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/********************************************************************** |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004 by Chris Morley |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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//Contains SMIFormat and FIXFormat classes |
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// TODO: Rewrite. Use std::string in place of char * to avoid buffer overflow |
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// use std::string::reserve (or different allocator) to avoid resize slowdown |
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|
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#include "mol.hpp" |
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#include "obconversion.hpp" |
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#include "obmolecformat.hpp" |
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|
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using namespace std; |
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|
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namespace OpenBabel |
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{ |
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class SMIFormat : public OBMoleculeFormat |
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{ |
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public: |
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//Register this format type ID |
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SMIFormat() |
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{ |
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OBConversion::RegisterFormat("smi",this, "chemical/x-daylight-smiles"); |
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OBConversion::RegisterOptionParam("n", this); |
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OBConversion::RegisterOptionParam("t", this); |
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} |
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|
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virtual const char* GetMIMEType() |
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{ return "chemical/x-daylight-smiles"; }; |
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|
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//////////////////////////////////////////////////// |
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/// The "API" interface functions |
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virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv); |
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virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
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|
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/////////////////////////////////////////////////////// |
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|
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virtual const char* Description() |
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{ |
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return |
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"SMILES format\n \ |
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A linear text format which can describe the connectivity\n \ |
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and chirality of a molecule\n \ |
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Write Options e.g. -xt\n \ |
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-n no molecule name\n \ |
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-t molecule name only\n \ |
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-r radicals lower case eg ethyl is Cc\n\n"; |
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}; |
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|
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virtual unsigned int Flags() { return DEFAULTFORMAT;}; |
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virtual const char* TargetClassDescription(){return OBMol::ClassDescription();}; |
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|
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virtual const char* SpecificationURL() |
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{return "http://www.daylight.com/smiles/f_smiles.html";}; |
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|
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virtual int SkipObjects(int n, OBConversion* pConv) |
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{ |
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if(n==0) return 1; //already points after current line |
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string temp; |
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istream& ifs = *pConv->GetInStream(); |
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int i; |
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for(i=0;i<n && ifs.good();i++) |
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getline(ifs, temp); |
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return ifs.good() ? 1 : -1; |
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}; |
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}; |
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|
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//Make an instance of the format class |
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SMIFormat theSMIFormat; |
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|
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////////////////////////////////////////////////////////////////// |
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class OBSmiNode |
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{ |
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OBAtom *_atom,*_parent; |
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std::vector<OBSmiNode*> _nextnode; |
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std::vector<OBBond*> _nextbond; |
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public: |
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OBSmiNode(OBAtom *atom); |
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~OBSmiNode(); |
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int Size() |
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{ |
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return((_nextnode.empty())?0:_nextnode.size()); |
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} |
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void SetParent(OBAtom *a) |
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{ |
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_parent = a; |
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} |
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void SetNextNode(OBSmiNode*,OBBond*); |
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OBAtom *GetAtom() |
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{ |
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return(_atom); |
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} |
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OBAtom *GetParent() |
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{ |
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return(_parent); |
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} |
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OBAtom *GetNextAtom(int i) |
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{ |
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return(_nextnode[i]->GetAtom()); |
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} |
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OBBond *GetNextBond(int i) |
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{ |
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return(_nextbond[i]); |
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} |
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OBSmiNode *GetNextNode(int i) |
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{ |
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return(_nextnode[i]); |
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} |
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}; |
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|
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class OBMol2Smi |
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{ |
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std::vector<int> _atmorder; |
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std::vector<int> _storder; |
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std::vector<bool> _aromNH; |
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OBBitVec _uatoms,_ubonds; |
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std::vector<OBEdgeBase*> _vclose; |
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std::vector<std::pair<OBAtom*,std::pair<int,int> > > _vopen; |
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OBConversion* _pconv; |
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public: |
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OBMol2Smi() |
