/* * International Chemical Identifier (InChI) * Version 1 * Software version 1.04 * September 9, 2011 * * The InChI library and programs are free software developed under the * auspices of the International Union of Pure and Applied Chemistry (IUPAC). * Originally developed at NIST. Modifications and additions by IUPAC * and the InChI Trust. * * IUPAC/InChI-Trust Licence No.1.0 for the * International Chemical Identifier (InChI) Software version 1.04 * Copyright (C) IUPAC and InChI Trust Limited * * This library is free software; you can redistribute it and/or modify it * under the terms of the IUPAC/InChI Trust InChI Licence No.1.0, * or any later version. * * Please note that this library is distributed WITHOUT ANY WARRANTIES * whatsoever, whether expressed or implied. See the IUPAC/InChI Trust * Licence for the International Chemical Identifier (InChI) Software * version 1.04, October 2011 ("IUPAC/InChI-Trust InChI Licence No.1.0") * for more details. * * You should have received a copy of the IUPAC/InChI Trust InChI * Licence No. 1.0 with this library; if not, please write to: * * The InChI Trust * c/o FIZ CHEMIE Berlin * * Franklinstrasse 11 * 10587 Berlin * GERMANY * * or email to: ulrich@inchi-trust.org. * */ #include #include #include #include #include #include "mode.h" #include "inpdef.h" #include "util.h" #include "ichi.h" #include "strutil.h" #include "ichierr.h" #include "ichicomp.h" #include "extr_ct.h" #include "ichister.h" #include "ichi_io.h" #define FIX_P_IV_Plus_O_Minus /* added fix to remove_ion_pairs() -- 2010-03-17 DT */ /* local prototypes */ int cmp_components( const void *a1, const void *a2 ); /*int mark_one_struct_component( inp_ATOM* at, int j, AT_NUMB *mark, AT_NUMB num_disconnected_components );*/ INChI_Stereo *Alloc_INChI_Stereo(int num_at, int num_bonds); int RemoveInpAtBond( inp_ATOM *at, int iat, int k ); int DisconnectInpAtBond( inp_ATOM *at, AT_NUMB *nOldCompNumber, int iat, int neigh_ord ); int move_explicit_Hcation(inp_ATOM *at, int num_at, int iat, int iat_H, int bInAllComponents); int DisconnectOneLigand( inp_ATOM *at, AT_NUMB *nOldCompNumber, S_CHAR *bMetal, char *elnumber_Heteroat, int num_halogens, int num_atoms, int iMetal, int jLigand, INCHI_MODE *bTautFlagsDone ); int bIsAmmoniumSalt( inp_ATOM *at, int i, int *piO, int *pk, S_CHAR *num_explicit_H ); int DisconnectAmmoniumSalt ( inp_ATOM *at, int i, int iO, int k, S_CHAR *num_explicit_H ); /*int bIsMetalSalt( inp_ATOM *at, int i ); - moved to strutil,h */ int DisconnectMetalSalt( inp_ATOM *at, int i ); int bIsMetalToDisconnect(inp_ATOM *at, int i, int bCheckMetalValence); int get_iat_number( int el_number, const int el_num[], int el_num_len ); int tot_unsat( int unsat[] ); int max_unsat( int unsat[] ); double dist3D( inp_ATOM *at1, inp_ATOM *at2 ); double dist2D( inp_ATOM *at1, inp_ATOM *at2 ); double dist_from_segm( double x, double y, double x1, double y1, double x2, double y2); int segments_intersect( double x11, double y11, double x12, double y12, /* segment #1 */ double x21, double y21, double x22, double y22 ); double GetMinDistDistribution( inp_ATOM *at, int num_at, int iat, int iat_H, int bInAllComponents, double min_dist[], int num_segm ); int nFindOneOM(inp_ATOM *at, int at_no, int ord_OM[], int num_OM); int the_only_doublet_neigh(inp_ATOM *at, int i1, int *ineigh1, int *ineigh2); #ifndef NUMH #define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2]) #define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) #endif /************************************************************************/ int the_only_doublet_neigh(inp_ATOM *at, int i1, int *ineigh1, int *ineigh2) { int i, neigh1, num_rad1=0, num_rad2=0; inp_ATOM *a = at+i1, *b; if ( RADICAL_DOUBLET != a->radical ) return -1; for ( i = 0; i < a->valence; i ++ ) { b = at + (neigh1 = (int)a->neighbor[i]); if ( RADICAL_DOUBLET == b->radical ) { num_rad1 ++; *ineigh1 = i; } } if ( 1 == num_rad1 ) { a = at + (neigh1 = (int)a->neighbor[*ineigh1]); for ( i = 0; i < a->valence; i ++ ) { b = at +(int)a->neighbor[i]; if ( RADICAL_DOUBLET == b->radical ) { num_rad2 ++; *ineigh2 = i; } } if ( 1 == num_rad2 ) { return neigh1; } } return -1; } /************************************************************************/ int fix_odd_things( int num_atoms, inp_ATOM *at, int bFixBug, int bFixNonUniformDraw ) { /* 0 1 2 3 4 5 6 7 8 9 */ static const char el[] = "N;P;As;Sb;O;S;Se;Te;"; /* 8 elements + C, Si */ static U_CHAR en[10]; /* same number: 8 elements */ static int ne=0, ne2; /* will be 8 and 10 */ static int el_number_P; static int el_number_H; static int el_number_C; static int el_number_O; static int el_number_Si; #define FIRST_NEIGHB2 4 #define FIRST_CENTER2 5 #define NUM_CENTERS_N 4 int i1, i2, k1, k2, c, num_changes = 0; char elname[ATOM_EL_LEN]; /* constants for element numbers */ enum elems { dNone, dCl=17,dBr=35,dI=53,dAt=85,dO=8,dS=16,dSe=34,dTe=52, dP=15, dC=6, dN=7 } ; if (bFixNonUniformDraw) { /* Correct non-uniformly drawn oxoanions and amidinium cations. */ { /* For central halogen, apply the following correftion rules: O O(-) || | O=Hal(-)=O ===> O=Hal=O || || O O (perchlorate, etc.) O O(-) || | Hal(-)=O ===> Hal=O || || O O (chlorate, etc.) O O(-) || | Hal(-)=O ===> Hal=O (chlorite, etc.) Hal(-)=O ===> Hal-O(-) (hypochlorite, etc.) For halcogenes (S, Se, Te) Y Y(-) || | RnX(-) ===> RnX if: 1) (X = S, Y = O) || (X = Se, Y = S, O) || (X = Te, Y = O, S, Se) 2) valence of X exceeds 6, in initially drawn form So the following is corrected: O O(-) || | O=S(-)-R ===> O=S-R || || O O or O O- || | F5Te(-) ===> F5Te but the following remains unchanged: O || O=S(-)-R The central atom (of IUPAC Group 16-17) is shown as negative but it contains double bond(s) to terminal atom of greater electronegativity (of Group 16). The central atom is halcogen (S,Se,Te) in highest oxidation state or halogen. Fix: move negative charge to terminal atom and change double bond to a single one. Eligible central atom Eligible terminal atom at double bond's end Cl O Br O I O [At S,Se,Te] S O Se O,S Te O, S, Se Comments: 1. Central atoms of Groups 13-15 are not considered. 2. Pauling electronegativities are: F(3.98) > O(3.44) > Cl (3.16) > N (3.04) > Br(2.96) > I(2.66) > S(2.58) > Se(2.55) > At (2.2) > Te(2.1) */ static U_CHAR allowed_elnums_center_halogen[] = {dCl, dBr, dI, dAt} ; static U_CHAR allowed_elnums_center_halcogen[] = {dS, dSe, dTe} ; int en_center; int i, j, k; for (i=0; i 0? at[i].iso_atw_diff-1 : at[i].iso_atw_diff; continue; } /* From same-element candidates, select one with less isotopic mass (arbitrary choice). */ else if (en_term==min_en) { iso = at[j].iso_atw_diff > 0? at[i].iso_atw_diff-1 : at[i].iso_atw_diff; if ( iso =0) { at[i].charge = 0; at[jj].charge = -1; at[i].bond_type[kk] = BOND_TYPE_SINGLE; at[jj].bond_type[0] = BOND_TYPE_SINGLE; at[i].bond_stereo[kk] = at[jj].bond_stereo[0] = 0; at[i].chem_bonds_valence--; at[jj].chem_bonds_valence--; num_changes ++; } } } /* end of search for candidate centers. */ } /* end of correcting oxoanions */ /* Correct non-uniformly drawn amidinium cations. */ { /* Amidines include carboxamidines RC(=NR)NR2, sulfinamidines RS(=NR)NR2 and phosphinamidines, R2P(=NR)NR2. NR NR | | R"-Y-NHR' ===> R"-Y=N(+)HR' (+) Y = C, S, P Fix: move positive charge to nitrogen and change single bond to a double one. Comment: Fix is applied only if at least one of R's at N is hydrogen (otherwise we have just a '+' delocalization which is already recognized). */ static U_CHAR allowed_elnums_center[] = {dC, dS, dP} ; int en_center; int i, j, k, jj, kk; int mismatch = 0, nuH=0, nuN = 0, nitrogens[MAXVAL]; for (i=0; i 3 ) || ( at[j].chem_bonds_valence > 3 ) ) { mismatch = 1; break; } nuH+= NUMH(at,j); nuN++; if (jj<0) { jj = j; kk = k; } } } /* If OK, apply changes. */ if (mismatch) continue; if (nuN!=2) continue; if (nuH<1) continue; if (jj>=0) { at[i].charge = 0; at[jj].charge = 1; at[i].bond_type[kk] = BOND_TYPE_DOUBLE; for ( k1 = 0; k1 < at[jj].valence && i != at[jj].neighbor[k1]; k1 ++ ) ; at[jj].bond_type[k1] = BOND_TYPE_DOUBLE; at[i].chem_bonds_valence++; at[jj].chem_bonds_valence++; /* NB: do nothing with wedge stereo bonds (retain wedge) */ num_changes ++; } } /* end of search for candidate centers. */ } /* end of correcting amidiniums */ } /*( if (bFixNonUniformDraw) */ if ( !ne ) { /* one time initialization */ const char *b, *e; int len; for ( b = el; e = strchr( b, ';'); b = e+1 ) { len = e-b; memcpy( elname, b, len ); elname[len] = '\0'; en[ne++] = get_periodic_table_number( elname ); } ne2 = ne; el_number_P = get_periodic_table_number( "P" ); el_number_H = get_periodic_table_number( "H" ); el_number_O = get_periodic_table_number( "O" ); en[ne2++] = el_number_C = get_periodic_table_number( "C" ); en[ne2++] = el_number_Si = get_periodic_table_number( "Si" ); } /* H(-)-X -> H-X(-); H(+)-X -> H-X(+) */ for ( i1 = 0; i1 < num_atoms; i1 ++ ) { if ( 1 == at[i1].valence && 1 == abs(at[i1].charge) && (0 == at[i1].radical || RADICAL_SINGLET == at[i1].radical) && BOND_TYPE_SINGLE == at[i1].bond_type[0] && el_number_H == at[i1].el_number && el_number_H != at[i2=(int)at[i1].neighbor[0]].el_number && !NUMH(at,i1) && !NUMH(at,i2) ) { at[i2].charge += at[i1].charge; at[i1].charge = 0; } } /* replace XHm(-)--Y==XHn(+) with XHm==Y--XHn, (n>=0 ,m>=0, X=N,P,As,Sb,O,S,Se,Te) */ for ( i1 = 0; i1 < num_atoms; i1 ++ ) { if ( 1 != at[i1].charge || at[i1].radical && RADICAL_SINGLET != at[i1].radical || at[i1].chem_bonds_valence == at[i1].valence || !memchr(en, at[i1].el_number, ne) || get_el_valence( at[i1].el_number, at[i1].charge, 0 ) != at[i1].chem_bonds_valence+NUMH(at,i1) ) { continue; } /* found a candidate at[i1] for X in XHn(+) */ if ( 1 == at[i1].valence && BOND_TYPE_DOUBLE == at[i1].bond_type[0] ) { c = (int)at[i1].neighbor[0]; for ( k2 = 0; k2 < at[c].valence; k2 ++ ) { i2 = at[c].neighbor[k2]; if ( 1 == at[i2].valence && -1 == at[i2].charge && at[i2].el_number == at[i1].el_number && /* exact match */ (0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical) && BOND_TYPE_SINGLE == at[i2].bond_type[0] && /*memchr(en, at[i2].el_number, ne) &&*/ get_el_valence( at[i2].el_number, at[i2].charge, 0 ) == at[i2].chem_bonds_valence+NUMH(at,i2) ) { /* found both X(-) and X(+); change bonds and remove charges */ for ( k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1 ++ ) ; at[i1].charge = at[i2].charge = 0; at[i1].bond_type[0] = at[c].bond_type[k1] = BOND_TYPE_SINGLE; at[i1].chem_bonds_valence --; at[i2].bond_type[0] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; at[i2].chem_bonds_valence ++; num_changes ++; break; } } } else { /* explicit H case: detect H-neighbors and Y */ int ineigh, neigh, i1_c, i2_c, num_H_i1, num_H_i2; for ( ineigh = 0, num_H_i1 = 0, i1_c = -1; ineigh < at[i1].valence; ineigh ++ ) { neigh = at[i1].neighbor[ineigh]; if ( at[neigh].el_number == el_number_H ) { if ( at[neigh].chem_bonds_valence == 1 && (0 == at[neigh].radical || RADICAL_SINGLET == at[neigh].radical) ) { num_H_i1 ++; /* found H-neighbor */ } else { break; /* wrong neighbor */ } } else if ( at[i1].bond_type[ineigh] == BOND_TYPE_DOUBLE ) { /* found a candidate for Y; bond must be double */ i1_c = ineigh; c = neigh; } } if ( i1_c < 0 || num_H_i1 + 1 != at[i1].valence ) { continue; } for ( k2 = 0; k2 < at[c].valence; k2 ++ ) { i2 = at[c].neighbor[k2]; if (-1 == at[i2].charge && at[i2].el_number == at[i1].el_number && /* exact match */ (0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical) && get_el_valence( at[i2].el_number, at[i2].charge, 0 ) == at[i2].chem_bonds_valence+NUMH(at,i2) ) { for ( ineigh = 0, num_H_i2 = 0, i2_c = -1; ineigh < at[i2].valence; ineigh ++ ) { neigh = at[i2].neighbor[ineigh]; if ( at[neigh].el_number == el_number_H ) { if ( at[neigh].chem_bonds_valence == 1 && (0 == at[neigh].radical || RADICAL_SINGLET == at[neigh].radical) ) { num_H_i2 ++; /* found H-neighbor */ } else { break; /* wrong neighbor */ } } else if ( c == neigh && at[i2].bond_type[ineigh] == BOND_TYPE_SINGLE ) { i2_c = ineigh; /* position of Y neighbor; bond must be single */ } else { break; } } if ( num_H_i2 + (i2_c >= 0) != at[i2].valence ) { continue; } /* found both X(-) and X(+); change bonds and remove charges */ for ( k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1 ++ ) ; at[i1].charge = at[i2].charge = 0; at[i1].bond_type[i1_c] = at[c].bond_type[k1] = BOND_TYPE_SINGLE; at[i1].chem_bonds_valence --; at[i2].bond_type[i2_c] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; at[i2].chem_bonds_valence ++; num_changes ++; break; } } } } /* Replace X- X X=O,S,Se,Te -- terminal atoms (NEIGHB2) \ | \ || >Y++ with >Y Y=S,Se,Te -- central cation (CENTER2) / | / || X- X Y valence=4, original Y bond valence = 4 --- the following case of P is processed separately in remove_ion_pairs() --- therefire, it has been disabled here, see #ifndef FIX_P_IV_Plus_O_Minus -- 2010-03-17 DT X- X X=O,S,Se,Te -- terminal atoms (NEIGHB2) \ | \ || >P+ with >P / | / | X- X- Y valence=4, original Y bond valence = 4 */ for ( i1 = 0; i1 < num_atoms; i1 ++ ) { if ( 1 == at[i1].valence && -1 == at[i1].charge && (0 == at[i1].radical || RADICAL_SINGLET == at[i1].radical) && !NUMH(at,i1) && BOND_TYPE_SINGLE == at[i1].bond_type[0] && memchr( en+FIRST_NEIGHB2, at[i1].el_number, ne-FIRST_NEIGHB2 ) ) { int charge, i; /* found a candidate for X */ c = (int)at[i1].neighbor[0]; /* candidate for Y */ if ( ((charge=2) == at[c].charge && memchr( en+FIRST_CENTER2, at[c].el_number, ne-FIRST_CENTER2) #ifndef FIX_P_IV_Plus_O_Minus || (charge=1) == at[c].charge && el_number_P==at[c].el_number #endif ) && 4 == at[c].valence && (0 == at[c].radical || RADICAL_SINGLET == at[c].radical ) && at[c].valence == at[c].chem_bonds_valence && !NUMH(at,c) ) { ; /* accept */ } else { continue; /* ignore at[i1] */ } for ( k2 = 0; k2 < at[c].valence; k2 ++ ) { i2 = at[c].neighbor[k2]; if ( i2 == i1 ) { continue; } if ( 1 == at[i2].valence && -1 == at[i2].charge && memchr( en+FIRST_NEIGHB2, at[i2].el_number, ne-FIRST_NEIGHB2 ) && /*at[i2].el_number == at[i1].el_number &&*/ /* exact match */ (0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical) && !NUMH(at,i2) && BOND_TYPE_SINGLE == at[i2].bond_type[0] ) { /* found both X(-) and X(-); change bonds and remove charges */ for ( k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1 ++ ) ; for ( i = 0; i < charge; i ++ ) { /* in case of P it does not matter which X atom is neutralized because of tautomerism. However, neutral central atom is important for the neutralization of the components */ switch ( i ) { case 0: at[i1].charge ++; /* = 0; changed 2010-03-17 DT*/ at[i1].bond_type[0] = at[c].bond_type[k1] = BOND_TYPE_DOUBLE; at[i1].bond_stereo[0] = at[c].bond_stereo[k1] = 0; at[i1].chem_bonds_valence ++; at[c].chem_bonds_valence ++; if ( bFixBug ) at[c].charge --; /* added 2010-03-17 DT*/ num_changes ++; break; case 1: at[i2].charge ++; /*= 0; changed 2010-03-17 DT*/ at[i2].bond_type[0] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; at[i2].bond_stereo[0] = at[c].bond_stereo[k2] = 0; at[i2].chem_bonds_valence ++; at[c].chem_bonds_valence ++; if ( bFixBug ) at[c].charge --; /* added 2010-03-17 DT */ num_changes ++; break; } } /* -- removed -- 2010-03-17 DT #if ( FIX_ODD_THINGS_REM_Plus_BUG == 1 ) at[c].charge -= charge; #else if ( bFixBug ) { at[c].charge -= charge; } #endif */ break; } } } } /* A(doublet)-B(doublet) -> A=B (A and B have no other doublet neighbors) */ /* A(doublet)=B(doublet) -> A#B (A and B have no other doublet neighbors) */ for( i1 = 0; i1 < num_atoms; i1 ++ ) { if ( RADICAL_DOUBLET == at[i1].radical && 0 <= (i2=the_only_doublet_neigh(at, i1, &k1, &k2)) ) { if ( at[i1].bond_type[k1] <= BOND_TYPE_DOUBLE ) { at[i1].bond_type[k1] ++; at[i1].chem_bonds_valence ++; at[i2].bond_type[k2] ++; at[i2].chem_bonds_valence ++; at[i1].radical = 0; at[i2].radical = 0; } } } #if ( REMOVE_ION_PAIRS_EARLY == 1 ) num_changes += remove_ion_pairs( num_atoms, at ); #endif return num_changes; } /************************************************************************/ int post_fix_odd_things( int num_atoms, inp_ATOM *at ) { int num_changes = 0; /* currently does nothing */ return num_changes; } /************************************************************************/ int nFindOneOM(inp_ATOM *at, int at_no, int ord_OM[], int num_OM) { int i, n_OM, n_OM_best, best_value, cur_value, diff; int num_best; if ( 1 == num_OM ) { return ord_OM[0]; } if ( 1 > num_OM ) { return -1; } /* select neighbors with min. number of bonds */ num_best = 1; n_OM = (int)at[at_no].neighbor[ord_OM[0]]; best_value = (int)at[n_OM].valence; /* compare number of bonds; move indexes of the best neighbors to the first elements of ord_OM[] */ for ( i = 1; i < num_OM; i ++ ) { n_OM = at[at_no].neighbor[ord_OM[i]]; cur_value = (int)at[n_OM].valence; diff = cur_value - best_value; if ( diff < 0 ) { n_OM_best = n_OM; best_value = cur_value; ord_OM[0] = ord_OM[i]; num_best = 1; } else if ( diff == 0 ) { /* was '=', pointed by WDI */ ord_OM[num_best ++] = ord_OM[i]; } } num_OM = num_best; if ( 1 == num_OM ) { return ord_OM[0]; } /* select neighbors with min. periodic numbers */ num_best = 1; n_OM = (int)at[at_no].neighbor[ord_OM[0]]; best_value = (int)at[n_OM].el_number; /* compare periodic numbers; move indexes of the best neighbors to the first elements of ord_OM[] */ for ( i = 1; i < num_OM; i ++ ) { n_OM = at[at_no].neighbor[ord_OM[i]]; cur_value = (int)at[n_OM].el_number; diff = cur_value - best_value; if ( diff < 0 ) { n_OM_best = n_OM; best_value = cur_value; ord_OM[0] = ord_OM[i]; num_best = 1; } else if ( diff == 0 ) { /* was '=', pointed by WDI */ ord_OM[num_best ++] = ord_OM[i]; } } num_OM = num_best; if ( 1 == num_OM ) { return ord_OM[0]; } /* if neighbors are not terminal atoms then reject */ if ( 1 < at[n_OM].valence ) { return -1; } /* if neighbors are terminal atoms then the one without isotope or with lightest isotope */ num_best = 1; n_OM = (int)at[at_no].neighbor[ord_OM[0]]; best_value = (int)at[n_OM].iso_atw_diff; /* compare periodic numbers; move indexes of the best neighbors to the first elements of ord_OM[] */ for ( i = 1; i < num_OM; i ++ ) { n_OM = at[at_no].neighbor[ord_OM[i]]; cur_value = (int)at[n_OM].el_number; diff = cur_value - best_value; if ( (!cur_value && best_value) || diff < 0 ) { n_OM_best = n_OM; best_value = cur_value; ord_OM[0] = ord_OM[i]; num_best = 1; } else if ( diff == 0 ) { /* was '=', pointed by WDI */ ord_OM[num_best ++] = ord_OM[i]; } } num_OM = num_best; if ( 1 == num_OM ) { return ord_OM[0]; } /* return any */ return ord_OM[0]; } /************************************************************************/ /* the bonds are fixed in fix_special_bonds() */ int remove_ion_pairs( int num_atoms, inp_ATOM *at ) { int num_changes = 0; /* 0 1 2 3 4 5 6 7 8 9 8 9 */ #if ( FIX_REM_ION_PAIRS_Si_BUG == 1 ) static const char el[] = "N;P;As;Sb;O;S;Se;Te;C;Si;"; /* 8 elements + C, Si */ #else static const char el[] = "N;P;As;Sb;O;S;Se;Te;C;Si"; /* 8 elements + C, Si */ #endif static char en[12]; /* same number: 8 elements */ static int ne=0; /* will be 8 and 10 */ #define ELEM_N_FST 0 #define ELEM_N_LEN 4 #define ELEM_O_FST 4 #define ELEM_O_LEN 4 #define ELEM_C_FST 8 #define ELEM_C_LEN 2 #define MAX_NEIGH 6 int i, n, n2, i1, i2, i3, i4, type, chrg; int num_C_II=0, num_C_plus=0, num_C_minus=0, num_N_plus=0, num_N_minus=0, num_O_plus=0, num_O_minus=0, num_All; #ifdef FIX_P_IV_Plus_O_Minus int num_P_IV_plus=0; /* added 2010-03-17 DT */ #endif inp_ATOM *a; char elname[ATOM_EL_LEN], *p; if ( !ne ) { /* one time initialization */ const char *b, *e; int len; for ( b = el; e = strchr( b, ';'); b = e+1 ) { len = e-b; memcpy( elname, b, len ); elname[len] = '\0'; en[ne++] = get_periodic_table_number( elname ); } en[ne] = '\0'; } /****** count candidates ********/ for ( i = 0, a = at; i < num_atoms; i ++, a++ ) { if ( 1 == (chrg=a->charge) || -1 == chrg ) { if ( p = (char*)memchr( en, a->el_number, ne) ) { n = p - en; if ( n >= ELEM_C_FST ) { if ( chrg > 0 ) num_C_plus ++; else num_C_minus ++; } else if ( n >= ELEM_O_FST ) { if ( chrg > 0 ) num_O_plus ++; else num_O_minus ++; } else { if ( chrg > 0 ) num_N_plus ++; else num_N_minus ++; #ifdef FIX_P_IV_Plus_O_Minus num_P_IV_plus += n > 0 && chrg == 1 && a->valence == 4 && a->chem_bonds_valence == 4; /* added 2010-03-17 DT */ #endif } } } else if ( !chrg && a->chem_bonds_valence + NUMH(a, 0) == 2 && get_el_valence( a->el_number, 0, 0 ) == 4 && NULL != memchr( en+ELEM_C_FST, a->el_number, ELEM_C_LEN) ) { num_C_II ++; } } num_All = num_C_II + num_C_plus + num_C_minus + num_N_plus + num_N_minus + num_O_plus + num_O_minus; /* do not add num_P_IV_plus ! -- 2010-03-17 DT */ if ( !num_All ) { return 0; } /**************************************************************************/ /*************************** Terminal ion pairs ***************************/ /**************************************************************************/ /*------------------------------------------------------------------------- Pair type 1 N=N,P,As,Sb; O=O,S,Se,Te =========== X X if X is another -O(-) then neutralize O(-) | | that has the smallest periodic table number O=N(+)-O(-) => O=N=O i n --------------------------------------------------------------------------*/ for ( type = 1; type <= 18; type ++ ) { if ( (!type || 1 == type) ) { for ( i = 0; i < num_atoms && 0 < num_N_plus && 0 < num_O_minus; i ++ ) { if ( 1 == at[i].charge && 3 == nNoMetalNumBonds(at, i) && 4 == nNoMetalBondsValence(at, i) && NULL != memchr( en+ELEM_N_FST, at[i].el_number, ELEM_N_LEN) ) { int num_OM = 0, ord_OM[3]; /* -O(-) */ int num_O = 0; /* =O */ int num_O_other = 0; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( 1 == nNoMetalNumBonds(at, n) && 0 == num_of_H( at, n ) && NULL != (p = (char*)memchr( en+ELEM_O_FST, at[n].el_number, ELEM_O_LEN)) ) { if ( BOND_TYPE_SINGLE == at[i].bond_type[i1] && -1 == at[n].charge ) { ord_OM[num_OM ++] = i1; } else if ( BOND_TYPE_DOUBLE == at[n].bond_type[0] && 0 == at[n].charge ) { num_O ++; } else { num_O_other ++; } } } if ( num_OM > 0 && num_O > 0 && !num_O_other && 0 <= (i1=nFindOneOM(at, i, ord_OM, num_OM)) ) { /* remove charges and increase bond order */ n = at[i].neighbor[i1]; i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].charge --; at[n].charge ++; at[i].radical = 0; at[n].radical = 0; num_changes ++; num_N_plus --; num_O_minus --; num_All -= 2; } } } #ifdef FIX_P_IV_Plus_O_Minus /*------------------------------------------------------------------------- Pair type 1a P=P,As,Sb; O=O,S,Se,Te -- added 2010-03-17 ============= X X if X, Y, or Z is another -O(-) then neutralize O(-) | | that has the smallest periodic table number Y-P(+)-O(-) => Y-P=O |i n | Z Z --------------------------------------------------------------------------*/ for ( i = 0; i < num_atoms && 0 < num_P_IV_plus /*&& 0 < num_N_plus*/ && 0 < num_O_minus; i ++ ) { if ( 1 == at[i].charge && 4 == nNoMetalNumBonds(at, i) && 4 == nNoMetalBondsValence(at, i) && NULL != memchr( en+ELEM_N_FST+1, at[i].el_number, ELEM_N_LEN-1) ) { int num_OM = 0, ord_OM[4]; /* -O(-) */ /*int num_O = 0;*/ /* =O */ int num_O_other = 0; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( 1 == nNoMetalNumBonds(at, n) && 0 == num_of_H( at, n ) && NULL != (p = (char*)memchr( en+ELEM_O_FST, at[n].el_number, ELEM_O_LEN)) ) { if ( BOND_TYPE_SINGLE == at[i].bond_type[i1] && -1 == at[n].charge ) { ord_OM[num_OM ++] = i1; /* } if ( BOND_TYPE_DOUBLE == at[n].bond_type[0] && 0 == at[n].charge ) { num_O ++; */ } else { num_O_other ++; } } } if ( num_OM > 0 /*&& num_O > 0 && !num_O_other*/ && 0 <= (i1=nFindOneOM(at, i, ord_OM, num_OM)) ) { /* remove charges and increase bond order */ n = at[i].neighbor[i1]; i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].charge --; at[n].charge ++; at[i].radical = 0; at[n].radical = 0; num_changes ++; num_N_plus --; num_O_minus --; num_P_IV_plus --; num_All -= 2; } } } #endif /* FIX_P_IV_Plus_O_Minus */ } /*------------------------------------------------------------------------- Terminal pair types: 2,3,4,5,6,7,8,9 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si ==================================== type # 2 2: O=N-C(II)- => O=N#C- N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 3 9: O=O(+)-C(-)(III) => O=O=C(IV) 4 3: O(-)-N(+)(IV) => O=N(V) (input structure has at least 1 double bond) 5 4: O(-)-O(+)(III) => O=O(IV) 6 8: O(-)-O-C(+)(III) => O=O=C(IV) 7 5: N(-)=N(+)(IV) => N#N(V) allow terminal H on N(-) 8 6: N(-)=O(+)(III) => N#O- 9 7: N(-)=C(+)(III) => N#C- --------------------------------------------------------------------------*/ if ( !type || 2 <= type && type <= 9 ) { for ( i = 0; i < num_atoms && 0 < num_All; i ++ ) { if ( 0 == at[i].charge && 1 == nNoMetalNumBonds(at, i) && 2 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && NULL != memchr( en+ELEM_O_FST, at[i].el_number, ELEM_O_LEN) && 0 <= ( i1 = nNoMetalNeighIndex(at, i)) && at[i].bond_type[i1] <= BOND_TYPE_TRIPLE ) { /* terminal O= */ n = at[i].neighbor[i1]; if ( (!type || type == 2) && 0 < num_C_II ) { /* avoid alternating bonds */ if ( 0 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_N_FST, at[n].el_number, ELEM_N_LEN) && 0 <= (i2 = nNoMetalOtherNeighIndex( at, n, i ) ) && at[n].bond_type[i2] <= BOND_TYPE_TRIPLE ) { /* i2 = index of opposite to at[i] neighbor of at[n] */ /*i2 = (at[n].neighbor[0] == i);*/ n2 = at[n].neighbor[i2]; if ( 0 == at[n2].charge && 2 == at[n2].valence && 2 == at[n2].chem_bonds_valence && 0 == num_of_H( at, n2 ) && NULL != memchr( en+ELEM_C_FST, at[n2].el_number, ELEM_C_LEN) ) { /* i n n2 */ /* found O=N-C(II)- */ /* convert O=N-C(II)- => O=N#C- */ i3 = (at[n2].neighbor[0] != n); /* index of at[n] neighbor of n2 */ at[ n].chem_bonds_valence = 5; /* N */ at[n2].chem_bonds_valence = 4; /* C */ at[ n].bond_type[i2] = BOND_TYPE_TRIPLE; at[n2].bond_type[i3] = BOND_TYPE_TRIPLE; at[n2].radical = 0; num_changes ++; num_C_II --; num_All --; continue; } } } if ( (!type || type == 3) && 0 < num_O_plus && 0 < num_C_minus ) { if ( 1 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_O_FST, at[n].el_number, ELEM_O_LEN) && 0 <= (i2 = nNoMetalOtherNeighIndex( at, n, i ) ) && at[n].bond_type[i2] <= BOND_TYPE_TRIPLE ) { /* found O=O(+)- */ /* i2 = index of opposite to at[i] neighbor of at[n] */ /*i2 = (at[n].neighbor[0] == i);*/ n2 = at[n].neighbor[i2]; if ( -1 == at[n2].charge && 3 >= nNoMetalNumBonds(at, n2) && 3 == nNoMetalBondsValence(at, n2)+NUMH(at,n2) && NULL != memchr( en+ELEM_C_FST, at[n2].el_number, ELEM_C_LEN) ) { /* i n n2 */ /* found found O=O(+)-C(-)(III) */ /* convert O=O(+)-C(-)(III) => O=O=C(IV) */ i3 = (at[n2].neighbor[0] != n); /* index of at[n] neighbor of n2 */ at[ n].charge --; at[n2].charge ++; at[ n].chem_bonds_valence += 1; /* =O- => =O= */ at[n2].chem_bonds_valence += 1; /* -C => =C */ at[ n].bond_type[i2] = BOND_TYPE_DOUBLE; at[n2].bond_type[i3] = BOND_TYPE_DOUBLE; num_changes ++; num_O_plus --; num_C_minus --; num_All -= 2; continue; } } } } else if ( -1 == at[i].charge && 0 < num_O_minus + num_N_minus && 0 < num_N_plus + num_O_plus + num_C_plus && 1 == nNoMetalNumBonds(at, i) && 1 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && NULL != memchr( en+ELEM_O_FST, at[i].el_number, ELEM_O_LEN) && 0 <= (i1 = nNoMetalNeighIndex( at, i )) && at[i].bond_type[i1] <= BOND_TYPE_TRIPLE ) { /* terminal O(-)- */ n = at[i].neighbor[i1]; if ( (!type || type == 4) && 0 < num_O_minus && 0 < num_N_plus && /* O(-)-N(+)(IV) */ 1 == at[n].charge && 3 >= nNoMetalNumBonds(at, n) && 4 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_N_FST, at[n].el_number, ELEM_N_LEN) /* except >O(+)- */ ) { /* found O(-)-N(+)(IV) */ /* convert O(-)-N(+)(IV) => O=N(V) */ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; /* index of at[i] neighbor of at[n] */ at[i].charge ++; at[n].charge --; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_O_minus --; num_N_plus --; num_All -= 2; continue; } if ( (!type || type == 5) && 0 < num_O_minus && 0 < num_O_plus &&/* O(-)-O(+)(III) */ 1 == at[n].charge && 3 >= nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_O_FST, at[n].el_number, ELEM_O_LEN) /* except >O(+)- */ ) { /* found O(+)(III) */ /* convert O(-)-O(+)(III) => O=O(IV) */ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; /* index of at[i] neighbor of at[n] */ at[i].charge ++; at[n].charge --; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_O_minus --; num_O_plus --; num_All -= 2; continue; } /* i n n2 */ if ( (!type || type == 6) && /* O(-)-O-C(+)(III) */ 0 < num_O_minus && 0 < num_C_plus && 0 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 2 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_O_FST, at[n].el_number, ELEM_O_LEN) && 0 <= (i2=nNoMetalOtherNeighIndex( at, n, i )) && at[n].bond_type[i2] <= BOND_TYPE_TRIPLE ) { /* found O(-)-O- */ /* i2 = index of opposite to at[i] neighbor of at[n] */ /*i2 = (at[n].neighbor[0] == i);*/ n2 = at[n].neighbor[i2]; if ( 1 == at[n2].charge && 3 >= nNoMetalNumBonds(at, n2) && 3 == nNoMetalBondsValence(at, n2)+NUMH(at,n2) && NULL != memchr( en+ELEM_C_FST, at[n2].el_number, ELEM_C_LEN) ) { /* i n n2 */ /* found O(-)-O-C(+)(III) */ /* convert O(-)-O-C(+)(III) => O=O=C(IV) */ /*i3 = (at[n2].neighbor[0] != n);*/ /* i3 = index of at[n] neighbor of at[n2] */ i3 = is_in_the_list( at[n2].neighbor, (AT_NUMB)n, at[n2].valence ) - at[n2].neighbor; /*i4 = index of at[i] in the adjacency list of at[n] */ i4 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[ i].charge ++; at[n2].charge --; at[ i].chem_bonds_valence += 1; /* O- => O= */ at[ n].chem_bonds_valence += 2; /* -O- => =O= */ at[n2].chem_bonds_valence += 1; /* -C => =C */ at[ i].bond_type[i1] = BOND_TYPE_DOUBLE; at[ n].bond_type[i4] = BOND_TYPE_DOUBLE; at[ n].bond_type[i2] = BOND_TYPE_DOUBLE; at[n2].bond_type[i3] = BOND_TYPE_DOUBLE; num_changes ++; num_O_minus --; num_C_plus --; num_All -= 2; continue; } } } else if ( -1 == at[i].charge && 0 < num_N_minus && 0 < num_N_plus+num_O_plus+num_C_plus && 1 == nNoMetalNumBonds(at, i) && 2 == nNoMetalBondsValence(at, i)+NUMH(at, i) && /*0 == num_of_H( at, i ) &&*/ NULL != memchr( en+ELEM_N_FST, at[i].el_number, ELEM_N_LEN) && 0 <= (i1 = nNoMetalNeighIndex( at, i )) && at[i].bond_type[i1] <= BOND_TYPE_TRIPLE ) { /* terminal N(-)= */ n = at[i].neighbor[i1 = 0]; if ( (!type || type == 7) && 0 < num_N_plus && /* N(-)=N(+)(IV) */ 1 == at[n].charge && 3 >= nNoMetalNumBonds(at, n) && 4 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_N_FST, at[n].el_number, ELEM_N_LEN) ) { /* found N(-)-N(+)(IV) */ /* convert N(-)=N(+)(IV) => N#N(V) */ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; /* index of at[i] neighbor of at[n] */ at[i].charge ++; at[n].charge --; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_N_minus --; num_N_plus --; num_All -= 2; continue; } if ( (!type || type == 8) && 0 < num_O_plus && /* N(-)=O(+)(III) */ 1 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_O_FST, at[n].el_number, ELEM_O_LEN) ) { /* found N(-)-O(+)(III) */ /* convert N(-)=O(+)(III) => N#O(IV)- */ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; /* index of at[i] neighbor of at[n] */ at[i].charge ++; at[n].charge --; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_N_minus --; num_O_plus --; num_All -= 2; continue; } if ( (!type || type == 9) && 0 < num_C_plus && /* N(-)=C(+)(III) */ 1 == at[n].charge && 2 == at[n].valence && 3 == at[n].chem_bonds_valence && 0 == num_of_H( at, n ) && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { /* found N(-)=C(+)(III) */ /* convert N(-)=C(+)(III) => N#C(IV)- */ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; /* index of at[i] neighbor of at[n] */ at[i].charge ++; at[n].charge --; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_N_minus --; num_C_plus --; num_All -= 2; continue; } } } } /**************************************************************************/ /*********************** NON-Terminal ion pairs ***************************/ /**************************************************************************/ /*------------------------------------------------------------------------- Non-Terminal pair types: 10,11,12,13,14 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si ======================================== 10: N(+)(IV)-C(-)(III) => N(V)=C(IV) (N has 3 or 2 bonds) 11: N(+)(IV)=C(-)(III) => N(V)#C(IV) (N has 3 or 2 bonds) 12: N(+)(IV)-N(-)(II) => N(V)=N(III) (allow terminal H on N(-)) 13: -O(+)-C(-)(III) => -O=C- 14: -O(+)=C(-)(III) => -O#C- 15: O(+)(III)-N(-)(II) => O(IV)=N(III) (allow terminal H on N(-)) --------------------------------------------------------------------------*/ if ( !type || 10 <= type && type <= 15 ) { for ( i = 0; i < num_atoms && 0 < num_All; i ++ ) { if ( 1 == at[i].charge && 0 < num_N_plus + num_O_plus && 0 < num_C_minus + num_N_minus && 4 >= nNoMetalNumBonds(at, i) && 4 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && NULL != memchr( en+ELEM_N_FST, at[i].el_number, ELEM_N_LEN) ) { /* found non-terminal N(+)(IV) */ if ( (!type || 10 == type) && 0 < num_N_plus && 0 < num_C_minus ) { int num_neigh = 0, pos_neigh = -1; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( -1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence+NUMH(at,n) && /*0 == at[n].num_H &&*/ at[i].bond_type[i1] == BOND_TYPE_SINGLE && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { /* found N(+)(IV)-C(-)(III); prepare conversion to N(V)=C(IV) */ num_neigh ++; pos_neigh = i1; } } i1=pos_neigh; if ( 1 == num_neigh && at[i].bond_type[i1] <= BOND_TYPE_TRIPLE && !has_other_ion_neigh( at, i, n=at[i].neighbor[i1], en, ne ) && !has_other_ion_neigh( at, n, i, en, ne )) { /*n = at[i].neighbor[i1=pos_neigh];*/ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].charge --; at[n].charge ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_C_minus --; num_N_plus --; num_All -= 2; continue; } } if ( (!type || 11 == type) && 0 < num_N_plus && 0 < num_C_minus ) { int num_neigh = 0, pos_neigh = -1; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( -1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence+NUMH(at,n) && /*0 == at[n].num_H &&*/ at[i].bond_type[i1] == BOND_TYPE_DOUBLE && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { /* found N(+)(IV)=C(-)(III); prepare conversion to N(V)#C(IV) */ num_neigh ++; pos_neigh = i1; } } if ( 1 == num_neigh && !has_other_ion_neigh( at, i, n=at[i].neighbor[i1=pos_neigh], en, ne ) && !has_other_ion_neigh( at, n, i, en, ne )) { /*n = at[i].neighbor[i1=pos_neigh];*/ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].charge --; at[n].charge ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_C_minus --; num_N_plus --; num_All -= 2; continue; } } if ( !type || 12 == type && 0 < num_N_plus && 0 < num_N_minus ) { int num_neigh = 0, pos_neigh = -1; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( -1 == at[n].charge && 2 >= nNoMetalNumBonds(at, n) && 2 == nNoMetalBondsValence(at, n)+NUMH(at, n) && /*0 == num_of_H( at, n ) &&*/ at[i].bond_type[i1] == BOND_TYPE_SINGLE && NULL != memchr( en+ELEM_N_FST, at[n].el_number, ELEM_N_LEN) ) { /* found N(+)(IV)=N(-)(II); prepare conversion to N(V)#N(III) */ num_neigh ++; pos_neigh = i1; } } if ( 1 == num_neigh && !has_other_ion_neigh( at, i, n=at[i].neighbor[i1=pos_neigh], en, ne ) && !has_other_ion_neigh( at, n, i, en, ne )) { /*n = at[i].neighbor[i1=pos_neigh];*/ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].charge --; at[n].charge ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_N_minus --; num_N_plus --; num_All -= 2; continue; } } } else if ( 1 == at[i].charge && 0 < num_O_plus && 0 < num_C_minus + num_N_minus && 3 >= nNoMetalNumBonds(at, i) && 3 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && NULL != memchr( en+ELEM_O_FST, at[i].el_number, ELEM_O_LEN) ) { /* found non-terminal O(+)(III) */ if ( (!type || 13 == type) && 0 < num_C_minus ) { int num_neigh = 0, pos_neigh = -1; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( -1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence+NUMH(at,n) && /*0 == at[n].num_H &&*/ at[i].bond_type[i1] == BOND_TYPE_SINGLE && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { /* found O(+)(III)-C(-)(II); prepare conversion to O(IV)=C(IV) */ num_neigh ++; pos_neigh = i1; } } if ( 1 == num_neigh && !has_other_ion_neigh( at, i, n=at[i].neighbor[i1=pos_neigh], en, ne ) && !has_other_ion_neigh( at, n, i, en, ne )) { /*n = at[i].neighbor[i1=pos_neigh];*/ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].charge --; at[n].charge ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_C_minus --; num_O_plus --; num_All -= 2; continue; } } if ( (!type || 14 == type) && 0 < num_C_minus ) { int num_neigh = 0, pos_neigh = -1; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( -1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence+NUMH(at,n) && /*0 == at[n].num_H &&*/ at[i].bond_type[i1] == BOND_TYPE_DOUBLE && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { /* found O(+)(III)=C(-)(III); prepare conversion to O(IV)#C(IV) */ num_neigh ++; pos_neigh = i1; } } if ( 1 == num_neigh && !has_other_ion_neigh( at, i, n=at[i].neighbor[i1=pos_neigh], en, ne ) && !has_other_ion_neigh( at, n, i, en, ne )) { /*n = at[i].neighbor[i1=pos_neigh];*/ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].charge --; at[n].charge ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_C_minus --; num_O_plus --; num_All -= 2; continue; } } if ( (!type || 15 == type) && 0 < num_N_minus ) { int num_neigh = 0, pos_neigh = -1; for ( i1 = 0; i1 < at[i].valence; i1 ++ ) { n = at[i].neighbor[i1]; if ( -1 == at[n].charge && 2 >= nNoMetalNumBonds(at, n) && 2 == nNoMetalBondsValence(at, n)+NUMH(at, n) && /*0 == num_of_H( at, n ) &&*/ at[i].bond_type[i1] == BOND_TYPE_SINGLE && NULL != memchr( en+ELEM_N_FST, at[n].el_number, ELEM_N_LEN) ) { /* found O(+)(III)=N(-)(II); prepare conversion to O(IV)#N(III) */ num_neigh ++; pos_neigh = i1; } } if ( 1 == num_neigh && !has_other_ion_neigh( at, i, n=at[i].neighbor[i1=pos_neigh], en, ne ) && !has_other_ion_neigh( at, n, i, en, ne )) { /*n = at[i].neighbor[i1=pos_neigh];*/ i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].charge --; at[n].charge ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; num_changes ++; num_N_minus --; num_O_plus --; num_All -= 2; continue; } } } } } /**************************************************************************/ /*********************** NON-Terminal ion triples *************************/ /**************************************************************************/ /*------------------------------------------------------------------------- Non-Terminal triple types: 16, 17, 18 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si ======================================== 16: C(+)(III)-O-N(-)(II) => C(IV)=O=N(III) (allow terminal H on N(-)) | | 17: C(+)(III)-N-C(-)(III) => C(IV)=N=C(IV) 18: C(-)(III)-N=C(+)(III) => C(IV)=N#C(IV) (may have two or no charges) C(IV)=N-C(II) => C(IV)=N#C(IV) */ if ( (!type || 16 == type) && 0 < num_C_plus && 0 < num_N_minus ) { int m[2], j[2], k; for ( i = 0; i < num_atoms; i ++ ) { if ( 0 == at[i].charge && 2 == nNoMetalNumBonds(at, i) && 2 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && 0 <= (j[0] = nNoMetalNeighIndex( at, i )) && at[m[0]=at[i].neighbor[j[0]]].charge && 0 <= (j[1] = nNoMetalOtherNeighIndex( at, i, m[0] )) && 0 == at[m[0]].charge + at[m[1]=at[i].neighbor[j[1]]].charge && 5 >= nNoMetalBondsValence(at, m[0]) + nNoMetalBondsValence(at, m[1]) && /*5 >= at[m[0]].chem_bonds_valence + at[m[1]].chem_bonds_valence &&*/ NULL != memchr( en+ELEM_O_FST, at[i].el_number, ELEM_O_LEN) ) { /* found non-terminal A(+)-O-B(-); chem_bond_val of A+B <= 5 */ int n_N=-1, n_C=-1, i_C=-1; for ( k = 0; k < 2; k ++ ) { n = m[k]; if ( -1 == at[n].charge && 2 == nNoMetalNumBonds(at, n)+NUMH(at, n) && /*0 == num_of_H( at, n ) &&*/ NULL != memchr( en+ELEM_N_FST, at[n].el_number, ELEM_N_LEN) ) { n_N = n; } else if ( 1 == at[n].charge && 3 == at[n].chem_bonds_valence+NUMH(at,n) && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { n_C = n; i_C = k; } } if ( n_C < 0 || n_N < 0 || has_other_ion_in_sphere_2(at, n_C, n_N, en, ne ) || has_other_ion_in_sphere_2(at, n_N, n_C, en, ne ) ) { continue; } /* C(+)(III)-O-N(-)(II) => C(IV)=O=N(III) */ for ( k = 0; k < 2; k ++ ) { n = k? n_C : n_N; i1 = k? j[i_C] : j[1-i_C]; i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[n].charge += (k? -1:1); } num_changes ++; num_N_minus --; num_C_plus --; num_All -= 2; } } } if ( (!type || 17 == type) && 0 < num_C_plus && 0 < num_C_minus ) { int m[3], c[3], j[3], k; for ( i = 0; i < num_atoms; i ++ ) { if ( 0 == at[i].charge && 3 == nNoMetalNumBonds(at, i) && 3 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && 0 <= ( j[0] = nNoMetalNeighIndex(at, i) ) && 0 <= ( j[1] = nNoMetalOtherNeighIndex( at, i, m[0] = at[i].neighbor[j[0]] ) ) && 0 <= ( j[2] = nNoMetalOtherNeighIndex2( at, i, m[0], m[1] = at[i].neighbor[j[1]] ) ) && 1 == !(c[0]=at[m[0]].charge) + !(c[1]=at[m[1]].charge) + !(c[2]=at[m[2]=at[i].neighbor[j[2]]].charge) && 0 == c[0] + c[1] + c[2] && 2 == (3== (c[0]? at[m[0]].chem_bonds_valence+NUMH(at,m[0]):0)) + (3== (c[1]? at[m[1]].chem_bonds_valence+NUMH(at,m[1]):0)) + (3== (c[2]? at[m[2]].chem_bonds_valence+NUMH(at,m[2]):0)) && NULL != memchr( en+ELEM_N_FST, at[i].el_number, ELEM_N_LEN) ) { /* found non-terminal A(+)-O-B(-) */ int n_Cp=-1, n_Cm=-1, i_Cp=-1, i_Cm=-1; /* p = positive, m = negatice ion C */ for ( k = 0; k < 3; k ++ ) { if ( c[k] ) { n = m[k]; if ( -1 == at[n].charge && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { n_Cm = n; i_Cm = k; } else if ( 1 == at[n].charge && NULL != memchr( en+ELEM_C_FST, at[n].el_number, ELEM_C_LEN) ) { n_Cp = n; i_Cp = k; } } } if ( n_Cp < 0 || n_Cm < 0 || has_other_ion_in_sphere_2(at, n_Cp, n_Cm, en, ne ) || has_other_ion_in_sphere_2(at, n_Cm, n_Cp, en, ne )) { continue; } /* | | */ /* C(+)(III)-N-C(-)(III) => C(IV)=N=C(IV) */ for ( k = 0; k < 2; k ++ ) { n = k? n_Cp : n_Cm; i1 = k? j[i_Cp] : j[i_Cm]; i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].bond_type[i1] ++; at[n].bond_type[i2] ++; at[i].chem_bonds_valence ++; at[n].chem_bonds_valence ++; at[n].charge += (k? -1:1); } num_changes ++; num_C_minus --; num_C_plus --; num_All -= 2; } } } if ( (!type || 18 == type) && (0 < num_C_plus && 0 < num_C_minus || 0 < num_C_II) ) { int m[2], v[2], j[2], k; for ( i = 0; i < num_atoms; i ++ ) { if ( 0 == at[i].charge && 2 == nNoMetalNumBonds(at, i) && 3 == nNoMetalBondsValence(at, i) && 0 == num_of_H( at, i ) && 0 <= (j[0] = nNoMetalNeighIndex( at, i )) && 0 <= (j[1] = nNoMetalOtherNeighIndex( at, i, m[0] = at[i].neighbor[j[0]] )) && 0 == at[m[0]].charge +at[m[1]=at[i].neighbor[j[1]]].charge && 6 == (v[0]=at[m[0]].chem_bonds_valence+NUMH(at,m[0])) +(v[1]=at[m[1]].chem_bonds_valence+NUMH(at,m[1])) && 2 >= abs(v[0]-v[1]) && NULL != memchr( en+ELEM_N_FST, at[i].el_number, ELEM_N_LEN) && NULL != memchr( en+ELEM_C_FST, at[m[0]].el_number, ELEM_C_LEN) && NULL != memchr( en+ELEM_C_FST, at[m[1]].el_number, ELEM_C_LEN) ) { /* n_Cm i n_Cp */ /* found non-terminal C(-)(III)-N=C(+)(III) or C(IV)=N-C(II): Cm-N-Cp */ /* convert to C(IV)=N#C(IV) */ int n_Cp=-1, n_Cm=-1, i_Cp=-1, i_Cm=-1; /* p = positive, m = negatice ion C */ for ( k = 0; k < 2; k ++ ) { n = m[k]; if ( v[k] == 4 || v[k] == 3 && at[i].bond_type[j[k]] == BOND_TYPE_SINGLE ) { n_Cm = n; i_Cm = k; } else if ( v[k] == 2 || v[k] == 3 && at[i].bond_type[j[k]] == BOND_TYPE_DOUBLE ) { n_Cp = n; i_Cp = k; } } if ( n_Cp < 0 || n_Cm < 0 || at[n_Cp].valence+NUMH(at,n_Cp) != 2 ) { continue; /* guarantees at[n_Cp].valence <= 2 */ } if ( v[i_Cp] == 2 || !at[n_Cp].charge ) { if ( at[n_Cp].valence == 2 ) { /* neighbor of at[n_Cp] opposite to at[i] */ k = at[n_Cp].neighbor[at[n_Cp].neighbor[0]==i]; if ( NULL != memchr( en+ELEM_N_FST, at[k].el_number, ELEM_N_LEN) ) { continue; } } } else if ( at[n_Cp].charge ) { if ( has_other_ion_in_sphere_2(at, n_Cp, n_Cm, en, ne ) || has_other_ion_in_sphere_2(at, n_Cm, n_Cp, en, ne )) { continue; } } else { continue; /* unknown case */ } /* */ /* C(-)(III)-N=C(+)(III) => C(IV)=N#C(IV) */ /* C(IV)=N-C(II) => C(IV)=N#C(IV) */ if ( at[n_Cp].charge ) { num_C_minus --; num_C_plus --; num_All -= 2; } else { num_C_II --; num_All --; } for ( k = 0; k < 2; k ++ ) { n = k? n_Cp : n_Cm; i3 = k? i_Cp : i_Cm; /* added to fix the bug */ /*i1 = k? j[i_Cp] : j[i_Cm];*/ /* replaced with next line */ i1 = j[i3]; if ( v[i3 /*was i1*/] < 4 ) { /* WDI found a bug here: bounds violation */ int delta = 4 - v[i3 /*was i1*/]; i2 = is_in_the_list( at[n].neighbor, (AT_NUMB)i, at[n].valence ) - at[n].neighbor; at[i].bond_type[i1] += delta; at[n].bond_type[i2] += delta; at[i].chem_bonds_valence += delta; at[n].chem_bonds_valence += delta; at[n].charge = 0; at[n].radical = 0; } } at[i].charge = 0; at[i].radical = 0; num_changes ++; } } } } return num_changes; } /*#if ( DISCONNECT_SALTS == 1 )*/ /* { */ /*************************************************************************************************/ int RemoveInpAtBond( inp_ATOM *atom, int iat, int k ) { int i, j, m, m2, k2; inp_ATOM *at = atom + iat; inp_ATOM *at2 = NULL; int val = at->valence - 1; if ( val >= 0 ) { int bond = at->bond_type[k]; if ( bond > BOND_TYPE_TRIPLE ) bond = BOND_TYPE_SINGLE; /* added 08-06-2003 */ /* update CML tetrahedral atom parity. */ if ( at->p_parity ) { for( m = 0; m < MAX_NUM_STEREO_ATOM_NEIGH; m ++ ) { if ( at->p_orig_at_num[m] == at->orig_at_number ) { at->p_parity = 0; break; /* only 3 bonds are present; removing one bond removes stereo */ } } if ( at->p_parity /* at->valence == MAX_NUM_STEREO_ATOM_NEIGH*/ ) { for ( m = 0; m < at->valence; m ++ ) { if ( atom[(int)at->neighbor[k]].orig_at_number == at->p_orig_at_num[m] ) { break; } } if ( m < at->valence ) { at->p_orig_at_num[m] = at->orig_at_number; } else { at->p_parity = 0; /* wrong neighbors: at->neighbor[k] is not in the list of a stereo neighbors */ } } } /* update CML stereogenic bond parities; at this point no removed explicit H exist yet */ if ( at->sb_parity[0] ) { for ( m = 0; m < MAX_NUM_STEREO_BONDS && at->sb_parity[m]; ) { if ( k == at->sb_ord[m] || k == at->sn_ord[m] && val < 2 && ATOM_PARITY_WELL_DEF(at->sb_parity[m]) ) { /* !!! FLAW: does take into account removed H !!! */ /* stereogenic bond is being removed OR */ /* remove stereogenic bond because its only neighbor is being removed */ int pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; int len= get_opposite_sb_atom( atom, iat, at->sb_ord[m], &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord ); if ( len ) { i = pinxt_sb_parity_ord; at2 = atom + pnxt_atom; k2 = pinxt2cur; } else { i = MAX_NUM_STEREO_BONDS; } /* at2 = atom + at->neighbor[ (int)at->sb_ord[m] ]; for ( i = 0; i < MAX_NUM_STEREO_BONDS && at2->sb_parity[i]; i ++ ) { if ( iat == at2->neighbor[ (int)at2->sb_ord[i] ] ) break; } */ if ( i < MAX_NUM_STEREO_BONDS && at2->sb_parity[i] ) { m2 = i; /* remove bond parity from at */ if ( m < MAX_NUM_STEREO_BONDS-1 ) { memmove( at->sb_parity+m, at->sb_parity+m+1, (MAX_NUM_STEREO_BONDS-1 - m) * sizeof(at->sb_parity[0])); memmove( at->sb_ord+m, at->sb_ord+m+1, (MAX_NUM_STEREO_BONDS-1 - m) * sizeof(at->sb_ord[0])); memmove( at->sn_ord+m, at->sn_ord+m+1, (MAX_NUM_STEREO_BONDS-1 - m) * sizeof(at->sn_ord[0])); memmove( at->sn_orig_at_num+m, at->sn_orig_at_num+m+1, (MAX_NUM_STEREO_BONDS-1 - m) * sizeof(at->sn_orig_at_num[0])); } at->sb_parity[MAX_NUM_STEREO_BONDS-1] = 0; at->sb_ord[MAX_NUM_STEREO_BONDS-1] = 0; at->sn_ord[MAX_NUM_STEREO_BONDS-1] = 0; at->sn_orig_at_num[MAX_NUM_STEREO_BONDS-1] = 0; /* remove bond parity from at2 */ if ( m2 < MAX_NUM_STEREO_BONDS-1 ) { memmove( at2->sb_parity+m2, at2->sb_parity+m2+1, (MAX_NUM_STEREO_BONDS-1 - m2) * sizeof(at2->sb_parity[0])); memmove( at2->sb_ord+m2, at2->sb_ord+m2+1, (MAX_NUM_STEREO_BONDS-1 - m2) * sizeof(at2->sb_ord[0])); memmove( at2->sn_ord+m2, at2->sn_ord+m2+1, (MAX_NUM_STEREO_BONDS-1 - m2) * sizeof(at2->sn_ord[0])); memmove( at2->sn_orig_at_num+m2, at2->sn_orig_at_num+m2+1, (MAX_NUM_STEREO_BONDS-1 - m2) * sizeof(at2->sn_orig_at_num[0])); } at2->sb_parity[MAX_NUM_STEREO_BONDS-1] = 0; at2->sb_ord[MAX_NUM_STEREO_BONDS-1] = 0; at2->sn_ord[MAX_NUM_STEREO_BONDS-1] = 0; at2->sn_orig_at_num[MAX_NUM_STEREO_BONDS-1] = 0; /* do not increment m here because the array elements have been shifted */ } else { m ++; /* program error: inconsistent stereobond parity */ } } else if ( k == at->sn_ord[m] ) { /* stereogenic bond neighbor is being removed; another neighbor remains */ /* !!! FLAW: does take into account removed H !!! */ for ( j = 0, i = -1; j < at->valence; j ++ ) { if ( j != k && j != at->sb_ord[m] ) { i = j; break; } } /* i is the position of the neighbor that will become a new neighbor */ /*************************************************************************** * at->sb_parity[m] is the direction (EVEN=clockwise, ODD=counterclockwise) * from stereobond to the neighbor. If the neighbor is removed then * the parity should invert, otherwise it should be unchanged. ***************************************************************************/ if ( i < 0 ) { /* no alternative neighbor is available */ if ( ATOM_PARITY_WELL_DEF(at->sb_parity[m] ) ) { /* parity cannot be not well-defined anymore */ int pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; int len= get_opposite_sb_atom( atom, iat, at->sb_ord[m], &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord ); if ( len > 0 ) { atom[pnxt_atom].sb_parity[pinxt_sb_parity_ord] = at->sb_parity[m] = AB_PARITY_UNDF; } #ifdef _DEBUG else { int stop = 1; /* sb parities error */ } #endif } at->sn_ord[m] = -99; /* sb neighbor has been disconnected */ at->sb_ord[m] -= (at->sb_ord[m] > k); /* same as above */ at->sn_orig_at_num[m] = 0; } else if ( i < at->valence ) { /* choose another stereogenic bond neighbor, its ord. number is i before bond removal */ if ( ATOM_PARITY_WELL_DEF(at->sb_parity[m]) ) { /* ALL WRONG: 'move' previous stereo bond neighbor to the last position (pos. 2 out of 0,1,2) */ /* the parity of the transpositions is (2 - at->sn_ord[m])%2 = at->sn_ord[m] % 2 */ /* and replace the neighbor with another; the contribution to the parity is 1 */ /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + at->sn_ord[m] + 1 ) % 2;*/ /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + k + i + (i > k) + (i > at->sb_ord[m]) ) % 2;*/ /*=== parity should be INVERTED ===*/ at->sb_parity[m] = 3 - at->sb_parity[m]; } at->sn_ord[m] = i - (i > k); /* ord. number shifted because preceding bond is removed */ at->sb_ord[m] -= (at->sb_ord[m] > k); /* same as above */ at->sn_orig_at_num[m] = atom[(int)at->neighbor[i]].orig_at_number; /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + 1 ) % 2;*/ } else { at->sb_parity[m] = 0; /* program error: inconsistent stereobond parity */ } m ++; } else { /* removing another neighbor, k: first move it to the last position (pos. 2 out of 0,1,2) */ if ( k < 2 && ATOM_PARITY_WELL_DEF(at->sb_parity[m]) ) { /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + k ) % 2;*/ /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + (at->sn_ord[m] > k) + (at->sb_ord[m] > k) ) % 2;*/ ;/*==== Parity should remain UNCHANGED ===*/ } if ( at->sb_ord[m] > k ) { at->sb_ord[m] --; } if ( at->sn_ord[m] > k ) { at->sn_ord[m] --; } m ++; } } } if ( k < val ) { memmove( at->neighbor+k, at->neighbor+k+1, sizeof(at->neighbor[0])*(val-k) ); memmove( at->bond_stereo+k, at->bond_stereo+k+1, sizeof(at->bond_stereo[0])*(val-k) ); memmove( at->bond_type+k, at->bond_type+k+1, sizeof(at->bond_type[0])*(val-k) ); } at->neighbor[val] = 0; at->bond_stereo[val] = 0; at->bond_type[val] = 0; at->valence = val; at->chem_bonds_valence -= bond; return 1; } return 0; } /*************************************************************************************************/ int DisconnectInpAtBond( inp_ATOM *at, AT_NUMB *nOldCompNumber, int iat, int neigh_ord ) { int neigh, i, ret = 0; int component; neigh = at[iat].neighbor[neigh_ord]; for ( i = 0; i < at[neigh].valence; i ++ ) { if ( iat == (int)at[neigh].neighbor[i] ) break; } if ( i < at[neigh].valence ) { ret += RemoveInpAtBond( at, iat, neigh_ord ); ret += RemoveInpAtBond( at, neigh, i ); if ( nOldCompNumber && ret ) { if ( component = at[iat].component ) { nOldCompNumber[component-1] = 0; } if ( component = at[neigh].component ) { nOldCompNumber[component-1] = 0; } } } return (ret == 2); } /*************************************************************************************************/ int bIsAmmoniumSalt( inp_ATOM *at, int i, int *piO, int *pk, S_CHAR *num_explicit_H ) { /* NH4(+charge)-O(-charge)-C -> NH3 + HO-C; any charge including 0, any C except charged or radical */ /* F, Cl, Br, I */ static U_CHAR el_number_C=0, el_number_O=0, el_number_H=0, el_number_N=0; static U_CHAR el_number_F=0, el_number_Cl=0, el_number_Br=0, el_number_I=0; int num_H, num_non_iso_H, num_impl_iso_H, bDisconnect = 1; int j, val, neigh, iO=-1, iC, k=-1; if ( 0 == el_number_C ) { /* one time initialization */ el_number_C = get_periodic_table_number( "C" ); el_number_O = get_periodic_table_number( "O" ); el_number_H = get_periodic_table_number( "H" ); el_number_N = get_periodic_table_number( "N" ); el_number_F = get_periodic_table_number( "F" ); el_number_Cl= get_periodic_table_number( "Cl" ); el_number_Br= get_periodic_table_number( "Br" ); el_number_I = get_periodic_table_number( "I" ); } if ( at[i].el_number != el_number_N ) return 0; /* check for NH4-O-C... -> NH3 + HO-C... */ val = at[i].valence; num_impl_iso_H = NUM_ISO_H(at,i); num_non_iso_H = at[i].num_H; num_H = num_non_iso_H + num_impl_iso_H; if ( val + num_H == 5 ) { int num_O = 0; memset( num_explicit_H, 0, (NUM_H_ISOTOPES+1)*sizeof(num_explicit_H[0]) ); for ( j = 0; j < val; j ++ ) { /* looking for O: H4N-O-C... */ neigh = at[i].neighbor[j]; if ( at[neigh].num_H || at[neigh].charge && (at[neigh].el_number != el_number_O || at[neigh].charge + at[i].charge) || at[neigh].radical && at[neigh].radical != RADICAL_SINGLET ) { bDisconnect = 0; break; /* reject */ } if ( at[neigh].el_number == el_number_H && at[neigh].valence == 1 && !at[neigh].charge && !at[neigh].radical ) { num_H ++; /* at this point at[].num_H does not include explicit H count */ num_non_iso_H += (0==at[neigh].iso_atw_diff); num_explicit_H[at[neigh].iso_atw_diff] ++; /* explicit H on N */ } else if ( at[neigh].el_number == el_number_O && at[neigh].valence == 2 && !num_O ) { num_O ++; /* found O: N-O- */ iO = neigh; k = j; iC = at[iO].neighbor[at[iO].neighbor[0] == i]; if ( at[iC].el_number != el_number_C || /* at[iC].num_H || at[iC].chem_bonds_valence != 4 || */ at[iC].charge || at[iC].radical && at[iC].radical != RADICAL_SINGLET /*|| at[iC].valence == at[iC].chem_bonds_valence*/ ) { bDisconnect = 0; break; /* reject */ } } else if ( (at[neigh].el_number == el_number_F || at[neigh].el_number == el_number_Cl || at[neigh].el_number == el_number_Br || at[neigh].el_number == el_number_I ) && at[neigh].valence == 1 && at[neigh].chem_bonds_valence == 1 && !at[neigh].charge && !NUMH(at,neigh) && !num_O ) { num_O ++; /* found O: N-O- */ iO = neigh; k = j; iC = -1; } else { bDisconnect = 0; break; /* reject */ } } if ( bDisconnect && (num_O != 1 || num_H != 4) ) { bDisconnect = 0; /* reject */ } } else { bDisconnect = 0; } if ( bDisconnect ) { *piO = iO; *pk = k; } return bDisconnect; } /*************************************************************************************************/ int DisconnectAmmoniumSalt ( inp_ATOM *at, int iN, int iO, int k, S_CHAR *num_explicit_H ) { /* disconnect NH4-O from O */ /* Note: iO = at[iN].neighbor[k], at[iN] is N, at[iO].neighbor[0] is either N=at[iN] or C=at[iC] */ int nMove_H_iso_diff = -1; /* do not move explicit H */ int j, neigh, iso_diff, neigh_pos; static U_CHAR el_number_H = 0; int val = at[iN].valence; if ( !el_number_H ) { el_number_H = get_periodic_table_number( "H" ); } if ( at[iN].charge && !(at[iN].charge + at[iO].charge) ) { at[iN].charge = at[iO].charge = 0; /* remove charges */ } neigh_pos = (at[iO].valence == 2)? (at[iO].neighbor[1] == iN) : 0; /* position of at[iN] in the neigh list of iO */ /* disconnect bond O-N */ RemoveInpAtBond( at, iO, neigh_pos ); RemoveInpAtBond( at, iN, k ); val --; /* move 1 H from NH4 to O- or Cl */ /* find non-isotopic or the lightest isotopic H to move from N to O */ for ( iso_diff = 0; iso_diff <= NUM_H_ISOTOPES; iso_diff ++ ) { if ( !iso_diff ) { /* find non-isotopic H */ if ( at[iN].num_H ) { at[iN].num_H --; /* move non-isotopic implicit H */ at[iO].num_H ++; break; } else if ( num_explicit_H[0] ) { nMove_H_iso_diff = 0; /* flag: move explicit non-isotopic H */ break; } } else { /* find isotopic H */ if ( at[iN].num_iso_H[iso_diff] ) { at[iN].num_iso_H[iso_diff] --; /* move implicit isotopic H, atw = 1 */ at[iO].num_iso_H[iso_diff] ++; break; } else if ( num_explicit_H[iso_diff] ) { nMove_H_iso_diff = iso_diff; /* flag: move explicit isotopic H, atw = 1 */ break; } } } if ( nMove_H_iso_diff >= 0 ) { /* move explicit H, it is isotopic if nMove_H_iso_diff > 0 */ double dist2_H_O, min_dist2_H_O = -1.0; int jH = -1, iH = -1; for ( j = 0; j < val; j ++ ) { /* looking H in N-H such that H-O is shortest */ neigh = at[iN].neighbor[j]; if ( at[neigh].el_number == el_number_H && at[neigh].iso_atw_diff == nMove_H_iso_diff ) { dist2_H_O = (at[neigh].x - at[iO].x) * (at[neigh].x - at[iO].x) + (at[neigh].y - at[iO].y) * (at[neigh].y - at[iO].y) + (at[neigh].z - at[iO].z) * (at[neigh].z - at[iO].z); if ( min_dist2_H_O < 0.0 || min_dist2_H_O > dist2_H_O ) { min_dist2_H_O = dist2_H_O; iH = neigh; jH = j; } } } /* reconnect; bonds do not need changes except stereo */ neigh_pos = at[iO].valence; at[iO].neighbor[neigh_pos] = iH; at[iO].bond_stereo[neigh_pos] = 0; at[iO].bond_type[neigh_pos] = at[iH].bond_type[0]; at[iO].chem_bonds_valence += at[iH].bond_type[0]; at[iO].valence ++; at[iH].neighbor[0] = iO; at[iH].bond_stereo[0] = 0; /* disconnect H from N */ RemoveInpAtBond( at, iN, jH ); val --; if ( k > jH ) { k --; } } return 1; } /*************************************************************************************************/ int bIsMetalSalt( inp_ATOM *at, int i ) { int type, val, k, iO, iC, j, neigh; int bDisconnect = 1; static U_CHAR el_number_C=0, el_number_O=0, el_number_H=0; static U_CHAR el_number_F=0, el_number_Cl=0, el_number_Br=0, el_number_I=0; if ( 0 == el_number_C ) { /* one time initialization */ el_number_C = get_periodic_table_number( "C" ); el_number_O = get_periodic_table_number( "O" ); el_number_H = get_periodic_table_number( "H" ); el_number_F = get_periodic_table_number( "F" ); el_number_Cl= get_periodic_table_number( "Cl" ); el_number_Br= get_periodic_table_number( "Br" ); el_number_I = get_periodic_table_number( "I" ); } /* check for a metal atom: metal atom should be connected and be a metal */ if ( !(val = at[i].valence) || !(type = get_el_type( at[i].el_number )) || !(type & IS_METAL) ) { bDisconnect = 0; /* reject */ } else /* metal atom should not have adjacent H or multiple bonds or radical */ if ( at[i].num_H ) { bDisconnect = 0; /* reject */ } else /* check valence */ if ( at[i].charge == 0 && ( (type & 1) && val == get_el_valence( at[i].el_number, 0, 0 ) || (type & 2) && val == get_el_valence( at[i].el_number, 0, 1 ) ) || at[i].charge > 0 && (type & 1) && val == get_el_valence( at[i].el_number, at[i].charge, 0 ) ) { ; /* accept */ } else { bDisconnect = 0; /* reject */ } if ( bDisconnect ) { /************************************************************************* * | * * check M neighbors. Disconnect if all neighbors are M-O-C# or M-O-C= * * | * *************************************************************************/ for ( k = 0; k < at[i].valence; k ++ ) { iO = at[i].neighbor[k]; /* halogenide 2004-07-08 */ if ( (at[iO].el_number == el_number_F || at[iO].el_number == el_number_Cl || at[iO].el_number == el_number_Br || at[iO].el_number == el_number_I ) && at[iO].valence == 1 && at[iO].chem_bonds_valence == 1 && !at[iO].charge && !(at[iO].radical && at[iO].radical != RADICAL_SINGLET) && !NUMH(at,iO) ) { ; /* found */ } else { /* -O-C= */ if ( at[iO].el_number != el_number_O || NUMH(at, iO) || at[iO].valence != 2 || at[iO].charge || at[iO].radical && at[iO].radical != RADICAL_SINGLET || at[iO].valence != at[iO].chem_bonds_valence ) { bDisconnect = 0; /* reject */ break; } iC = at[iO].neighbor[at[iO].neighbor[0] == i]; if ( at[iC].el_number != el_number_C || at[iC].num_H || at[iC].chem_bonds_valence != 4 || at[iC].charge || at[iC].radical && at[iC].radical != RADICAL_SINGLET || at[iC].valence == at[iC].chem_bonds_valence ) { bDisconnect = 0; /* reject */ break; } for ( j = 0; j < at[iC].valence; j ++ ) { neigh = at[iC].neighbor[j]; if ( at[neigh].el_number == el_number_H ) { break; } } if ( j != at[iC].valence ) { bDisconnect = 0; /* reject */ break; } } } } return bDisconnect; } /*************************************************************************************************/ int DisconnectMetalSalt( inp_ATOM *at, int i ) { int k, iO; /* disconnect metal atom or ion at[i] */ for ( k = 0; k < at[i].valence; k ++ ) { iO = at[i].neighbor[k]; if ( at[iO].valence == 2 ) { if ( at[iO].neighbor[0] == i ) { /* assuming atom O always has 2 bonds */ /* copy the remaining neighbor to the 0 position */ at[iO].neighbor[0] = at[iO].neighbor[1]; at[iO].bond_stereo[0] = at[iO].bond_stereo[1]; at[iO].bond_type[0] = at[iO].bond_type[1]; } /* clear neighbor at position 1 */ at[iO].neighbor[1] = 0; at[iO].bond_stereo[1] = 0; at[iO].bond_type[1] = 0; } else { /* clear neighbor at position 1 */ at[iO].neighbor[0] = 0; at[iO].bond_stereo[0] = 0; at[iO].bond_type[0] = 0; } /* make O negatively charged */ at[iO].charge = -1; /* reduce O valence to account for the removed single bond */ at[iO].valence --; at[iO].chem_bonds_valence --; /* clear metal neighbor (O) */ at[i].neighbor[k] = 0; at[i].bond_stereo[k] = 0; at[i].bond_type[k] = 0; /* add a positive charge to the metal */ at[i].charge ++; } /* set metal valence to zero because it has been disconnected */ at[i].valence = 0; at[i].chem_bonds_valence = 0; return k; } /*************************************************************************************************/ int DisconnectSalts( ORIG_ATOM_DATA *orig_inp_data, int bDisconnect ) { int i, k, iO, num_changes, val; S_CHAR num_explicit_H[NUM_H_ISOTOPES+1]; inp_ATOM *at = orig_inp_data->at; int num_at = orig_inp_data->num_inp_atoms; /* check each atom */ for ( i = 0, num_changes = 0; i < num_at; i ++ ) { if ( !