thioxo_c(a_ref)) then fg[fg_thioxohetarene] := true; if (is_exocyclic_imino_c(a_ref,r_id)) then fg[fg_iminohetarene] := true; end; end; end; procedure chk_ion(a_ref:integer); var i : integer; nb : neighbor_rec; charge : integer; begin fillchar(nb,sizeof(neighbor_rec),0); nb := get_neighbors(a_ref); charge := atom^[a_ref].formal_charge; if charge <> 0 then begin // check if charge is neutralized by an adjacent opposite charge for i := 1 to atom^[a_ref].neighbor_count do begin charge := charge + atom^[(nb[i])].formal_charge; end; if charge > 0 then fg[fg_cation] := true; if charge < 0 then fg[fg_anion] := true; end; end; procedure chk_functionalgroups; var i : integer; a1,a2 : integer; bt : char; pos_chg, neg_chg : integer; begin if (n_atoms < 1) or (n_bonds < 1) then exit; pos_chg := 0; neg_chg := 0; for i := 1 to n_atoms do // a few groups are best discovered in the atom list begin if (atom^[i].atype = 'SO2') then chk_so2_deriv(i); //if (atom^[i].atype = 'SO ') then fg[fg_sulfoxide] := true; // do another check in the bond list!! if (atom^[i].element = 'P ') then chk_p_deriv(i); if (atom^[i].element = 'B ') then chk_b_deriv(i); if (atom^[i].atype = 'N3+') or (atom^[i].formal_charge > 0) then chk_ammon(i); if (atom^[i].atype = 'C3 ') and (hetbond_count(i) = 2) then chk_carbonyl_deriv_sp3(i); if (atom^[i].atype = 'C3 ') and (hetbond_count(i) = 3) then chk_carboxyl_deriv_sp3(i); if (atom^[i].atype = 'O3 ') and (atom^[i].neighbor_count = 2) then chk_anhydride(i); if ((atom^[i].atype = 'N3 ') or (atom^[i].atype = 'NAM')) and (atom^[i].neighbor_count >= 2) then chk_imide(i); if (atom^[i].formal_charge > 0) then pos_chg := pos_chg + atom^[i].formal_charge; if (atom^[i].formal_charge < 0) then neg_chg := neg_chg + atom^[i].formal_charge; chk_ion(i); end; for i := 1 to n_bonds do // most groups are best discovered in the bond list begin a1 := bond^[i].a1; a2 := bond^[i].a2; bt := bond^[i].btype; if (is_heavyatom(a1)) and (is_heavyatom(a2)) then begin orient_bond(a1,a2); if (bt = 'T') then chk_triple(a1,a2); if (bt = 'D') then chk_double(a1,a2); if (bt = 'S') then chk_single(a1,a2); if (bond^[i].arom) then chk_arom_fg(a1,a2); end; end; if (n_rings > 0) then begin for i := 1 to n_rings do begin chk_oxo_thioxo_imino_hetarene(i); if (is_arene(i)) then fg[fg_aromatic] := true; if (is_heterocycle(i)) then fg[fg_heterocycle] := true; end; end; if (pos_chg + neg_chg) > 0 then fg[fg_cation] := true; if (pos_chg + neg_chg) < 0 then fg[fg_anion] := true; end; procedure mod_wrt_noln_fg_text; begin if fg[fg_cation] then mod_wrt_ln('cation'); if fg[fg_anion] then mod_wrt_ln('anion'); // if fg[fg_carbonyl] then mod_wrt_ln('carbonyl compound'); if fg[fg_aldehyde] then mod_wrt_ln('aldehyde'); if fg[fg_ketone] then mod_wrt_ln('ketone'); // if fg[fg_thiocarbonyl] then mod_wrt_ln('thiocarbonyl compound'); if fg[fg_thioaldehyde] then mod_wrt_ln('thioaldehyde'); if fg[fg_thioketone] then mod_wrt_ln('thioketone'); if fg[fg_imine] then mod_wrt_ln('imine'); if fg[fg_hydrazone] then mod_wrt_ln('hydrazone'); if fg[fg_semicarbazone] then mod_wrt_ln('semicarbazone'); if fg[fg_thiosemicarbazone] then mod_wrt_ln('thiosemicarbazone'); if fg[fg_oxime] then mod_wrt_ln('oxime'); if fg[fg_oxime_ether] then mod_wrt_ln('oxime ether'); if fg[fg_ketene] then mod_wrt_ln('ketene'); if fg[fg_ketene_acetal_deriv] then mod_wrt_ln('ketene acetal or derivative'); if fg[fg_carbonyl_hydrate] then mod_wrt_ln('carbonyl hydrate'); if fg[fg_hemiacetal] then mod_wrt_ln('hemiacetal'); if fg[fg_acetal] then mod_wrt_ln('acetal'); if fg[fg_hemiaminal] then mod_wrt_ln('hemiaminal'); if fg[fg_aminal] then mod_wrt_ln('aminal'); if fg[fg_thiohemiaminal] then mod_wrt_ln('hemithioaminal'); if fg[fg_thioacetal] then mod_wrt_ln('thioacetal'); if fg[fg_enamine] then mod_wrt_ln('enamine'); if fg[fg_enol] then mod_wrt_ln('enol'); if fg[fg_enolether] then mod_wrt_ln('enol ether'); // if fg[fg_hydroxy] then mod_wrt_ln('hydroxy compound'); // if fg[fg_alcohol] then mod_wrt_ln('alcohol'); if fg[fg_prim_alcohol] then mod_wrt_ln('primary alcohol'); if fg[fg_sec_alcohol] then mod_wrt_ln('secondary alcohol'); if fg[fg_tert_alcohol] then mod_wrt_ln('tertiary alcohol'); if fg[fg_1_2_diol] then mod_wrt_ln('1,2-diol'); if fg[fg_1_2_aminoalcohol] then mod_wrt_ln('1,2-aminoalcohol'); if fg[fg_phenol] then mod_wrt_ln('phenol or hydroxyhetarene'); if fg[fg_1_2_diphenol] then mod_wrt_ln('1,2-diphenol'); if fg[fg_enediol] then mod_wrt_ln('enediol'); // if fg[fg_ether] then mod_wrt_ln('ether'); if fg[fg_dialkylether] then mod_wrt_ln('dialkyl ether'); if fg[fg_alkylarylether] then mod_wrt_ln('alkyl aryl ether '); if fg[fg_diarylether] then mod_wrt_ln('diaryl ether'); if fg[fg_thioether] then mod_wrt_ln('thioether'); if fg[fg_disulfide] then mod_wrt_ln('disulfide'); if fg[fg_peroxide] then mod_wrt_ln('peroxide'); if fg[fg_hydroperoxide] then mod_wrt_ln('hydroperoxide '); if fg[fg_hydrazine] then mod_wrt_ln('hydrazine derivative'); if fg[fg_hydroxylamine] then mod_wrt_ln('hydroxylamine'); // if fg[fg_amine] then mod_wrt_ln('amine'); if fg[fg_prim_amine] then mod_wrt_ln('primary amine'); if fg[fg_prim_aliph_amine] then mod_wrt_ln('primary aliphatic amine (alkylamine)'); if fg[fg_prim_arom_amine] then mod_wrt_ln('primary aromatic amine'); if fg[fg_sec_amine] then mod_wrt_ln('secondary amine'); if fg[fg_sec_aliph_amine] then mod_wrt_ln('secondary aliphatic amine (dialkylamine)'); if fg[fg_sec_mixed_amine] then mod_wrt_ln('secondary aliphatic/aromatic amine (alkylarylamine)'); if fg[fg_sec_arom_amine] then mod_wrt_ln('secondary aromatic amine (diarylamine)'); if fg[fg_tert_amine] then mod_wrt_ln('tertiary amine'); if fg[fg_tert_aliph_amine] then mod_wrt_ln('tertiary aliphatic amine (trialkylamine)'); if fg[fg_tert_mixed_amine] then mod_wrt_ln('tertiary aliphatic/aromatic amine (alkylarylamine)'); if fg[fg_tert_arom_amine] then mod_wrt_ln('tertiary aromatic amine (triarylamine)'); if fg[fg_quart_ammonium] then mod_wrt_ln('quaternary ammonium salt'); if fg[fg_n_oxide] then mod_wrt_ln('N-oxide'); // if fg[fg_halogen_deriv] then mod_wrt_ln('halogen derivative'); // if fg[fg_alkyl_halide] then mod_wrt_ln('alkyl halide'); if fg[fg_alkyl_fluoride] then mod_wrt_ln('alkyl fluoride'); if fg[fg_alkyl_chloride] then mod_wrt_ln('alkyl chloride'); if fg[fg_alkyl_bromide] then mod_wrt_ln('alkyl bromide'); if fg[fg_alkyl_iodide] then mod_wrt_ln('alkyl iodide'); // if fg[fg_aryl_halide] then mod_wrt_ln('aryl halide'); if fg[fg_aryl_fluoride] then mod_wrt_ln('aryl fluoride'); if fg[fg_aryl_chloride] then mod_wrt_ln('aryl chloride'); if fg[fg_aryl_bromide] then mod_wrt_ln('aryl bromide'); if fg[fg_aryl_iodide] then mod_wrt_ln('aryl iodide'); if fg[fg_organometallic] then mod_wrt_ln('organometallic compound'); if fg[fg_organolithium] then mod_wrt_ln('organolithium compound'); if fg[fg_organomagnesium] then mod_wrt_ln('organomagnesium compound'); // if fg[fg_carboxylic_acid_deriv] then mod_wrt_ln('carboxylic acid derivative'); if fg[fg_carboxylic_acid] then mod_wrt_ln('carboxylic acid'); if fg[fg_carboxylic_acid_salt] then mod_wrt_ln('carboxylic acid salt'); if fg[fg_carboxylic_acid_ester] then mod_wrt_ln('carboxylic acid ester'); if fg[fg_lactone] then mod_wrt_ln('lactone'); // if fg[fg_carboxylic_acid_amide] then mod_wrt_ln('carboxylic acid amide'); if fg[fg_carboxylic_acid_prim_amide] then mod_wrt_ln('primary carboxylic acid amide'); if fg[fg_carboxylic_acid_sec_amide] then mod_wrt_ln('secondary carboxylic acid amide'); if fg[fg_carboxylic_acid_tert_amide] then mod_wrt_ln('tertiary carboxylic acid amide'); if fg[fg_lactam] then mod_wrt_ln('lactam'); if fg[fg_carboxylic_acid_hydrazide] then mod_wrt_ln('carboxylic acid hydrazide'); if fg[fg_carboxylic_acid_azide] then mod_wrt_ln('carboxylic acid azide'); if fg[fg_hydroxamic_acid] then mod_wrt_ln('hydroxamic acid'); if fg[fg_carboxylic_acid_amidine] then mod_wrt_ln('carboxylic acid amidine'); if fg[fg_carboxylic_acid_amidrazone] then mod_wrt_ln('carboxylic acid amidrazone'); if fg[fg_nitrile] then mod_wrt_ln('carbonitrile'); // if fg[fg_acyl_halide] then mod_wrt_ln('acyl halide'); if fg[fg_acyl_fluoride] then mod_wrt_ln('acyl fluoride'); if fg[fg_acyl_chloride] then mod_wrt_ln('acyl chloride'); if fg[fg_acyl_bromide] then mod_wrt_ln('acyl bromide'); if fg[fg_acyl_iodide] then mod_wrt_ln('acyl iodide'); if fg[fg_acyl_cyanide] then mod_wrt_ln('acyl cyanide'); if fg[fg_imido_ester] then mod_wrt_ln('imido ester'); if fg[fg_imidoyl_halide] then mod_wrt_ln('imidoyl halide'); // if fg[fg_thiocarboxylic_acid_deriv] then mod_wrt_ln('thiocarboxylic acid derivative'); if fg[fg_thiocarboxylic_acid] then mod_wrt_ln('thiocarboxylic acid'); if fg[fg_thiocarboxylic_acid_ester] then mod_wrt_ln('thiocarboxylic acid ester'); if fg[fg_thiolactone] then mod_wrt_ln('thiolactone'); if fg[fg_thiocarboxylic_acid_amide] then mod_wrt_ln('thiocarboxylic acid amide'); if fg[fg_thiolactam] then mod_wrt_ln('thiolactam'); if fg[fg_imido_thioester] then mod_wrt_ln('imidothioester'); if fg[fg_oxohetarene] then mod_wrt_ln('oxo(het)arene'); if fg[fg_thioxohetarene] then mod_wrt_ln('thioxo(het)arene'); if fg[fg_iminohetarene] then mod_wrt_ln('imino(het)arene'); if fg[fg_orthocarboxylic_acid_deriv] then mod_wrt_ln('orthocarboxylic acid derivative'); if fg[fg_carboxylic_acid_orthoester] then mod_wrt_ln('orthoester'); if fg[fg_carboxylic_acid_amide_acetal] then mod_wrt_ln('amide acetal'); if fg[fg_carboxylic_acid_anhydride] then mod_wrt_ln('carboxylic acid anhydride'); // if fg[fg_carboxylic_acid_imide] then mod_wrt_ln('carboxylic acid imide'); if fg[fg_carboxylic_acid_unsubst_imide] then mod_wrt_ln('carboxylic acid imide, N-unsubstituted'); if fg[fg_carboxylic_acid_subst_imide] then