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{ |
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_vclose.clear(); |
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} |
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~OBMol2Smi() |
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{} |
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int GetUnusedIndex(); |
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void Init(OBConversion* pconv=NULL); |
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void CreateSmiString(OBMol&,char*); |
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void GetClosureAtoms(OBAtom*,std::vector<OBNodeBase*>&); |
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void FindClosureBonds(OBMol&); |
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void ToSmilesString(OBSmiNode *node,char *buffer); |
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void RemoveUsedClosures(); |
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void AssignCisTrans(OBSmiNode*); |
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bool BuildTree(OBSmiNode*); |
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bool GetSmilesElement(OBSmiNode*,char*); |
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bool GetChiralStereo(OBSmiNode*,char*); |
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void CorrectAromaticAmineCharge(OBMol&); |
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std::vector<std::pair<int,OBBond*> > GetClosureDigits(OBAtom*); |
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std::vector<int> &GetOutputOrder() |
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{ |
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return(_atmorder); |
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} |
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}; |
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|
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bool WriteTheSmiles(OBMol & mol,char *out); |
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|
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///////////////////////////////////////////////////////////////// |
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class OBSmilesParser |
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{ |
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int _bondflags; |
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int _order; |
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int _prev; |
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char *_ptr; |
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vector<int> _vprev; |
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vector<vector<int> > _rclose; |
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vector<vector<int> > _extbond; |
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vector<int> _path; |
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vector<bool> _avisit; |
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vector<bool> _bvisit; |
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char _buffer[BUFF_SIZE]; |
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bool chiralWatch; // set when a chiral atom is read |
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map<OBAtom*,OBChiralData*> _mapcd; // map of ChiralAtoms and their data |
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public: |
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|
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OBSmilesParser() { } |
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~OBSmilesParser() { } |
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|
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bool SmiToMol(OBMol&,string&); |
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bool ParseSmiles(OBMol&); |
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bool ParseSimple(OBMol&); |
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bool ParseComplex(OBMol&); |
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bool ParseRingBond(OBMol&); |
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bool ParseExternalBond(OBMol&); |
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bool CapExternalBonds(OBMol &mol); |
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void FindAromaticBonds(OBMol &mol,OBAtom*,int); |
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void FindAromaticBonds(OBMol&); |
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void FindOrphanAromaticAtoms(OBMol &mol); //CM 18 Sept 2003 |
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}; |
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|
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///////////////////////////////////////////////////////////////// |
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bool SMIFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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|
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//Define some references so we can use the old parameter names |
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istream &ifs = *pConv->GetInStream(); |
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OBMol &mol = *pmol; |
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const char* title = pConv->GetTitle(); |
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|
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//Taken unchanged from ReadSmiles |
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char buffer[BUFF_SIZE]; |
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|
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if (!ifs.getline(buffer,BUFF_SIZE)) |
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return(false); |
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vector<string> vs; |
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tokenize(vs,buffer); |
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|
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// RWT 10/3/2000 |
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// |
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// added the following to allow spaces in compound names (titles). |
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// Essentially everything after the first space on a SMILES file line |
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// is treated as the name. |
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// Also had to change the condition a few lines below from: |
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// if (vs.size() == 2) ... to |
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// if (vs.size() >= 2) |
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|
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if (vs.size() > 2) |
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{ |
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for (unsigned int i=2;i<vs.size(); i++) |
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{ |
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vs[1]=vs[1]+" "+vs[i]; |
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} |
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} |
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|
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if (vs.empty()) |
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return false; |
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mol.SetDimension(0); |
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|
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if (vs.size() >= 2) |
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mol.SetTitle(vs[1].c_str()); |
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else |
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mol.SetTitle(title); |
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|
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OBSmilesParser sp; |
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return sp.SmiToMol(mol,vs[0]); |
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} |
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|
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////////////////////////////////////////////////// |
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bool SMIFormat::WriteMolecule(OBBase* pOb,OBConversion* pConv) |
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{ |
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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|
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//Define some references so we can use the old parameter names |
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ostream &ofs = *pConv->GetOutStream(); |
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OBMol &mol = *pmol; |
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|
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if(pConv->IsOption("t")) //Title only option |
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{ |
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ofs << mol.GetTitle() <<endl; |
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return true; |