(val = at[i].valence) || /* disconnected atom */ val != at[i].chem_bonds_valence || /* a bond has higher multiplicity than 1 */ at[i].radical && at[i].radical != RADICAL_SINGLET /* radical */ ) { continue; /* reject */ } if ( bIsAmmoniumSalt( at, i, &iO, &k, num_explicit_H ) ) { if ( bDisconnect ) { DisconnectAmmoniumSalt ( at, i, iO, k, num_explicit_H ); orig_inp_data->num_inp_bonds --; } /* count disconnected atoms */ num_changes ++; } else if ( bIsMetalSalt( at, i ) ) { if ( bDisconnect ) { k = DisconnectMetalSalt( at, i ); orig_inp_data->num_inp_bonds -= k; } num_changes ++; } } return num_changes; } /*****************************************************************************/ /* Important: Salt disconnection is independent from coord. disconnection: */ /* because different atoms are disconnected. */ /* However, sal disconnection may need to be rerun after metal disconnection */ /* because metal disconnection may make certain atoms be eligible for salt */ /* disconnection */ /*****************************************************************************/ int bIsMetalToDisconnect(inp_ATOM *at, int i, int bCheckMetalValence) { int type, at_valence, num_H; /* if ( !at[i].valence ) */ if ( !(type = get_el_type( at[i].el_number )) || !(type & IS_METAL ) ) { return 0; } num_H = NUMH(at,i); at_valence = num_H + at[i].chem_bonds_valence; if ( !at_valence ) { return 0; /* nothing to disconnect */ } if ( bCheckMetalValence ) { if ( abs(at[i].charge) > 1 ) { return 1; /* multiple charges */ } for ( i = 0; i < 2 && (i & type); i ++ ) { if ( at_valence == get_el_valence( at[i].el_number, at[i].charge, i ) ) { return 2; /* atom has normal valence */ } } } return 1; } /*****************************************************************************/ int bMayDisconnectMetals( ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone ) { int i, j, k, iO, num_changes, val, bRadOrMultBonds, num_impl_H = 0; S_CHAR num_explicit_H[NUM_H_ISOTOPES+1]; inp_ATOM *at = orig_inp_data->at; int num_at = orig_inp_data->num_inp_atoms; int *nNumImplH = &orig_inp_data->bDisconnectCoord; /* check each atom */ for ( i = 0, num_changes = 0; i < num_at; i ++ ) { if ( !(val = at[i].valence) && !NUMH(at,i) ) { continue; /* disconnected atom */ } bRadOrMultBonds = (val == 0) || (val != at[i].chem_bonds_valence) || /* a bond has higher multiplicity than 1 */ (at[i].radical && at[i].radical != RADICAL_SINGLET); /* radical */ if ( !bRadOrMultBonds && bIsAmmoniumSalt( at, i, &iO, &k, num_explicit_H ) ) { ; } else if ( !bRadOrMultBonds && bIsMetalSalt( at, i ) ) { ; } else if ( 1 == (j = bIsMetalToDisconnect(at, i, bCheckMetalValence)) ) { num_impl_H += NUMH(at,i); num_changes ++; } else if ( 2 == j && bTautFlagsDone ) { *bTautFlagsDone |= TG_FLAG_CHECK_VALENCE_COORD_DONE; } } if ( nNumImplH ) *nNumImplH = num_changes? num_impl_H+1 : 0; return num_changes; } /*****************************************************************************/ #if ( bRELEASE_VERSION == 0 && (EXTR_HAS_METAL_ATOM & (EXTR_MASK | EXTR_FLAG) ) ) int bHasMetalAtom( ORIG_ATOM_DATA *orig_inp_data ) { int i; inp_ATOM *at; if ( orig_inp_data && (at = orig_inp_data->at) ) { int num_at = orig_inp_data->num_inp_atoms; /* check each atom */ for ( i = 0; i < num_at; i ++ ) { if ( IS_METAL & get_el_type( at[i].el_number ) ) { return 1; } } } return 0; } #endif /***************************************************************************** { "F", 19, 19, 18.998403220, 0 , 0, {{0,}, {0,}, {1,}, {2,}, {3,5}, },}, { "Cl", 35, 35, 34.968852730, 0 , 0, {{0,}, {0,}, {1,3,5,7}, {2,4,6}, {3,5,}, },}, { "Br", 80, 79, 78.918336100, 0 , 0, {{0,}, {0,}, {1,3,5,7,}, {2,4,6,}, {3,5,}, },}, { "I", 127, 127, 126.904500000, 0 , 0, {{0,}, {0,}, {1,3,5,7,}, {2,4,6}, {3,5,}, },}, { "At", 210, 210, 209.987100000, 0 , 0, {{0,}, {0,}, {1,3,5,7,}, {2,4,6}, {3,5,}, },}, { "N", 14, 14, 14.003074000, 0 , 0, {{1,}, {2,}, {3,5}, {4,}, {3,}, },}, { "P", 31, 31, 30.973762000, 0 , 0, {{1,3,5,7,}, {2,4,6,}, {3,5,}, {4,}, {3,}, },}, { "As", 75, 75, 74.921594200, 0 , 0, {{0,}, {2,4,6,}, {3,5,}, {4,}, {3,}, },}, { "Sb", 122, 121, 120.903800000, 0 , 0, {{1,3,5,7,}, {2,4,6,}, {3,5,}, {2,4,}, {3,}, },}, { "O", 16, 16, 15.994914630, 0 , 0, {{0,}, {1,}, {2,}, {3,5,}, {4,}, },}, { "S", 32, 32, 31.972070700, 0 , 0, {{0,}, {1,3,5,7,}, {2,4,6}, {3,5,}, {4,}, },}, { "Se", 79, 80, 79.916519600, 0 , 0, {{0,}, {1,3,5,7,}, {2,4,6,}, {3,5,}, {4,}, },}, { "Te", 128, 130, 129.906200000, 0 , 0, {{0,}, {1,3,5,7,}, {2,4,6,}, {3,5,}, {2,4,}, },}, { "Po", 209, 209, 208.982400000, 0 , 0, {{0,}, {1,3,5,7,}, {2,4,6,}, {3,5,}, {2,4,}, },}, { "B", 11, 11, 11.009300000, 0 , 0, {{3,}, {4,}, {3,}, {2,}, {1,}, },}, *****************************************************************************/ int DisconnectMetals( ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone ) /*inp_ATOM *atom, int num_atoms, int nNumExplH, int *new_num_atoms */ { int i, j, k, n, iO, num_changes, val, bRadOrMultBonds; int num_impl_H, num_at, err, num_disconnected; S_CHAR num_explicit_H[NUM_H_ISOTOPES+1]; static char elnumber_Heteroat[16] = {'\0', }; static int num_halogens; inp_ATOM *at = NULL; S_CHAR *bMetal = NULL; inp_ATOM *atom = orig_inp_data->at; int num_atoms = orig_inp_data->num_inp_atoms; int nNumExplH = (orig_inp_data->bDisconnectCoord > 0)? orig_inp_data->bDisconnectCoord - 1 : 0; AT_NUMB *nOldCompNumber = orig_inp_data->nOldCompNumber; err = 0; num_impl_H = 0; num_at = num_atoms; num_disconnected = 0; if ( !(at = (inp_ATOM *)inchi_calloc( num_at + nNumExplH, sizeof(at[0] ) )) || !(bMetal = ( S_CHAR *)inchi_calloc( num_at + nNumExplH, sizeof(bMetal[0]) )) ) { err = 1; goto exit_function; } if (!elnumber_Heteroat[0] ) { i = 0; /* halogens */ elnumber_Heteroat[i++] = (char)get_periodic_table_number( "F" ); /* 0 */ elnumber_Heteroat[i++] = (char)get_periodic_table_number( "Cl" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "Br" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "I" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "At" ); /* 4 */ num_halogens = i; /* other non-metal */ elnumber_Heteroat[i++] = (char)get_periodic_table_number( "N" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "P" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "As" ); /*elnumber_Heteroat[i++] = get_periodic_table_number( "Sb" );*/ /* metal 10-28-2003 */ elnumber_Heteroat[i++] = (char)get_periodic_table_number( "O" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "S" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "Se" ); elnumber_Heteroat[i++] = (char)get_periodic_table_number( "Te" ); /*elnumber_Heteroat[i++] = get_periodic_table_number( "Po" );*/ /* metal 10-28-2003 */ elnumber_Heteroat[i++] = (char)get_periodic_table_number( "B" ); elnumber_Heteroat[i++] = 0; } memcpy( at, atom, num_atoms * sizeof(at[0]) ); /* check each atom, mark metals */ for ( i = 0, k = 0, num_changes = 0; i < num_atoms; i ++ ) { if ( !(val = at[i].valence) && !NUMH(at,i) ) { continue; /* disconnected atom */ } bRadOrMultBonds = (val == 0) || (val != at[i].chem_bonds_valence) || /* a bond has higher multiplicity than 1 */ (at[i].radical && at[i].radical != RADICAL_SINGLET); /* radical */ if ( !bRadOrMultBonds && bIsAmmoniumSalt( at, i, &iO, &k, num_explicit_H ) ) { ; } else if ( !bRadOrMultBonds && bIsMetalSalt( at, i ) ) { ; } else if ( 1 == (j = bIsMetalToDisconnect(at, i, bCheckMetalValence)) ) { num_impl_H += (k = NUMH(at,i)); bMetal[i] = 1+k; num_changes ++; } else if ( 2 == j && bTautFlagsDone ) { *bTautFlagsDone |= TG_FLAG_CHECK_VALENCE_COORD_DONE; } } if ( num_impl_H != nNumExplH ) { err = 2; goto exit_function; } /* replace implicit H atoms with explicit H atoms */ for ( i = 0; i < num_atoms && 0 < num_impl_H; i ++ ) { if ( bMetal[i] <= 1 ) { continue; } for ( k = 0; k < NUM_H_ISOTOPES+1; k ++ ) { n = k? at[i].num_iso_H[k-1] : at[i].num_H; for ( j = 0; j < n; j ++ ) { if ( num_at >= num_atoms + nNumExplH ) { err = 3; goto exit_function; } at[num_at].elname[0] = 'H'; at[num_at].el_number = get_periodic_table_number(at[num_at].elname); at[num_at].iso_atw_diff = k; at[num_at].component = at[i].component; move_explicit_Hcation(at, num_at+1, i, num_at, 1); at[num_at].orig_at_number = num_at+1; num_at ++; num_impl_H --; bMetal[i] --; if ( k ) { at[i].num_iso_H[k-1] --; } else { at[i].num_H --; } } } if ( bMetal[i] != 1 ) { err = 4; goto exit_function; } } if ( num_at != num_atoms + nNumExplH ) { err = 5; goto exit_function; } /* disconnect metal - ligand bonds */ for ( i = 0; i < num_atoms; i ++ ) { if ( !bMetal[i] ) { continue; } /* disconnect metal atom M Note: Defect in case of bridging ligands: M M M M M M(+) \ / will be transformed to , not to N(+) N(+) N(-) / \ / \ / \ R R R R R R Non-bridging are OK: M R M(+) R \ / / N(+) ---> N / \ / \ R R R R */ for ( j = at[i].valence-1; 0 <= j; j -- ) { if ( j < at[i].valence && !bMetal[ (int)at[i].neighbor[j] ] ) { /* do not break metal-metal bond here */ num_disconnected += DisconnectOneLigand( at, nOldCompNumber, bMetal, elnumber_Heteroat, num_halogens, num_atoms, i, j, bTautFlagsDone ); } } } /* disconnect metal-metal bonds */ for ( i = 0; i < num_atoms; i ++ ) { if ( !bMetal[i] ) { continue; } for ( j = at[i].valence-1; 0 <= j; j -- ) { if ( j < at[i].valence && bMetal[ (int)at[i].neighbor[j] ] ) { /* break metal-metal bond here */ num_disconnected += DisconnectOneLigand( at, nOldCompNumber, bMetal, elnumber_Heteroat, num_halogens, num_atoms, i, j, bTautFlagsDone ); } } } exit_function: if ( !num_disconnected ) { err = 6; } if ( at && err ) { inchi_free( at ); at = NULL; } if ( atom && at ) { /* changed if ( at ) to if ( atom && at ) 2004-04-03 */ inchi_free( atom ); atom = NULL; } if ( bMetal ) inchi_free( bMetal ); if ( at ) { orig_inp_data->at = at; orig_inp_data->num_inp_atoms = num_at; } return err? -err : num_disconnected; } /*****************************************************************************/ int DisconnectOneLigand( inp_ATOM *at, AT_NUMB *nOldCompNumber, S_CHAR *bMetal, char *elnumber_Heteroat, int num_halogens, int num_atoms, int iMetal, int jLigand, INCHI_MODE *bTautFlagsDone ) { int i, j, iLigand, neigh, val; int metal_neigh_ord[MAXVAL], num_neigh_arom_bonds[MAXVAL]; int num_metal_neigh, num_disconnections; int num_del_arom_bonds, num_tot_arom_bonds, new_charge; char *p; iLigand = at[iMetal].neighbor[jLigand]; num_metal_neigh = 0; num_disconnections = 0; num_del_arom_bonds = num_tot_arom_bonds = 0; /* find bonds to disconnect */ for ( i = 0; i < at[iLigand].valence; i ++ ) { num_neigh_arom_bonds[i] = 0; neigh = (int)at[iLigand].neighbor[i]; if ( neigh < num_atoms && bMetal[ neigh ] ) { metal_neigh_ord[ num_metal_neigh ++ ] = i; if ( at[iLigand].bond_type[i] > BOND_TYPE_TRIPLE ) { /* aromatic bond */ for ( j = 0; j < at[neigh].valence; j ++ ) { num_neigh_arom_bonds[i] += ( at[neigh].bond_type[j] > BOND_TYPE_TRIPLE ); } num_del_arom_bonds ++; } } num_tot_arom_bonds += (at[iLigand].bond_type[i] > BOND_TYPE_TRIPLE); } /* Disconnect */ if ( num_del_arom_bonds ) { /* fix chem_valence of the ligand and its neighbors in case of disconnecting arom. bonds */ /* because in this case special care should be taken of updating at[].chem_bonds_valence */ for ( i = 0; i < num_metal_neigh; i ++ ) { j = metal_neigh_ord[i]; if ( num_neigh_arom_bonds[j] ) { neigh = at[iLigand].neighbor[j]; at[neigh].chem_bonds_valence -= num_neigh_arom_bonds[j]/2 - (num_neigh_arom_bonds[j]-1)/2; } } at[iLigand].chem_bonds_valence -= num_tot_arom_bonds/2 - (num_tot_arom_bonds-num_del_arom_bonds)/2; } /* disconnect in reverse order, otherwise the metal_neigh_ord[i] becomes invalid after the first disconnection */ for ( i = num_metal_neigh-1; 0 <= i; i -- ) { num_disconnections += DisconnectInpAtBond( at, nOldCompNumber, iLigand, metal_neigh_ord[i] ); } /* attempt to change ligand charge to make its valence 'natural' */ i = num_tot_arom_bonds - num_del_arom_bonds; if ( i && i != 2 && i != 3 || at[iLigand].radical && at[iLigand].radical != RADICAL_SINGLET || !(p = strchr( elnumber_Heteroat, at[iLigand].el_number ) ) ) { goto exit_function; /* non-standard atom */ } val = at[iLigand].chem_bonds_valence + NUMH(at, iLigand); new_charge = MAX_ATOMS; /* impossible value */ if ( !val ) { if ( p - elnumber_Heteroat < num_halogens ) { new_charge = -1; } } else { for ( i = -1; i <= 1; i ++ ) { if ( val == get_el_valence( at[iLigand].el_number, i, 0 ) ) { new_charge = i; /* found charge that fits chem. valence */ break; } } } if ( new_charge != MAX_ATOMS ) { if ( (new_charge != at[iLigand].charge || (at[iLigand].radical && at[iLigand].radical != RADICAL_SINGLET)) && 1 == num_metal_neigh ) { if ( 1 == new_charge && 4 == val && 2 == at[iLigand].valence && 4 == at[iLigand].chem_bonds_valence && at[iLigand].bond_type[0] == at[iLigand].bond_type[1] ) { ; /* do not add +1 charge to disconnected =N=, etc. 2004-10-27 */ } else { if ( bTautFlagsDone && new_charge != at[iLigand].charge ) { *bTautFlagsDone |= TG_FLAG_MOVE_CHARGE_COORD_DONE; } at[iMetal].charge -= new_charge - at[iLigand].charge; at[iLigand].charge = new_charge; /*at[iLigand].radical = 0;*/ } } } exit_function: return num_disconnections; /* ret;*/ } /****************************************************************************************/ double dist3D( inp_ATOM *at1, inp_ATOM *at2 ) { double dx = at1->x - at2->x; double dy = at1->y - at2->y; double dz = at1->z - at2->z; return sqrt( dx*dx+dy*dy+dz*dz ); } /****************************************************************************************/ #define MIN_BOND_LENGTH (1.0e-6) #define MIN_COS (1.0e-6) #define MIN_BOND_LENGTH2 (MIN_BOND_LENGTH*MIN_BOND_LENGTH) #define MAX_BOND_LENGTH (1.0e30) /****************************************************************************************/ double GetMinDistDistribution( inp_ATOM *at, int num_at, int iat, int iat_H, int bInAllComponents, double min_dist[], int num_segm ) { /* const double one_pi = 2.0*atan2(1.0 , 0.0 ); */ const double one_pi = 3.14159265358979323846; /* M_PI */ const double two_pi = 2.0*one_pi; const double f_step = two_pi / num_segm; const double h_step = f_step/2.0; int i, j, k, kk, ki, kn, n, num_bonds; double xi, yi, xn, yn, cross_prod_in, dot_prod_in, xni, yni, rni, tni, rmin; double fi, fk, fn, ft, rt, rk, ri, rn, c, ave_bond_len; for ( i = 0; i < num_segm; i ++ ) { min_dist[i] = MAX_BOND_LENGTH; /* more than any distance */ } num_bonds = 0; ave_bond_len = 0.0; for ( i = 0; i < num_at; i ++ ) { if ( i != iat && i != iat_H && (bInAllComponents || at[i].component == at[iat].component) ) { for ( j = 0; j < at[i].valence; j ++ ) { n = at[i].neighbor[j]; if ( (n > i && n != iat) || n == iat_H ) continue; #if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) if ( n == iat ) { int stop = 1; /* */ } #endif xi = at[i].x - at[iat].x; /* ri; i != iat */ yi = at[i].y - at[iat].y; xn = at[n].x - at[iat].x; /* rn; possibly n == iat */ yn = at[n].y - at[iat].y; cross_prod_in = xi*yn - xn*yi; /* ((r(i)-r(iat)) x (r(n)-r(iat)) */ if ( cross_prod_in < -0.01*MIN_BOND_LENGTH2 ) { /* make sure the r(i)->r(n) vector is counterclockwise around at[iat] */ inchi_swap( (char*)&xi, (char*)&xn, sizeof(xi) ); inchi_swap( (char*)&yi, (char*)&yn, sizeof(yi) ); cross_prod_in = -cross_prod_in; } xni = xn - xi; /* r(n)->r(i) */ yni = yn - yi; rni = xni*xni + yni*yni; if ( rni > 0.01*MIN_BOND_LENGTH2 ) { /* vector length |ri->rn| is not too small */ /* arrowhead of the vector r(t) = ri + (rn-ri)*t; 0 <= t <= 1 points to the bond ri->rn */ /* r(tni) is perpendicular to the bond ri->rn so that min|r(t)| = r(tni) = |tni|*rni */ tni = -(xni*xi + yni*yi)/rni; /* find min. distance from n-i bond to at[iat] */ if ( tni < 0.0 ) { rmin = sqrt( xi*xi + yi*yi ); } else if ( tni > 1.0 ) { rmin = sqrt( xn*xn + yn*yn ); } else { rmin = sqrt(tni*tni*rni); } ave_bond_len += sqrt( rni ); num_bonds ++; } else { /* zero length i-n bond */ tni = 0.5; /* fake */ rmin = sqrt( xi*xi + yi*yi ); /* arbitrarily choose one */ } if ( rmin >= 0.1*MIN_BOND_LENGTH ) { /* at[iat] does not belong to at[i]-at[n] bond */ int bCalc_rt = 1; fi = atan2( yi, xi ); fn = (n == iat)? fi : atan2( yn, xn ); if ( fi > fn ) { /* make sure fn - fi >= 0 */ fn += two_pi; } if ( fi < 0.0 ) { fi += two_pi; fn += two_pi; } ki = (int)floor((fi+h_step)/f_step); /* cast does not match function type */ kn = (int)floor((fn+h_step)/f_step); /* the bond may affect several segments */ for ( k = ki; k <= kn; k ++ ) { kk = k % num_segm; if ( min_dist[kk] < rmin ) continue; if ( bCalc_rt ) { if ( n == iat ) { ft = fi; rt = rmin; } else { double xt, yt; xt = xi + xni*tni; yt = yi + yni*tni; ft = atan2( yt, xt ); rt = sqrt(xt*xt + yt*yt); } bCalc_rt = 0; } fk = f_step * kk; c = fabs(cos( fk - ft )); if ( c < MIN_COS ) c = MIN_COS; rk = rt / c; if ( min_dist[kk] > rk ) { min_dist[kk] = rk; } } } else { /* rmin < 0.1*MIN_BOND_LENGTH */ ri = xi*xi + yi*yi; rn = xn*xn + yn*yn; if ( ri > MIN_BOND_LENGTH2 && rn > MIN_BOND_LENGTH2 ) { dot_prod_in = xn*xi + yn*yi; /* a very short bond */ if ( dot_prod_in > 0.01*MIN_BOND_LENGTH2 ) { /* bond does not cross at[iat] */ double fyixi = atan2( yi, xi ); if ( fyixi < 0.0 ) fyixi += two_pi; kk = (int)floor((fyixi+h_step)/f_step) % num_segm; if ( min_dist[kk] > rmin ) { min_dist[kk] = rmin; } } else if ( dot_prod_in < -0.01*MIN_BOND_LENGTH2 ) { /* bond does cross at[iat] */ double fyixi = atan2( yi, xi ); if ( fyixi < 0.0 ) fyixi += two_pi; kk = (int)floor((fyixi+h_step)/f_step) % num_segm; if ( min_dist[kk] > rmin ) { min_dist[kk] = rmin; } fyixi += one_pi; kk = (int)floor((fyixi+h_step)/f_step) % num_segm; if ( min_dist[kk] > rmin ) { min_dist[kk] = rmin; } } else { ; /* error, should not happen */ } } else if ( ri <= MIN_BOND_LENGTH2 && rn <= MIN_BOND_LENGTH2 ) { /* a very short bond coincides with at[iat]; ignore */ ; } else { /* one end of the bond coincides with at[iat] */ fi = ri>rn? atan2( yi, xi) : atan2( yn, xn ); if ( fi < 0.0 ) fi += two_pi; kk = (int)floor((fi+h_step)/f_step) % num_segm; if ( min_dist[kk] > rmin ) { min_dist[kk] = rmin; } } } } } } if ( num_bonds ) { return ave_bond_len / (double)num_bonds; } else { return 0.0; } } /****************************************************************************************/ int move_explicit_Hcation(inp_ATOM *at, int num_at, int iat, int iat_H, int bInAllComponents) { #define NUM_SEGM 20 /* const double one_pi = 2.0*atan2(1.0 , 0.0 ); */ const double one_pi = 3.14159265358979323846; /* M_PI */ const double two_pi = 2.0*one_pi; const double f_step = two_pi / NUM_SEGM; const double h_step = f_step/2.0; double min_dist[NUM_SEGM]; int nB, i, k, kk, next, val; double r, r0, xd, yd, zd, xr, yr, zr, ave_bond_len; /*double step = 4.0*atan(1.0)/NUM_SEGM;*/ /* find at[iat] neighbors coordinates */ xd=yd=zd=0.0; if ( at[iat].valence ) { for ( i = 0, nB=0, r = 0.0; i < at[iat].valence; i ++ ) { next = at[iat].neighbor[i]; xd += at[next].x; yd += at[next].y; zd += at[next].z; r += dist3D( at+iat, at+next ); nB ++; } xd /= (double)nB; yd /= (double)nB; zd /= (double)nB; r /= (double)nB; r0 = sqrt((double)(xd-at[iat].x)*(xd-at[iat].x) + (double)(yd-at[iat].y)*(yd-at[iat].y)); } else { if ( at[iat_H].valence ) { r = dist3D( at+iat_H, at+ (int)at[iat_H].neighbor[0] ); } else { r = 0.0; } r0 = 0.0; } ave_bond_len = GetMinDistDistribution( at, num_at, iat, iat_H, bInAllComponents, min_dist, NUM_SEGM ); if ( r < MIN_BOND_LENGTH && ave_bond_len > MIN_BOND_LENGTH ) { r = ave_bond_len; /* ave_bond_len = 0.0 may mean that it is 0D structure */ } if ( r > MIN_BOND_LENGTH ) { /* process non-zero bond lengths */ double f; if ( 10.0*r0 < r ) { xr = -r; /* arbitrary */ yr = 0.0; zr = 0.0; } else { /* if ( r0 < MIN_BOND_LENGTH ) { r0 = 1.0; } */ xr = r * ( at[iat].x - xd )/r0; yr = r * ( at[iat].y - yd )/r0; /* length = r */ zr = r * ( at[iat].z - zd )/r0; /* -- test: opposire direction -- xr = -r * ( at[iat].x - xd )/r0; yr = -r * ( at[iat].y - yd )/r0; zr = -r * ( at[iat].z - zd )/r0; */ if ( xr*xr + yr*yr < 0.04*r*r ) { xr = -r; yr = 0.0; } } r = sqrt( xr*xr + yr*yr ); f = atan2( yr, xr ); if ( f < 0.0 ) f += two_pi; kk = (int)floor((f+h_step)/f_step) % NUM_SEGM; /* cast does not match function type by design */ if ( min_dist[kk] < 1.5* r ) { double dist = 1.5*r; int start=-1, len=0, start_max=-1, len_max=0; again: /* look for longest kk interval with min_dist[kk] >= dist */ for ( k = 0, start = 0, len = 0, len_max = 0; k < 2*NUM_SEGM; k ++ ) { kk = k % NUM_SEGM; if ( min_dist[kk] >= dist ) { if ( !len ++) { start = k; } } else { if ( len > len_max ) { len_max = len; start_max = start; } len = 0; } } if ( !len_max ) { if ( dist > 0.1*r ) { dist *= 0.75; goto again; } else { goto done; /* do it anyway */ } } else { /* found a good sector */ f = f_step * (start_max + (double)(len_max - 1)/2.0); r0 = dist / 1.5; xr = r0 * cos(f); yr = r0 * sin(f); zr = zr/r*r0; } } } else { xr = yr = zr = 0; } done: if ( at[iat_H].valence ) { /* disconnect H */ next = at[iat_H].neighbor[0]; for ( i = 0; i < at[next].valence; i ++ ) { if ( at[next].neighbor[i] == iat_H ) { RemoveInpAtBond( at, next, i ); i = 0; /* success */ break; } } } else { /* isolated H+ cation */ next = iat_H; i = 0; at[iat_H].valence = 1; at[iat_H].chem_bonds_valence = 1; at[iat_H].bond_type[0] = BOND_TYPE_SINGLE; } if ( 0 == i /*i < at[next].valence*/ ) { /* move charge */ if ( at[next].charge > 0 && at[iat].charge < 0 ) { at[next].charge --; at[iat].charge ++; } /* connect H to at[iat] */ val = at[iat].valence; at[iat].neighbor[val] = iat_H; at[iat].bond_type[val] = at[iat_H].bond_type[0]; at[iat].bond_stereo[val] = 0; at[iat].chem_bonds_valence += at[iat_H].bond_type[0]; at[iat].valence = val+1; at[iat_H].component = at[iat].component; at[iat_H].neighbor[0] = iat; at[iat_H].bond_stereo[0] = 0; /* possible loss of stereo info */ at[iat_H].x = at[iat].x + xr; at[iat_H].y = at[iat].y + yr; at[iat_H].z = at[iat].z + zr; return 1; /* success */ } return 0; /* failed */ } /****************************************************************************************/ int get_iat_number( int el_number, const int el_num[], int el_num_len ) { int i; for ( i = 0; i < el_num_len; i ++ ) { if ( el_num[i] == el_number ) return i; } return -1; } /*#endif*/ /* } DISCONNECT_SALTS */ typedef enum tagIonAtomType { IAT_H=0, IAT_C, IAT_N, IAT_P, IAT_O, IAT_S, IAT_Se, IAT_Te, IAT_F, IAT_Cl, IAT_Br, IAT_I, IAT_MAX } ION_ATOM_TYPE; #if ( READ_INCHI_STRING == 1 ) /****************************************************************************************/ int bHeteroAtomMayHaveXchgIsoH( inp_ATOM *atom, int iat ) { inp_ATOM *at = atom + iat, *at2; static int el_num[IAT_MAX]; int j, val, is_O=0, is_Cl=0, is_N=0, is_H=0, num_H, iat_numb, bAccept, cur_num_iso_H; if ( !el_num[IAT_H]) { el_num[IAT_H ] = get_periodic_table_number( "H" ); el_num[IAT_C ] = get_periodic_table_number( "C" ); el_num[IAT_N ] = get_periodic_table_number( "N" ); el_num[IAT_P ] = get_periodic_table_number( "P" ); el_num[IAT_O ] = get_periodic_table_number( "O" ); el_num[IAT_S ] = get_periodic_table_number( "S" ); el_num[IAT_Se] = get_periodic_table_number( "Se"); el_num[IAT_Te] = get_periodic_table_number( "Te"); el_num[IAT_F ] = get_periodic_table_number( "F" ); el_num[IAT_Cl] = get_periodic_table_number( "Cl"); el_num[IAT_Br] = get_periodic_table_number( "Br"); el_num[IAT_I ] = get_periodic_table_number( "I" ); } if ( 0 > (iat_numb = get_iat_number( at->el_number, el_num, IAT_MAX )) ) { return 0; } if ( abs(at->charge) > 1 || at->radical && RADICAL_SINGLET != at->radical ) { return 0; } val = -1; switch( iat_numb ) { case IAT_N: case IAT_P: is_N = 1; val = 3+at->charge; break; case IAT_O: case IAT_S: case IAT_Se: case IAT_Te: is_O = 1; val = 2+at->charge; break; case IAT_F: case IAT_Cl: case IAT_Br: case IAT_I: if ( at->charge == 0 ) { is_Cl = 1; /* isolated HCl */ val = 1; } break; case IAT_H: if ( at->valence == 0 && at->charge == 1 ) { is_H = 1; /* isolated proton */ val = 0; } } if ( val < 0 ) { return 0; } num_H = NUMH(at,0); if ( val != at->chem_bonds_valence + num_H ) { return 0; } if ( is_H ) { return 2; /* H atom */ } else { cur_num_iso_H = 0; for ( j = 0, bAccept = 1; j < at->valence && bAccept; j ++ ) { at2 = atom + (int)at->neighbor[j]; if ( at2->charge && at->charge || (at2->radical && RADICAL_SINGLET != at2->radical ) ) { return 0; /* adjacent charged/radical atoms: do not neutralizate */ } } } return 1; } #endif /****************************************************************************************/ int bNumHeterAtomHasIsotopicH( inp_ATOM *atom, int num_atoms ) { static int el_num[IAT_MAX]; int i, j, val, is_O=0, is_Cl=0, is_N=0, is_H=0, num_H, iat_numb, bAccept, num_iso_H, cur_num_iso_H, num_iso_atoms; inp_ATOM *at, *at2; /* one time initialization */ if ( !el_num[IAT_H]) { el_num[IAT_H ] = get_periodic_table_number( "H" ); el_num[IAT_C ] = get_periodic_table_number( "C" ); el_num[IAT_N ] = get_periodic_table_number( "N" ); el_num[IAT_P ] = get_periodic_table_number( "P" ); el_num[IAT_O ] = get_periodic_table_number( "O" ); el_num[IAT_S ] = get_periodic_table_number( "S" ); el_num[IAT_Se] = get_periodic_table_number( "Se"); el_num[IAT_Te] = get_periodic_table_number( "Te"); el_num[IAT_F ] = get_periodic_table_number( "F" ); el_num[IAT_Cl] = get_periodic_table_number( "Cl"); el_num[IAT_Br] = get_periodic_table_number( "Br"); el_num[IAT_I ] = get_periodic_table_number( "I" ); } num_iso_H = 0; num_iso_atoms = 0; for ( i = 0, at = atom; i < num_atoms; i ++, at ++ ) { num_iso_atoms += ( at->iso_atw_diff != 0 || NUM_ISO_H(at,0) ); /* isotopic atoms and implicit isotopic H */ if ( 0 > (iat_numb = get_iat_number( at->el_number, el_num, IAT_MAX )) ) { continue; } if ( abs(at->charge) > 1 || at->radical && RADICAL_SINGLET != at->radical ) { continue; } val = -1; switch( iat_numb ) { case IAT_N: case IAT_P: is_N = 1; val = 3+at->charge; break; case IAT_O: case IAT_S: case IAT_Se: case IAT_Te: is_O = 1; val = 2+at->charge; break; case IAT_F: case IAT_Cl: case IAT_Br: case IAT_I: if ( at->charge == 0 ) { is_Cl = 1; /* isolated HCl */ val = 1; } break; case IAT_H: if ( at->valence == 0 && at->charge == 1 ) { is_H = 1; /* isolated proton */ val = 0; } } if ( val < 0 ) { continue; } num_H = NUMH(at,0); if ( val != at->chem_bonds_valence + num_H ) { continue; } if ( is_H ) { bAccept = 1; cur_num_iso_H = (at->iso_atw_diff != 0); } else { cur_num_iso_H = 0; for ( j = 0, bAccept = 1; j < at->valence && bAccept; j ++ ) { at2 = atom + (int)at->neighbor[j]; if ( at2->charge && at->charge || (at2->radical && RADICAL_SINGLET != at2->radical ) ) { bAccept = 0; /* adjacent charged/radical atoms: do not neutralizate */ break; } else if ( at2->el_number == el_num[IAT_H ] && at2->valence == 1 && at2->iso_atw_diff ) { cur_num_iso_H ++; /* isotopic explicit H */ } } if ( bAccept ) { num_iso_atoms -= cur_num_iso_H; /* avoid counting explicit H as isotopic atom */ cur_num_iso_H += NUM_ISO_H(at,0); } } num_iso_H += (bAccept && cur_num_iso_H); /* number of acceptable heteroatoms that have isotopic H */ } return ((num_iso_H? 1:0) | (num_iso_atoms? 2:0)); } /****************************************************/ /* Mark and count disconnected structure components */ /* by Depth-first searching each component */ /****************************************************/ int cmp_components( const void *a1, const void *a2 ) { int ret; AT_NUMB n1; AT_NUMB n2; n1 = ((const AT_NUMB *)a1)[0]; /* number of atoms in the component -- descending order */ n2 = ((const AT_NUMB *)a2)[0]; if ( ret = (int)n2 - (int)n1 ) { return ret; } /* stable sort */ n1 = ((const AT_NUMB *)a1)[1]; /* component ordering number -- ascending order */ n2 = ((const AT_NUMB *)a2)[1]; ret = (int)n1 - (int)n2; return ret; } /*************************************************************************************************/ int MarkDisconnectedComponents( ORIG_ATOM_DATA *orig_at_data, int bProcessOldCompNumbers ) { typedef AT_NUMB AT_TRIPLE[3]; inp_ATOM *at = orig_at_data->at; int num_at = orig_at_data->num_inp_atoms; AT_NUMB *nCurAtLen = NULL; AT_NUMB *nNewCompNumber = NULL; AT_NUMB *nPrevAtom = NULL; S_CHAR *iNeigh = NULL; AT_NUMB *nOldCompNumber = NULL; int i, j, num_components, ret; int new_comp_no; AT_NUMB old_comp_no, another_comp_no, no_component; /* component_nbr[i][0] = number of atoms in the component i-1 * component_nbr[i][1] = original component number (id-1) = i * after sorting: * component_nbr[j][2] = new number of component #(component_nbr[i][1]+1) */ AT_TRIPLE *component_nbr = NULL; /* initialize */ if ( bProcessOldCompNumbers && !orig_at_data->nOldCompNumber ) { bProcessOldCompNumbers = 0; } num_components = 0; /* for ( j = 0; j < num_at; j ++ ) { at[j].component = 0; } */ ret = -1; if ( !num_at ) { return 0; } if ( !( nNewCompNumber = (AT_NUMB *) inchi_calloc( num_at, sizeof(nNewCompNumber[0]) ) ) || /* for non-recursive DFS only: */ !( nPrevAtom = (AT_NUMB *) inchi_calloc( num_at, sizeof(nPrevAtom[0]) ) ) || !( iNeigh = (S_CHAR *) inchi_calloc( num_at, sizeof(iNeigh[0]) ) )) { goto exit_function; } /* mark and count; avoid deep DFS recursion: it may make verifying software unhappy */ /* nNewCompNumber[i] will contain new component number for atoms at[i], i=0..num_at-1 */ for ( j = 0; j < num_at; j++ ) { if ( !nNewCompNumber[j] ) { /* mark starting with at[j] */ int fst_at, nxt_at, cur_at = j; num_components ++; /* first time at at[j] */ nNewCompNumber[fst_at = cur_at] = (AT_NUMB) num_components; /* find next neighbor */ while ( 1 ) { if ( iNeigh[cur_at] < at[cur_at].valence ) { nxt_at = at[cur_at].neighbor[(int)iNeigh[cur_at] ++]; if ( !nNewCompNumber[nxt_at] ) { /* forward edge: found new atom */ nNewCompNumber[nxt_at] = (AT_NUMB) num_components; nPrevAtom[nxt_at] = (AT_NUMB) cur_at; cur_at = nxt_at; } } else if ( cur_at == fst_at ) { break; /* done */ } else { cur_at = nPrevAtom[cur_at]; /* retract */ } } } } inchi_free( nPrevAtom ); nPrevAtom = NULL; inchi_free( iNeigh ); iNeigh = NULL; /* Allocate more memory */ i = inchi_max( num_components, orig_at_data->num_components ); if ( !(nCurAtLen = (AT_NUMB *) inchi_calloc( num_components+1, sizeof(nCurAtLen[0]) ) ) || !(nOldCompNumber = (AT_NUMB *) inchi_calloc( i +1, sizeof(nOldCompNumber[0]) ) ) || !