mod_wrt_ln('carboxylic acid imide, N-substituted'); if fg[fg_co2_deriv] then mod_wrt_ln('CO2 derivative (general)'); // if fg[fg_carbonic_acid_deriv] then mod_wrt_ln('carbonic acid dervivative'); if fg[fg_carbonic_acid_monoester] then mod_wrt_ln('carbonic acid monoester'); if fg[fg_carbonic_acid_diester] then mod_wrt_ln('carbonic acid diester'); if fg[fg_carbonic_acid_ester_halide] then mod_wrt_ln('carbonic acid ester halide (alkyl/aryl haloformate)'); if fg[fg_thiocarbonic_acid_deriv] then mod_wrt_ln('thiocarbonic acid derivative'); if fg[fg_thiocarbonic_acid_monoester] then mod_wrt_ln('thiocarbonic acid monoester'); if fg[fg_thiocarbonic_acid_diester] then mod_wrt_ln('thiocarbonic acid diester'); if fg[fg_thiocarbonic_acid_ester_halide] then mod_wrt_ln('thiocarbonic acid halide (alkyl/aryl halothioformate)'); // if fg[fg_carbamic_acid_deriv] then mod_wrt_ln('carbamic acid derivative'); if fg[fg_carbamic_acid] then mod_wrt_ln('carbamic acid'); if fg[fg_carbamic_acid_ester] then mod_wrt_ln('carbamic acid ester (urethane)'); if fg[fg_carbamic_acid_halide] then mod_wrt_ln('carbamic acid halide (haloformic acid amide)'); // if fg[fg_thiocarbamic_acid_deriv] then mod_wrt_ln('thiocarbamic acid derivative'); if fg[fg_thiocarbamic_acid] then mod_wrt_ln('thiocarbamic acid'); if fg[fg_thiocarbamic_acid_ester] then mod_wrt_ln('thiocarbamic acid ester'); if fg[fg_thiocarbamic_acid_halide] then mod_wrt_ln('thiocarbamic acid halide (halothioformic acid amide)'); if fg[fg_urea] then mod_wrt_ln('urea'); if fg[fg_isourea] then mod_wrt_ln('isourea'); if fg[fg_thiourea] then mod_wrt_ln('thiourea'); if fg[fg_isothiourea] then mod_wrt_ln('isothiourea'); if fg[fg_guanidine] then mod_wrt_ln('guanidine'); if fg[fg_semicarbazide] then mod_wrt_ln('semicarbazide'); if fg[fg_thiosemicarbazide] then mod_wrt_ln('thiosemicarbazide'); if fg[fg_azide] then mod_wrt_ln('azide'); if fg[fg_azo_compound] then mod_wrt_ln('azo compound'); if fg[fg_diazonium_salt] then mod_wrt_ln('diazonium salt'); if fg[fg_isonitrile] then mod_wrt_ln('isonitrile'); if fg[fg_cyanate] then mod_wrt_ln('cyanate'); if fg[fg_isocyanate] then mod_wrt_ln('isocyanate'); if fg[fg_thiocyanate] then mod_wrt_ln('thiocyanate'); if fg[fg_isothiocyanate] then mod_wrt_ln('isothiocyanate'); if fg[fg_carbodiimide] then mod_wrt_ln('carbodiimide'); if fg[fg_nitroso_compound] then mod_wrt_ln('nitroso compound'); if fg[fg_nitro_compound] then mod_wrt_ln('nitro compound'); if fg[fg_nitrite] then mod_wrt_ln('nitrite'); if fg[fg_nitrate] then mod_wrt_ln('nitrate'); // if fg[fg_sulfuric_acid_deriv] then mod_wrt_ln('sulfuric acid derivative'); if fg[fg_sulfuric_acid] then mod_wrt_ln('sulfuric acid'); if fg[fg_sulfuric_acid_monoester] then mod_wrt_ln('sulfuric acid monoester'); if fg[fg_sulfuric_acid_diester] then mod_wrt_ln('sulfuric acid diester'); if fg[fg_sulfuric_acid_amide_ester] then mod_wrt_ln('sulfuric acid amide ester'); if fg[fg_sulfuric_acid_amide] then mod_wrt_ln('sulfuric acid amide'); if fg[fg_sulfuric_acid_diamide] then mod_wrt_ln('sulfuric acid diamide'); if fg[fg_sulfuryl_halide] then mod_wrt_ln('sulfuryl halide'); // if fg[fg_sulfonic_acid_deriv] then mod_wrt_ln('sulfonic acid derivative '); if fg[fg_sulfonic_acid] then mod_wrt_ln('sulfonic acid'); if fg[fg_sulfonic_acid_ester] then mod_wrt_ln('sulfonic acid ester'); if fg[fg_sulfonamide] then mod_wrt_ln('sulfonamide'); if fg[fg_sulfonyl_halide] then mod_wrt_ln('sulfonyl halide'); if fg[fg_sulfone] then mod_wrt_ln('sulfone'); if fg[fg_sulfoxide] then mod_wrt_ln('sulfoxide'); // if fg[fg_sulfinic_acid_deriv] then mod_wrt_ln('sulfinic acid derivative'); if fg[fg_sulfinic_acid] then mod_wrt_ln('sulfinic acid'); if fg[fg_sulfinic_acid_ester] then mod_wrt_ln('sulfinic acid ester'); if fg[fg_sulfinic_acid_halide] then mod_wrt_ln('sulfinic acid halide'); if fg[fg_sulfinic_acid_amide] then mod_wrt_ln('sulfinic acid amide'); // if fg[fg_sulfenic_acid_deriv] then mod_wrt_ln('sulfenic acid derivative'); if fg[fg_sulfenic_acid] then mod_wrt_ln('sulfenic acid'); if fg[fg_sulfenic_acid_ester] then mod_wrt_ln('sulfenic acid ester'); if fg[fg_sulfenic_acid_halide] then mod_wrt_ln('sulfenic acid halide'); if fg[fg_sulfenic_acid_amide] then mod_wrt_ln('sulfenic acid amide'); if fg[fg_thiol] then mod_wrt_ln('thiol (sulfanyl compound)'); if fg[fg_alkylthiol] then mod_wrt_ln('alkylthiol'); if fg[fg_arylthiol] then mod_wrt_ln('arylthiol'); // if fg[fg_phosphoric_acid_deriv] then mod_wrt_ln('phosphoric acid derivative'); if fg[fg_phosphoric_acid] then mod_wrt_ln('phosphoric acid'); if fg[fg_phosphoric_acid_ester] then mod_wrt_ln('phosphoric acid ester'); if fg[fg_phosphoric_acid_halide] then mod_wrt_ln('phosphoric acid halide'); if fg[fg_phosphoric_acid_amide] then mod_wrt_ln('phosphoric acid amide'); // if fg[fg_thiophosphoric_acid_deriv] then mod_wrt_ln('thiophosphoric acid derivative'); if fg[fg_thiophosphoric_acid] then mod_wrt_ln('thiophosphoric acid'); if fg[fg_thiophosphoric_acid_ester] then mod_wrt_ln('thiophosphoric acid ester'); if fg[fg_thiophosphoric_acid_halide] then mod_wrt_ln('thiophosphoric acid halide'); if fg[fg_thiophosphoric_acid_amide] then mod_wrt_ln('thiophosphoric acid amide'); if fg[fg_phosphonic_acid_deriv] then mod_wrt_ln('phosphonic acid derivative '); if fg[fg_phosphonic_acid] then mod_wrt_ln('phosphonic acid'); if fg[fg_phosphonic_acid_ester] then mod_wrt_ln('phosphonic acid ester'); if fg[fg_phosphine] then mod_wrt_ln('phosphine'); if fg[fg_phosphinoxide] then mod_wrt_ln('phosphine oxide'); if fg[fg_boronic_acid_deriv] then mod_wrt_ln('boronic acid derivative'); if fg[fg_boronic_acid] then mod_wrt_ln('boronic acid'); if fg[fg_boronic_acid_ester] then mod_wrt_ln('boronic acid ester'); if fg[fg_alkene] then mod_wrt_ln('alkene'); if fg[fg_alkyne] then mod_wrt_ln('alkyne'); if fg[fg_aromatic] then mod_wrt_ln('aromatic compound'); if fg[fg_heterocycle] then mod_wrt_ln('heterocyclic compound'); if fg[fg_alpha_aminoacid] then mod_wrt_ln('alpha-aminoacid'); if fg[fg_alpha_hydroxyacid] then mod_wrt_ln('alpha-hydroxyacid'); end; procedure mod_wrt_noln_fg_text_de; begin if fg[fg_cation] then mod_wrt_ln('Kation'); if fg[fg_anion] then mod_wrt_ln('Anion'); // if fg[fg_carbonyl] then mod_wrt_ln('Carbonylverbindung'); if fg[fg_aldehyde] then mod_wrt_ln('Aldehyd'); if fg[fg_ketone] then mod_wrt_ln('Keton'); // if fg[fg_thiocarbonyl] then mod_wrt_ln('Thiocarbonylverbindung'); if fg[fg_thioaldehyde] then mod_wrt_ln('Thioaldehyd'); if fg[fg_thioketone] then mod_wrt_ln('Thioketon'); if fg[fg_imine] then mod_wrt_ln('Imin'); if fg[fg_hydrazone] then mod_wrt_ln('Hydrazon'); if fg[fg_semicarbazone] then mod_wrt_ln('Semicarbazon'); if fg[fg_thiosemicarbazone] then mod_wrt_ln('Thiosemicarbazon'); if fg[fg_oxime] then mod_wrt_ln('Oxim'); if fg[fg_oxime_ether] then mod_wrt_ln('Oximether'); if fg[fg_ketene] then mod_wrt_ln('Keten'); if fg[fg_ketene_acetal_deriv] then mod_wrt_ln('Keten-Acetal oder Derivat'); if fg[fg_carbonyl_hydrate] then mod_wrt_ln('Carbonyl-Hydrat'); if fg[fg_hemiacetal] then mod_wrt_ln('Halbacetal'); if fg[fg_acetal] then mod_wrt_ln('Acetal'); if fg[fg_hemiaminal] then mod_wrt_ln('Halbaminal'); if fg[fg_aminal] then mod_wrt_ln('Aminal'); if fg[fg_thiohemiaminal] then mod_wrt_ln('Thiohalbaminal'); if fg[fg_thioacetal] then mod_wrt_ln('Thioacetal'); if fg[fg_enamine] then mod_wrt_ln('Enamin'); if fg[fg_enol] then mod_wrt_ln('Enol'); if fg[fg_enolether] then mod_wrt_ln('Enolether'); // if fg[fg_hydroxy] then mod_wrt_ln('Hydroxy-Verbindung'); // if fg[fg_alcohol] then mod_wrt_ln('Alkohol'); if fg[fg_prim_alcohol] then mod_wrt_ln('primärer Alkohol'); if fg[fg_sec_alcohol] then mod_wrt_ln('sekundärer Alkohol'); if fg[fg_tert_alcohol] then mod_wrt_ln('tertiärer Alkohol'); if fg[fg_1_2_diol] then mod_wrt_ln('1,2-Diol'); if fg[fg_1_2_aminoalcohol] then mod_wrt_ln('1,2-Aminoalkohol'); if fg[fg_phenol] then mod_wrt_ln('Phenol oder Hydroxyhetaren'); if fg[fg_1_2_diphenol] then mod_wrt_ln('1,2-Diphenol'); if fg[fg_enediol] then mod_wrt_ln('Endiol'); // if fg[fg_ether] then mod_wrt_ln('Ether'); if fg[fg_dialkylether] then mod_wrt_ln('Dialkylether'); if fg[fg_alkylarylether] then mod_wrt_ln('Alkylarylether '); if fg[fg_diarylether] then mod_wrt_ln('Diarylether'); if fg[fg_thioether] then mod_wrt_ln('Thioether'); if fg[fg_disulfide] then mod_wrt_ln('Disulfid'); if fg[fg_peroxide] then mod_wrt_ln('Peroxid'); if fg[fg_hydroperoxide] then mod_wrt_ln('Hydroperoxid'); if fg[fg_hydrazine] then mod_wrt_ln('Hydrazin-Derivat'); if fg[fg_hydroxylamine] then mod_wrt_ln('Hydroxylamin'); // if fg[fg_amine] then mod_wrt_ln('Amin'); if fg[fg_prim_amine] then mod_wrt_ln('primäres Amin'); if fg[fg_prim_aliph_amine] then mod_wrt_ln('primäres aliphatisches Amin (Alkylamin)'); if fg[fg_prim_arom_amine] then mod_wrt_ln('primäres aromatisches Amin'); if fg[fg_sec_amine] then mod_wrt_ln('sekundäres Amin'); if fg[fg_sec_aliph_amine] then mod_wrt_ln('sekundäres aliphatisches Amin (Dialkylamin)'); if fg[fg_sec_mixed_amine] then mod_wrt_ln('sekundäres aliphatisches/aromatisches Amin (Alkylarylamin)'); if fg[fg_sec_arom_amine] then mod_wrt_ln('sekundäres aromatisches Amin (Diarylamin)'); if fg[fg_tert_amine] then mod_wrt_ln('tertiäres Amin'); if fg[fg_tert_aliph_amine] then mod_wrt_ln('tertiäres aliphatisches Amin (Trialkylamin)'); if fg[fg_tert_mixed_amine] then mod_wrt_ln('tertiäres aliphatisches/aromatisches Amin (Alkylarylamin)'); if fg[fg_tert_arom_amine] then mod_wrt_ln('tertiäres aromatisches Amin (Triarylamin)'); if fg[fg_quart_ammonium] then mod_wrt_ln('quartäres Ammoniumsalz'); if fg[fg_n_oxide] then mod_wrt_ln('N-Oxid'); // if fg[fg_halogen_deriv] then mod_wrt_ln('Halogenverbindung'); // if fg[fg_alkyl_halide] then