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} |
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char buffer[BUFF_SIZE]; |
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*buffer='\0'; //empty buffer |
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|
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// This is a hack to prevent recursion problems. |
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// we still need to fix the underlying problem (mainly chiral centers) -GRH |
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if (mol.NumAtoms() > 1000) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << "SMILES Conversion failed: Molecule is too large to convert. Open Babel is currently limited to 1000 atoms." << endl; |
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errorMsg << " Molecule size: " << mol.NumAtoms() << " atoms " << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obWarning); |
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return(false); |
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} |
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|
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if(mol.NumAtoms()!=0) |
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{ |
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OBMol2Smi m2s; |
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m2s.Init(pConv); |
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m2s.CorrectAromaticAmineCharge(mol); |
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m2s.CreateSmiString(mol,buffer); |
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} |
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|
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ofs << buffer ; |
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if(!pConv->IsOption("n")) |
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ofs << '\t' << mol.GetTitle(); |
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ofs << endl; |
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|
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return true; |
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} |
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|
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////////////////////////////////////////////// |
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|
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//CM not needed extern OBAromaticTyper aromtyper; |
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//OBAtomTyper atomtyperx; //CM |
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|
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bool OBSmilesParser::SmiToMol(OBMol &mol,string &s) |
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{ |
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strncpy(_buffer,s.c_str(), BUFF_SIZE); |
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_buffer[BUFF_SIZE - 1] = '\0'; |
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|
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_vprev.clear(); |
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_rclose.clear(); |
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_prev=0; |
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chiralWatch=false; |
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|
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if (!ParseSmiles(mol)) |
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{ |
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mol.Clear(); |
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return(false); |
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} |
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|
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// SMILES always sets formal charges -- don't throw them away |
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mol.SetAutomaticFormalCharge(false); |
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|
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return(true); |
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} |
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|
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bool OBSmilesParser::ParseSmiles(OBMol &mol) |
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{ |
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mol.BeginModify(); |
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|
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for (_ptr=_buffer;*_ptr;_ptr++) |
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{ |
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if (isspace(*_ptr)) |
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continue; |
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else if (isdigit(*_ptr) || *_ptr == '%') //ring open/close |
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{ |
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if (!ParseRingBond(mol)) |
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return false; |
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continue; |
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} |
| 328 |
else if(*_ptr == '&') //external bond |
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{ |
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ParseExternalBond(mol); |
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continue; |
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} |
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else |
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switch(*_ptr) |
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{ |
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case '.': |
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_prev=0; |
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break; |
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case '(': |
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_vprev.push_back(_prev); |
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break; |
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case ')': |
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if(_vprev.empty()) //CM |
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return false; |
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_prev = _vprev.back(); |
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_vprev.pop_back(); |
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break; |
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case '[': |
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if (!ParseComplex(mol)) |
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{ |
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mol.EndModify(); |
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mol.Clear(); |
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return(false); |
| 354 |
} |
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break; |
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case '-': |
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_order = 1; |
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break; |
| 359 |
case '=': |
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_order = 2; |
| 361 |
break; |
| 362 |
case '#': |
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_order = 3; |
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break; |
| 365 |
case ':': |
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_order = 5; |
| 367 |
break; |
| 368 |
case '/': |
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_bondflags |= OB_TORUP_BOND; |
| 370 |
break; |
| 371 |
case '\\': |
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_bondflags |= OB_TORDOWN_BOND; |
| 373 |
break; |
| 374 |
default: |
| 375 |
if (!ParseSimple(mol)) |
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{ |
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mol.EndModify(); |
| 378 |
mol.Clear(); |
| 379 |
return(false); |
| 380 |
} |
| 381 |
} // end switch |
| 382 |
} // end for _ptr |
| 383 |
|
| 384 |
// place dummy atoms for each unfilled external bond |
| 385 |
if(!_extbond.empty()) |
| 386 |
CapExternalBonds(mol); |
| 387 |
|
| 388 |
//set aromatic bond orders |
| 389 |
mol.SetAromaticPerceived(); |
| 390 |
FindAromaticBonds(mol); |
| 391 |
FindOrphanAromaticAtoms(mol);// CM 18 Sept 2003 |
| 392 |
mol.AssignSpinMultiplicity(); |
| 393 |
mol.UnsetAromaticPerceived(); |
| 394 |
|
| 395 |
mol.EndModify(); |
| 396 |
|
| 397 |
//NE add the OBChiralData stored inside the _mapcd to the atoms now after end |
| 398 |
// modify so they don't get lost. |
| 399 |
if(_mapcd.size()>0) |
| 400 |
{ |
| 401 |
OBAtom* atom; |
| 402 |
OBChiralData* cd; |
| 403 |
map<OBAtom*,OBChiralData*>::iterator ChiralSearch; |
| 404 |
for(ChiralSearch=_mapcd.begin();ChiralSearch!=_mapcd.end();ChiralSearch++) |
| 405 |
{ |
| 406 |
atom=ChiralSearch->first; |
| 407 |
cd=ChiralSearch->second; |
| 408 |
atom->SetData(cd); |
| 409 |
} |
| 410 |
} |
| 411 |
|
| 412 |
return(true); |
| 413 |
} |
| 414 |
|
| 415 |
// CM 18 Sept 2003 |
| 416 |
void OBSmilesParser::FindOrphanAromaticAtoms(OBMol &mol) |
| 417 |
{ |
| 418 |
//Facilitates the use lower case shorthand for radical entry |