(component_nbr = (AT_TRIPLE *) inchi_calloc( num_components+1, sizeof(component_nbr[0]) ) ) ) { goto exit_function; } /* count atoms per component and renumber the components */ for ( i = 0; i < num_components; i ++ ) { component_nbr[i][0] = 0; /* number of atoms in the component */ component_nbr[i][1] = i; /* component ordering number */ } for ( j = 0; j < num_at; j ++ ) { component_nbr[(int)nNewCompNumber[j]-1][0] ++; /* count atoms in each component */ } /* sort key: number of atoms; order: descending */ qsort( (void*)component_nbr[0], num_components, sizeof(component_nbr[0]), cmp_components); /* invert the transposition */ for ( i = 0; i < num_components; i ++ ) { nCurAtLen[i] = component_nbr[i][0]; component_nbr[ component_nbr[i][1] ][2] = i+1; } /* renumber the components so that the component with the greatest number of atoms is the first */ no_component = num_at+1; for ( j = 0; j < num_at; j ++ ) { /* new component number for at[j] */ new_comp_no = component_nbr[(int)nNewCompNumber[j]-1][2]-1; /* starts from 0 */ if ( bProcessOldCompNumbers ) { /* old component number for at[j] */ old_comp_no = at[j].component; /* fill out nOldCompNumber[]; initially it contains zeroes */ if ( !old_comp_no ) { nOldCompNumber[new_comp_no] = no_component; /* atom did not have component number */ } else if ( nOldCompNumber[new_comp_no] != old_comp_no ) { if ( !nOldCompNumber[new_comp_no] ) { nOldCompNumber[new_comp_no] = old_comp_no; } else { /* at[j] moved from old comp #old_comp_no to old comp #nOldCompNumber[new_comp_no] Both components cannot be equal to any current component */ another_comp_no = nOldCompNumber[new_comp_no]; for ( i = 0; i < num_components; i ++ ) { if ( nOldCompNumber[i] == old_comp_no || nOldCompNumber[i] == another_comp_no ) { nOldCompNumber[i] = no_component; } } /* nOldCompNumber[new_comp_no] = num_at+1; */ } } } /* orig_at_data->nOldCompNumber */ at[j].component = new_comp_no+1; /* starts from 1 */ } if ( bProcessOldCompNumbers ) { for ( j = 0; j < num_components; j ++ ) { if ( nOldCompNumber[j] == no_component ) { /* the component has atom from another component */ nOldCompNumber[j] = 0; } else if ( nOldCompNumber[j] && !orig_at_data->nOldCompNumber[nOldCompNumber[j]-1] ) { /* the component has changed in the previous processing */ nOldCompNumber[j] = 0; } } } else { for ( j = 0; j < num_components; j ++ ) { nOldCompNumber[j] = j + 1; } } ret = num_components; exit_function: if ( nNewCompNumber ) inchi_free( nNewCompNumber ); if ( component_nbr ) inchi_free( component_nbr ); if ( ret < 0 ) { if ( nPrevAtom ) { inchi_free( nPrevAtom ); nPrevAtom = NULL; } if ( iNeigh ) { inchi_free( iNeigh ); iNeigh = NULL; } if ( nCurAtLen ) { inchi_free( nCurAtLen ); nCurAtLen = NULL; } if ( nOldCompNumber ) { inchi_free( nOldCompNumber ); nOldCompNumber = NULL; } num_components = ret; } /* avoid memory leaks */ if ( orig_at_data->nCurAtLen ) inchi_free ( orig_at_data->nCurAtLen ); if ( orig_at_data->nOldCompNumber ) inchi_free ( orig_at_data->nOldCompNumber ); orig_at_data->nCurAtLen = nCurAtLen; orig_at_data->nOldCompNumber = nOldCompNumber; orig_at_data->num_components = num_components; return ret; /* number of disconnected components; 1=>single connected structure*/ } /******************************************************************************/ /* Extract one (connected) component */ /******************************************************************************/ int ExtractConnectedComponent( inp_ATOM *at, int num_at, int component_number, inp_ATOM *component_at ) { int i, j, num_component_at; AT_NUMB *number; if ( NULL == (number = (AT_NUMB*)inchi_calloc(num_at, sizeof(AT_NUMB)))){ return CT_OUT_OF_RAM; /* out of memory */ /* */ } /* copy atoms */ for ( i = 0, num_component_at = 0; i < num_at; i ++ ) { if ( at[i].component == component_number ) { number[i] = num_component_at; component_at[num_component_at ++] = at[i]; } } /* renumber neighbors */ for ( i = 0; i < num_component_at; i ++ ) { component_at[i].orig_compt_at_numb = (AT_NUMB)(i + 1); for ( j = 0; j < component_at[i].valence; j ++ ) { component_at[i].neighbor[j] = number[(int)component_at[i].neighbor[j]]; } } inchi_free( number ); return num_component_at; } /****************************************************************/ int SetConnectedComponentNumber( inp_ATOM *at, int num_at, int component_number ) { int i; for ( i = 0; i < num_at; i ++ ) { at[i].component = (AT_NUMB)component_number; } return 0; } /****************************************************************/ int Free_INChI_Stereo( INChI_Stereo *pINChI_Stereo ) { if ( pINChI_Stereo ) { qzfree( pINChI_Stereo->nNumber ); qzfree( pINChI_Stereo->t_parity ); qzfree( pINChI_Stereo->nNumberInv ); qzfree( pINChI_Stereo->t_parityInv ); qzfree( pINChI_Stereo->nBondAtom1 ); qzfree( pINChI_Stereo->nBondAtom2 ); qzfree( pINChI_Stereo->b_parity ); } return 0; } /****************************************************************/ INChI_Stereo *Alloc_INChI_Stereo(int num_at, int num_bonds) { INChI_Stereo *pINChI_Stereo = (INChI_Stereo *)inchi_calloc(1, sizeof(INChI_Stereo)); if ( pINChI_Stereo ) { if ( num_at && (pINChI_Stereo->nNumber = (AT_NUMB *)inchi_calloc(num_at, sizeof(pINChI_Stereo->nNumber[0]))) && (pINChI_Stereo->t_parity = (S_CHAR *)inchi_calloc(num_at, sizeof(pINChI_Stereo->t_parity[0]))) && (pINChI_Stereo->nNumberInv = (AT_NUMB *)inchi_calloc(num_at, sizeof(pINChI_Stereo->nNumberInv[0]))) && (pINChI_Stereo->t_parityInv = (S_CHAR *)inchi_calloc(num_at, sizeof(pINChI_Stereo->t_parityInv[0]))) ) { ; } else if ( num_at ) { goto out_of_RAM; } if ( num_bonds && (pINChI_Stereo->nBondAtom1 =(AT_NUMB *)inchi_calloc(num_bonds, sizeof(pINChI_Stereo->nBondAtom1[0]))) && (pINChI_Stereo->nBondAtom2 =(AT_NUMB *)inchi_calloc(num_bonds, sizeof(pINChI_Stereo->nBondAtom2[0]))) && (pINChI_Stereo->b_parity =(S_CHAR *)inchi_calloc(num_bonds, sizeof(pINChI_Stereo->b_parity[0]))) ) { ; } else if ( num_bonds ) { goto out_of_RAM; } return pINChI_Stereo; out_of_RAM: Free_INChI_Stereo( pINChI_Stereo ); qzfree( pINChI_Stereo ); } return NULL; } /****************************************************************/ int Free_INChI(INChI **ppINChI) { INChI *pINChI; if ( pINChI = *ppINChI ) { #if ( bREUSE_INCHI == 1 ) if ( pINChI->nRefCount -- > 0 ) return 1; #endif Free_INChI_Members(pINChI); qzfree( pINChI ); *ppINChI = NULL; } return 0; } /****************************************************************/ int Free_INChI_Members(INChI *pINChI) { if ( pINChI ) { Free_INChI_Stereo(pINChI->Stereo ); Free_INChI_Stereo(pINChI->StereoIsotopic ); qzfree(pINChI->nAtom ); qzfree(pINChI->nConnTable ); qzfree(pINChI->nTautomer ); qzfree(pINChI->nNum_H ); qzfree(pINChI->nNum_H_fixed ); qzfree(pINChI->IsotopicAtom ); qzfree(pINChI->IsotopicTGroup ); qzfree(pINChI->nPossibleLocationsOfIsotopicH); qzfree(pINChI->Stereo ); qzfree(pINChI->StereoIsotopic ); qzfree(pINChI->szHillFormula ); } return 0; } /****************************************************************/ INChI *Alloc_INChI( inp_ATOM *at, int num_at, int *found_num_bonds, int *found_num_isotopic, int nAllocMode ) { int i, num_bonds, num_isotopic_atoms; INChI *pINChI; int bIsotopic = (nAllocMode & REQ_MODE_ISO); /* int bTautomeric = (nAllocMode & REQ_MODE_TAUT); */ if ( num_at <= 0 || NULL == (pINChI = (INChI *)inchi_calloc( 1, sizeof(INChI)))) { return NULL; } for ( i = 0, num_bonds = 0, num_isotopic_atoms = 0; i < num_at; i ++ ) { num_bonds += at[i].valence; /* if ( bIsotopic ) { */ num_isotopic_atoms += (0 != at[i].iso_atw_diff || !strcmp(at[i].elname, "D") || !strcmp(at[i].elname, "T") || at[i].num_iso_H[0] || at[i].num_iso_H[1] || at[i].num_iso_H[2]); /* } */ } num_bonds /= 2; *found_num_bonds = num_bonds; *found_num_isotopic = num_isotopic_atoms; if ( (pINChI->nAtom = (U_CHAR*) inchi_calloc( num_at, sizeof(pINChI->nAtom[0]))) && (pINChI->nConnTable = (AT_NUMB*)inchi_calloc( num_at+num_bonds, sizeof(pINChI->nConnTable[0]))) && (pINChI->nTautomer = (AT_NUMB*)inchi_calloc( ((3+INCHI_T_NUM_MOVABLE)*num_at)/2+1, sizeof(pINChI->nTautomer[0]))) && (pINChI->nNum_H = (S_CHAR*) inchi_calloc( num_at, sizeof(pINChI->nNum_H[0]))) && (pINChI->nNum_H_fixed= (S_CHAR*) inchi_calloc( num_at, sizeof(pINChI->nNum_H_fixed[0]))) ) { ; /* nTautomer length: max. number of tautomeric groups is num_at/2 1 word -> number of t-groups each group has: 1 word -> number of endpoints+INCHI_T_NUM_MOVABLE INCHI_T_NUM_MOVABLE words -> number(s) of moveable attachments numbers of endpoints words -> canon. numbers max. occurs if each t-group has 2 atoms (num_at/2 t-groups) and all atoms belong to t-groups (num_at endpoints) Total: 1 + (number of t-groups)*(1+INCHI_T_NUM_MOVABLE) + (number of endpoints) <= 1 + (num_at/2) * (1+INCHI_T_NUM_MOVABLE) + num_at <= 1 + (3+INCHI_T_NUM_MOVABLE)*num_at/2 words. */ } else { goto out_of_RAM; } pINChI->szHillFormula = NULL; /* the length is unknown */ if ( bIsotopic ) { if ( num_isotopic_atoms && (pINChI->IsotopicAtom = (INChI_IsotopicAtom *)inchi_calloc(num_isotopic_atoms, sizeof(INChI_IsotopicAtom) )) && (pINChI->IsotopicTGroup = (INChI_IsotopicTGroup *)inchi_calloc(num_isotopic_atoms, sizeof(INChI_IsotopicTGroup) )) ) { ; } else if ( num_isotopic_atoms ) { goto out_of_RAM; } if ( !(pINChI->nPossibleLocationsOfIsotopicH = (AT_NUMB *)inchi_calloc( num_at+1, sizeof(pINChI->nPossibleLocationsOfIsotopicH[0]) ) ) ) { goto out_of_RAM; } } if ((pINChI->Stereo = Alloc_INChI_Stereo(num_at, num_bonds)) ) { ; } else { goto out_of_RAM; } if ( bIsotopic ) { if ((pINChI->StereoIsotopic = Alloc_INChI_Stereo(num_at, num_bonds)) ) { ; } else { goto out_of_RAM; } } return pINChI; out_of_RAM: if ( pINChI ) { Free_INChI(&pINChI); /* inchi_free(pINChI); */ } return NULL; } /****************************************************************/ int Free_INChI_Aux( INChI_Aux **ppINChI_Aux ) { INChI_Aux *pINChI_Aux = *ppINChI_Aux; if ( pINChI_Aux ) { #if ( bREUSE_INCHI == 1 ) if ( pINChI_Aux->nRefCount -- > 0 ) return 1; #endif qzfree( pINChI_Aux->nOrigAtNosInCanonOrd ); qzfree( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd ); qzfree( pINChI_Aux->nOrigAtNosInCanonOrdInv ); qzfree( pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv ); qzfree( pINChI_Aux->szOrigCoord ); qzfree( pINChI_Aux->OrigInfo ); /* qzfree( pINChI_Aux->nOriginalAtomNumber ); qzfree( pINChI_Aux->nCanonicalTGroupNumbers ); qzfree( pINChI_Aux->nIsotopicCanonicalTGroupNumbers); qzfree( pINChI_Aux->nTautomer ); qzfree( pINChI_Aux->nNontautomericCanonicalNumbers ); qzfree( pINChI_Aux->nIsotopicCanonicalNumbers ); qzfree( pINChI_Aux->nNontautomericIsotopicCanonicalNumbers ); qzfree( pINChI_Aux->nNontautomericEquNumbers ); qzfree( pINChI_Aux->nNontautomericIsotopicEquNumbers ); */ qzfree( pINChI_Aux->nConstitEquNumbers ); qzfree( pINChI_Aux->nConstitEquTGroupNumbers ); qzfree( pINChI_Aux->nConstitEquIsotopicNumbers ); qzfree( pINChI_Aux->nConstitEquIsotopicTGroupNumbers ); qzfree( pINChI_Aux ); *ppINChI_Aux = NULL; } return 0; } /****************************************************************/ INChI_Aux *Alloc_INChI_Aux( int num_at, int num_isotopic_atoms, int nAllocMode, int bOrigCoord ) { INChI_Aux *pINChI_Aux; int bIsotopic = (nAllocMode & REQ_MODE_ISO); int num_at_tg = num_at + num_at/2; /* int bTautomeric = (nAllocMode & REQ_MODE_TAUT); */ if ( num_at <= 0 || NULL == (pINChI_Aux = (INChI_Aux *)inchi_calloc(sizeof(INChI_Aux), 1))) { return NULL; } if ( (pINChI_Aux->nOrigAtNosInCanonOrd = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nOrigAtNosInCanonOrd[0]), num_at_tg)) && (pINChI_Aux->nOrigAtNosInCanonOrdInv = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nOrigAtNosInCanonOrd[0]), num_at_tg)) && (pINChI_Aux->nConstitEquNumbers = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nConstitEquNumbers[0]), num_at_tg)) ) { ; } else { goto out_of_RAM; } if ( num_at > 1 && (pINChI_Aux->nConstitEquTGroupNumbers = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nConstitEquTGroupNumbers[0]), num_at/2+1)) ) { ; } else if ( num_at > 1 ) { goto out_of_RAM; } if ( num_at > 0 ) { pINChI_Aux->OrigInfo = (ORIG_INFO *)inchi_calloc(sizeof(pINChI_Aux->OrigInfo[0]), num_at); if ( !pINChI_Aux->OrigInfo ) goto out_of_RAM; } if ( bOrigCoord && num_at > 0 ) { pINChI_Aux->szOrigCoord = (MOL_COORD *)inchi_calloc(sizeof(pINChI_Aux->szOrigCoord[0]), num_at); if ( !pINChI_Aux->szOrigCoord ) goto out_of_RAM; } if ( bIsotopic ) { if ( /*num_isotopic_atoms &&*/ (pINChI_Aux->nIsotopicOrigAtNosInCanonOrd = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0]), num_at_tg)) && (pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0]), num_at_tg)) && (pINChI_Aux->nConstitEquIsotopicNumbers = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nConstitEquIsotopicNumbers[0]), num_at_tg)) ) { ; } else if ( num_isotopic_atoms ) { goto out_of_RAM; } if ( /*num_isotopic_atoms && num_at > 1 &&*/ (pINChI_Aux->nConstitEquIsotopicTGroupNumbers = (AT_NUMB*)inchi_calloc(sizeof(pINChI_Aux->nConstitEquIsotopicTGroupNumbers[0]), num_at/2+1)) ) { ; } else if ( num_isotopic_atoms && num_at > 1 ) { goto out_of_RAM; } } return pINChI_Aux; out_of_RAM: if ( pINChI_Aux ) { Free_INChI_Aux(&pINChI_Aux); /* inchi_free(pINChI_Aux); */ } return NULL; } /***********************************************************************************/ #define IS_DEUTERIUM(i) (!strcmp( at[i].elname, "D" ) || at[i].iso_atw_diff == 2 && !strcmp( at[i].elname, "H" )) #define IS_TRITIUM(i) (!strcmp( at[i].elname, "T" ) || at[i].iso_atw_diff == 3 && !strcmp( at[i].elname, "H" )) #define ABNORMAL_ISO(i) (at[i].iso_atw_diff == 1 || at[i].iso_atw_diff < -3 || at[i].iso_atw_diff > 5 ) #define ABNORMAL_CHG(i) (abs(at[i].charge) > 3) #define ABNORMAL_RAD(i) (RADICAL_SINGLET <= at[i].radical && at[i].radical <= RADICAL_TRIPLET ) #define ANY_ISO(i, X) ((X)? (at[i].iso_atw_diff && !IS_DEUTERIUM(i) && !IS_TRITIUM(i)) :\ (at[i].iso_atw_diff || IS_DEUTERIUM(i) || IS_TRITIUM(i))) #define ANY_CHG(i) (0 != at[i].charge) #define ANY_RAD(i) (RADICAL_SINGLET <= at[i].radical && at[i].radical <= RADICAL_TRIPLET ) #define NORMAL_ISO(i, X) (ANY_ISO(i, X) && !ABNORMAL_ISO(i)) /* needs additional M CHG. M RAD, M ISO line */ /* due to ISIS/Draw feature always include M RAD for any radical */ #define ABNORMAL_AT(i) ( at[i].radical || abs(at[i].charge) > 3 || \ ABNORMAL_ISO(i) ) /* always add M ISO, M RAD, M CHG; Except: (bAtomsDT && D or T) */ #define ADD_LINE_AT(i) ( at[i].charge || \ at[i].radical || \ at[i].iso_atw_diff && (bAtomsDT? (at[i].iso_atw_diff != 1 || strcmp(at[i].elname, "H")) : 1) ) #define ALIASED_AT(i) (0 < NUM_ISO_H(at, i)) /***********************************************************************************/ #if ( TEST_RENUMB_ATOMS_SAVE_LONGEST == 1 || TEST_RENUMB_SWITCH == 1 ) int WriteToSDfile( const INP_ATOM_DATA *inp_at_data, INCHI_IOSTREAM* fcb, const char* name, const char* comment, const char *szLabel, const char *szValue) { int i, j, k, num_bonds=0, ret=0, bAtomsDT = 1 /* treat D, T as normal atoms */, bV2000 = 0 /*V2000 Molfile */; int bAtomNeedsAlias; int flag_bad_charge=0, flag_bad_iso=0, nNumAddLines=0, nNumIsoLines=0, nNumChargeLines=0, nNumRadicalLines=0, nNumAliasLines=0; int nNumNecessaryIsoLines = 0, nNumNecessaryChgLines = 0, nNumNecessaryRadLines = 0; /*sp_ATOM *at; */ /*float fzero=0.0F;*/ double x, y, z; int bNext /*, s*/; const inp_ATOM *at = inp_at_data->at_fixed_bonds? inp_at_data->at_fixed_bonds : inp_at_data->at; int num_atoms = inp_at_data->num_at; /*at = species->atom;*/ /*inchi_ios_eprint(fcb,"%ld.MOL\n",species->casno);*/ { /* block start */ char strLocName[82]; memset(strLocName, 0, sizeof(strLocName) ); if ( name && *name ) { strncpy( strLocName, name, 80 ); } inchi_ios_print_nodisplay( fcb,"%s\n", strLocName ); } /* block end */ /**********************************************************************/ /** **/ /** Important: Atoms with alias cannot have charge, radical, or **/ /** isotope differences. **/ /** **/ /** Atoms with alias cannot be abnormal. **/ /** **/ /** Abnormal atoms are atoms which need M CHG, M RAD, M ISO **/ /** **/ /**********************************************************************/ /* F10.5 F12.5 I6 IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR inchi_ios_eprint( fcb,"NISTTRANHP09089809272D 1 1.0 0.0 %6ld\n", lEpa);*/ /*^^^ inchi_ios_print_nodisplay( fcb," -%s v%s SDfile Output \n", INCHI_NAME, INCHI_VERSION); Changed 01/10/2009 to conform CTFile specification (by Symyx request)*/ inchi_ios_print_nodisplay( fcb, /* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR*/ " InChIV10 \n"); /*y_fprintf(fcb, " -CPSS- 1213981200n\n");*/ { /*block start*/ char strLocName[82]; memset(strLocName, 0, sizeof(strLocName) ); if ( comment && *comment ) { strncpy( strLocName, comment, 80 ); } inchi_ios_print_nodisplay( fcb,"%s\n", strLocName ); } /*block end*/ for (i=0; i< num_atoms; i++) num_bonds += at[i].valence; num_bonds /= 2; /*find if we need "M CHG", "M RAD", "M ISO" */ for (i=0, nNumAddLines = 0; i < num_atoms; i++) { if ( bAtomNeedsAlias = ALIASED_AT(i) ) { nNumAliasLines += 2 * bAtomNeedsAlias; } else { nNumNecessaryIsoLines += ABNORMAL_ISO(i); nNumNecessaryChgLines += ABNORMAL_CHG(i); nNumNecessaryRadLines += ABNORMAL_RAD(i); nNumIsoLines += ANY_ISO(i, bAtomsDT); nNumChargeLines += ANY_CHG(i); nNumRadicalLines += ANY_RAD(i); } } if ( !bV2000 ) { if ( !nNumNecessaryRadLines && !nNumNecessaryChgLines ) { nNumRadicalLines = 0; nNumChargeLines = 0; } if ( !nNumNecessaryIsoLines ) { nNumIsoLines = 0; } } /* count additional M lines*/ nNumChargeLines = ( nNumChargeLines + 7 ) / 8; nNumRadicalLines = ( nNumRadicalLines + 7 ) / 8; nNumIsoLines = ( nNumIsoLines + 7 ) / 8; nNumAddLines = nNumChargeLines + nNumRadicalLines + nNumIsoLines + nNumAliasLines; /* 1 for M END*/ if ( nNumAddLines || bV2000 ) { nNumAddLines += 1; /* add 1 for "M END" line*/ } /* aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv*/ inchi_ios_print_nodisplay(fcb,"%3d%3d 0 0 0 0 0 0 0 0%3d%s\n",num_atoms, num_bonds, nNumAddLines,nNumAddLines?" V2000":""); /* atoms block*/ for (i=0; i < num_atoms; i++) { char elname[ATOM_EL_LEN]; int iso = 0; int charge = 0; int valence = 0; int nIsotopeH = IS_DEUTERIUM(i)? 