46d45
<         "  a  Ignore Astex Conect Record Mode\n\n";
71c70
<   static bool parseConectRecord(char *buffer, OBMol & mol, bool IgnoreAstexMode);
---
>   static bool parseConectRecord(char *buffer, OBMol & mol);
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<             parseConectRecord(buffer,mol, pConv->IsOption("a",OBConversion::INOPTIONS));
---
>             parseConectRecord(buffer,mol);
291c290
<   bool parseConectRecord(char *buffer,OBMol &mol, bool IgnoreAstexMode)
---
>   bool parseConectRecord(char *buffer,OBMol &mol)
440d438
< 	if(IgnoreAstexMode){
442,453c440,446
<             unsigned char order = 0;
<             while(     boundedAtomsSerialNumbersValid[k+order+1] 
<                    && (boundedAtomsSerialNumbers[k+order] == boundedAtomsSerialNumbers[k+order+1]) )
<             {
<               order++;
<             }
<             k += order;
< 
<             // Generate the bond
<             mol.AddBond(firstAtom->GetIdx(), connectedAtom->GetIdx(), order+1);
<     	}
< 	else{
---
>         unsigned char order = 0;
>         while(     boundedAtomsSerialNumbersValid[k+order+1] 
>                && (boundedAtomsSerialNumbers[k+order] == boundedAtomsSerialNumbers[k+order+1]) )
>         {
>           order++;
>         }
>         k += order;
456,467c449
< 
< //the astex way: only consider those conect records which have the first index less than the second
<             if(firstAtom->GetIdx() < connectedAtom->GetIdx()){
<                 OBBond *bond = mol.GetBond(firstAtom, connectedAtom);
<                 if(bond){
<                     bond->SetBondOrder(bond->GetBondOrder() + 1);
<                 }
<                 else{
<                     mol.AddBond(firstAtom->GetIdx(), connectedAtom->GetIdx(), 1);
<                 }
<             }
<         }
---
>         mol.AddBond(firstAtom->GetIdx(), connectedAtom->GetIdx(), order+1);