| 419 |
//Atoms which are marked as aromatic but have no aromatic bonds |
| 420 |
//are taken to be radical centres |
| 421 |
OBAtom *atom; |
| 422 |
vector<OBNodeBase*>::iterator j; |
| 423 |
|
| 424 |
for (atom = mol.BeginAtom(j);atom;atom = mol.NextAtom(j)) |
| 425 |
if(atom->IsAromatic()) |
| 426 |
{ |
| 427 |
if(atom->CountBondsOfOrder(5)<2) //bonds order 5 set in FindAromaticBonds() |
| 428 |
//not proper aromatic atoms - could be conjugated chain or radical centre |
| 429 |
atom->UnsetAromatic(); |
| 430 |
else |
| 431 |
{ |
| 432 |
//recognized as aromatic, so are not radicals |
| 433 |
atom->SetSpinMultiplicity(0); |
| 434 |
} |
| 435 |
} |
| 436 |
} |
| 437 |
|
| 438 |
void OBSmilesParser::FindAromaticBonds(OBMol &mol) |
| 439 |
{ |
| 440 |
_path.clear(); |
| 441 |
_avisit.clear(); |
| 442 |
_bvisit.clear(); |
| 443 |
_avisit.resize(mol.NumAtoms()+1); |
| 444 |
_bvisit.resize(mol.NumBonds()); |
| 445 |
_path.resize(mol.NumAtoms()+1); |
| 446 |
|
| 447 |
OBBond *bond; |
| 448 |
vector<OBEdgeBase*>::iterator i; |
| 449 |
for (bond = mol.BeginBond(i);bond;bond = mol.NextBond(i)) |
| 450 |
if (!bond->GetBeginAtom()->IsAromatic() || |
| 451 |
!bond->GetEndAtom()->IsAromatic()) |
| 452 |
_bvisit[bond->GetIdx()] = true; |
| 453 |
|
| 454 |
OBAtom *atom; |
| 455 |
vector<OBNodeBase*>::iterator j; |
| 456 |
|
| 457 |
for (atom = mol.BeginAtom(j);atom;atom = mol.NextAtom(j)) |
| 458 |
if(!_avisit[atom->GetIdx()] && atom->IsAromatic()) |
| 459 |
FindAromaticBonds(mol,atom,0); |
| 460 |
} |
| 461 |
|
| 462 |
void OBSmilesParser::FindAromaticBonds(OBMol &mol,OBAtom *atom,int depth ) |
| 463 |
{ |
| 464 |
OBBond *bond; |
| 465 |
vector<OBEdgeBase*>::iterator k; |
| 466 |
|
| 467 |
if (_avisit[atom->GetIdx()]) |
| 468 |
{ |
| 469 |
int j = depth-1; |
| 470 |
bond=mol.GetBond(_path[j--]); |
| 471 |
bond->SetBO(5); |
| 472 |
while( j >= 0 ) |
| 473 |
{ |
| 474 |
bond=mol.GetBond(_path[j--]); |
| 475 |
bond->SetBO(5); |
| 476 |
if(bond->GetBeginAtom() == atom || bond->GetEndAtom() == atom) |
| 477 |
break; |
| 478 |
} |
| 479 |
} |
| 480 |
else |
| 481 |
{ |
| 482 |
_avisit[atom->GetIdx()] = true; |
| 483 |
for(bond = atom->BeginBond(k);bond;bond = atom->NextBond(k)) |
| 484 |
if( !_bvisit[bond->GetIdx()]) |
| 485 |
{ |
| 486 |
_path[depth] = bond->GetIdx(); |
| 487 |
_bvisit[bond->GetIdx()] = true; |
| 488 |
FindAromaticBonds(mol,bond->GetNbrAtom(atom),depth+1); |
| 489 |
} |
| 490 |
} |
| 491 |
} |
| 492 |
|
| 493 |
|
| 494 |
bool OBSmilesParser::ParseSimple(OBMol &mol) |
| 495 |
{ |
| 496 |
char symbol[3]; |
| 497 |
int element; |
| 498 |
bool arom=false; |
| 499 |
memset(symbol,'\0',sizeof(char)*3); |
| 500 |
|
| 501 |
if (isupper(*_ptr)) |
| 502 |
switch(*_ptr) |
| 503 |
{ |
| 504 |
case 'C': |
| 505 |
_ptr++; |
| 506 |
if (*_ptr == 'l') |
| 507 |
{ |
| 508 |
strcpy(symbol,"Cl"); |
| 509 |
element = 17; |
| 510 |
} |
| 511 |
else |
| 512 |
{ |
| 513 |
symbol[0] = 'C'; |
| 514 |
element = 6; |
| 515 |
_ptr--; |
| 516 |
} |
| 517 |
break; |
| 518 |
|
| 519 |
case 'N': |
| 520 |
element = 7; |
| 521 |
symbol[0] = 'N'; |
| 522 |
break; |
| 523 |
case 'O': |
| 524 |
element = 8; |
| 525 |
symbol[0] = 'O'; |
| 526 |
break; |
| 527 |
case 'S': |
| 528 |
element = 16; |
| 529 |
symbol[0] = 'S'; |
| 530 |
break; |
| 531 |
case 'P': |
| 532 |
element = 15; |
| 533 |
symbol[0] = 'P'; |
| 534 |
break; |
| 535 |
case 'F': |
| 536 |
element = 9; |
| 537 |
symbol[0] = 'F'; |
| 538 |
break; |
| 539 |
case 'I': |
| 540 |
element = 53; |
| 541 |
symbol[0] = 'I'; |
| 542 |
break; |
| 543 |
|
| 544 |
case 'B': |
| 545 |
_ptr++; |
| 546 |
if (*_ptr == 'r') |
| 547 |
{ |
| 548 |
element = 35; |
| 549 |
strcpy(symbol,"Br"); |
| 550 |
} |
| 551 |
else |
| 552 |
{ |
| 553 |
element = 5; |
| 554 |
symbol[0] = 'B'; |
| 555 |
_ptr--; |
| 556 |
} |
| 557 |
break; |
| 558 |
default: |
| 559 |
return(false); |
| 560 |
} |
| 561 |
else |
| 562 |
{ |
| 563 |
arom = true; |
| 564 |
switch(*_ptr) |
| 565 |
{ |
| 566 |
case 'c': |
| 567 |
element = 6; |
| 568 |
symbol[0] = 'C'; |
| 569 |
break; |
| 570 |
case 'n': |
| 571 |
element = 7; |
| 572 |
symbol[0] = 'N'; |
| 573 |
break; |
| 574 |
case 'o': |
| 575 |
element = 8; |
| 576 |
symbol[0] = 'O'; |
| 577 |
break; |
| 578 |
case 'p': |
| 579 |
element = 15; |
| 580 |
symbol[0] = 'P'; |
| 581 |
break; |
| 582 |
case 's': |
| 583 |
element = 16; |
| 584 |
symbol[0] = 'S'; |
| 585 |
break; |
| 586 |
case '*': |
| 587 |
element = 0; |
| 588 |
strcpy(symbol,"Du"); |
| 589 |
break; |
| 590 |
default: |
| 591 |
return(false); |
| 592 |
} |
| 593 |
} |
| 594 |
|
| 595 |
OBAtom *atom = mol.NewAtom(); |
| 596 |
atom->SetAtomicNum(element); |
| 597 |
atom->SetType(symbol); |
| 598 |
if (arom) |
| 599 |
{ |
| 600 |
atom->SetAromatic(); |
| 601 |
atom->SetSpinMultiplicity(2); // CM 18 Sept 2003 |
| 602 |
} |
| 603 |
|
| 604 |
if (_prev) //need to add bond |
| 605 |
{ |
| 606 |
/* CM 18 Sept 2003 |
| 607 |
An extension to the SMILES format has been added so that lower case c,n,o can |
| 608 |
represent a radical centre: CcC is isopropyl radical; |
| 609 |
and cccc... a carbon chain bonded by conjugated double bonds. |
| 610 |
Fails sometimes when using c as both aromatic and as the extened form. |
| 611 |
For benzyl radical C6H5CH2. c1ccccc1c is ok; c1cc(c)ccc1 fails. |
| 612 |
Radical centres should not be involved in ring closure: |
| 613 |
for cyclohexyl radical C1cCCCC1 is ok, c1CCCCC1 is not. |
| 614 |
|
| 615 |
Implementation |
| 616 |
Atoms c,n,o, etc initially added as a radical centre |
| 617 |
unless _prev is a radical centre when both are made a normal atoms |
| 618 |
connected by a double bond. |
| 619 |
Since they are still marked as aromatic, FindAromaticBonds() will |
| 620 |
replace the bonds by aromatic bonds if they are in a ring. |
| 621 |
FindOrphanAromand removes the aromatic tag from the atoms not found in this way |
| 622 |
and removes stray radical centres in . |
| 623 |
|
| 624 |
To avoid difficulties in complex aromatics with 5 membered rings containing N and O, |
| 625 |
the above scheme modified to prevent recognition of aromatic structures is not confused. |
| 626 |
- the double bond is made single if it would exceed valence of atom (not all aromatics have conjugated bonds) |
| 627 |
- the radical centre is removed on both atoms when forming a ring (in ParseRingBond()) |
| 628 |
and on the new atom if the valence of the prev atom is being exceeded. |
| 629 |
Note that the bond orders made here are reassigned in aromatic structures in FindAromaticBonds() |
| 630 |
*/ |
| 631 |
if(arom) |
| 632 |
{ |
| 633 |
OBAtom* prevatom = mol.GetAtom(_prev); |
| 634 |
|
| 635 |
//Calculate available valency on prevatom |
| 636 |
//This is far more difficult than it should be! |
| 637 |
//Data not always updated during molecule constuction. |
| 638 |
int val=0; |
| 639 |
if(prevatom->IsCarbon()) |
| 640 |
val=4; |
| 641 |
else if(prevatom->IsNitrogen()) |
| 642 |
val=3; |
| 643 |
else if(prevatom->IsPhosphorus()) |
| 644 |
val=3; |
| 645 |
else if(prevatom->IsOxygen()) |
| 646 |
val=2; |
| 647 |
else if(prevatom->IsSulfur()) |
| 648 |
val=2; |
| 649 |
|
| 650 |
/* int sumBO=0; |
| 651 |
vector<OBEdgeBase*>::iterator itr; |
| 652 |
OBBond* bond = prevatom->BeginBond(itr); |
| 653 |
while(bond) |
| 654 |
{ |
| 655 |
sumBO +=bond->GetBO(); |
| 656 |
bond=prevatom->NextBond(itr); |
| 657 |
} |
| 658 |
if(prevatom->BOSum() != sumBO) |
| 659 |
cerr << "BOSum != sumBO" << endl; |
| 660 |
*/ |
| 661 |
int AvailableValence = val + prevatom->GetFormalCharge() - prevatom->BOSum();//sumBO; |
| 662 |
|
| 663 |
if (prevatom->GetSpinMultiplicity()) |
| 664 |
{ |
| 665 |
prevatom->SetSpinMultiplicity(0); |
| 666 |
atom->SetSpinMultiplicity(0); |
| 667 |
|
| 668 |
//Make the new bond potentially aromatic, unless a double |
| 669 |
// bond might be impossible given the valence |
| 670 |
_order = AvailableValence>=2 ? 5 : 1 ; |
| 671 |
} |
| 672 |
else |
| 673 |
if(AvailableValence<1) //Must be complex aromatic with O, N |
| 674 |
atom->SetSpinMultiplicity(0); //radical centres not appropriate in complex aromatics |
| 675 |
} |
| 676 |
// CM end |
| 677 |
mol.AddBond(_prev,mol.NumAtoms(),_order,_bondflags); |
| 678 |
|
| 679 |
//NE iterate through and see if atom is bonded to chiral atom |
| 680 |
map<OBAtom*,OBChiralData*>::iterator ChiralSearch; |
| 681 |
ChiralSearch=_mapcd.find(mol.GetAtom(_prev)); |
| 682 |
if (ChiralSearch!=_mapcd.end() && ChiralSearch->second != NULL) |
| 683 |
{ |
| 684 |
(ChiralSearch->second)->AddAtomRef(mol.NumAtoms(), input); |
| 685 |
// cout << "Line 650: Adding "<<mol.NumAtoms()<<" to "<<ChiralSearch->second<<endl; |
| 686 |
} |
| 687 |
} |
| 688 |
//set values |
| 689 |
_prev = mol.NumAtoms(); |
| 690 |
_order = 1; |
| 691 |
_bondflags = 0; |
| 692 |
|
| 693 |
return(true); |
| 694 |
} |
| 695 |
|
| 696 |
bool OBSmilesParser::ParseComplex(OBMol &mol) |
| 697 |
{ |
| 698 |
char symbol[7]; |
| 699 |
int element=0; |
| 700 |
int isotope=0; |
| 701 |
int isoPtr=0; |
| 702 |
bool arom=false; |
| 703 |
memset(symbol,'\0',sizeof(char)*7); |
| 704 |
|
| 705 |
_ptr++; |
| 706 |
|
| 707 |
//grab isotope information |
| 708 |
for (;*_ptr && isdigit(*_ptr) && (isoPtr <= 6); _ptr++) |
| 709 |
{ |
| 710 |
symbol[isoPtr] = *_ptr; |
| 711 |
isoPtr++; |
| 712 |
} |
| 713 |
