845 int mark_atoms_ap( inp_ATOM *at, AT_NUMB start, R2C_ATPAIR *ap, int num_ap, int num, AT_NUMB cFlags…
901         at[i].cFlags          = 0;  in UnMarkOtherIndicators()
1003 int mark_atoms_ap( inp_ATOM *at, AT_NUMB start, R2C_ATPAIR *ap, int num_ap, int num, AT_NUMB cFlags…  in mark_atoms_ap()  argument
1008         at[start].at_type = cFlags;  in mark_atoms_ap()
1014             num = mark_atoms_ap( at, neigh, ap, num_ap, num, cFlags );  in mark_atoms_ap()
1068 int mark_atoms_cFlags( inp_ATOM *at, int start, int num, char cFlags );
1069 int un_mark_atoms_cFlags( inp_ATOM *at, int start, int num, char cFlags, char cInvFlags );
1072 int is_C_Alk( inp_ATOM *at, int i, char cFlags );
1075 int is_possibly_deriv_neigh( inp_ATOM *at, int iat, int iord, int type, char cFlags );
1076 int get_traversed_deriv_type( inp_ATOM *at, DERIV_AT *da, int k, DERIV_AT *da1, char cFlags );
1078 int mark_atoms_deriv( inp_ATOM *at, DERIV_AT *da, int start, int num, char cFlags, int *pbFound );
1079 int count_one_bond_atoms( inp_ATOM *at, DERIV_AT *da, int start, int ord, char cFlags, int *bFound …
1094 int mark_atoms_cFlags( inp_ATOM *at, int start, int num, char cFlags )  in mark_atoms_cFlags()  argument
1096     if ( !(at[start].cFlags & cFlags) ) {  in mark_atoms_cFlags()
1098         at[start].cFlags |= cFlags;  in mark_atoms_cFlags()
1101             num = mark_atoms_cFlags( at, at[start].neighbor[i], num, cFlags );  in mark_atoms_cFlags()
1108 int un_mark_atoms_cFlags( inp_ATOM *at, int start, int num, char cFlags, char cInvFlags )  in un_mark_atoms_cFlags()  argument
1110     if ( at[start].cFlags & cFlags ) {  in un_mark_atoms_cFlags()
1112         at[start].cFlags &= cInvFlags;  in un_mark_atoms_cFlags()
1115             num = un_mark_atoms_cFlags( at, at[start].neighbor[i], num, cFlags, cInvFlags );  in un_mark_atoms_cFlags()
1164 int is_C_Alk( inp_ATOM *at, int i, char cFlags )  in is_C_Alk()  argument
1172             if ( at[k].cFlags & cFlags )  in is_C_Alk()
1209 int is_possibly_deriv_neigh( inp_ATOM *at, int iat, int iord, int type, char cFlags )  in is_possibly_deriv_neigh()  argument
1231                 is_C_Alk( at, neigh, cFlags ) ||  in is_possibly_deriv_neigh()
1237                 is_C_Alk( at, neigh, cFlags ) ||  in is_possibly_deriv_neigh()
1247 int get_traversed_deriv_type( inp_ATOM *at, DERIV_AT *da, int k, DERIV_AT *da1, char cFlags )  in get_traversed_deriv_type()  argument
1251     if ( at[k].cFlags & cFlags ) {  in get_traversed_deriv_type()
1254     for ( m = 0; m < at[k].valence && !(at[(int)at[k].neighbor[m]].cFlags & cFlags); m ++ )  in get_traversed_deriv_type()
1286         if ( is_possibly_deriv_neigh( at, k, !m, DERIV_BRIDGE_O, cFlags ) ) {  in get_traversed_deriv_type()
1310             if ( is_possibly_deriv_neigh( at, k, (m+1)%3, DERIV_AMINE_tN, cFlags ) ) {  in get_traversed_deriv_type()
1313             if ( is_possibly_deriv_neigh( at, k, (m+2)%3, DERIV_AMINE_tN, cFlags ) ) {  in get_traversed_deriv_type()
1324             if ( rm1 && is_possibly_deriv_neigh( at, k, (m+2)%3, DERIV_AMINE_tN, cFlags ) ) {  in get_traversed_deriv_type()
1327             if ( rm2 && is_possibly_deriv_neigh( at, k, (m+1)%3, DERIV_AMINE_tN, cFlags ) ) {  in get_traversed_deriv_type()
1378             at[k].cFlags |= CFLAG_MARK_BLOCK;  in get_traversed_deriv_type()
1385                 if ( at[j].cFlags & CFLAG_MARK_BLOCK ) {  in get_traversed_deriv_type()
1472 int mark_atoms_deriv( inp_ATOM *at, DERIV_AT *da, int start, int num, char cFlags, int *pbFound )  in mark_atoms_deriv()  argument
1476     if ( !(at[start].cFlags & cFlags) ) {  in mark_atoms_deriv()
1477         if ( DERIV_NOT == get_traversed_deriv_type( at, da, start, &da1, cFlags ) ) {  in mark_atoms_deriv()
1481         at[start].cFlags |= cFlags;  in mark_atoms_deriv()
1489 …         n1 = mark_atoms_deriv( at, da, at[start].neighbor[(int)da1.ord[0]], 0, cFlags, &nFound1 );  in mark_atoms_deriv()
1498 …           n1 = mark_atoms_deriv( at, da, at[start].neighbor[i1=da1.ord[0]], 0, cFlags, &nFound1 );  in mark_atoms_deriv()
1500 …           n2 = mark_atoms_deriv( at, da, at[start].neighbor[i2=da1.ord[1]], 0, cFlags, &nFound2 );  in mark_atoms_deriv()
1523 …        if ( i != da1.ord[0] && i != da1.ord[1] && !(at[at[start].neighbor[i]].cFlags & cFlags) ) {  in mark_atoms_deriv()
1525 …                    n1 = mark_atoms_deriv( at, da, at[start].neighbor[i1=i], 0, cFlags, &nFound1 );  in mark_atoms_deriv()
1527 …                    n2 = mark_atoms_deriv( at, da, at[start].neighbor[i2=i], 0, cFlags, &nFound2 );  in mark_atoms_deriv()
1554             num = mark_atoms_deriv( at, da, at[start].neighbor[i], num, cFlags, pbFound );  in mark_atoms_deriv()
1563 int count_one_bond_atoms( inp_ATOM *at, DERIV_AT *da, int start, int ord, char cFlags, int *bFound )  in count_one_bond_atoms()  argument
1566     if ( !(at[at[start].neighbor[ord]].cFlags & cFlags) ) {  in count_one_bond_atoms()
1567         at[at[start].neighbor[ord]].cFlags |= cFlags;  in count_one_bond_atoms()
1569         num = mark_atoms_deriv( at, da, start, num, cFlags, bFound );   in count_one_bond_atoms()