mod_wrt_ln('Alkylhalogenid'); if fg[fg_alkyl_fluoride] then mod_wrt_ln('Alkylfluorid'); if fg[fg_alkyl_chloride] then mod_wrt_ln('Alkylchlorid'); if fg[fg_alkyl_bromide] then mod_wrt_ln('Alkylbromid'); if fg[fg_alkyl_iodide] then mod_wrt_ln('Alkyliodid'); // if fg[fg_aryl_halide] then mod_wrt_ln('Arylhalogenid'); if fg[fg_aryl_fluoride] then mod_wrt_ln('Arylfluorid'); if fg[fg_aryl_chloride] then mod_wrt_ln('Arylchlorid'); if fg[fg_aryl_bromide] then mod_wrt_ln('Arylbromid'); if fg[fg_aryl_iodide] then mod_wrt_ln('Aryliodid'); if fg[fg_organometallic] then mod_wrt_ln('Organometall-Verbindung'); if fg[fg_organolithium] then mod_wrt_ln('Organolithium-Verbindung'); if fg[fg_organomagnesium] then mod_wrt_ln('Organomagnesium-Verbindung'); // if fg[fg_carboxylic_acid_deriv] then mod_wrt_ln('Carbonsäure-Derivat'); if fg[fg_carboxylic_acid] then mod_wrt_ln('Carbonsäure'); if fg[fg_carboxylic_acid_salt] then mod_wrt_ln('Carbonsäuresalz'); if fg[fg_carboxylic_acid_ester] then mod_wrt_ln('Carbonsäureester'); if fg[fg_lactone] then mod_wrt_ln('Lacton'); // if fg[fg_carboxylic_acid_amide] then mod_wrt_ln('Carbonsäureamid'); if fg[fg_carboxylic_acid_prim_amide] then mod_wrt_ln('primäres Carbonsäureamid'); if fg[fg_carboxylic_acid_sec_amide] then mod_wrt_ln('sekundäres Carbonsäureamid'); if fg[fg_carboxylic_acid_tert_amide] then mod_wrt_ln('tertiäres Carbonsäureamid'); if fg[fg_lactam] then mod_wrt_ln('Lactam'); if fg[fg_carboxylic_acid_hydrazide] then mod_wrt_ln('Carbonsäurehydrazid'); if fg[fg_carboxylic_acid_azide] then mod_wrt_ln('Carbonsäureazid'); if fg[fg_hydroxamic_acid] then mod_wrt_ln('Hydroxamsäure'); if fg[fg_carboxylic_acid_amidine] then mod_wrt_ln('Carbonsäureamidin'); if fg[fg_carboxylic_acid_amidrazone] then mod_wrt_ln('Carbonsäureamidrazon'); if fg[fg_nitrile] then mod_wrt_ln('Carbonitril'); // if fg[fg_acyl_halide] then mod_wrt_ln('Acylhalogenid'); if fg[fg_acyl_fluoride] then mod_wrt_ln('Acylfluorid'); if fg[fg_acyl_chloride] then mod_wrt_ln('Acylchlorid'); if fg[fg_acyl_bromide] then mod_wrt_ln('Acylbromid'); if fg[fg_acyl_iodide] then mod_wrt_ln('Acyliodid'); if fg[fg_acyl_cyanide] then mod_wrt_ln('Acylcyanid'); if fg[fg_imido_ester] then mod_wrt_ln('Imidoester'); if fg[fg_imidoyl_halide] then mod_wrt_ln('Imidoylhalogenid'); // if fg[fg_thiocarboxylic_acid_deriv] then mod_wrt_ln('Thiocarbonsäure-Derivat'); if fg[fg_thiocarboxylic_acid] then mod_wrt_ln('Thiocarbonsäure'); if fg[fg_thiocarboxylic_acid_ester] then mod_wrt_ln('Thiocarbonsäureester'); if fg[fg_thiolactone] then mod_wrt_ln('Thiolacton'); if fg[fg_thiocarboxylic_acid_amide] then mod_wrt_ln('Thiocarbonsäureamid'); if fg[fg_thiolactam] then mod_wrt_ln('Thiolactam'); if fg[fg_imido_thioester] then mod_wrt_ln('Imidothioester'); if fg[fg_oxohetarene] then mod_wrt_ln('Oxo(het)aren'); if fg[fg_thioxohetarene] then mod_wrt_ln('Thioxo(het)aren'); if fg[fg_iminohetarene] then mod_wrt_ln('Imino(het)aren'); if fg[fg_orthocarboxylic_acid_deriv] then mod_wrt_ln('Orthocarbonsäure-Derivat'); if fg[fg_carboxylic_acid_orthoester] then mod_wrt_ln('Orthoester'); if fg[fg_carboxylic_acid_amide_acetal] then mod_wrt_ln('Amidacetal'); if fg[fg_carboxylic_acid_anhydride] then mod_wrt_ln('Carbonsäureanhydrid'); // if fg[fg_carboxylic_acid_imide] then mod_wrt_ln('Carbonsäureimid'); if fg[fg_carboxylic_acid_unsubst_imide] then mod_wrt_ln('Carbonsäureimid, N-unsubstituiert'); if fg[fg_carboxylic_acid_subst_imide] then mod_wrt_ln('Carbonsäureimid, N-substituiert'); if fg[fg_co2_deriv] then mod_wrt_ln('CO2-Derivat (allgemein)'); // if fg[fg_carbonic_acid_deriv] then mod_wrt_ln('Kohlensäure-Dervivat'); if fg[fg_carbonic_acid_monoester] then mod_wrt_ln('Kohlensäuremonoester'); if fg[fg_carbonic_acid_diester] then mod_wrt_ln('Kohlensäurediester'); if fg[fg_carbonic_acid_ester_halide] then mod_wrt_ln('Kohlensäureesterhalogenid (Alkyl/Aryl-Halogenformiat)'); if fg[fg_thiocarbonic_acid_deriv] then mod_wrt_ln('Thiokohlensäure-Derivat'); if fg[fg_thiocarbonic_acid_monoester] then mod_wrt_ln('Thiokohlensäuremonoester'); if fg[fg_thiocarbonic_acid_diester] then mod_wrt_ln('Thiokohlensäurediester'); if fg[fg_thiocarbonic_acid_ester_halide] then mod_wrt_ln('Thiokohlensäurehalogenid (Alkyl/Aryl-Halogenthioformiat)'); // if fg[fg_carbamic_acid_deriv] then mod_wrt_ln('Carbaminsäure-Derivat'); if fg[fg_carbamic_acid] then mod_wrt_ln('Carbaminsäure'); if fg[fg_carbamic_acid_ester] then mod_wrt_ln('Carbaminsäureester (Urethan)'); if fg[fg_carbamic_acid_halide] then mod_wrt_ln('Carbaminsäurehalogenid (Halogenformamid)'); // if fg[fg_thiocarbamic_acid_deriv] then mod_wrt_ln('Thiocarbaminsäure-Derivat'); if fg[fg_thiocarbamic_acid] then mod_wrt_ln('Thiocarbaminsäure'); if fg[fg_thiocarbamic_acid_ester] then mod_wrt_ln('Thiocarbaminsäureester'); if fg[fg_thiocarbamic_acid_halide] then mod_wrt_ln('Thiocarbaminsäurehalogenid (Halogenthioformamid)'); if fg[fg_urea] then mod_wrt_ln('Harnstoff'); if fg[fg_isourea] then mod_wrt_ln('Isoharnstoff'); if fg[fg_thiourea] then mod_wrt_ln('Thioharnstoff'); if fg[fg_isothiourea] then mod_wrt_ln('Isothioharnstoff'); if fg[fg_guanidine] then mod_wrt_ln('Guanidin'); if fg[fg_semicarbazide] then mod_wrt_ln('Semicarbazid'); if fg[fg_thiosemicarbazide] then mod_wrt_ln('Thiosemicarbazid'); if fg[fg_azide] then mod_wrt_ln('Azid'); if fg[fg_azo_compound] then mod_wrt_ln('Azoverbindung'); if fg[fg_diazonium_salt] then mod_wrt_ln('Diazoniumsalz'); if fg[fg_isonitrile] then mod_wrt_ln('Isonitril'); if fg[fg_cyanate] then mod_wrt_ln('Cyanat'); if fg[fg_isocyanate] then mod_wrt_ln('Isocyanat'); if fg[fg_thiocyanate] then mod_wrt_ln('Thiocyanat'); if fg[fg_isothiocyanate] then mod_wrt_ln('Isothiocyanat'); if fg[fg_carbodiimide] then mod_wrt_ln('Carbodiimid'); if fg[fg_nitroso_compound] then mod_wrt_ln('Nitroso-Verbindung'); if fg[fg_nitro_compound] then mod_wrt_ln('Nitro-Verbindung'); if fg[fg_nitrite] then mod_wrt_ln('Nitrit'); if fg[fg_nitrate] then mod_wrt_ln('Nitrat'); // if fg[fg_sulfuric_acid_deriv] then mod_wrt_ln('Schwefelsäure-Derivat'); if fg[fg_sulfuric_acid] then mod_wrt_ln('Schwefelsäure'); if fg[fg_sulfuric_acid_monoester] then mod_wrt_ln('Schwefelsäuremonoester'); if fg[fg_sulfuric_acid_diester] then mod_wrt_ln('Schwefelsäurediester'); if fg[fg_sulfuric_acid_amide_ester] then mod_wrt_ln('Schwefelsäureamidester'); if fg[fg_sulfuric_acid_amide] then mod_wrt_ln('Schwefelsäureamid'); if fg[fg_sulfuric_acid_diamide] then mod_wrt_ln('Schwefelsäurediamid'); if fg[fg_sulfuryl_halide] then mod_wrt_ln('Sulfurylhalogenid'); // if fg[fg_sulfonic_acid_deriv] then mod_wrt_ln('Sulfonsäure-Derivat '); if fg[fg_sulfonic_acid] then mod_wrt_ln('Sulfonsäure'); if fg[fg_sulfonic_acid_ester] then mod_wrt_ln('Sulfonsäureester'); if fg[fg_sulfonamide] then mod_wrt_ln('Sulfonamid'); if fg[fg_sulfonyl_halide] then mod_wrt_ln('Sulfonylhalogenid'); if fg[fg_sulfone] then mod_wrt_ln('Sulfon'); if fg[fg_sulfoxide] then mod_wrt_ln('Sulfoxid'); // if fg[fg_sulfinic_acid_deriv] then mod_wrt_ln('Sulfinsäure-Derivat'); if fg[fg_sulfinic_acid] then mod_wrt_ln('Sulfinsäure'); if fg[fg_sulfinic_acid_ester] then mod_wrt_ln('Sulfinsäureester'); if fg[fg_sulfinic_acid_halide] then mod_wrt_ln('Sulfinsäurehalogenid'); if fg[fg_sulfinic_acid_amide] then mod_wrt_ln('Sulfinsäureamid'); // if fg[fg_sulfenic_acid_deriv] then mod_wrt_ln('Sulfensäure-Derivat'); if fg[fg_sulfenic_acid] then mod_wrt_ln('Sulfensäure'); if fg[fg_sulfenic_acid_ester] then mod_wrt_ln('Sulfensäureester'); if fg[fg_sulfenic_acid_halide] then mod_wrt_ln('Sulfensäurehalogenid'); if fg[fg_sulfenic_acid_amide] then mod_wrt_ln('Sulfensäureamid'); if fg[fg_thiol] then mod_wrt_ln('Thiol (Sulfanyl-Verbindung, Mercaptan)'); if fg[fg_alkylthiol] then mod_wrt_ln('Alkylthiol'); if fg[fg_arylthiol] then mod_wrt_ln('Arylthiol'); // if fg[fg_phosphoric_acid_deriv] then mod_wrt_ln('Phosphorsäure-Derivat'); if fg[fg_phosphoric_acid] then mod_wrt_ln('Phosphorsäure'); if fg[fg_phosphoric_acid_ester] then mod_wrt_ln('Phosphorsäureester'); if fg[fg_phosphoric_acid_halide] then mod_wrt_ln('Phosphorsäurehalogenid'); if fg[fg_phosphoric_acid_amide] then mod_wrt_ln('Phosphorsäureamid'); // if fg[fg_thiophosphoric_acid_deriv] then mod_wrt_ln('Thiophosphorsäure-Derivat'); if fg[fg_thiophosphoric_acid] then mod_wrt_ln('Thiophosphorsäure'); if fg[fg_thiophosphoric_acid_ester] then mod_wrt_ln('Thiophosphorsäureester'); if fg[fg_thiophosphoric_acid_halide] then mod_wrt_ln('Thiophosphorsäurehalogenid'); if fg[fg_thiophosphoric_acid_amide] then mod_wrt_ln('Thiophosphorsäureamid'); if fg[fg_phosphonic_acid_deriv] then mod_wrt_ln('Phosphonsäure-Derivat '); if fg[fg_phosphonic_acid] then mod_wrt_ln('Phosphonsäure'); if fg[fg_phosphonic_acid_ester] then mod_wrt_ln('Phosphonsäureester'); if fg[fg_phosphine] then mod_wrt_ln('Phosphin'); if fg[fg_phosphinoxide] then mod_wrt_ln('Phosphinoxid'); if fg[fg_boronic_acid_deriv] then mod_wrt_ln('Boronsäure-Derivat'); if fg[fg_boronic_acid] then mod_wrt_ln('Boronsäure'); if fg[fg_boronic_acid_ester] then mod_wrt_ln('Boronsäureester'); if fg[fg_alkene] then mod_wrt_ln('Alken'); if fg[fg_alkyne] then mod_wrt_ln('Alkin'); if fg[fg_aromatic] then mod_wrt_ln('aromatische Verbindung'); if fg[fg_heterocycle] then mod_wrt_ln('heterocyclische Verbindung'); if fg[fg_alpha_aminoacid] then mod_wrt_ln('alpha-Aminosäure'); if fg[fg_alpha_hydroxyacid] then mod_wrt_ln('alpha-Hydroxysäure'); end; procedure mod_wrt_noln_fg_code; const sc = ';'; begin if fg[fg_cation] then mod_wrt_noln('000000T2',sc); if fg[fg_anion] then mod_wrt_noln('000000T1',sc); // if fg[fg_carbonyl] then mod_wrt_noln('C2O10000',sc); if fg[fg_aldehyde] then mod_wrt_noln('C2O1H000',sc); if fg[fg_ketone] then mod_wrt_noln('C2O1C000',sc); // if