if (isoPtr >= 6) |
| 714 |
return false; |
| 715 |
isotope = atoi(symbol); |
| 716 |
|
| 717 |
//parse element data |
| 718 |
if (isupper(*_ptr)) |
| 719 |
switch(*_ptr) |
| 720 |
{ |
| 721 |
case 'C': |
| 722 |
_ptr++; |
| 723 |
switch(*_ptr) |
| 724 |
{ |
| 725 |
case 'a': |
| 726 |
element = 20; |
| 727 |
strcpy(symbol,"Ca"); |
| 728 |
break; |
| 729 |
case 'd': |
| 730 |
element = 48; |
| 731 |
strcpy(symbol,"Cd"); |
| 732 |
break; |
| 733 |
case 'e': |
| 734 |
element = 58; |
| 735 |
strcpy(symbol,"Ce"); |
| 736 |
break; |
| 737 |
case 'f': |
| 738 |
element = 98; |
| 739 |
strcpy(symbol,"Cf"); |
| 740 |
break; |
| 741 |
case 'l': |
| 742 |
element = 17; |
| 743 |
strcpy(symbol,"Cl"); |
| 744 |
break; |
| 745 |
case 'm': |
| 746 |
element = 96; |
| 747 |
strcpy(symbol,"Cm"); |
| 748 |
break; |
| 749 |
case 'o': |
| 750 |
element = 27; |
| 751 |
strcpy(symbol,"Co"); |
| 752 |
break; |
| 753 |
case 'r': |
| 754 |
element = 24; |
| 755 |
strcpy(symbol,"Cr"); |
| 756 |
break; |
| 757 |
case 's': |
| 758 |
element = 55; |
| 759 |
strcpy(symbol,"Cs"); |
| 760 |
break; |
| 761 |
case 'u': |
| 762 |
element = 29; |
| 763 |
strcpy(symbol,"Cu"); |
| 764 |
break; |
| 765 |
default: |
| 766 |
element = 6; |
| 767 |
symbol[0] = 'C'; |
| 768 |
_ptr--; |
| 769 |
} |
| 770 |
break; |
| 771 |
|
| 772 |
case 'N': |
| 773 |
_ptr++; |
| 774 |
switch(*_ptr) |
| 775 |
{ |
| 776 |
case 'a': |
| 777 |
element = 11; |
| 778 |
strcpy(symbol,"Na"); |
| 779 |
break; |
| 780 |
case 'b': |
| 781 |
element = 41; |
| 782 |
strcpy(symbol,"Nb"); |
| 783 |
break; |
| 784 |
case 'd': |
| 785 |
element = 60; |
| 786 |
strcpy(symbol,"Nd"); |
| 787 |
break; |
| 788 |
case 'e': |
| 789 |
element = 10; |
| 790 |
strcpy(symbol,"Ne"); |
| 791 |
break; |
| 792 |
case 'i': |
| 793 |
element = 28; |
| 794 |
strcpy(symbol,"Ni"); |
| 795 |
break; |
| 796 |
case 'o': |
| 797 |
element = 102; |
| 798 |
strcpy(symbol,"No"); |
| 799 |
break; |
| 800 |
case 'p': |
| 801 |
element = 93; |
| 802 |
strcpy(symbol,"Np"); |
| 803 |
break; |
| 804 |
default: |
| 805 |
element = 7; |
| 806 |
symbol[0] = 'N'; |
| 807 |
_ptr--; |
| 808 |
} |
| 809 |
break; |
| 810 |
|
| 811 |
case('O'): |
| 812 |
_ptr++; |
| 813 |
if(*_ptr == 's') |
| 814 |
{ |
| 815 |
element = 76; |
| 816 |
strcpy(symbol,"Os"); |
| 817 |
} |
| 818 |
else |
| 819 |
{ |
| 820 |
element = 8; |
| 821 |
symbol[0] = 'O'; |
| 822 |
_ptr--; |
| 823 |
} |
| 824 |
break; |
| 825 |
|
| 826 |
case 'P': |
| 827 |
_ptr++; |
| 828 |
switch(*_ptr) |
| 829 |
{ |
| 830 |
case 'a': |
| 831 |
element = 91; |
| 832 |
strcpy(symbol,"Pa"); |
| 833 |
break; |
| 834 |
case 'b': |
| 835 |
element = 82; |
| 836 |
strcpy(symbol,"Pb"); |
| 837 |
break; |
| 838 |
case 'd': |
| 839 |
element = 46; |
| 840 |
strcpy(symbol,"Pd"); |
| 841 |
break; |
| 842 |
case 'm': |
| 843 |
element = 61; |
| 844 |
strcpy(symbol,"Pm"); |
| 845 |
break; |
| 846 |
case 'o': |
| 847 |
element = 84; |
| 848 |
strcpy(symbol,"Po"); |
| 849 |
break; |
| 850 |
case 'r': |
| 851 |
element = 59; |
| 852 |
strcpy(symbol,"Pr"); |
| 853 |
break; |
| 854 |
case 't': |
| 855 |
element = 78; |
| 856 |
strcpy(symbol,"Pt"); |
| 857 |
break; |
| 858 |
case 'u': |
| 859 |
element = 94; |
| 860 |
strcpy(symbol,"Pu"); |
| 861 |
break; |
| 862 |
default: |
| 863 |
element = 15; |
| 864 |
symbol[0] = 'P'; |
| 865 |
_ptr--; |
| 866 |
} |
| 867 |
break; |
| 868 |
|
| 869 |
case('S'): |
| 870 |
_ptr++; |
| 871 |
switch(*_ptr) |
| 872 |
{ |
| 873 |
case 'b': |
| 874 |
element = 51; |
| 875 |
strcpy(symbol,"Sb"); |
| 876 |
break; |
| 877 |
case 'c': |
| 878 |
element = 21; |
| 879 |
strcpy(symbol,"Sc"); |
| 880 |
break; |
| 881 |
case 'e': |
| 882 |
element = 34; |
| 883 |
strcpy(symbol,"Se"); |
| 884 |
break; |
| 885 |
case 'i': |
| 886 |
element = 14; |
| 887 |
strcpy(symbol,"Si"); |
| 888 |
break; |
| 889 |
case 'm': |
| 890 |
element = 62; |
| 891 |
strcpy(symbol,"Sm"); |
| 892 |
break; |
| 893 |
case 'n': |
| 894 |
element = 50; |
| 895 |
strcpy(symbol,"Sn"); |
| 896 |
break; |
| 897 |
case 'r': |
| 898 |
element = 38; |
| 899 |
strcpy(symbol,"Sr"); |
| 900 |
break; |
| 901 |
default: |
| 902 |
element = 16; |
| 903 |
symbol[0] = 'S'; |
| 904 |
_ptr--; |
| 905 |
} |
| 906 |
break; |
| 907 |
|
| 908 |
case 'B': |
| 909 |
_ptr++; |
| 910 |
switch(*_ptr) |
| 911 |
{ |
| 912 |
case 'a': |
| 913 |
element = 56; |
| 914 |
strcpy(symbol,"Ba"); |
| 915 |
break; |
| 916 |
case 'e': |
| 917 |
element = 4; |
| 918 |
strcpy(symbol,"Be"); |
| 919 |
break; |
| 920 |
case 'i': |
| 921 |
element = 83; |
| 922 |
strcpy(symbol,"Bi"); |
| 923 |
break; |
| 924 |
case 'k': |
| 925 |
element = 97; |
| 926 |
strcpy(symbol,"Bk"); |
| 927 |
break; |
| 928 |
case 'r': |
| 929 |
element = 35; |
| 930 |
strcpy(symbol,"Br"); |
| 931 |
break; |
| 932 |
default: |
| 933 |
element = 5; |
| 934 |
symbol[0] = 'B'; |
| 935 |
_ptr--; |
| 936 |
} |
| 937 |
break; |
| 938 |
|
| 939 |
case 'F': |
| 940 |
_ptr++; |
| 941 |
switch(*_ptr) |
| 942 |
{ |
| 943 |
case 'e': |
| 944 |
element = 26; |
| 945 |
strcpy(symbol,"Fe"); |
| 946 |
break; |
| 947 |
case 'm': |
| 948 |
element = 100; |
| 949 |
strcpy(symbol,"Fm"); |
| 950 |
break; |
| 951 |
case 'r': |
| 952 |
element = 87; |
| 953 |
strcpy(symbol,"Fr"); |
| 954 |
break; |
| 955 |
default: |
| 956 |
element = 9; |
| 957 |
symbol[0] = 'F'; |
| 958 |
_ptr--; |
| 959 |
} |
| 960 |
break; |
| 961 |
|
| 962 |
case 'I': |
| 963 |
_ptr++; |
| 964 |
switch(*_ptr) |
| 965 |
{ |
| 966 |
case 'n': |
| 967 |
element = 49; |
| 968 |
strcpy(symbol,"In"); |
| 969 |
break; |
| 970 |
case 'r': |
| 971 |
element = 77; |
| 972 |
strcpy(symbol,"Ir"); |
| 973 |
break; |
| 974 |
default: |
| 975 |
element = 53; |
| 976 |
symbol[0] = 'I'; |
| 977 |
_ptr--; |
| 978 |
} |
| 979 |
break; |
| 980 |
|
| 981 |
case 'A': |
| 982 |
_ptr++; |
| 983 |
switch(*_ptr) |
| 984 |
{ |
| 985 |
case 'c': |
| 986 |
element = 89; |
| 987 |
strcpy(symbol,"Ac"); |
| 988 |
break; |
| 989 |
case 'g': |
| 990 |
element = 47; |
| 991 |
strcpy(symbol,"Ag"); |
| 992 |
break; |
| 993 |
case 'l': |
| 994 |
element = 13; |
| 995 |
strcpy(symbol,"Al"); |
| 996 |
break; |
| 997 |
case 'm': |
| 998 |
element = 95; |
| 999 |
strcpy(symbol,"Am"); |
| 1000 |
break; |
| 1001 |
case 'r': |
| 1002 |
element = 18; |
| 1003 |
strcpy(symbol,"Ar"); |
| 1004 |
break; |
| 1005 |
case 's': |
| 1006 |
element = 33; |
| 1007 |
strcpy(symbol,"As"); |
| 1008 |
break; |
| 1009 |
case 't': |
| 1010 |
element = 85; |
| 1011 |
strcpy(symbol,"At"); |
| 1012 |
break; |
| 1013 |
case 'u': |
| 1014 |
element = 79; |
| 1015 |
strcpy(symbol,"Au"); |
| 1016 |
break; |
| 1017 |
default: |
| 1018 |
_ptr--; |
| 1019 |
return(false); |
| 1020 |
} |
| 1021 |
break; |
| 1022 |
|
| 1023 |
case 'D': |
| 1024 |
_ptr++; |
| 1025 |
if (*_ptr == 'y') |
| 1026 |
{ |
| 1027 |
element = 66; |
| 1028 |
strcpy(symbol,"Dy"); |
| 1029 |
} |
| 1030 |
else |
| 1031 |
{ |
| 1032 |
_ptr--; |
| 1033 |
return(false); |
| 1034 |
} |
| 1035 |
break; |
| 1036 |
|
| 1037 |
case 'E': |
| 1038 |
_ptr++; |
| 1039 |
switch(*_ptr) |
| 1040 |
{ |
| 1041 |
case 'r': |
| 1042 |
element = 68; |
| 1043 |
strcpy(symbol,"Er"); |
| 1044 |
break; |
| 1045 |
case 's': |
| 1046 |
element = 99; |
| 1047 |
strcpy(symbol,"Es"); |
| 1048 |
break; |
| 1049 |
case 'u': |
| 1050 |
element = 63; |
| 1051 |
strcpy(symbol,"Eu"); |
| 1052 |
break; |
| 1053 |
default: |
| 1054 |
_ptr--; |
| 1055 |
return(false); |
| 1056 |
} |
| 1057 |
break; |
| 1058 |
|
| 1059 |
case 'G': |
| 1060 |
_ptr++; |
| 1061 |
switch (*_ptr) |
| 1062 |
{ |
| 1063 |
case 'a': |
| 1064 |
element = 31; |
| 1065 |
strcpy(symbol,"Ga"); |
| 1066 |
break; |
| 1067 |
case 'd': |
| 1068 |
element = 64; |
| 1069 |
strcpy(symbol,"Gd"); |
| 1070 |
break; |
| 1071 |
case 'e': |
| 1072 |
element = 32; |
| 1073 |
strcpy(symbol,"Ge"); |
| 1074 |
break; |
| 1075 |
default: |
| 1076 |
_ptr--; |
| 1077 |
return(false); |
| 1078 |
} |
| 1079 |
break; |
| 1080 |
|
| 1081 |
case 'H': |
| 1082 |
_ptr++; |
| 1083 |
switch (*_ptr) |
| 1084 |
{ |
| 1085 |
case 'e': |
| 1086 |
element = 2; |
| 1087 |
strcpy(symbol,"He"); |
| 1088 |
break; |
| 1089 |
case 'f': |
| 1090 |
element = 72; |
| 1091 |
strcpy(symbol,"Hf"); |
| 1092 |
break; |
| 1093 |
case 'g': |
| 1094 |
element = 80; |
| 1095 |
strcpy(symbol,"Hg"); |
| 1096 |
break; |
| 1097 |
case 'o': |
| 1098 |
element = 67; |
| 1099 |
strcpy(symbol,"Ho"); |
| 1100 |
break; |
| 1101 |
default: |
| 1102 |
element = 1; |
| 1103 |
symbol[0] = 'H'; |
| 1104 |
_ptr--; |
| 1105 |
} |
| 1106 |
break; |
| 1107 |
|
| 1108 |
case 'K': |
| 1109 |
_ptr++; |
| 1110 |
if(*_ptr == 'r') |
| 1111 |
{ |
| 1112 |
element = 36; |
| 1113 |
strcpy(symbol,"Kr"); |
| 1114 |
} |
| 1115 |
else |
| 1116 |
{ |
| 1117 |
element = 19; |
| 1118 |
symbol[0] = 'K'; |
| 1119 |
_ptr--; |
| 1120 |
} |
| 1121 |
break; |
| 1122 |
|
| 1123 |
case 'L': |
| 1124 |
_ptr++; |
| 1125 |
switch(*_ptr) |
| 1126 |
{ |
| 1127 |
case 'a': |
| 1128 |
element = 57; |
| 1129 |
strcpy(symbol,"La"); |
| 1130 |
break; |
| 1131 |
case 'i': |
| 1132 |
element = 3; |
| 1133 |
strcpy(symbol,"Li"); |
| 1134 |
break; |
| 1135 |
case 'r': |
| 1136 |
element = 103; |
| 1137 |
strcpy(symbol,"Lr"); |
| 1138 |
break; |
| 1139 |
case 'u': |
| 1140 |
element = 71; |
| 1141 |
strcpy(symbol,"Lu"); |
| 1142 |
break; |
| 1143 |
default: |
| 1144 |
_ptr--; |
| 1145 |
return(false); |