1 : IS_TRITIUM(i)? 2 : 0; bAtomNeedsAlias = ALIASED_AT(i); /* Has implicit D and/or T neighbors */ memset( elname, 0, sizeof(elname) ); if ( bAtomNeedsAlias ) { /* alias */ strcpy ( elname, "C" ); } else { /* isotope*/ if ( nIsotopeH ) { strcpy( elname, bAtomsDT? ( nIsotopeH==1? "D" : "T" ) : "H" ); } else { strncpy ( elname, at[i].elname, sizeof(elname)-1 ); } if ( !ABNORMAL_CHG(i) && !ANY_RAD(i) ) { /* charge*/ /* Only atoms without alias can be here*/ switch ( at[i].charge ) { case 3: charge = 1; break; case 2: charge = 2; break; case 1: charge = 3; break; case -1: charge = 5; break; case -2: charge = 6; break; case -3: charge = 7; break; case 0: charge = 0; break; default: flag_bad_charge = 1; break; }; } /* radical*/ if ( ANY_RAD(i) && !ANY_CHG(i) ) { if ( at[i].radical == RADICAL_DOUBLET ) { charge = 4; } } } /* allow isotopic shift for aliased atoms */ if ( NORMAL_ISO(i, bAtomsDT) ) { iso = at[i].iso_atw_diff > 0? at[i].iso_atw_diff-1: at[i].iso_atw_diff < 0? at[i].iso_atw_diff : nIsotopeH? nIsotopeH : (flag_bad_iso ++, 0); } x = at[i].x; y = at[i].y; z = at[i].z; if( at[i].num_H > 0 ) { for ( j = 0, valence = 0; j < at[i].valence; j++ ) { switch( k = at[i].bond_type[j] ) { /* fixed valence calculation 12-23-99 DCh.*/ case 2: case 3: valence += 2*k; break; case 4: valence += 3; break; default: valence += 2; } } valence = valence/2 + at[i].num_H; } else /* Added 07-09-2003 DCh*/ if ( at[i].chem_bonds_valence > 0 ) { valence = at[i].chem_bonds_valence; } else /* Added 07-09-2003 DCh*/ if ( !at[i].valence && !at[i].num_H && !at[i].chem_bonds_valence ) { valence = 15; } /*inchi_ios_eprint(fcb,"%10.4f%10.4f%10.4f %-3.3s%2d%3d 0 0 0 0 0 0 0\n",*/ /* (float)at[i].x, (float)(-at[i].y), fzero, at[i].elname, iso, charge);*/ /* xxxxxxyyyyyyzzzzzz aaa____ddcccsssnnnbbbvvvrrriiimmmeee */ inchi_ios_print_nodisplay(fcb,"%10.4f%10.4f%10.4f %-3.3s%2d%3d 0 0%3d 0 0 0 0\n", x, y, z, elname, (int)iso, (int)charge, valence /* at[i].special*/); /* reflect image against x-axis; when transforming MOLfile back to STDATA in mol_to_stdata(...), make one more reflection to restore original orientation. Reason: in MS Search y-axis is directed from top to bottom, while in MOLfile y-axis goes from bottom to top. */ } bNext = 0; /* debug only*/ /* bonds*/ for (i=0; i< num_atoms; i++) { for (j=0; j 1 ) { sprintf( str_m + strlen(str_m), "%d", num_H ); } } if ( num_H = at[i].num_iso_H[1] ) { /* deuterium */ strcat( str_m, "D" ); if ( num_H > 1 ) { sprintf( str_m + strlen(str_m), "%d", num_H ); } } if ( num_H = at[i].num_iso_H[2] ) { /* Tritium */ strcat( str_m, "T" ); if ( num_H > 1 ) { sprintf( str_m + strlen(str_m), "%d", num_H ); } } /* Add charge to the Alias */ if ( at[i].charge){ strcat(str_m, at[i].charge>0? "+" : "-"); if ( 1 < (j=abs(at[i].charge)) ) sprintf( str_m+strlen(str_m), "%d", j ); } /* Add radical to the Alias */ switch( at[i].radical ) { case RADICAL_SINGLET: strcat( str_m, ":" ); break; case RADICAL_DOUBLET: strcat( str_m, "^" ); break; case RADICAL_TRIPLET: strcat( str_m, "^^" ); break; } inchi_ios_print_nodisplay( fcb, "%s\n", str_m ); num_m ++; } } if ( num_m != nNumAliasLines ) { /* error in lines counting*/ ret ++; } } /* charges*/ str_m[0] = 0; num_m = 0; if ( nNumChargeLines ) { for (i=0; i < num_atoms; i++) { if ( ANY_CHG(i) && !ALIASED_AT(i) ) { sprintf( entry, " %3d %3d", i+1, (int)at[i].charge ); strcat( str_m, entry ); num_m ++; } if ( i == num_atoms-1 && num_m || num_m == 8 ) { inchi_ios_print_nodisplay( fcb, "M CHG%3d%s\n", num_m, str_m ); str_m[0] = 0; num_m = 0; } } } /* radicals*/ str_m[0] = 0; num_m = 0; if ( nNumRadicalLines ) { for (i=0; i < num_atoms; i++) { if ( ANY_RAD(i) && !ALIASED_AT(i) ) { int radical = (at[i].radical==RADICAL_SINGLET || at[i].radical==RADICAL_DOUBLET || at[i].radical==RADICAL_TRIPLET)? at[i].radical : 0; if ( radical ) { sprintf( entry, " %3d %3d", i+1, radical ); strcat( str_m, entry ); num_m ++; } } if ( i == num_atoms-1 && num_m || num_m == 8 ) { inchi_ios_print_nodisplay( fcb, "M RAD%3d%s\n", num_m, str_m ); str_m[0] = 0; num_m = 0; } } } /* isotopes*/ str_m[0] = 0; num_m = 0; if ( nNumIsoLines ) { int el_num, iso; for (i=0; i < num_atoms; i++) { if ( ANY_ISO(i,bAtomsDT) && !ALIASED_AT(i) ) { if ( IS_DEUTERIUM(i) ) { iso = 1; el_num = 1; } else if ( IS_TRITIUM(i) ) { iso = 2; el_num = 1; } else { iso = at[i].iso_atw_diff > 0? at[i].iso_atw_diff-1 : at[i].iso_atw_diff; el_num = at[i].el_number; } iso += get_atw_from_elnum( el_num ); sprintf( entry, " %3d %3d", i+1, iso ); strcat( str_m, entry ); num_m ++; } if ( i == num_atoms-1 && num_m || num_m == 8 ) { inchi_ios_print_nodisplay( fcb, "M ISO%3d%s\n", num_m, str_m ); str_m[0] = 0; num_m = 0; } } } inchi_ios_print_nodisplay( fcb, "M END\n" ); } if ( szValue && szValue[0] ) { if ( szLabel && szLabel[0] ) { inchi_ios_print_nodisplay( fcb, "> <%s>\n", szLabel ); } else { inchi_ios_print_nodisplay( fcb, "> \n" ); } inchi_ios_print_nodisplay( fcb, "%s\n\n", szValue ); } inchi_ios_print_nodisplay(fcb, "$$$$\n"); return ret; } #endif /***************************************************************************************************/ int WriteOrigAtomDataToSDfile(const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM * fcb, const char* name, const char* comment, int bChiralFlag, int bAtomsDT, const char *szLabel, const char *szValue) { int i, j, k, num_bonds=0, ret=0; int bAtomNeedsAlias; int flag_bad_charge=0, flag_bad_iso = 0; int nNumAddLines=0, nNumIsoLines=0, nNumChargeLines=0, nNumRadicalLines=0, nNumAliasLines=0; int nNumNecessaryIsoLines = 0, nNumNecessaryChgLines = 0, nNumNecessaryRadLines = 0; int bV2000 = SDF_OUTPUT_V2000; double x, y, z; int bNext /*, s*/; const inp_ATOM *at = inp_at_data->at; int num_atoms = inp_at_data->num_inp_atoms; /*at = species->atom;*/ /*inchi_ios_eprint(fcb,"%ld.MOL\n",species->casno);*/ { /* block start */ char strLocName[82]; memset(strLocName, 0, sizeof(strLocName) ); if ( name && *name ) { strncpy( strLocName, name, 80 ); /* --- debug only --- if ( strstr( name, "#3959" ) ) { int stop = 1; } */ } inchi_ios_print_nodisplay( fcb,"%s\n", strLocName ); } /* block end */ /**********************************************************************/ /** **/ /** Important: Atoms with alias cannot have charge, radical **/ /** isotope differences are allowed **/ /** **/ /** Atoms with alias cannot be abnormal. **/ /** **/ /** Abnormal atoms are atoms which need M CHG, M RAD, M ISO **/ /** **/ /** Output aliased atoms if they have implicit D or T **/ /** **/ /**********************************************************************/ /* F10.5 F12.5 I6 IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR inchi_ios_eprint( fcb,"NISTTRANHP09089809272D 1 1.0 0.0 %6ld\n", lEpa);*/ /*^^^ inchi_ios_print_nodisplay( fcb," %s v%s SDfile Output \n", INCHI_NAME, INCHI_VERSION); Changed 01/10/2009 to conform CTFile specification (by Symyx request)*/ inchi_ios_print_nodisplay( fcb, /* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR*/ " InChIV10 \n"); /*y_fprintf(fcb, " -CPSS- 1213981200n\n");*/ { /*block start*/ char strLocName[82]; memset(strLocName, 0, sizeof(strLocName) ); if ( comment && *comment ) { strncpy( strLocName, comment, 80 ); } inchi_ios_print_nodisplay( fcb,"%s\n", strLocName ); } /*block end*/ for (i=0; i< num_atoms; i++) num_bonds += at[i].valence; num_bonds /= 2; /*find if we need "M CHG" and "M RAD"*/ for (i=0; i < num_atoms; i++) { if ( bAtomNeedsAlias = ALIASED_AT(i) ) { /* has isotopic implicit D or T; ignoring pure 1H */ nNumAliasLines += 2 * bAtomNeedsAlias; } else { /* abnormal means atom needs CHG, RAD, or ISO entry */ /* nNumAddLines += ABNORMAL_AT(i); */ /* nNumIso += ( 0 == strcmp( at[i].elname, "D" ) || ( 0 == strcmp( at[i].elname, "T" ) || at[i].iso_atw_diff ) ); */ /* nNumAddIso += at[i].iso_atw_diff && (at[i].iso_atw_diff == 1 || at[i].iso_atw_diff < -3 || at[i].iso_atw_diff > 5 ); */ nNumNecessaryIsoLines += ABNORMAL_ISO(i); nNumNecessaryChgLines += ABNORMAL_CHG(i); nNumNecessaryRadLines += ABNORMAL_RAD(i); nNumIsoLines += ANY_ISO(i, bAtomsDT); nNumChargeLines += ANY_CHG(i); nNumRadicalLines += ANY_RAD(i); } } nNumChargeLines = ( nNumChargeLines + 7 ) / 8; nNumRadicalLines = ( nNumRadicalLines + 7 ) / 8; nNumIsoLines = ( nNumIsoLines + 7 ) / 8; if ( !bV2000 ) { if ( !nNumNecessaryRadLines && !nNumNecessaryChgLines ) { nNumRadicalLines = 0; nNumChargeLines = 0; } if ( !nNumNecessaryIsoLines ) { nNumIsoLines = 0; } } /* recalculate number of added lines */ nNumAddLines = nNumChargeLines + nNumRadicalLines + nNumIsoLines + nNumAliasLines; /* 1 for M END*/ if ( nNumAddLines || bV2000 ) { nNumAddLines += 1; /* add 1 for "M END" line*/ } /* aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv*/ inchi_ios_print_nodisplay(fcb,"%3d%3d 0 0%3d 0 0 0 0 0%3d%s\n", num_atoms, num_bonds, bChiralFlag?1:0, nNumAddLines,nNumAddLines?" V2000":""); /* atoms block*/ for (i=0; i < num_atoms; i++) { char elname[ATOM_EL_LEN] = "\0\0\0\0\0"; int iso = 0; int charge = 0; int valence = 0; int nIsotopeH = IS_DEUTERIUM(i)? 1 : IS_TRITIUM(i)? 2 : 0; int bonds_val; bAtomNeedsAlias = ALIASED_AT(i); memset( elname, 0, sizeof(elname) ); if ( bAtomNeedsAlias ) { /* alias */ strcpy ( elname, "C" ); } else { /* isotope*/ if ( nIsotopeH ) { strcpy( elname, bAtomsDT? ( nIsotopeH==1? "D" : "T" ) : "H" ); } else { strncpy ( elname, at[i].elname, sizeof(elname)-1 ); } if ( !ABNORMAL_CHG(i) && !ANY_RAD(i) ) { /* charge*/ /* Only atoms without alias can be here*/ switch ( at[i].charge ) { case 3: charge = 1; break; case 2: charge = 2; break; case 1: charge = 3; break; case -1: charge = 5; break; case -2: charge = 6; break; case -3: charge = 7; break; case 0: charge = 0; break; default: flag_bad_charge = 1; break; }; } /* radical*/ if ( ANY_RAD(i) && !ANY_CHG(i) ) { if ( at[i].radical == RADICAL_DOUBLET ) { charge = 4; } } } /* allow isotopic shift for aliased atoms */ if ( NORMAL_ISO(i, bAtomsDT) ) { iso = at[i].iso_atw_diff > 0? at[i].iso_atw_diff-1: at[i].iso_atw_diff < 0? at[i].iso_atw_diff : nIsotopeH? nIsotopeH : (flag_bad_iso ++, 0); } x = at[i].x; y = at[i].y; z = at[i].z; /* valence -- set only if needed */ bonds_val = nBondsValenceInpAt( at+i, NULL, NULL ); valence=needed_unusual_el_valence( at[i].el_number, at[i].charge, at[i].radical, at[i].chem_bonds_valence, bonds_val, NUMH(at, i), at[i].valence ); if ( valence < 0 ) { valence = 15; /* means no bonds nor H */ } /*inchi_ios_eprint(fcb,"%10.4f%10.4f%10.4f %-3.3s%2d%3d 0 0 0 0 0 0 0\n",*/ /* (float)at[i].x, (float)(-at[i].y), fzero, at[i].elname, iso, charge);*/ /* xxxxxxyyyyyyzzzzzz aaa____ddcccsssnnnbbbvvvrrriiimmmeee */ inchi_ios_print_nodisplay(fcb,"%10.4f%10.4f%10.4f %-3.3s%2d%3d 0 0%3d 0 0 0 0\n", x, y, z, elname, (int)iso, (int)charge, valence /* at[i].special*/); /* reflect image against x-axis; when transforming MOLfile back to STDATA in mol_to_stdata(...), make one more reflection to restore original orientation. Reason: in MS Search y-axis is directed from top to bottom, while in MOLfile y-axis goes from bottom to top. */ } bNext = 0; /* debug only*/ /* bonds*/ for (i=0; i< num_atoms; i++) { for (j=0; j0? "+" : "-"); if ( 1 < (j=abs(at[i].charge)) ) { len += sprintf( str_m+len, "%d", j ); } } /* Add radical to the Alias */ if ( at[i].radical == RADICAL_SINGLET ) { len += sprintf( str_m+len, "%s", ":" ); } else if ( at[i].radical == RADICAL_DOUBLET ) { len += sprintf( str_m+len, "%s", "^" ); } else if ( at[i].radical == RADICAL_TRIPLET ) { len += sprintf( str_m+len, "%s", "^^" ); } inchi_ios_print_nodisplay( fcb, "%s\n", str_m ); num_m ++; } } if ( num_m != nNumAliasLines ) { /* error in lines counting*/ ret ++; } } /* charges*/ str_m[0] = 0; num_m = 0; if ( nNumChargeLines ) { for (i=0; i < num_atoms; i++) { if ( at[i].charge && !ALIASED_AT(i) ) { sprintf( entry, " %3d %3d", i+1, (int)at[i].charge ); strcat( str_m, entry ); num_m ++; } if ( i == num_atoms-1 && num_m || num_m == 8 ) { inchi_ios_print_nodisplay( fcb, "M CHG%3d%s\n", num_m, str_m ); str_m[0] = 0; num_m = 0; } } } /* radicals*/ str_m[0] = 0; num_m = 0; if ( nNumRadicalLines ) { for (i=0; i < num_atoms; i++) { if ( at[i].radical && !ALIASED_AT(i) ) { int radical = (at[i].radical==RADICAL_SINGLET || at[i].radical==RADICAL_DOUBLET || at[i].radical==RADICAL_TRIPLET)? at[i].radical : 0; if ( radical ) { sprintf( entry, " %3d %3d", i+1, radical ); strcat( str_m, entry ); num_m ++; } } if ( i == num_atoms-1 && num_m || num_m == 8 ) { inchi_ios_print_nodisplay( fcb, "M RAD%3d%s\n", num_m, str_m ); str_m[0] = 0; num_m = 0; } } } /* isotopes*/ str_m[0] = 0; num_m = 0; if ( nNumIsoLines ) { int el_num, iso; for (i=0; i < num_atoms; i++) { /* if ( 0 == strcmp( at[i].elname, "D" ) ) { sprintf( entry, " %3d %3d", i+1, 2 ); strcat( str_m, entry ); num_m ++; } else if ( 0 == strcmp( at[i].elname, "T" ) ) { sprintf( entry, " %3d %3d", i+1, 3 ); strcat( str_m, entry ); num_m ++; } else if ( k = at[i].iso_atw_diff ) { int mw = get_atw_from_elnum( at[i].el_number ); mw += (k > 0)? k-1 : k; sprintf( entry, " %3d %3d", i+1, mw ); strcat( str_m, entry ); num_m ++; } */ if ( ANY_ISO(i, bAtomsDT) && !ALIASED_AT(i) ) { if ( IS_DEUTERIUM(i) ) { iso = 1; el_num = 1; } else if ( IS_TRITIUM(i) ) { iso = 2; el_num = 1; } else { iso = at[i].iso_atw_diff > 0? at[i].iso_atw_diff-1 : at[i].iso_atw_diff; el_num = at[i].el_number; } iso += get_atw_from_elnum( el_num ); sprintf( entry, " %3d %3d", i+1, iso ); strcat( str_m, entry ); num_m ++; } if ( i == num_atoms-1 && num_m || num_m == 8 ) { inchi_ios_print_nodisplay( fcb, "M ISO%3d%s\n", num_m, str_m ); str_m[0] = 0; num_m = 0; } } } inchi_ios_print_nodisplay( fcb, "M END\n" ); } if ( szValue && szValue[0] ) { if ( szLabel && szLabel[0] ) { inchi_ios_print_nodisplay( fcb, "> <%s>\n", szLabel ); } else { inchi_ios_print_nodisplay( fcb, "> \n" ); } inchi_ios_print_nodisplay( fcb, " %s\n\n", szValue ); } inchi_ios_print_nodisplay(fcb, "$$$$\n"); return ret; } #if ( FIX_ADJ_RAD == 1 ) /*************************************************************************/ int FixNextRadicals( int cur_at, inp_ATOM *at ); int FixNextRadicals( int cur_at, inp_ATOM *at ) { int j, neigh, num_found = 0; for ( j = 0; j < at[cur_at].valence; j ++ ) { neigh = at[cur_at].neighbor[j]; if ( at[neigh].radical == RADICAL_DOUBLET ) { at[neigh].radical = 0; num_found ++; num_found += FixNextRadicals( neigh, at ); } } return num_found; } /*************************************************************************/ int FixAdjacentRadicals( int num_inp_atoms, inp_ATOM *at ) { int i, j; char *bVisited = NULL; int nNumFound = 0, neigh, cur_found; for ( i = 0; i < num_inp_atoms; i ++ ) { if ( at[i].radical == RADICAL_DOUBLET ) { cur_found = 1; for ( j = 0; j < at[i].valence; j ++ ) { neigh = at[i].neighbor[j]; if ( at[neigh].radical == RADICAL_DOUBLET ) { cur_found ++; } } if ( cur_found >= 3 ) { nNumFound ++; at[i].radical = 0; nNumFound += FixNextRadicals( i, at ); } } } return nNumFound; } #endif #ifdef COMPILE_ANSI_ONLY #ifndef TARGET_API_LIB /* #include #include "inpdef.h" */ void PrintFileName( const char *fmt, FILE *output_file, /* INCHI_IOSTREAM *output_file, */ const char *szFname ) { inchi_print_nodisplay( output_file, fmt, szFname ); } #endif #endif