fg[fg_thiocarbonyl] then mod_wrt_noln('C2S10000',sc); if fg[fg_thioaldehyde] then mod_wrt_noln('C2S1H000',sc); if fg[fg_thioketone] then mod_wrt_noln('C2S1C000',sc); if fg[fg_imine] then mod_wrt_noln('C2N10000',sc); if fg[fg_hydrazone] then mod_wrt_noln('C2N1N000',sc); if fg[fg_semicarbazone] then mod_wrt_noln('C2NNC4ON',sc); if fg[fg_thiosemicarbazone] then mod_wrt_noln('C2NNC4SN',sc); if fg[fg_oxime] then mod_wrt_noln('C2N1OH00',sc); if fg[fg_oxime_ether] then mod_wrt_noln('C2N1OC00',sc); if fg[fg_ketene] then mod_wrt_noln('C3OC0000',sc); if fg[fg_ketene_acetal_deriv] then mod_wrt_noln('C3OCC000',sc); if fg[fg_carbonyl_hydrate] then mod_wrt_noln('C2O2H200',sc); if fg[fg_hemiacetal] then mod_wrt_noln('C2O2HC00',sc); if fg[fg_acetal] then mod_wrt_noln('C2O2CC00',sc); if fg[fg_hemiaminal] then mod_wrt_noln('C2NOHC10',sc); if fg[fg_aminal] then mod_wrt_noln('C2N2CC10',sc); if fg[fg_thiohemiaminal] then mod_wrt_noln('C2NSHC10',sc); if fg[fg_thioacetal] then mod_wrt_noln('C2S2CC00',sc); if fg[fg_enamine] then mod_wrt_noln('C2CNH000',sc); if fg[fg_enol] then mod_wrt_noln('C2COH000',sc); if fg[fg_enolether] then mod_wrt_noln('C2COC000',sc); // if fg[fg_hydroxy] then mod_wrt_noln('O1H00000',sc); // if fg[fg_alcohol] then mod_wrt_noln('O1H0C000',sc); if fg[fg_prim_alcohol] then mod_wrt_noln('O1H1C000',sc); if fg[fg_sec_alcohol] then mod_wrt_noln('O1H2C000',sc); if fg[fg_tert_alcohol] then mod_wrt_noln('O1H3C000',sc); if fg[fg_1_2_diol] then mod_wrt_noln('O1H0CO1H',sc); if fg[fg_1_2_aminoalcohol] then mod_wrt_noln('O1H0CN1C',sc); if fg[fg_phenol] then mod_wrt_noln('O1H1A000',sc); if fg[fg_1_2_diphenol] then mod_wrt_noln('O1H2A000',sc); if fg[fg_enediol] then mod_wrt_noln('C2COH200',sc); // if fg[fg_ether] then mod_wrt_noln('O1C00000',sc); if fg[fg_dialkylether] then mod_wrt_noln('O1C0CC00',sc); if fg[fg_alkylarylether] then mod_wrt_noln('O1C0CA00',sc); if fg[fg_diarylether] then mod_wrt_noln('O1C0AA00',sc); if fg[fg_thioether] then mod_wrt_noln('S1C00000',sc); if fg[fg_disulfide] then mod_wrt_noln('S1S1C000',sc); if fg[fg_peroxide] then mod_wrt_noln('O1O1C000',sc); if fg[fg_hydroperoxide] then mod_wrt_noln('O1O1H000',sc); if fg[fg_hydrazine] then mod_wrt_noln('N1N10000',sc); if fg[fg_hydroxylamine] then mod_wrt_noln('N1O1H000',sc); // if fg[fg_amine] then mod_wrt_noln('N1C00000',sc); // if fg[fg_prim_amine] then mod_wrt_noln('N1C10000',sc); if fg[fg_prim_aliph_amine] then mod_wrt_noln('N1C1C000',sc); if fg[fg_prim_arom_amine] then mod_wrt_noln('N1C1A000',sc); // if fg[fg_sec_amine] then mod_wrt_noln('N1C20000',sc); if fg[fg_sec_aliph_amine] then mod_wrt_noln('N1C2CC00',sc); if fg[fg_sec_mixed_amine] then mod_wrt_noln('N1C2AC00',sc); if fg[fg_sec_arom_amine] then mod_wrt_noln('N1C2AA00',sc); // if fg[fg_tert_amine] then mod_wrt_noln('N1C30000',sc); if fg[fg_tert_aliph_amine] then mod_wrt_noln('N1C3CC00',sc); if fg[fg_tert_mixed_amine] then mod_wrt_noln('N1C3AC00',sc); if fg[fg_tert_arom_amine] then mod_wrt_noln('N1C3AA00',sc); if fg[fg_quart_ammonium] then mod_wrt_noln('N1C400T2',sc); if fg[fg_n_oxide] then mod_wrt_noln('N0O10000',sc); // if fg[fg_halogen_deriv] then mod_wrt_noln('XX000000',sc); // if fg[fg_alkyl_halide] then mod_wrt_noln('XX00C000',sc); if fg[fg_alkyl_fluoride] then mod_wrt_noln('XF00C000',sc); if fg[fg_alkyl_chloride] then mod_wrt_noln('XC00C000',sc); if fg[fg_alkyl_bromide] then mod_wrt_noln('XB00C000',sc); if fg[fg_alkyl_iodide] then mod_wrt_noln('XI00C000',sc); // if fg[fg_aryl_halide] then mod_wrt_noln('XX00A000',sc); if fg[fg_aryl_fluoride] then mod_wrt_noln('XF00A000',sc); if fg[fg_aryl_chloride] then mod_wrt_noln('XC00A000',sc); if fg[fg_aryl_bromide] then mod_wrt_noln('XB00A000',sc); if fg[fg_aryl_iodide] then mod_wrt_noln('XI00A000',sc); if fg[fg_organometallic] then mod_wrt_noln('000000MX',sc); if fg[fg_organolithium] then mod_wrt_noln('000000ML',sc); if fg[fg_organomagnesium] then mod_wrt_noln('000000MM',sc); // if fg[fg_carboxylic_acid_deriv] then mod_wrt_noln('C3O20000',sc); if fg[fg_carboxylic_acid] then mod_wrt_noln('C3O2H000',sc); if fg[fg_carboxylic_acid_salt] then mod_wrt_noln('C3O200T1',sc); if fg[fg_carboxylic_acid_ester] then mod_wrt_noln('C3O2C000',sc); if fg[fg_lactone] then mod_wrt_noln('C3O2CZ00',sc); // if fg[fg_carboxylic_acid_amide] then mod_wrt_noln('C3ONC000',sc); if fg[fg_carboxylic_acid_prim_amide] then mod_wrt_noln('C3ONC100',sc); if fg[fg_carboxylic_acid_sec_amide] then mod_wrt_noln('C3ONC200',sc); if fg[fg_carboxylic_acid_tert_amide] then mod_wrt_noln('C3ONC300',sc); if fg[fg_lactam] then mod_wrt_noln('C3ONCZ00',sc); if fg[fg_carboxylic_acid_hydrazide] then mod_wrt_noln('C3ONN100',sc); if fg[fg_carboxylic_acid_azide] then mod_wrt_noln('C3ONN200',sc); if fg[fg_hydroxamic_acid] then mod_wrt_noln('C3ONOH00',sc); if fg[fg_carboxylic_acid_amidine] then mod_wrt_noln('C3N2H000',sc); if fg[fg_carboxylic_acid_amidrazone] then mod_wrt_noln('C3NNN100',sc); if fg[fg_nitrile] then mod_wrt_noln('C3N00000',sc); // if fg[fg_acyl_halide] then mod_wrt_noln('C3OXX000',sc); if fg[fg_acyl_fluoride] then mod_wrt_noln('C3OXF000',sc); if fg[fg_acyl_chloride] then mod_wrt_noln('C3OXC000',sc); if fg[fg_acyl_bromide] then mod_wrt_noln('C3OXB000',sc); if fg[fg_acyl_iodide] then mod_wrt_noln('C3OXI000',sc); if fg[fg_acyl_cyanide] then mod_wrt_noln('C2OC3N00',sc); if fg[fg_imido_ester] then mod_wrt_noln('C3NOC000',sc); if fg[fg_imidoyl_halide] then mod_wrt_noln('C3NXX000',sc); // if fg[fg_thiocarboxylic_acid_deriv] then mod_wrt_noln('C3SO0000',sc); if fg[fg_thiocarboxylic_acid] then mod_wrt_noln('C3SOH000',sc); if fg[fg_thiocarboxylic_acid_ester] then mod_wrt_noln('C3SOC000',sc); if fg[fg_thiolactone] then mod_wrt_noln('C3SOCZ00',sc); if fg[fg_thiocarboxylic_acid_amide] then mod_wrt_noln('C3SNH000',sc); if fg[fg_thiolactam] then mod_wrt_noln('C3SNCZ00',sc); if fg[fg_imido_thioester] then mod_wrt_noln('C3NSC000',sc); if fg[fg_oxohetarene] then mod_wrt_noln('C3ONAZ00',sc); if fg[fg_thioxohetarene] then mod_wrt_noln('C3SNAZ00',sc); if fg[fg_iminohetarene] then mod_wrt_noln('C3NNAZ00',sc); if fg[fg_orthocarboxylic_acid_deriv] then mod_wrt_noln('C3O30000',sc); if fg[fg_carboxylic_acid_orthoester] then mod_wrt_noln('C3O3C000',sc); if fg[fg_carboxylic_acid_amide_acetal] then mod_wrt_noln('C3O3NC00',sc); if fg[fg_carboxylic_acid_anhydride] then mod_wrt_noln('C3O2C3O2',sc); // if fg[fg_carboxylic_acid_imide] then mod_wrt_noln('C3ONC000',sc); if fg[fg_carboxylic_acid_unsubst_imide] then mod_wrt_noln('C3ONCH10',sc); if fg[fg_carboxylic_acid_subst_imide] then mod_wrt_noln('C3ONCC10',sc); if fg[fg_co2_deriv] then mod_wrt_noln('C4000000',sc); if fg[fg_carbonic_acid_deriv] then mod_wrt_noln('C4O30000',sc); if fg[fg_carbonic_acid_monoester] then mod_wrt_noln('C4O3C100',sc); if fg[fg_carbonic_acid_diester] then mod_wrt_noln('C4O3C200',sc); if fg[fg_carbonic_acid_ester_halide] then mod_wrt_noln('C4O3CX00',sc); if fg[fg_thiocarbonic_acid_deriv] then mod_wrt_noln('C4SO0000',sc); if fg[fg_thiocarbonic_acid_monoester] then mod_wrt_noln('C4SOC100',sc); if fg[fg_thiocarbonic_acid_diester] then mod_wrt_noln('C4SOC200',sc); if fg[fg_thiocarbonic_acid_ester_halide] then mod_wrt_noln('C4SOX_00',sc); if fg[fg_carbamic_acid_deriv] then mod_wrt_noln('C4O2N000',sc); if fg[fg_carbamic_acid] then mod_wrt_noln('C4O2NH00',sc); if fg[fg_carbamic_acid_ester] then mod_wrt_noln('C4O2NC00',sc); if fg[fg_carbamic_acid_halide] then mod_wrt_noln('C4O2NX00',sc); if fg[fg_thiocarbamic_acid_deriv] then mod_wrt_noln('C4SN0000',sc); if fg[fg_thiocarbamic_acid] then mod_wrt_noln('C4SNOH00',sc); if fg[fg_thiocarbamic_acid_ester] then mod_wrt_noln('C4SNOC00',sc); if fg[fg_thiocarbamic_acid_halide] then mod_wrt_noln('C4SNXX00',sc); if fg[fg_urea] then mod_wrt_noln('C4O1N200',sc); if fg[fg_isourea] then mod_wrt_noln('C4N2O100',sc); if fg[fg_thiourea] then mod_wrt_noln('C4S1N200',sc); if fg[fg_isothiourea] then mod_wrt_noln('C4N2S100',sc); if fg[fg_guanidine] then mod_wrt_noln('C4N30000',sc); if fg[fg_semicarbazide] then mod_wrt_noln('C4ON2N00',sc); if fg[fg_thiosemicarbazide] then mod_wrt_noln('C4SN2N00',sc); if fg[fg_azide] then mod_wrt_noln('N4N20000',sc); if fg[fg_azo_compound] then mod_wrt_noln('N2N10000',sc); if fg[fg_diazonium_salt] then mod_wrt_noln('N3N100T2',sc); if fg[fg_isonitrile] then mod_wrt_noln('N3C10000',sc); if fg[fg_cyanate] then mod_wrt_noln('C4NO1000',sc); if fg[fg_isocyanate] then mod_wrt_noln('C4NO2000',sc); if fg[fg_thiocyanate] then mod_wrt_noln('C4NS1000',sc); if fg[fg_isothiocyanate] then mod_wrt_noln('C4NS2000',sc); if fg[fg_carbodiimide] then mod_wrt_noln('C4N20000',sc); if fg[fg_nitroso_compound] then mod_wrt_noln('N2O10000',sc); if fg[fg_nitro_compound] then mod_wrt_noln('N4O20000',sc); if fg[fg_nitrite] then mod_wrt_noln('N3O20000',sc); if fg[fg_nitrate] then mod_wrt_noln('N4O30000',sc); if fg[fg_sulfuric_acid_deriv] then mod_wrt_noln('S6O00000',sc); if fg[fg_sulfuric_acid] then mod_wrt_noln('S6O4H000',sc); if fg[fg_sulfuric_acid_monoester] then mod_wrt_noln('S6O4HC00',sc); if fg[fg_sulfuric_acid_diester] then mod_wrt_noln('S6O4CC00',sc); if fg[fg_sulfuric_acid_amide_ester] then mod_wrt_noln('S6O3NC00',sc); if fg[fg_sulfuric_acid_amide] then mod_wrt_noln('S6O3N100',sc); if fg[fg_sulfuric_acid_diamide] then mod_wrt_noln('S6O2N200',sc); if fg[fg_sulfuryl_halide] then mod_wrt_noln('S6O3XX00',sc); if fg[fg_sulfonic_acid_deriv] then mod_wrt_noln('S5O00000',sc); if fg[fg_sulfonic_acid] then mod_wrt_noln('S5O3H000',sc); if fg[fg_sulfonic_acid_ester] then mod_wrt_noln('S5O3C000',sc); if fg[fg_sulfonamide] then mod_wrt_noln('S5O2N000',sc); if fg[fg_sulfonyl_halide] then mod_wrt_noln('S5O2XX00',sc); if fg[fg_sulfone] then mod_wrt_noln('S4O20000',sc); if fg[fg_sulfoxide] then