| 1146 |
} |
| 1147 |
break; |
| 1148 |
|
| 1149 |
case 'M': |
| 1150 |
_ptr++; |
| 1151 |
switch(*_ptr) |
| 1152 |
{ |
| 1153 |
case 'd': |
| 1154 |
element = 101; |
| 1155 |
strcpy(symbol,"Md"); |
| 1156 |
break; |
| 1157 |
case 'g': |
| 1158 |
element = 12; |
| 1159 |
strcpy(symbol,"Mg"); |
| 1160 |
break; |
| 1161 |
case 'n': |
| 1162 |
element = 25; |
| 1163 |
strcpy(symbol,"Mn"); |
| 1164 |
break; |
| 1165 |
case 'o': |
| 1166 |
element = 42; |
| 1167 |
strcpy(symbol,"Mo"); |
| 1168 |
break; |
| 1169 |
default: |
| 1170 |
_ptr--; |
| 1171 |
return(false); |
| 1172 |
} |
| 1173 |
break; |
| 1174 |
|
| 1175 |
case 'R': |
| 1176 |
_ptr++; |
| 1177 |
switch(*_ptr) |
| 1178 |
{ |
| 1179 |
case 'a': |
| 1180 |
element = 88; |
| 1181 |
strcpy(symbol,"Ra"); |
| 1182 |
break; |
| 1183 |
case 'b': |
| 1184 |
element = 37; |
| 1185 |
strcpy(symbol,"Rb"); |
| 1186 |
break; |
| 1187 |
case 'e': |
| 1188 |
element = 75; |
| 1189 |
strcpy(symbol,"Re"); |
| 1190 |
break; |
| 1191 |
case 'h': |
| 1192 |
element = 45; |
| 1193 |
strcpy(symbol,"Rh"); |
| 1194 |
break; |
| 1195 |
case 'n': |
| 1196 |
element = 86; |
| 1197 |
strcpy(symbol,"Rn"); |
| 1198 |
break; |
| 1199 |
case 'u': |
| 1200 |
element = 44; |
| 1201 |
strcpy(symbol,"Ru"); |
| 1202 |
break; |
| 1203 |
default: |
| 1204 |
_ptr--; |
| 1205 |
return(false); |
| 1206 |
} |
| 1207 |
break; |
| 1208 |
|
| 1209 |
case 'T': |
| 1210 |
_ptr++; |
| 1211 |
switch(*_ptr) |
| 1212 |
{ |
| 1213 |
case 'a': |
| 1214 |
element = 73; |
| 1215 |
strcpy(symbol,"Ta"); |
| 1216 |
break; |
| 1217 |
case 'b': |
| 1218 |
element = 65; |
| 1219 |
strcpy(symbol,"Tb"); |
| 1220 |
break; |
| 1221 |
case 'c': |
| 1222 |
element = 43; |
| 1223 |
strcpy(symbol,"Tc"); |
| 1224 |
break; |
| 1225 |
case 'e': |
| 1226 |
element = 52; |
| 1227 |
strcpy(symbol,"Te"); |
| 1228 |
break; |
| 1229 |
case 'h': |
| 1230 |
element = 90; |
| 1231 |
strcpy(symbol,"Th"); |
| 1232 |
break; |
| 1233 |
case 'i': |
| 1234 |
element = 22; |
| 1235 |
strcpy(symbol,"Ti"); |
| 1236 |
break; |
| 1237 |
case 'l': |
| 1238 |
element = 81; |
| 1239 |
strcpy(symbol,"Tl"); |
| 1240 |
break; |
| 1241 |
case 'm': |
| 1242 |
element = 69; |
| 1243 |
strcpy(symbol,"Tm"); |
| 1244 |
break; |
| 1245 |
default: |
| 1246 |
_ptr--; |
| 1247 |
return(false); |
| 1248 |
} |
| 1249 |
break; |
| 1250 |
|
| 1251 |
case('U'): element = 92; |
| 1252 |
symbol[0] = 'U'; |
| 1253 |
break; |
| 1254 |
case('V'): element = 23; |
| 1255 |
symbol[0] = 'V'; |
| 1256 |
break; |
| 1257 |
case('W'): element = 74; |
| 1258 |
symbol[0] = 'W'; |
| 1259 |
break; |
| 1260 |
|
| 1261 |
case('X'): |
| 1262 |
_ptr++; |
| 1263 |
if (*_ptr == 'e') |
| 1264 |
{ |
| 1265 |
element = 54; |
| 1266 |
strcpy(symbol,"Xe"); |
| 1267 |
} |
| 1268 |
else |
| 1269 |
{ |
| 1270 |
_ptr--; |
| 1271 |
return(false); |
| 1272 |
} |
| 1273 |
break; |
| 1274 |
|
| 1275 |
case('Y'): |
| 1276 |
_ptr++; |
| 1277 |
if (*_ptr == 'b') |
| 1278 |
{ |
| 1279 |
element = 70; |
| 1280 |
strcpy(symbol,"Yb"); |
| 1281 |
} |
| 1282 |
else |
| 1283 |
{ |
| 1284 |
element = 39; |
| 1285 |
symbol[0] = 'Y'; |
| 1286 |
_ptr--; |
| 1287 |
} |
| 1288 |
break; |
| 1289 |
|
| 1290 |
case('Z'): |
| 1291 |
_ptr++; |
| 1292 |
switch(*_ptr) |
| 1293 |
{ |
| 1294 |
case 'n': |
| 1295 |
element = 30; |
| 1296 |
strcpy(symbol,"Zn"); |
| 1297 |
break; |
| 1298 |
case 'r': |
| 1299 |
element = 40; |
| 1300 |
strcpy(symbol,"Zr"); |
| 1301 |
break; |
| 1302 |
default: |
| 1303 |
_ptr--; |
| 1304 |
return(false); |
| 1305 |
} |
| 1306 |
break; |
| 1307 |
} |
| 1308 |
else |
| 1309 |
{ |
| 1310 |
arom = true; |
| 1311 |
switch(*_ptr) |
| 1312 |
{ |
| 1313 |
case 'c': |
| 1314 |
element = 6; |
| 1315 |
symbol[0] = 'C'; |
| 1316 |
break; |
| 1317 |
case 'n': |
| 1318 |
element = 7; |
| 1319 |
symbol[0] = 'N'; |
| 1320 |
break; |
| 1321 |
case 'o': |
| 1322 |
element = 8; |
| 1323 |
symbol[0] = 'O'; |
| 1324 |
break; |
| 1325 |
case 'p': |
| 1326 |
element = 15; |
| 1327 |
symbol[0] = 'P'; |
| 1328 |
break; |
| 1329 |
case 's': |
| 1330 |
_ptr++; |
| 1331 |
if (*_ptr == 'e') |
| 1332 |
{ |
| 1333 |
element = 34; |
| 1334 |
strcpy(symbol,"Se"); |
| 1335 |
} |
| 1336 |
else |
| 1337 |
{ |
| 1338 |
element = 16; |
| 1339 |
symbol[0] = 'S'; |
| 1340 |
_ptr--; |
| 1341 |
} |
| 1342 |
break; |
| 1343 |
case 'a': |
| 1344 |
_ptr++; |
| 1345 |
if (*_ptr == 's') |
| 1346 |
{ |
| 1347 |
element = 33; |
| 1348 |
strcpy(symbol,"As"); |
| 1349 |
} |
| 1350 |
else |
| 1351 |
return(false); |
| 1352 |
break; |
| 1353 |
default: |
| 1354 |
return(false); |
| 1355 |
} |
| 1356 |
} |
| 1357 |
|
| 1358 |
//handle hydrogen count, stereochemistry, and charge |
| 1359 |
|
| 1360 |
OBAtom *atom = mol.NewAtom(); |
| 1361 |
int hcount = 0; |
| 1362 |
int charge=0; |
| 1363 |
int rad=0; |
| 1364 |
char tmpc[2]; |
| 1365 |
tmpc[1] = '\0'; |
| 1366 |
for (_ptr++;*_ptr && *_ptr != ']';_ptr++) |
| 1367 |
{ |
| 1368 |
switch(*_ptr) |
| 1369 |
{ |
| 1370 |
case '@': |
| 1371 |
_ptr++; |
| 1372 |
chiralWatch=true; |
| 1373 |
_mapcd[atom]= new OBChiralData; |
| 1374 |
if (*_ptr == '@') |
| 1375 |
atom->SetClockwiseStereo(); |
| 1376 |
else |
| 1377 |
{ |
| 1378 |
atom->SetAntiClockwiseStereo(); |
| 1379 |
_ptr--; |
| 1380 |
} |
| 1381 |
break; |
| 1382 |
case '-': |
| 1383 |
_ptr++; |
| 1384 |
if (isdigit(*_ptr)) |
| 1385 |
{ |
| 1386 |
tmpc[0] = *_ptr; |
| 1387 |
charge = -atoi(tmpc); |
| 1388 |
} |
| 1389 |
else |
| 1390 |
{ |
| 1391 |
charge--; |
| 1392 |
_ptr--; |
| 1393 |
} |
| 1394 |
break; |
| 1395 |
case '+': |
| 1396 |
_ptr++; |
| 1397 |
if (isdigit(*_ptr)) |
| 1398 |
{ |
| 1399 |
tmpc[0] = *_ptr; |
| 1400 |
charge = atoi(tmpc); |
| 1401 |
} |
| 1402 |
else |
| 1403 |
{ |
| 1404 |
charge++; |
| 1405 |
_ptr--; |
| 1406 |
} |
| 1407 |
break; |
| 1408 |
|
| 1409 |
case 'H': |
| 1410 |
_ptr++; |
| 1411 |
if (isdigit(*_ptr)) |
| 1412 |
{ |
| 1413 |
tmpc[0] = *_ptr; |
| 1414 |
hcount = atoi(tmpc); |
| 1415 |
} |
| 1416 |
else |
| 1417 |
{ |
| 1418 |
hcount = 1; |
| 1419 |
_ptr--; |
| 1420 |
} |
| 1421 |
break; |
| 1422 |
case '.': //CM Feb05 |
| 1423 |
rad=2; |
| 1424 |
if(*(++_ptr)=='.') |
| 1425 |
rad=3; |
| 1426 |
else |
| 1427 |
_ptr--; |
| 1428 |
break; |
| 1429 |
|
| 1430 |
default: |
| 1431 |
return(false); |
| 1432 |
} |
| 1433 |
} |
| 1434 |
|
| 1435 |
if (charge) |
| 1436 |
atom->SetFormalCharge(charge); |
| 1437 |
if (rad) |
| 1438 |
atom->SetSpinMultiplicity(rad); |
| 1439 |
atom->SetAtomicNum(element); |
| 1440 |
atom->SetIsotope(isotope); |
| 1441 |
atom->SetType(symbol); |
| 1442 |
if (arom) |
| 1443 |
atom->SetAromatic(); |
| 1444 |
|
| 1445 |
if (_prev) //need to add bond |
| 1446 |
{ |
| 1447 |
mol.AddBond(_prev,mol.NumAtoms(),_order,_bondflags); |
| 1448 |
if(chiralWatch) // if chiral atom need to add its previous into atom4ref |
| 1449 |
{ |
| 1450 |
if (_mapcd[atom] == NULL) |
| 1451 |
_mapcd[atom]= new OBChiralData; |
| 1452 |
|
| 1453 |
(_mapcd[atom])->AddAtomRef((unsigned int)_prev,input); |
| 1454 |
// cout <<"line 1405: Added atom ref "<<_prev<<" to "<<_mapcd[atom]<<endl; |
| 1455 |
} |
| 1456 |
map<OBAtom*,OBChiralData*>::iterator ChiralSearch; |
| 1457 |
ChiralSearch = _mapcd.find(mol.GetAtom(_prev)); |
| 1458 |
if (ChiralSearch!=_mapcd.end() && ChiralSearch->second != NULL) |
| 1459 |
{ |
| 1460 |
(ChiralSearch->second)->AddAtomRef(mol.NumAtoms(), input); |
| 1461 |
// cout <<"line 1431: Added atom ref "<<mol.NumAtoms()<<" to "<<ChiralSearch->second<<endl; |
| 1462 |
} |
| 1463 |
} |
| 1464 |
|
| 1465 |
//set values |
| 1466 |
_prev = mol.NumAtoms(); |
| 1467 |
_order = 1; |
| 1468 |
_bondflags = 0; |
| 1469 |
|
| 1470 |
//now add hydrogens |
| 1471 |
|
| 1472 |
for (int i = 0;i < hcount;i++) |
| 1473 |
{ |
| 1474 |
atom = mol.NewAtom(); |
| 1475 |
atom->SetAtomicNum(1); |
| 1476 |
atom->SetType("H"); |
| 1477 |
mol.AddBond(_prev,mol.NumAtoms(),1); |
| 1478 |
if(chiralWatch) |
| 1479 |
{ |
| 1480 |
if (_mapcd[mol.GetAtom(_prev)] != NULL) |
| 1481 |
(_mapcd[mol.GetAtom(_prev)])->AddAtomRef(mol.NumAtoms(),input); |
| 1482 |
// cout << "line 1434: Added atom ref "<<mol.NumAtoms()<<" to "<<_mapcd[mol.GetAtom(_prev)]<<endl; |
| 1483 |
|
| 1484 |
} |
| 1485 |
} |
| 1486 |
chiralWatch=false; |
| 1487 |
return(true); |
| 1488 |
} |
| 1489 |
|
| 1490 |
bool OBSmilesParser::CapExternalBonds(OBMol &mol) |
| 1491 |
{ |
| 1492 |
|
| 1493 |
if(_extbond.empty()) |
| 1494 |
return(true); |
| 1495 |
|
| 1496 |
OBAtom *atom; |
| 1497 |
vector<vector<int> >::iterator bond; |
| 1498 |
|
| 1499 |
for(bond = _extbond.begin();bond != _extbond.end();bond++) |
| 1500 |
{ |
| 1501 |
// create new dummy atom |
| 1502 |
atom = mol.NewAtom(); |
| 1503 |
atom->SetAtomicNum(0); |
| 1504 |
atom->SetType("*"); |
| 1505 |
|
| 1506 |
// bond dummy atom to mol via external bond |
| 1507 |
mol.AddBond((*bond)[1],atom->GetIdx(),(*bond)[2],(*bond)[3]); |
| 1508 |
OBBond *refbond = atom->GetBond(mol.GetAtom((*bond)[1])); |
| 1509 |
|
| 1510 |
//record external bond information |
| 1511 |
OBExternalBondData *xbd; |
| 1512 |
if(mol.HasData(OBGenericDataType::ExternalBondData)) |
| 1513 |
xbd = (OBExternalBondData*)mol.GetData(OBGenericDataType::ExternalBondData); |
| 1514 |
else |
| 1515 |
{ |
| 1516 |
xbd = new OBExternalBondData; |
| 1517 |
mol.SetData(xbd); |
| 1518 |
} |
| 1519 |
xbd->SetData(atom,refbond,(*bond)[0]); |
| 1520 |
|
| 1521 |
/* old code written by AGS -- mts |
| 1522 |
{ |
| 1523 |
externalbonds = (vector<pair<int,pair<OBAtom *,OBBond *> > > *)mol.GetData("extBonds"); |
| 1524 |
} |
| 1525 |
else |
| 1526 |
{ |
| 1527 |
externalbonds = new vector<pair<int,pair<OBAtom *,OBBond *> > >; |
| 1528 |
} |
| 1529 |
|
| 1530 |
//save data <external bond count, bond index> |
| 1531 |
externalbonds->push_back(pair<int,pair<OBAtom *,OBBond *> > ((*bond)[0], pair<OBAtom *,OBBond *> (atom,mol.GetBond((*bond)[1],atom->GetIdx())))); |
| 1532 |
mol.SetData("extBonds",externalbonds); |
| 1533 |
*/ |
| 1534 |
|
| 1535 |
//this data gets cleaned up in mol.Clear. |
| 1536 |
} |
| 1537 |
|
| 1538 |
return(true); |
| 1539 |
} |
| 1540 |
|
| 1541 |
bool OBSmilesParser::ParseExternalBond(OBMol &mol) |
| 1542 |
{ |
| 1543 |
int digit; |
| 1544 |
char str[10]; |
| 1545 |
|
| 1546 |
//*_ptr should == '&' |
| 1547 |
_ptr++; |
| 1548 |
|
| 1549 |
switch (*_ptr) // check for bond order indicators CC&=1.C&1 |
| 1550 |
{ |
| 1551 |
case '-': |
| 1552 |
_order = 1; |
| 1553 |
_ptr++; |
| 1554 |
break; |
| 1555 |
case '=': |
| 1556 |
_order = 2; |
| 1557 |
_ptr++; |
| 1558 |
break; |
| 1559 |
case '#': |
| 1560 |
_order = 3; |
| 1561 |
_ptr++; |
| 1562 |
break; |
| 1563 |
case ';': |
| 1564 |
_order = 5; |
| 1565 |
_ptr++; |
| 1566 |
break; |
| 1567 |
case '/': //chiral, but _order still == 1 |
| 1568 |
_bondflags |= OB_TORUP_BOND; |
| 1569 |
_ptr++; |
| 1570 |
break; |
| 1571 |
_ptr++; |
| 1572 |
case '\\': // chiral, but _order still == 1 |
| 1573 |
_bondflags |= OB_TORDOWN_BOND; |
| 1574 |
_ptr++; |
| 1575 |
break; |
| 1576 |
default: // no bond indicator just leave order = 1 |
| 1577 |
break; |
| 1578 |
} |
| 1579 |
|
| 1580 |
if (*_ptr == '%') // external bond indicator > 10 |
| 1581 |
{ |
| 1582 |
_ptr++; |
| 1583 |
str[0] = *_ptr; |
| 1584 |
_ptr++; |
| 1585 |
str[1] = *_ptr; |
| 1586 |
str[2] = '\0'; |
| 1587 |
} |
| 1588 |
else // simple single digit external bond indicator |
| 1589 |
{ |
| 1590 |
str[0] = *_ptr; |
| 1591 |
str[1] = '\0'; |
| 1592 |
} |
| 1593 |
digit = atoi(str); // convert indicator to digit |
| 1594 |
|
| 1595 |
//check for dot disconnect closures |
| 1596 |
vector<vector<int> >::iterator j; |
| 1597 |
int bondFlags,bondOrder; |
| 1598 |
for(j = _extbond.begin();j != _extbond.end();j++) |
| 1599 |
{ |
| 1600 |
if((*j)[0] == digit) |
| 1601 |
{ |
| 1602 |
bondFlags = (_bondflags > (*j)[3]) ? _bondflags : (*j)[3]; |
| 1603 |
bondOrder = (_order > (*j)[2]) ? _order : (*j)[2]; |
| 1604 |
mol.AddBond((*j)[1],_prev,bondOrder,bondFlags); |
| 1605 |
|
| 1606 |
// after adding a bond to atom "_prev" |
| 1607 |
// search to see if atom is bonded to a chiral atom |
| 1608 |
map<OBAtom*,OBChiralData*>::iterator ChiralSearch; |
| 1609 |
ChiralSearch = _mapcd.find(mol.GetAtom(_prev)); |
| 1610 |
if (ChiralSearch!=_mapcd.end() && ChiralSearch->second != NULL) |
| 1611 |
{ |
| 1612 |
(ChiralSearch->second)->AddAtomRef((*j)[1], input); |
| 1613 |
// cout << "Added external "<<(*j)[1]<<" to "<<ChiralSearch->second<<endl; |
| 1614 |
} |
| 1615 |
|
| 1616 |
_extbond.erase(j); |
| 1617 |
_bondflags = 0; |
| 1618 |
_order = 0; |
| 1619 |
return(true); |
| 1620 |
} |
| 1621 |
} |
| 1622 |
|
| 1623 |
//since no closures save another ext bond |
| 1624 |
vector<int> vtmp(4); |
| 1625 |
vtmp[0] = digit; |
| 1626 |
vtmp[1] = _prev; |
| 1627 |
vtmp[2] = _order; |
| 1628 |
vtmp[3] = _bondflags; |
| 1629 |
|
| 1630 |
_extbond.push_back(vtmp); |
| 1631 |
_order = 1; |
| 1632 |
_bondflags = 0; |
| 1633 |
|
| 1634 |
return(true); |
| 1635 |
|
| 1636 |
} |
| 1637 |
|
| 1638 |
bool OBSmilesParser::ParseRingBond(OBMol &mol) |
| 1639 |
{ |
| 1640 |
int digit; |
| 1641 |
char str[10]; |
| 1642 |
|
| 1643 |
if (*_ptr == '%') |
| 1644 |
{ |
| 1645 |
_ptr++; |
| 1646 |
str[0] = *_ptr; |
| 1647 |
_ptr++; |
| 1648 |
str[1] = *_ptr; |
| 1649 |
str[2] = '\0'; |
| 1650 |
} |
| 1651 |
else |
| 1652 |
{ |
| 1653 |
str[0] = *_ptr; |
| 1654 |
str[1] = '\0'; |
| 1655 |
} |
| 1656 |
digit = atoi(str); |
| 1657 |
|
| 1658 |
int bf,ord; |
| 1659 |
vector<vector<int> >::iterator j; |
| 1660 |
for (j = _rclose.begin();j != _rclose.end();j++) |
| 1661 |
if ((*j)[0] == digit) |
| 1662 |
{ |
| 1663 |
bf = (_bondflags > (*j)[3]) ? _bondflags : (*j)[3]; |
| 1664 |
ord = (_order > (*j)[2]) ? _order : (*j)[2]; |
| 1665 |
mol.AddBond((*j)[1],_prev,ord,bf,(*j)[4]); |
| 1666 |
|
| 1667 |
// after adding a bond to atom "_prev" |
| 1668 |
// search to see if atom is bonded to a chiral atom |
| 1669 |
// need to check both _prev and (*j)[1] as closure is direction independant |
| 1670 |
map<OBAtom*,OBChiralData*>::iterator ChiralSearch,cs2; |
| 1671 |
ChiralSearch = _mapcd.find(mol.GetAtom(_prev)); |
| 1672 |
cs2=_mapcd.find(mol.GetAtom((*j)[1])); |
| 1673 |
if (ChiralSearch!=_mapcd.end() && ChiralSearch->second != NULL) |
| 1674 |
{ |
| 1675 |
(ChiralSearch->second)->AddAtomRef((*j)[1], input); |
| 1676 |
//cout << "Added ring closure "<<(*j)[1]<<" to "<<ChiralSearch->second<<endl; |
| 1677 |
} |
| 1678 |
if (cs2!=_mapcd.end() && cs2->second != NULL) |
| 1679 |
{ |
| 1680 |
(cs2->second)->AddAtomRef(_prev,input); |
| 1681 |
// cout <<"Added ring opening "<<_prev<<" to "<<cs2->second<<endl; |
| 1682 |
} |
| 1683 |
|
| 1684 |
//CM ensure neither atoms in ring closure is a radical centre |
| 1685 |
OBAtom* patom = mol.GetAtom(_prev); |
| 1686 |
patom->SetSpinMultiplicity(0); |
| 1687 |
patom = mol.GetAtom((*j)[1]); |
| 1688 |
patom->SetSpinMultiplicity(0); |
| 1689 |
//CM end |
| 1690 |
_rclose.erase(j); |
| 1691 |
_bondflags = 0; |
| 1692 |
_order = 1; |
| 1693 |
return(true); |
| 1694 |
} |
| 1695 |
|
| 1696 |
vector<int> vtmp(5); |
| 1697 |
vtmp[0] = digit; |
| 1698 |
vtmp[1] = _prev; |
| 1699 |
vtmp[2] = _order; |
| 1700 |
vtmp[3] = _bondflags; |
| 1701 |
OBAtom* atom = mol.GetAtom(_prev); |
| 1702 |
if(!atom) |
| 1703 |
{ |
| 1704 |
obErrorLog.ThrowError(__func__,"Number not parsed correctly as a ring bond", obWarning); |
| 1705 |
return false; |
| 1706 |
} |
| 1707 |
|
| 1708 |
vtmp[4] = atom->GetValence(); //store position to insert closure bond |
| 1709 |
for (j = _rclose.begin();j != _rclose.end();j++) //correct for multiple closure bonds to a single atom |
| 1710 |
if ((*j)[1] == _prev) |
| 1711 |
vtmp[4]++; |
| 1712 |
|
| 1713 |
_rclose.push_back(vtmp); |
| 1714 |
_order = 1; |
| 1715 |
_bondflags = 0; |
| 1716 |
|
| 1717 |
return(true); |
| 1718 |
} |
| 1719 |
|
| 1720 |
static bool IsCisOrTransH(OBAtom *atom) |
| 1721 |
{ |
| 1722 |
if (!atom->IsHydrogen()) |
| 1723 |
return false; |
| 1724 |
else |
| 1725 |
FOR_BONDS_OF_ATOM(bond, atom) |
| 1726 |
{ |
| 1727 |
if (bond->IsUp() || bond->IsDown()) |
| 1728 |
return true; |
| 1729 |
} |
| 1730 |
return false; |
| 1731 |
} |
| 1732 |
|
| 1733 |
void OBMol2Smi::CreateSmiString(OBMol &mol,char *buffer) |
| 1734 |
{ |
| 1735 |
OBAtom *atom; |
| 1736 |
OBSmiNode *root =NULL; |
| 1737 |
buffer[0] = '\0'; |
| 1738 |
vector<OBNodeBase*>::iterator i; |
| 1739 |
|
| 1740 |
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
| 1741 |
// don't use a hydrogen as the root node unless it's not bonded |
| 1742 |
// or it's involved in a cis/trans '/' or '\' specification |
| 1743 |
if ((!atom->IsHydrogen() || atom->GetValence() == 0 || IsCisOrTransH(atom)) |
| 1744 |
&& !_uatoms[atom->GetIdx()]) |
| 1745 |
if (!atom->IsChiral() || !mol.HasNonZeroCoords()) |
| 1746 |
// don't use chiral root atoms unless this is from a SMILES |
| 1747 |
{ |
| 1748 |
//clear out closures in case structure is dot disconnected |
| 1749 |
_vclose.clear(); |
| 1750 |
_atmorder.clear(); |
| 1751 |
_storder.clear(); |
| 1752 |
_vopen.clear(); |
| 1753 |
//dot disconnected structure |
| 1754 |
if (strlen(buffer) > 0) |
| 1755 |
strcat(buffer,"."); |
| 1756 |
root = new OBSmiNode (atom); |
| 1757 |
BuildTree(root); |
| 1758 |
FindClosureBonds(mol); |
| 1759 |
if (mol.Has2D()) |
| 1760 |
AssignCisTrans(root); |
| 1761 |
ToSmilesString(root,buffer); |
| 1762 |
delete root; |
| 1763 |
} |
| 1764 |
|
| 1765 |
//If no starting node found e.g. [H][H] CM 21Mar05 |
| 1766 |
if(root==NULL) |
| 1767 |
{ |
| 1768 |
root = new OBSmiNode(mol.GetFirstAtom()); |
| 1769 |
BuildTree(root); |
| 1770 |
ToSmilesString(root,buffer); |
| 1771 |
delete root; |
| 1772 |
} |
| 1773 |
} |
| 1774 |
|
| 1775 |
bool OBMol2Smi::BuildTree(OBSmiNode *node) |
| 1776 |
{ |
| 1777 |
vector<OBEdgeBase*>::iterator i; |
| 1778 |
OBAtom *nbr,*atom = node->GetAtom(); |
| 1779 |
|
| 1780 |
_uatoms.SetBitOn(atom->GetIdx()); //mark the atom as visited |
| 1781 |
_atmorder.push_back(atom->GetIdx()); //store the atom ordering |
| 1782 |
_storder.push_back(atom->GetIdx()); //store the atom ordering for stereo |
| 1783 |
|
| 1784 |
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i)) |
| 1785 |
{ |
| 1786 |
// Normally skip hydrogens |
| 1787 |
// but D,T is explicit and so is H2 |
| 1788 |
// or an H atom involved in a cis/trans '/' or '\' bond spec |
| 1789 |
if ( (!nbr->IsHydrogen() || nbr->GetIsotope() || atom->IsHydrogen() || |
| 1790 |
(((OBBond*)*i)->IsUp() || ((OBBond*)*i)->IsDown()) ) |
| 1791 |
&& !_uatoms[nbr->GetIdx()]) |
| 1792 |
{ |
| 1793 |
_ubonds.SetBitOn((*i)->GetIdx()); |
| 1794 |
OBSmiNode *next = new OBSmiNode (nbr); |
| 1795 |
next->SetParent(atom); |
| 1796 |
node->SetNextNode(next,(OBBond*)*i); |
| 1797 |
BuildTree(next); |
| 1798 |