mod_wrt_noln('S2O10000',sc); if fg[fg_sulfinic_acid_deriv] then mod_wrt_noln('S3O00000',sc); if fg[fg_sulfinic_acid] then mod_wrt_noln('S3O2H000',sc); if fg[fg_sulfinic_acid_ester] then mod_wrt_noln('S3O2C000',sc); if fg[fg_sulfinic_acid_halide] then mod_wrt_noln('S3O1XX00',sc); if fg[fg_sulfinic_acid_amide] then mod_wrt_noln('S3O1N000',sc); if fg[fg_sulfenic_acid_deriv] then mod_wrt_noln('S1O00000',sc); if fg[fg_sulfenic_acid] then mod_wrt_noln('S1O1H000',sc); if fg[fg_sulfenic_acid_ester] then mod_wrt_noln('S1O1C000',sc); if fg[fg_sulfenic_acid_halide] then mod_wrt_noln('S1O0XX00',sc); if fg[fg_sulfenic_acid_amide] then mod_wrt_noln('S1O0N100',sc); // if fg[fg_thiol] then mod_wrt_noln('S1H10000',sc); if fg[fg_alkylthiol] then mod_wrt_noln('S1H1C000',sc); if fg[fg_arylthiol] then mod_wrt_noln('S1H1A000',sc); if fg[fg_phosphoric_acid_deriv] then mod_wrt_noln('P5O0H000',sc); if fg[fg_phosphoric_acid] then mod_wrt_noln('P5O4H200',sc); if fg[fg_phosphoric_acid_ester] then mod_wrt_noln('P5O4HC00',sc); if fg[fg_phosphoric_acid_halide] then mod_wrt_noln('P5O3HX00',sc); if fg[fg_phosphoric_acid_amide] then mod_wrt_noln('P5O3HN00',sc); if fg[fg_thiophosphoric_acid_deriv] then mod_wrt_noln('P5O0S000',sc); if fg[fg_thiophosphoric_acid] then mod_wrt_noln('P5O3SH00',sc); if fg[fg_thiophosphoric_acid_ester] then mod_wrt_noln('P5O3SC00',sc); if fg[fg_thiophosphoric_acid_halide] then mod_wrt_noln('P5O2SX00',sc); if fg[fg_thiophosphoric_acid_amide] then mod_wrt_noln('P5O2SN00',sc); if fg[fg_phosphonic_acid_deriv] then mod_wrt_noln('P4O30000',sc); if fg[fg_phosphonic_acid] then mod_wrt_noln('P4O3H000',sc); if fg[fg_phosphonic_acid_ester] then mod_wrt_noln('P4O3C000',sc); if fg[fg_phosphine] then mod_wrt_noln('P3000000',sc); if fg[fg_phosphinoxide] then mod_wrt_noln('P2O00000',sc); if fg[fg_boronic_acid_deriv] then mod_wrt_noln('B2O20000',sc); if fg[fg_boronic_acid] then mod_wrt_noln('B2O2H000',sc); if fg[fg_boronic_acid_ester] then mod_wrt_noln('B2O2C000',sc); if fg[fg_alkene] then mod_wrt_noln('000C2C00',sc); if fg[fg_alkyne] then mod_wrt_noln('000C3C00',sc); if fg[fg_aromatic] then mod_wrt_noln('0000A000',sc); if fg[fg_heterocycle] then mod_wrt_noln('0000CZ00',sc); if fg[fg_alpha_aminoacid] then mod_wrt_noln('C3O2HN1C',sc); if fg[fg_alpha_hydroxyacid] then mod_wrt_noln('C3O2HO1H',sc); end; procedure mod_wrt_noln_fg_binary; var i : integer; n : integer; o : char; begin for i := 1 to (max_fg div 8) do begin n := 0; if fg[8*i] then inc(n); if fg[8*i-1] then inc(n,2); if fg[8*i-2] then inc(n,4); if fg[8*i-3] then inc(n,8); if fg[8*i-4] then inc(n,16); if fg[8*i-5] then inc(n,32); if fg[8*i-6] then inc(n,64); if fg[8*i-7] then inc(n,128); o := chr(n); mod_wrt_noln(o); end; end; procedure mod_wrt_noln_fg_bitstring; var i : integer; begin for i := 1 to max_fg do if fg[i] then mod_wrt_noln('1') else mod_wrt_noln('0'); end; procedure readinputfile(molfilename:string); var rfile : text; rline : string; begin molbufindex := 0; if not opt_stdin then begin assign(rfile,molfilename); reset(rfile); rline := ''; while not eof(rfile) do begin readln(rfile,rline); mol_in_queue := false; if molbufindex < (max_atoms+max_bonds+8192) then begin inc(molbufindex); molbuf^[molbufindex] := rline; end else begin mod_wrt_ln('Not enough memory for molfile! ',molbufindex); close(rfile); halt(1); end; end; close(rfile); end else // read from standard input begin rline := ''; mol_in_queue := false; while (not eof) and (pos('$$$$',rline) = 0) do begin readln(rline); if molbufindex < (max_atoms+max_bonds+64) then begin inc(molbufindex); molbuf^[molbufindex] := rline; end else begin mod_wrt_ln('Not enough memory!'); halt(1); end; if pos('$$$$',rline) > 0 then mol_in_queue := true; end; end; end; procedure copy_mol_to_needle; var i, j : integer; begin if (n_atoms = 0) or (n_bonds = 0) then exit; try getmem(ndl_atom,n_atoms*sizeof(atom_rec)); getmem(ndl_bond,n_bonds*sizeof(bond_rec)); getmem(ndl_ring,sizeof(ringlist)); except on e:Eoutofmemory do begin mod_wrt_ln('Not enough memory'); halt(4); end; end; ndl_n_atoms := n_atoms; ndl_n_bonds := n_bonds; ndl_n_rings := n_rings; ndl_n_heavyatoms := n_heavyatoms; ndl_n_heavybonds := n_heavybonds; ndl_molname := molname; for i := 1 to n_atoms do begin ndl_atom^[i].element := atom^[i].element; ndl_atom^[i].atype := atom^[i].atype; ndl_atom^[i].x := atom^[i].x; ndl_atom^[i].y := atom^[i].y; ndl_atom^[i].z := atom^[i].z; ndl_atom^[i].formal_charge := atom^[i].formal_charge; ndl_atom^[i].real_charge := atom^[i].real_charge; ndl_atom^[i].Hexp := atom^[i].Hexp; ndl_atom^[i].Htot := atom^[i].Htot; ndl_atom^[i].neighbor_count := atom^[i].neighbor_count; ndl_atom^[i].ring_count := atom^[i].ring_count; ndl_atom^[i].arom := atom^[i].arom; end; for i := 1 to n_bonds do begin ndl_bond^[i].a1 := bond^[i].a1; ndl_bond^[i].a2 := bond^[i].a2; ndl_bond^[i].btype := bond^[i].btype; ndl_bond^[i].arom := bond^[i].arom; end; if n_rings > 0 then begin for i := 1 to n_rings do begin for j := 1 to max_ringsize do ndl_ring^[i,j] := ring^[i,j]; end; end; with ndl_molstat do begin n_QA := molstat.n_QA; n_QB := molstat.n_QB; n_chg := molstat.n_chg; n_C1 := molstat.n_C1; n_C2 := molstat.n_C2; n_C := molstat.n_C; n_CHB1p := molstat.n_CHB1p; n_CHB2p := molstat.n_CHB2p; n_CHB3p := molstat.n_CHB3p; n_CHB4 := molstat.n_CHB4; n_O2 := molstat.n_O2; n_O3 := molstat.n_O3; n_N1 := molstat.n_N1; n_N2 := molstat.n_N2; n_N3 := molstat.n_N3; n_S := molstat.n_S; n_SeTe := molstat.n_SeTe; n_F := molstat.n_F; n_Cl := molstat.n_Cl; n_Br := molstat.n_Br; n_I := molstat.n_I; n_P := molstat.n_P; n_B := molstat.n_B; n_Met := molstat.n_Met; n_X := molstat.n_X; n_b1 := molstat.n_b1; n_b2 := molstat.n_b2; n_b3 := molstat.n_b3; n_bar := molstat.n_bar; n_C1O := molstat.n_C1O; n_C2O := molstat.n_C2O; n_CN := molstat.n_CN; n_XY := molstat.n_XY; n_r3 := molstat.n_r3; n_r4 := molstat.n_r4; n_r5 := molstat.n_r5; n_r6 := molstat.n_r6; n_r7 := molstat.n_r7; n_r8 := molstat.n_r8; n_r9 := molstat.n_r9; n_r10 := molstat.n_r10; n_r11 := molstat.n_r11; n_r12 := molstat.n_r12; n_r13p := molstat.n_r13p; n_rN := molstat.n_rN; n_rN1 := molstat.n_rN1; n_rN2 := molstat.n_rN2; n_rN3p := molstat.n_rN3p; n_rO := molstat.n_rO; n_rO1 := molstat.n_rO1; n_rO2p := molstat.n_rO2p; n_rS := molstat.n_rS; n_rX := molstat.n_rX; n_rar := molstat.n_rar; end; end; procedure get_ringstat(r_id:integer); var i,j : integer; testring : ringpath_type; ring_size : integer; a_ref : integer; elem : str2; nN, nO, nS, nX : integer; begin nN := 0; nO := 0; nS := 0; nX := 0; if (r_id < 1) or (r_id > n_rings) then exit; fillchar(testring,sizeof(ringpath_type),0); for j := 1 to max_ringsize do if ring^[r_id,j] > 0 then testring[j] := ring^[r_id,j]; ring_size := path_length(testring); if (ring_size > 2) then begin for i := 1 to ring_size do begin a_ref := testring[i]; elem := atom^[a_ref].element; if (elem <> 'C ') and (elem <> 'A ') then begin inc(nX); // general heteroatom count if elem = 'N ' then inc(nN); if elem = 'O ' then inc(nO); if elem = 'S ' then inc(nS); end; end; if nN > 0 then begin inc(molstat.n_rN); if nN = 1 then inc(molstat.n_rN1); if nN = 2 then inc(molstat.n_rN2); if nN > 2 then inc(molstat.n_rN3p); end; if nO > 0 then begin inc(molstat.n_rO); if nO = 1 then inc(molstat.n_rO1); if nO = 2 then inc(molstat.n_rO2p); end; if nS > 0 then inc(molstat.n_rS); if nX > 0 then inc(molstat.n_rX); end; end; procedure get_molstat; var i : integer; elem : str2; atype : str3; a1, a2 : integer; a1el, a2el : str2; btype : char; hbc : integer; begin if n_atoms = 0 then exit; with molstat do begin for i := 1 to n_atoms do begin if is_heavyatom(i) then begin elem := atom^[i].element; atype := atom^[i].atype; if (atype = 'C1 ') then inc(n_C1); if (atype = 'C2 ') or (atype = 'CAR') then inc(n_C2); if (elem = 'C ') then inc(n_C); if (atype = 'O2 ') then inc(n_O2); if (atype = 'O3 ') then inc(n_O3); if (atype = 'N1 ') then inc(n_N1); if (atype = 'N2 ') or (atype = 'NAR') then inc(n_N2); if (atype = 'N3 ') or (atype = 'NPL') or (atype = 'N3+') or (atype = 'NAM') then inc(n_N3); if (elem = 'A ') then inc(n_QA); // query atom if (elem = 'Q ') then inc(n_QA); // query atom if (elem = 'S ') then inc(n_S); if (elem = 'SE') then inc(n_SeTe); if (elem = 'TE') then inc(n_SeTe); if (elem = 'F ') then inc(n_F); if (elem = 'CL') then inc(n_Cl); if (elem = 'BR') then inc(n_Br); if (elem = 'I ') then inc(n_I); if (elem = 'P ') then inc(n_P); if (elem = 'B ') then inc(n_B); // still missing: metals, unknown elements // check number of heteroatom bonds per C atom if elem = 'C ' then begin hbc := hetbond_count(i); if hbc >= 1 then inc(n_CHB1p); if hbc >= 2 then inc(n_CHB2p); if hbc >= 3 then inc(n_CHB3p); if hbc = 4 then inc(n_CHB4); end; if atom^[i].formal_charge <> 0 then begin inc(n_chg); inc(n_charges); end; end; end; // atoms if n_bonds > 0 then begin for i := 1 to n_bonds do begin a1 := bond^[i].a1; a2 := bond^[i].a2; a1el := atom^[a1].element; a2el := atom^[a2].element; btype := bond^[i].btype; if bond^[i].arom then inc(n_bar) else begin if (btype = 'S') then inc(n_b1); if (btype = 'D') then inc(n_b2); if (btype = 'T') then inc(n_b3); end; if ((a1el = 'C ') and (a2el = 'O ')) or ((a1el = 'O ') and (a2el = 'C ')) then begin if (btype = 'S') then inc(n_C1O); if (btype = 'D') then inc(n_C2O); end; if ((a1el = 'C ') and (a2el = 'N ')) or ((a1el = 'N ') and (a2el = 'C ')) then inc(n_CN); if ((a1el <> 'C ') and (is_heavyatom(a1))) and ((a2el <> 'C ') and (is_heavyatom(a2))) then inc(n_XY); end; end; // bonds if n_rings > 0 then begin for i := 1 to n_rings do begin if is_arene(i) then inc(n_rar); get_ringstat(i); end; end; // rings end; end; procedure mod_wrt_noln_molstat; begin with molstat do begin mod_wrt_noln('n_atoms:',n_heavyatoms,';'); // count only non-H atoms (some molfiles contain explicit H's) if n_bonds > 0 then mod_wrt_noln('n_bonds:',n_heavybonds,';'); // count only bonds between non-H atoms if n_rings > 0 then mod_wrt_noln('n_rings:',n_rings,';'); // if n_QA > 0 then mod_wrt_noln('n_QA:',n_QA,';'); // if n_QB > 0 then mod_wrt_noln('n_QB:',n_QB,';'); if n_chg > 0 then mod_wrt_noln('n_chg:',n_chg,';'); if n_C1 > 0 then mod_wrt_noln('n_C1:',n_C1,';'); if n_C2 > 0 then mod_wrt_noln('n_C2:',n_C2,';'); // requirement of a given number of sp3 carbons might be too restrictive, // so we use the total number of carbons instead (initially used variable n_C3 is now n_C) if n_C > 0 then mod_wrt_noln('n_C:',n_C,';'); if n_CHB1p > 0 then mod_wrt_noln('n_CHB1p:',n_CHB1p,';'); if n_CHB2p > 0 then mod_wrt_noln('n_CHB2p:',n_CHB2p,';'); if n_CHB3p > 0 then mod_wrt_noln('n_CHB3p:',n_CHB3p,';'); if n_CHB4 > 0 then mod_wrt_noln('n_CHB4:',n_CHB4,';'); if n_O2 > 0 then mod_wrt_noln('n_O2:',n_O2,';'); if n_O3 > 0 then mod_wrt_noln('n_O3:',n_O3,';'); if n_N1 > 0 then mod_wrt_noln('n_N1:',n_N1,';'); if n_N2 > 0 then mod_wrt_noln('n_N2:',n_N2,';'); if n_N3 > 0 then mod_wrt_noln('n_N3:',n_N3,';'); if n_S > 0 then mod_wrt_noln('n_S:',n_S,';'); if n_SeTe > 0 then mod_wrt_noln('n_SeTe:',n_SeTe,';'); if n_F > 0 then mod_wrt_noln('n_F:',n_F,';'); if n_Cl > 0 then mod_wrt_noln('n_Cl:',n_Cl,';'); if n_Br > 0 then mod_wrt_noln('n_Br:',n_Br,';'); if n_I > 0 then mod_wrt_noln('n_I:',n_I,';'); if n_P > 0 then mod_wrt_noln('n_P:',n_P,';'); if n_B > 0 then mod_wrt_noln('n_B:',n_B,';'); if n_Met > 0 then mod_wrt_noln('n_Met:',n_Met,';'); if n_X > 0 then mod_wrt_noln('n_X:',n_X,';'); if n_b1 > 0 then mod_wrt_noln('n_b1:',n_b1,';'); if n_b2 > 0 then mod_wrt_noln('n_b2:',n_b2,';'); if n_b3 > 0 then mod_wrt_noln('n_b3:',n_b3,';'); if n_bar > 0 then mod_wrt_noln('n_bar:',n_bar,';'); if n_C1O > 0 then mod_wrt_noln('n_C1O:',n_C1O,';'); if n_C2O > 0 then mod_wrt_noln('n_C2O:',n_C2O,';'); if n_CN > 0 then mod_wrt_noln('n_CN:',n_CN,';'); if n_XY > 0 then mod_wrt_noln('n_XY:',n_XY,';'); if n_r3 > 0 then mod_wrt_noln('n_r3:',n_r3,';'); if n_r4 > 0 then mod_wrt_noln('n_r4:',n_r4,';'); if n_r5 > 0 then mod_wrt_noln('n_r5:',n_r5,';'); if n_r6 > 0 then mod_wrt_noln('n_r6:',n_r6,';'); if n_r7 > 0 then mod_wrt_noln('n_r7:',n_r7,';'); if n_r8 > 0 then mod_wrt_noln('n_r8:',n_r8,';'); if n_r9 > 0 then mod_wrt_noln('n_r9:',n_r9,';'); if n_r10 > 0 then mod_wrt_noln('n_r10:',n_r10,';'); if n_r11 > 0 then mod_wrt_noln('n_r11:',n_r11,';'); if n_r12 > 0 then mod_wrt_noln('n_r12:',n_r12,';'); if n_r13p > 0 then mod_wrt_noln('n_r13p:',n_r13p,';'); if n_rN > 0 then mod_wrt_noln('n_rN:',n_rN,';'); if n_rN1 > 0 then mod_wrt_noln('n_rN1:',n_rN1,';'); if n_rN2 > 0 then mod_wrt_noln('n_rN2:',n_rN2,';'); if n_rN3p > 0 then mod_wrt_noln('n_rN3p:',n_rN3p,';'); if n_rO > 0 then mod_wrt_noln('n_rO:',n_rO,';'); if n_rO1 > 0 then mod_wrt_noln('n_rO1:',n_rO1,';'); if n_rO2p > 0 then mod_wrt_noln('n_rO2p:',n_rO2p,';'); if n_rS > 0 then mod_wrt_noln('n_rS:',n_rS,';'); if n_rX > 0 then mod_wrt_noln('n_rX:',n_rX,';'); if n_rar > 0 then mod_wrt_ln('n_rar:',n_rar,';'); end; end; procedure mod_wrt_noln_molstat_X; begin with molstat do begin mod_wrt_noln(n_heavyatoms,','); mod_wrt_noln(n_heavybonds,','); mod_wrt_noln(n_rings,','); mod_wrt_noln(n_QA,','); mod_wrt_noln(n_QB,','); mod_wrt_noln(n_chg,','); mod_wrt_noln(n_C1,','); mod_wrt_noln(n_C2,','); mod_wrt_noln(n_C,','); mod_wrt_noln(n_CHB1p,','); mod_wrt_noln(n_CHB2p,','); mod_wrt_noln(n_CHB3p,','); mod_wrt_noln(n_CHB4,','); mod_wrt_noln(n_O2,','); mod_wrt_noln(n_O3,','); mod_wrt_noln(n_N1,','); mod_wrt_noln(n_N2,','); mod_wrt_noln(n_N3,','); mod_wrt_noln(n_S,','); mod_wrt_noln(n_SeTe,','); mod_wrt_noln(n_F,','); mod_wrt_noln(n_Cl,','); mod_wrt_noln(n_Br,','); mod_wrt_noln(n_I,','); mod_wrt_noln(n_P,','); mod_wrt_noln(n_B,','); mod_wrt_noln(n_Met,','); mod_wrt_noln(n_X,','); mod_wrt_noln(n_b1,','); mod_wrt_noln(n_b2,','); mod_wrt_noln(n_b3,','); mod_wrt_noln(n_bar,','); mod_wrt_noln(n_C1O,','); mod_wrt_noln(n_C2O,','); mod_wrt_noln(n_CN,','); mod_wrt_noln(n_XY,','); mod_wrt_noln(n_r3,','); mod_wrt_noln(n_r4,','); mod_wrt_noln(n_r5,','); mod_wrt_noln(n_r6,','); mod_wrt_noln(n_r7,','); mod_wrt_noln(n_r8,','); mod_wrt_noln(n_r9,','); mod_wrt_noln(n_r10,','); mod_wrt_noln(n_r11,','); mod_wrt_noln(n_r12,','); mod_wrt_noln(n_r13p,','); mod_wrt_noln(n_rN,','); mod_wrt_noln(n_rN1,','); mod_wrt_noln(n_rN2,','); mod_wrt_noln(n_rN3p,','); mod_wrt_noln(n_rO,','); mod_wrt_noln(n_rO1,','); mod_wrt_noln(n_rO2p,','); mod_wrt_noln(n_rS,','); mod_wrt_noln(n_rX,','); mod_wrt_ln(n_rar); end; end; // routines for substructure matching function find_ndl_ref_atom: integer; var i : integer; score : integer; index : integer; n_nb, n_hc : integer; begin // finds a characteristic atom in the needle molecule, // i.e., one with as many substituents as possible and // with as many heteroatom substitutents as possible if ndl_n_atoms = 0 then exit; score := 0; for i := 1 to ndl_n_atoms do begin n_nb := ndl_atom^[i].neighbor_count; n_hc := ndl_hetatom_count(i); if n_nb + n_hc > score then begin index := i; score := n_nb + n_hc; end; end; find_ndl_ref_atom := index; end; function atomtypes_OK(ndl_a, hst_a : integer):boolean; var ndl_el : str2; hst_el : str2; ndl_nbc : integer; hst_nbc : integer; ndl_Hexp : smallint; hst_Htot : smallint; res : boolean; begin if (ndl_a < 1) or (ndl_a > ndl_n_atoms) or (hst_a < 1) or (hst_a > n_atoms) then begin atomtypes_OK := false; exit; end; res := false; ndl_el := ndl_atom^[ndl_a].element; ndl_nbc := ndl_atom^[ndl_a].neighbor_count; ndl_Hexp := ndl_atom^[ndl_a].Hexp; hst_el := atom^[hst_a].element; hst_nbc := atom^[hst_a].neighbor_count; hst_Htot := atom^[hst_a].Htot; if (ndl_el = hst_el) then res := true; // very simplified... if (ndl_el = 'A ') and (is_heavyatom(hst_a)) then res := true; if ndl_el = 'Q ' then begin if (is_heavyatom(hst_a)) and (hst_el <> 'C ') then res := true; end; if ndl_el = 'X ' then begin if (hst_el = 'F ') or (hst_el = 'CL') or (hst_el = 'BR') or (hst_el = 'I ') then res := true; end; // if needle atom has more substituents than haystack atom ==> no match if (ndl_nbc > hst_nbc) then res := false; // check for explicit hydrogens if (ndl_Hexp > hst_Htot) then res := false; if res then debugoutput('atom types OK ('+inttostr(ndl_a)+'/'+inttostr(hst_a)+')') else debugoutput('atom types not OK ('+inttostr(ndl_a)+'/'+inttostr(hst_a)+')'); atomtypes_OK := res; end; function bondtypes_OK(ndl_b, hst_b : integer):boolean; var ndl_arom : boolean; hst_arom : boolean; ndl_btype : char; hst_btype : char; res : boolean; na, ha : string; a1, a2 : integer; a1_el, a2_el : str2; begin if (ndl_b < 1) or (ndl_b > ndl_n_bonds) or (hst_b < 1) or (hst_b > n_bonds) then begin bondtypes_OK := false; exit; end; res := false; ndl_arom := ndl_bond^[ndl_b].arom; ndl_btype := ndl_bond^[ndl_b].btype; if ndl_arom then na := '(ar)' else na := ''; hst_arom := bond^[hst_b].arom; hst_btype := bond^[hst_b].btype; if hst_arom then ha := '(ar)' else ha := ''; if (ndl_arom = true) and (hst_arom = true) then res := true; if (ndl_arom = false) and (hst_arom = false) then begin if (ndl_btype = hst_btype) then res := true; if (ndl_btype = 'l') and ((hst_btype = 'S') or (hst_btype = 'D')) then res := true; if (ndl_btype = 's') and (hst_btype = 'S') then res := true; if (ndl_btype = 'd') and (hst_btype = 'D') then res := true; end; // a little exception: if (ndl_arom = false) and (hst_arom = true) then begin if (ndl_btype = 'A') then res := true; if (ndl_btype = 's') or (ndl_btype = 'd') then res := true; if (ndl_btype = 'D') then // added in 0.2d: do not accept C=O etc. begin // as C-O/arom a1 := ndl_bond^[ndl_b].a1; a2 := ndl_bond^[ndl_b].a2; a1_el := ndl_atom^[a1].element; a2_el := ndl_atom^[a2].element; if not ((a1_el = 'O ') or (a2_el = 'O ') or (a1_el = 'S ') or (a2_el = 'S ') or (a1_el = 'SE') or (a2_el = 'SE') or (a1_el = 'TE') or (a2_el = 'TE')) then res := true; end; end; if (ndl_btype = 'a') then res := true; if res then debugoutput('bond types OK '+inttostr(ndl_b)+':'+ndl_btype+na+'/'+inttostr(hst_b)+':'+hst_btype+ha+')') else debugoutput('bond types not OK '+inttostr(ndl_b)+':'+ndl_btype+na+'/'+inttostr(hst_b)+':'+hst_btype+ha+')'); bondtypes_OK := res; end; function matrix_OK(m:matchmatrix;ndl_dim:integer;hst_dim:integer):boolean; var mr : boolean; begin if (ndl_dim < 1) or (ndl_dim > 4) or (hst_dim < 1) or (hst_dim > 4) then begin matrix_OK := false; exit; end; mr := false; case ndl_dim of 1 : case hst_dim of 1 : begin if m[1,1] then mr := true; end; 2 : begin if m[1,1] or m[1,2] then mr := true; end; 3 : begin if m[1,1] or m[1,2] or m[1,3] then mr := true; end; 4 : begin if m[1,1] or m[1,2] or m[1,3] or m[1,4] then mr := true; end; end; 2 : case hst_dim of 2 : begin if m[1,1] and m[2,2] then mr := true; if m[1,2] and m[2,1] then mr := true; end; 3 : begin if m[1,1] and (m[2,2] or m[2,3]) then mr := true; if m[1,2] and (m[2,1] or m[2,3]) then mr := true; if m[1,3] and (m[2,1] or m[2,2]) then mr := true; end; 4 : begin if m[1,1] and (m[2,2] or m[2,3] or m[2,4]) then mr := true; if m[1,2] and (m[2,1] or m[2,3] or m[2,4]) then mr := true; if m[1,3] and (m[2,1] or m[2,2] or m[2,4]) then mr := true; if m[1,4] and (m[2,1] or m[2,2] or m[2,3]) then mr := true; end; end; 3 : case hst_dim of 3 : begin if m[1,1] and m[2,2] and m[3,3] then mr := true; if m[1,1] and m[2,3] and m[3,2] then mr := true; if m[1,2] and m[2,1] and m[3,3] then mr := true; if m[1,2] and m[2,3] and m[3,1] then mr := true; if m[1,3] and m[2,1] and m[3,2] then mr := true; if m[1,3] and m[2,2] and m[3,1] then mr := true; end; 4 : begin if m[1,1] and m[2,2] and (m[3,3] or m[3,4]) then mr := true; if m[1,1] and m[2,3] and (m[3,2] or m[3,4]) then mr := true; if m[1,1] and m[2,4] and (m[3,2] or m[3,3]) then mr := true; if m[1,2] and m[2,1] and (m[3,3] or m[3,4]) then mr := true; if m[1,2] and m[2,3] and (m[3,1] or m[3,4]) then mr := true; if m[1,2] and m[2,4] and (m[3,1] or m[3,3]) then mr := true; if m[1,3] and m[2,1] and (m[3,2] or m[3,4]) then mr := true; if m[1,3] and m[2,2] and (m[3,1] or m[3,4]) then mr := true; if m[1,3] and m[2,4] and (m[3,1] or m[3,2]) then mr := true; if m[1,4] and m[2,1] and (m[3,2] or m[3,3]) then mr := true; if m[1,4] and m[2,2] and (m[3,1] or m[3,3]) then mr := true; if m[1,4] and m[2,3] and (m[3,1] or m[3,2]) then mr := true; end; end; 4 : case hst_dim of 4 : begin if m[1,1] and m[2,2] and ((m[3,3] and m[4,4]) or (m[3,4] and m[4,3])) then mr := true; if m[1,1] and m[2,3] and ((m[3,2] and m[4,4]) or (m[3,4] and m[4,2])) then mr := true; if m[1,1] and m[2,4] and ((m[3,2] and m[4,3]) or (m[3,3] and m[4,2])) then mr := true; if m[1,2] and m[2,1] and ((m[3,3] and m[4,4]) or (m[3,4] and m[4,3])) then mr := true; if m[1,2] and m[2,3] and ((m[3,1] and m[4,4]) or (m[3,4] and m[4,1])) then mr := true; if m[1,2] and m[2,4] and ((m[3,1] and m[4,3]) or (m[3,3] and m[4,1])) then mr := true; if m[1,3] and m[2,1] and ((m[3,2] and m[4,4]) or (m[3,4] and m[4,2])) then mr := true; if m[1,3] and m[2,2] and ((m[3,1] and m[4,4]) or (m[3,4] and m[4,1])) then mr := true; if m[1,3] and m[2,4] and ((m[3,1] and m[4,2]) or (m[3,2] and m[4,1])) then mr := true; if m[1,4] and m[2,1] and ((m[3,2] and m[4,3]) or (m[3,3] and m[4,2])) then mr := true; if m[1,4] and m[2,2] and ((m[3,1] and m[4,3]) or (m[3,3] and m[4,1])) then mr := true; if m[1,4] and m[2,3] and ((m[3,1] and m[4,2]) or (m[3,2] and m[4,1])) then mr := true; end; end; end; // case matrix_OK := mr; end; function is_matching(ndl_xmp:matchpath_type;hst_xmp:matchpath_type):boolean; var i, j : integer; ndl_n_nb : integer; n_nb : integer; ndl_a : integer; hst_a : integer; ndl_b : integer; hst_b : integer; prev_ndl_a : integer; prev_hst_a : integer; next_ndl_a : integer; next_hst_a : integer; ndl_nb : neighbor_rec; hst_nb : neighbor_rec; mm : matchmatrix; ndl_mp_len : integer; hst_mp_len : integer; ndl_mp : matchpath_type; hst_mp : matchpath_type; emptyline : boolean; res : boolean; tmpstr : string; begin // initialize local matchpath variables fillchar(ndl_mp,sizeof(matchpath_type),0); fillchar(hst_mp,sizeof(matchpath_type),0); // copy content of external variables into local ones for i := 1 to max_matchpath_length do begin ndl_mp[i] := ndl_xmp[i]; hst_mp[i] := hst_xmp[i]; end; ndl_mp_len := matchpath_length(ndl_mp); hst_mp_len := matchpath_length(hst_mp); if ndl_mp_len <> hst_mp_len then begin // this should never happen.... debugoutput('needle and haystack matchpaths are of different length'); is_matching := false; exit; end; ndl_a := ndl_mp[ndl_mp_len]; hst_a := hst_mp[hst_mp_len]; ndl_b := 0; hst_b := 0; prev_ndl_a := 0; prev_hst_a := 0; if ndl_mp_len > 1 then begin prev_ndl_a := ndl_mp[ndl_mp_len-1]; prev_hst_a := hst_mp[hst_mp_len-1]; end; // check whatever can be checked as early as now: // e.g. different elements or more substituents on needle atom than on haystack if (not atomtypes_OK(ndl_a, hst_a)) then begin is_matching := false; exit; end; // positive scenarios: ndl_b := get_ndl_bond(prev_ndl_a,ndl_a); hst_b := get_bond(prev_hst_a,hst_a); debugoutput('Now checking atoms '+inttostr(ndl_a)+'/'+inttostr(hst_a)+', bonds '+inttostr(ndl_b)+'/'+inttostr(hst_b)); if (ndl_b > 0) and (hst_b > 0) then begin // do a quick check if bond types match if (not bondtypes_OK(ndl_b, hst_b)) then begin debugoutput(' failed match of bonds '+inttostr(ndl_b)+'/'+inttostr(hst_b)); is_matching := false; exit; end; end; // a) we reached the end of our needle fragment (and atom/bond types match) if (ndl_atom^[ndl_a].neighbor_count = 1) and (atomtypes_OK(ndl_a, hst_a)) and (bondtypes_OK(ndl_b, hst_b)) then begin is_matching := true; debugoutput(' ==> end of needle fragment at atom '+inttostr(ndl_a)+' (match)'); exit; end; // b) a ring is formed (ndl_a is already in the path) and atom/bond types match if (matchpath_pos(ndl_a,ndl_mp) > 0) and (matchpath_pos(ndl_a,ndl_mp) < matchpath_length(ndl_mp)) then begin if (matchpath_pos(ndl_a,ndl_mp) = matchpath_pos(hst_a, hst_mp)) and (atomtypes_OK(ndl_a, hst_a)) and (bondtypes_OK(ndl_b, hst_b)) then begin is_matching := true; debugoutput('matchpath forms ring at: '+inttostr(ndl_a)+' (match)'); exit; end else begin is_matching := false; debugoutput('matchpath forms ring at: '+inttostr(ndl_a)+' (no match)'); exit; end; end; // in all other cases: do the hard work: // first, get all heavy-atom neighbors of needle and haystack; // at the beginning of the search, this means all neighbors, then it means // all but the previous atom (where we came from) fillchar(ndl_nb, sizeof(neighbor_rec),0); fillchar(hst_nb, sizeof(neighbor_rec),0); if (matchpath_length(ndl_mp) = 1) then begin ndl_n_nb := ndl_atom^[ndl_a].neighbor_count; n_nb := atom^[hst_a].neighbor_count; ndl_nb := get_ndl_neighbors(ndl_a); hst_nb := get_neighbors(hst_a); end else begin ndl_n_nb := ndl_atom^[ndl_a].neighbor_count -1; n_nb := atom^[hst_a].neighbor_count -1; ndl_nb := get_ndl_nextneighbors(ndl_a,prev_ndl_a); hst_nb := get_nextneighbors(hst_a,prev_hst_a); end; // now that the neighbor-arrays are filled, get all // combinations of matches recursively; // first, initialize the match matrix for i := 1 to 4 do for j := 1 to 4 do mm[i,j] := false; // make sure there are not too many neighbors (max. 4) if (ndl_n_nb > 4) or (n_nb > 4) then begin debugoutput('too many neighbors - exiting'); is_matching := false; exit; end; // check if matchpath is not already filled up if matchpath_length(ndl_mp) = max_matchpath_length then begin debugoutput('matchpath too long - exiting'); is_matching := false; exit; end; // next, check which chain of the needle matches which chain of the haystack for i := 1 to ndl_n_nb do begin emptyline := true; next_ndl_a := ndl_nb[i]; for j := 1 to n_nb do begin next_hst_a := hst_nb[j]; ndl_mp[ndl_mp_len+1] := next_ndl_a; hst_mp[hst_mp_len+1] := next_hst_a; if is_matching(ndl_mp,hst_mp) then begin mm[i,j] := true; emptyline := false; end; end; // if a needle substituent does not match any of the haystack substituents, // stop any further work immediately if emptyline then begin is_matching := false; exit; end; end; // finally, check the content of the matrix res := matrix_OK(mm,ndl_n_nb,n_nb); is_matching := res; if res then tmpstr := ' MATCH' else tmpstr := ' NO MATCH'; debugoutput('result for atoms '+inttostr(ndl_a)+'/'+inttostr(hst_a)+', bonds '+inttostr(ndl_b)+'/'+inttostr(hst_b)+':'+tmpstr); end; function quick_match:boolean; // added in v0.2c var res : boolean; i : integer; begin if ((ndl_n_atoms < 1) or (n_atoms < 1)) or ((ndl_n_atoms > n_atoms) or (ndl_n_bonds > n_bonds)) then begin // just to be sure... quick_match := false; exit; end; res := true; for i := 1 to ndl_n_atoms do begin if atom^[i].atype <> ndl_atom^[i].atype then res := false; end; if ndl_n_bonds > 0 then begin for i := 1 to ndl_n_bonds do begin if (ndl_bond^[i].a1 <> bond^[i].a1) or (ndl_bond^[i].a2 <> bond^[i].a2) or (ndl_bond^[i].btype <> bond^[i].btype) then res := false; end; end; quick_match := res; end; procedure perform_match; var i, j : integer; ndl_ref_atom : integer; ndl_n_nb : integer; ndl_n_hc : integer; n_nb : integer; n_hc : integer; begin // if we perform an exact match, needle and haystack must have // the same number of atoms, bonds, and rings if opt_exact then begin if (n_heavyatoms <> ndl_n_heavyatoms) or (n_heavybonds <> ndl_n_heavybonds) then begin matchresult := false; debugoutput('different number of heavy atoms and/or bonds'); exit; end; end; // have a quick look iof needle and haystack are identical molfiles if quick_match then begin matchresult := true; exit; end; // first, look for a characteristic atom in the needle ndl_ref_atom := find_ndl_ref_atom; debugoutput('needle reference atom: '+inttostr(ndl_ref_atom)+' ('+ndl_atom^[ndl_ref_atom].atype+')'); ndl_n_nb := ndl_atom^[ndl_ref_atom].neighbor_count; ndl_n_hc := ndl_hetatom_count(ndl_ref_atom); debugoutput('neighbor atoms: '+inttostr(ndl_n_nb)+' heteroatom neighbors: '+inttostr(ndl_n_hc)); matchresult := false; for j := 1 to max_matchpath_length do begin ndl_matchpath[j] := 0; hst_matchpath[j] := 0; end; ndl_matchpath[1] := ndl_ref_atom; i := 0; while (i < n_atoms) and (matchresult = false) do begin inc(i); n_nb := atom^[i].neighbor_count; n_hc := hetatom_count(i); if (n_nb >= ndl_n_nb) and (n_hc >= ndl_n_hc) then begin debugoutput('trying atom '+inttostr(i)+'; neighbor atoms: '+inttostr(n_nb)+' heteroatom neighbors: '+inttostr(n_hc)); hst_matchpath[1] := i; matchresult := is_matching(ndl_matchpath, hst_matchpath); if matchresult then debugoutput('matching atom in haystack: '+inttostr(i)+' ('+atom^[i].atype+')'); end; end; end; procedure clear_rings; var i : integer; begin n_rings := 0; fillchar(ring^, sizeof(ringlist),0); if n_atoms > 0 then begin for i := 1 to n_atoms do atom^[i].ring_count := 0; end; if n_bonds > 0 then begin for i := 1 to n_bonds do bond^[i].ring_count := 0; end; end; function ring_lastpos(s:ringpath_type):integer; var i, j, rc, rlp : integer; begin rlp := 0; if n_rings > 0 then begin for i := 1 to n_rings do begin rc := ringcompare(s, ring^[i]); if rc_identical(rc) then rlp := i; end; end; ring_lastpos := rlp; end; procedure remove_redundant_rings; var i, j, k, rlp : integer; tmp_path : ringpath_type; begin if n_rings < 2 then exit; for i := 1 to (n_rings - 1) do begin tmp_path := ring^[i]; rlp := ring_lastpos(tmp_path); while rlp > i do begin debugoutput('removing redundant ring: '+inttostr(rlp)+' (identical to ring '+inttostr(i)+')'); for j := rlp to (n_rings - 1) do ring^[j] := ring^[(j+1)]; for k := 1 to max_ringsize do ring^[n_rings,k] := 0; dec(n_rings); rlp := ring_lastpos(tmp_path); end; end; end; {* begin // main routine progname := extractfilename(paramstr(0)); if pos('MATCHMOL',upcase(progname))>0 then progmode := pmMatchMol else begin if pos('CHECKMOL',upcase(progname))>0 then progmode := pmCheckMol else begin mod_wrt_ln('THOU SHALLST NOT RENAME ME!'); halt(9); end; end; if (paramcount = 0) then begin show_usage; halt(1); end; init_globals; init_molstat(molstat); parse_args; if ringsearch_mode = rs_sar then max_vringsize := max_ringsize else max_vringsize := 10; if opt_verbose then mod_wrt_ln(progname+' v',version,' N. Haider 2003'); if progmode = pmMatchMol then begin if (not fileexists(ndl_molfilename)) and (not opt_stdin) then begin mod_wrt_ln('file ',ndl_molfilename,' not found!'); halt(2); end; end; if (not fileexists(molfilename)) and (not opt_stdin) then begin mod_wrt_ln('file ',molfilename,' not found!'); halt(2); end; // read the first molecule and process it; if we are in "matchmol" mode, // this is the "needle" if progmode = pmMatchMol then readinputfile(ndl_molfilename) else readinputfile(molfilename); li := 1; // initialize line pointer for input buffer filetype := get_filetype(ndl_molfilename); if filetype = 'unknown' then begin mod_wrt_ln('unknown file format!'); if opt_verbose then begin mod_wrt_ln('==========================================='); for i := 1 to molbufindex do mod_wrt_ln(molbuf^[i]); end; halt(3); end; if filetype = 'alchemy' then read_molfile(ndl_molfilename); if filetype = 'sybyl' then read_mol2file(ndl_molfilename); if filetype = 'mdl' then read_MDLmolfile(ndl_molfilename); count_neighbors; if (not found_arominfo) or (progmode = pmCheckMol) then // added in v0.2b/0.2c begin debugoutput('no aromaticity information found - checking myself...'); chk_ringbonds; if ringsearch_mode = rs_ssr then remove_redundant_rings; if n_rings = max_rings then begin if opt_verbose then mod_wrt_ln('warning: max. number of rings exceeded, reverting to SSR search'); ringsearch_mode := rs_ssr; clear_rings; max_vringsize := 10; chk_ringbonds; remove_redundant_rings; end; update_ringcount; update_atypes; chk_arom; end else begin debugoutput('found aromaticity information in input file'); update_Htotal; // end v0.2b snippet end; if progmode = pmCheckMol then begin if opt_verbose then mod_wrt_noln_mol; get_molstat; if opt_molstat then begin if opt_molstat_X then mod_wrt_noln_molstat_X else mod_wrt_noln_molstat; end else begin if found_querymol then begin mod_wrt_ln('input structure contains query atom or query bond!'); halt(1); end; chk_functionalgroups; if opt_none then opt_text := true; if opt_text then mod_wrt_noln_fg_text; if opt_text_de then mod_wrt_noln_fg_text_de; if opt_code then mod_wrt_noln_fg_code; if opt_bin then mod_wrt_noln_fg_binary; if opt_bitstring then mod_wrt_noln_fg_bitstring; if opt_xmdlout then mod_wrt_noln_MDLmolfile; end; zap_molecule; end else begin // progmode = pmMatchMol // now transfer all data to the "needle" set of variables copy_mol_to_needle; if opt_verbose then mod_wrt_noln_needle_mol; mol_count := 0; // next, read the "haystack" file and process it li := 1; repeat begin if opt_stdin or (mol_count = 0) then begin readinputfile(molfilename); li := 1; end; filetype := get_filetype(molfilename); if filetype <> 'unknown' then begin found_arominfo := false; // added in v0.2b if filetype = 'alchemy' then read_molfile(molfilename); if filetype = 'sybyl' then read_mol2file(molfilename); if filetype = 'mdl' then read_MDLmolfile(molfilename); inc(mol_count); count_neighbors; if not found_arominfo then begin debugoutput('no aromaticity information found - checking myself...'); chk_ringbonds; if ringsearch_mode = rs_ssr then remove_redundant_rings; if n_rings = max_rings then begin if opt_verbose then mod_wrt_ln('warning: max. number of rings exceeded, reverting to SSR search'); ringsearch_mode := rs_ssr; clear_rings; max_vringsize := 10; chk_ringbonds; remove_redundant_rings; end; update_ringcount; update_atypes; chk_arom; end else begin debugoutput('found aromaticity information in input file'); update_Htotal; end; init_molstat(ndl_molstat); if opt_verbose then mod_wrt_noln_mol; // now that we have both molecules, perform the comparison perform_match; if matchresult = true then begin if opt_molout then begin for i := 1 to molbufindex do mod_wrt_ln(molbuf^[i]); end else mod_wrt_ln(inttostr(mol_count),':T'); end else begin if not opt_molout then mod_wrt_ln(inttostr(mol_count),':F'); end; zap_molecule; if opt_stdin then molbufindex := 0; end; // else mod_wrt_ln(mol_count,':unknown file format'); // if filetype <> 'unknown' end; //mod_wrt_ln(li,'/',molbufindex,': ',molbuf^[li]); until (mol_in_queue = false) or ((opt_stdin = false) and (li >= molbufindex)); zap_needle; end; *} {*******************************************************************************} {* ****** ** ** ****************************************} {* ******* ** ** ****************************************} {* ** ** ** ** ****************************************} {* ** ** ** ** ****************************************} {* ** ** ** ** ****************************************} {* ** ** ** ** ****************************************} {* ** ** ** ** ****************************************} {* ** ** ** ** ****************************************} {* ******** ********* ********* ****************************************} {* ****** ********* ********* ****************************************} {*******************************************************************************} procedure init_globals_DLL; var i : integer; begin opt_verbose := false; opt_debug := false; opt_exact := false; opt_stdin := false; opt_text := false; opt_code := false; opt_bin := false; opt_bitstring := false; opt_molout := false; opt_molstat := false; opt_molstat_X := false; opt_xmdlout := false; cm_mdlmolfile := false; found_arominfo := false; found_querymol := false; ringsearch_mode := rs_sar; for i := 1 to max_fg do fg[i] := false; if yet_initialized = false then begin try getmem(molbuf,sizeof(molbuftype)); except on e:Eoutofmemory do begin messagebox(0,'init_globals_dll error','ERROR',0); mod_wrt_ln('Not enough memory'); halt(4); end; end; yet_initialized:=true; end; end; procedure mm_InitMol(); begin init_globals_dll; init_molstat(molstat); if ringsearch_mode = rs_sar then max_vringsize := max_ringsize else max_vringsize := 10; zap_molecule; molbufindex := 0; end; procedure mm_ElabMol(); begin li := 1; // initialize line pointer for input buffer filetype := get_filetype(ndl_molfilename); if filetype = 'unknown' then begin messagebox (0,'Error in mm_ElabMol: Unknown file format','MATCHMOLDLL ERROR',0); halt(3); end; if filetype = 'alchemy' then read_molfile(ndl_molfilename); if filetype = 'sybyl' then read_mol2file(ndl_molfilename); if filetype = 'mdl' then read_MDLmolfile(ndl_molfilename); count_neighbors; chk_ringbonds; if ringsearch_mode = rs_ssr then remove_redundant_rings; if n_rings = max_rings then begin if opt_verbose then mod_wrt_ln('warning: max. number of rings exceeded, reverting to SSR search'); ringsearch_mode := rs_ssr; clear_rings; max_vringsize := 10; chk_ringbonds; remove_redundant_rings; end; update_ringcount; update_atypes; chk_arom; end; procedure mm_SetCurrentMolAsQuery(); export;stdcall; begin zap_needle; //mm_ElabMol; copy_mol_to_needle; molbufindex := 0; mol_count:=0; end; function mm_Match(ExactMatch:bool):integer; export;stdcall; begin mm_match:=0; opt_exact:=ExactMatch; mol_count:=1; // mm_ElabMol; init_molstat(ndl_molstat); perform_match; mol_count:=0; if matchresult then mm_Match:=1; zap_molecule; molbufindex := 0; end; procedure mm_ReadInputLine(st:Pchar); begin mol_in_queue := false; if molbufindex < (max_atoms+max_bonds+8192) then begin inc(molbufindex); molbuf^[molbufindex] := string(st); end else begin messagebox(0,'Error in mm_Readinputline; memory problem','ERROR',0); mod_wrt_ln('Not enough memory for molfile! ',molbufindex); halt(1); end; end; procedure mm_SetMol(st:pchar);export;stdcall; var bb:char; aa:char; i:integer; k:integer; J:integer; spt:integer; tt:pChar; bb10:char; bb13:char ; bb0:char; lenst:integer; d:string; begin bb10:=chr(10); bb0:=chr(0) ; bb13:=chr(13) ; lenst:=strlen(st); tt:=stralloc(1024); //messagebox(0,st,'',0); spt:=0 ; mm_InitMol; for i := spt to lenst do begin bb:=st[i]; if ((bb=bb10) or (i=lenst)) then begin J:=0; // d:=''; for k := spt to i do begin aa:=st[k]; if ((aa<>bb10)and(aa<>bb13)) then begin //d:=d+aa; tt[J]:=aa; inc(J); end; end; tt[J]:=bb0; spt:=i; //messagebox (0,tt,tt,0); mm_readinputline(tt); end; end; strdispose(tt); mm_elabmol; end; function mm_GetRings():integer;export;stdcall; begin mm_getrings:=n_rings; end; Function mm_GetAtomRing(AtomNumber:integer):integer;export;stdcall; var i, j, a1, a2, b, pl : integer; begin a1:= atom^[AtomNumber].ring_count; mm_getatomring:= 0; if n_rings > 0 then begin for i := 1 to n_rings do begin pl := path_length(ring^[i]); // a2 := ring^[i,pl]; for j := 1 to pl do begin a1 := ring^[i,j]; if AtomNumber = a1 then mm_getatomring:=i; // // inc(atom^[a1].ring_count); // b := get_bond(a1,a2); // inc(bond^[b].ring_count); // a2 := a1; end; end; end; end; Procedure mm_Version(st:pchar);export;stdcall; begin strpcopy(st,version); end; exports mm_SetMol; exports mm_GetAtomRing; exports mm_SetCurrentMolAsQuery; exports mm_Match; exports mm_GetRings; exports mm_Version; end.