} |
| 1799 |
} |
| 1800 |
|
| 1801 |
return(true); |
| 1802 |
} |
| 1803 |
|
| 1804 |
void OBMol2Smi::ToSmilesString(OBSmiNode *node,char *buffer) |
| 1805 |
{ |
| 1806 |
char tmpbuf[16]; |
| 1807 |
OBAtom *atom = node->GetAtom(); |
| 1808 |
|
| 1809 |
//write the current atom to the string |
| 1810 |
GetSmilesElement(node,tmpbuf); |
| 1811 |
strcat(buffer,tmpbuf); |
| 1812 |
|
| 1813 |
//handle ring closures here |
| 1814 |
vector<pair<int,OBBond*> > vc = GetClosureDigits(atom); |
| 1815 |
if (!vc.empty()) |
| 1816 |
{ |
| 1817 |
vector<pair<int,OBBond*> >::iterator i; |
| 1818 |
for (i = vc.begin();i != vc.end();i++) |
| 1819 |
{ |
| 1820 |
if (i->second) |
| 1821 |
{ |
| 1822 |
if (i->second->IsUp()) |
| 1823 |
{ |
| 1824 |
if ( (i->second->GetBeginAtom())->HasDoubleBond() || |
| 1825 |
(i->second->GetEndAtom())->HasDoubleBond() ) |
| 1826 |
strcat(buffer,"/"); |
| 1827 |
} |
| 1828 |
if (i->second->IsDown()) |
| 1829 |
{ |
| 1830 |
if ( (i->second->GetBeginAtom())->HasDoubleBond() || |
| 1831 |
(i->second->GetEndAtom())->HasDoubleBond() ) |
| 1832 |
strcat(buffer,"\\"); |
| 1833 |
} |
| 1834 |
#ifndef KEKULE |
| 1835 |
|
| 1836 |
if (i->second->GetBO() == 2 && !i->second->IsAromatic()) |
| 1837 |
strcat(buffer,"="); |
| 1838 |
#else |
| 1839 |
|
| 1840 |
if (i->second->GetBO() == 2) |
| 1841 |
strcat(buffer,"="); |
| 1842 |
#endif |
| 1843 |
|
| 1844 |
if (i->second->GetBO() == 3) |
| 1845 |
strcat(buffer,"#"); |
| 1846 |
} |
| 1847 |
|
| 1848 |
if (i->first > 9) |
| 1849 |
strcat(buffer,"%"); |
| 1850 |
snprintf(tmpbuf,sizeof(tmpbuf), "%d",i->first); |
| 1851 |
strcat(buffer,tmpbuf); |
| 1852 |
} |
| 1853 |
} |
| 1854 |
|
| 1855 |
//follow path to child atoms |
| 1856 |
OBBond *bond; |
| 1857 |
for (int i = 0;i < node->Size();i++) |
| 1858 |
{ |
| 1859 |
bond = node->GetNextBond(i); |
| 1860 |
if (i+1 < node->Size()) |
| 1861 |
strcat(buffer,"("); |
| 1862 |
if (bond->IsUp()) |
| 1863 |
{ |
| 1864 |
if ( (bond->GetBeginAtom())->HasDoubleBond() || |
| 1865 |
(bond->GetEndAtom())->HasDoubleBond() ) |
| 1866 |
strcat(buffer,"/"); |
| 1867 |
} |
| 1868 |
if (bond->IsDown()) |
| 1869 |
{ |
| 1870 |
if ( (bond->GetBeginAtom())->HasDoubleBond() || |
| 1871 |
(bond->GetEndAtom())->HasDoubleBond() ) |
| 1872 |
strcat(buffer,"\\"); |
| 1873 |
} |
| 1874 |
#ifndef KEKULE |
| 1875 |
|
| 1876 |
if (bond->GetBO() == 2 && !bond->IsAromatic()) |
| 1877 |
strcat(buffer,"="); |
| 1878 |
#else |
| 1879 |
|
| 1880 |
if (bond->GetBO() == 2) |
| 1881 |
strcat(buffer,"="); |
| 1882 |
#endif |
| 1883 |
|
| 1884 |
if (bond->GetBO() == 3) |
| 1885 |
strcat(buffer,"#"); |
| 1886 |
|
| 1887 |
ToSmilesString(node->GetNextNode(i),buffer); |
| 1888 |
if (i+1 < node->Size()) |
| 1889 |
strcat(buffer,")"); |
| 1890 |
} |
| 1891 |
} |
| 1892 |
|
| 1893 |
void OBMol2Smi::GetClosureAtoms(OBAtom *atom,vector<OBNodeBase*> &va) |
| 1894 |
{ |
| 1895 |
|
| 1896 |
//look through closure list for start atom |
| 1897 |
vector<OBEdgeBase*>::iterator i; |
| 1898 |
for (i = _vclose.begin();i != _vclose.end();i++) |
| 1899 |
if (*i) |
| 1900 |
{ |
| 1901 |
if (((OBBond*)*i)->GetBeginAtom() == atom) |
| 1902 |
va.push_back(((OBBond*)*i)->GetEndAtom()); |
| 1903 |
if (((OBBond*)*i)->GetEndAtom() == atom) |
| 1904 |
va.push_back(((OBBond*)*i)->GetBeginAtom()); |
| 1905 |
} |
| 1906 |
|
| 1907 |
OBAtom *nbr; |
| 1908 |
vector<pair<OBAtom*,pair<int,int> > >::iterator j; |
| 1909 |
for (j = _vopen.begin();j != _vopen.end();j++) |
| 1910 |
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i)) |
| 1911 |
if (nbr == j->first) |
| 1912 |
va.push_back(nbr); |
| 1913 |
} |
| 1914 |
|
| 1915 |
vector<pair<int,OBBond*> > OBMol2Smi::GetClosureDigits(OBAtom *atom) |
| 1916 |
{ |
| 1917 |
vector<pair<int,OBBond*> > vc; |
| 1918 |
vc.clear(); |
| 1919 |
|
| 1920 |
//look through closure list for start atom |
| 1921 |
int idx,bo; |
| 1922 |
OBBond *bond; |
| 1923 |
vector<OBEdgeBase*>::iterator i; |
| 1924 |
for (i = _vclose.begin();i != _vclose.end();i++) |
| 1925 |
if ((bond=(OBBond*)*i)) |
| 1926 |
if (bond->GetBeginAtom() == atom || bond->GetEndAtom() == atom) |
| 1927 |
{ |
| 1928 |
idx = GetUnusedIndex(); |
| 1929 |
vc.push_back(pair<int,OBBond*> (idx,bond)); |
| 1930 |
bo = (bond->IsAromatic())? 1 : bond->GetBO(); |
| 1931 |
_vopen.push_back(pair<OBAtom*,pair<int,int> > |
| 1932 |
(bond->GetNbrAtom(atom),pair<int,int>(idx,bo))); |
| 1933 |
*i = NULL;//remove bond from closure list |
| 1934 |
} |
| 1935 |
|
| 1936 |
//try to complete closures |
| 1937 |
if (!_vopen.empty()) |
| 1938 |
{ |
| 1939 |
vector<pair<OBAtom*,pair<int,int> > >::iterator j; |
| 1940 |
for (j = _vopen.begin();j != _vopen.end();) |
| 1941 |
if (j->first == atom) |
| 1942 |
{ |
| 1943 |
vc.push_back(pair<int,OBBond*> (j->second.first,(OBBond*)NULL)); |
| 1944 |
_vopen.erase(j); |
| 1945 |
j = _vopen.begin(); |
| 1946 |
} |
| 1947 |
else |
| 1948 |
j++; |
| 1949 |
} |
| 1950 |
|
| 1951 |
return(vc); |
| 1952 |
} |
| 1953 |
|
| 1954 |
void OBMol2Smi::FindClosureBonds(OBMol &mol) |
| 1955 |
{ |
| 1956 |
//find closure bonds |
| 1957 |
OBAtom *a1,*a2; |
| 1958 |
OBBond *bond; |
| 1959 |
vector<OBEdgeBase*>::iterator i; |
| 1960 |
OBBitVec bv; |
| 1961 |
bv.FromVecInt(_storder); |
| 1962 |
|
| 1963 |
for (bond = mol.BeginBond(i);bond;bond = mol.NextBond(i)) |
| 1964 |
if (!_ubonds[bond->GetIdx()] && bv[bond->GetBeginAtomIdx()]) |
| 1965 |
{ |
| 1966 |
a1 = bond->GetBeginAtom(); |
| 1967 |
a2 = bond->GetEndAtom(); |
| 1968 |
if (!a1->IsHydrogen() && !a2->IsHydrogen()) |
| 1969 |
_vclose.push_back(bond); |
| 1970 |
} |
| 1971 |
|
| 1972 |
vector<OBEdgeBase*>::reverse_iterator j; |
| 1973 |
vector<int>::iterator k; |
| 1974 |
|
| 1975 |
//modify _order to reflect ring closures |
| 1976 |
for (j = _vclose.rbegin();j != _vclose.rend();j++) |
| 1977 |
{ |
| 1978 |
bond = (OBBond*)*j; |
| 1979 |
a1 = a2 = NULL; |
| 1980 |
|
| 1981 |
for (k = _storder.begin();k != _storder.end();k++) |
| 1982 |
if (bond->GetBeginAtomIdx() == static_cast<unsigned int>(*k) || |
| 1983 |
bond-> |
| 1984 |
GetEndAtomIdx() == static_cast<unsigned int>(*k)) |
| 1985 |
if (!a1) a1 = mol.GetAtom(*k); |
| 1986 |
else if (!a2) |
| 1987 |
{ |
| 1988 |
a2 = mol.GetAtom(*k) |
| 1989 |
; |
| 1990 |
_storder.erase(k); |
| 1991 |
break; |
| 1992 |
} |
| 1993 |
|
| 1994 |
for (k = _storder.begin() |
| 1995 |
; |
| 1996 |
k != _storder.end(); |
| 1997 |
k++) |
| 1998 |
if (a1->GetIdx() |
| 1999 |
== static_cast<unsigned int>(*k)) |
| 2000 |
{ |
| 2001 |
k++; |
| 2002 |
if (k != _storder.end()) |
| 2003 |
_storder.insert(k,a2->GetIdx()); |
| 2004 |
else |
| 2005 |
_storder.push_back(a2->GetIdx()); |
| 2006 |
break; |
| 2007 |
} |
| 2008 |
} |
| 2009 |
} |
| 2010 |
|
| 2011 |
int OBMol2Smi::GetUnusedIndex() |
| 2012 |
{ |
| 2013 |
int idx=1; |
| 2014 |
|
| 2015 |
vector<pair<OBAtom*,pair<int,int> > >::iterator j; |
| 2016 |
for (j = _vopen.begin();j != _vopen.end();) |
| 2017 |
if (j->second.first == idx) |
| 2018 |
{ |
| 2019 |
idx++; //increment idx and start over if digit is already used |
| 2020 |
j = _vopen.begin(); |
| 2021 |
} |
| 2022 |
else |
| 2023 |
j++; |
| 2024 |
|
| 2025 |
return(idx); |
| 2026 |
} |
| 2027 |
|
| 2028 |
void OBMol2Smi::CorrectAromaticAmineCharge(OBMol &mol) |
| 2029 |
{ |
| 2030 |
OBAtom *atom; |
| 2031 |
vector<OBNodeBase*>::iterator i; |
| 2032 |
|
| 2033 |
_aromNH.clear(); |
| 2034 |
_aromNH.resize(mol.NumAtoms()+1); |
| 2035 |
|
| 2036 |
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
| 2037 |
if (atom->IsNitrogen() && atom->IsAromatic()) |
| 2038 |
if (atom->GetHvyValence() == 2) |
| 2039 |
{ |
| 2040 |
if (atom->GetValence() == 3 || atom->GetImplicitValence() == 3) |
| 2041 |
_aromNH[atom->GetIdx()] = true; |
| 2042 |
} |
| 2043 |
} |
| 2044 |
|
| 2045 |
void OBMol2Smi::AssignCisTrans(OBSmiNode *node) |
| 2046 |
{ |
| 2047 |
//traverse the tree searching for acyclic olefins - if it |
| 2048 |
//has at least one heavy atom attachment on each end assign stereochem |
| 2049 |
|
| 2050 |
OBBond *bond; |
| 2051 |
for (int i = 0;i < node->Size();i++) |
| 2052 |
{ |
| 2053 |
bond = node->GetNextBond(i); |
| 2054 |
if (bond->GetBO() == 2 && !bond->IsInRing()) |
| 2055 |
{ |
| 2056 |
OBAtom *b = node->GetAtom(); |
| 2057 |
OBAtom *c = bond->GetNbrAtom(b); |
| 2058 |
|
| 2059 |
//skip allenes |
| 2060 |
if (b->GetHyb() == 1 || c->GetHyb() == 1) |
| 2061 |
continue; |
| 2062 |
|
| 2063 |
if (b->GetHvyValence() > 1 && c->GetHvyValence() > 1) |
| 2064 |
{ |
| 2065 |
OBAtom *a,*d; |
| 2066 |
vector<OBEdgeBase*>::iterator j,k; |
| 2067 |
|
| 2068 |
//look for bond with assigned stereo as in poly-ene |
| 2069 |
for (a = b->BeginNbrAtom(j);a;a = b->NextNbrAtom(j)) |
| 2070 |
if (((OBBond*)*j)->IsUp() ||((OBBond*)*j)->IsDown()) |
| 2071 |
break; |
| 2072 |
|
| 2073 |
if (!a) |
| 2074 |
for (a = b->BeginNbrAtom(j);a;a = b->NextNbrAtom(j)) |
| 2075 |
if (a != c && !a->IsHydrogen()) |
| 2076 |
break; |
| 2077 |
for (d = c->BeginNbrAtom(k);d;d = c->NextNbrAtom(k)) |
| 2078 |
if (d != b && !d->IsHydrogen()) |
| 2079 |
break; |
| 2080 |
// obAssert(a); |
| 2081 |
// obAssert(d); |
| 2082 |
|
| 2083 |
if (((OBBond*)*j)->IsUp() || ((OBBond*)*j)->IsDown()) //stereo already assigned |
| 2084 |
{ |
| 2085 |
if (fabs(CalcTorsionAngle(a->GetVector(),b->GetVector(), |
| 2086 |
c->GetVector(),d->GetVector())) > 10.0) |
| 2087 |
if (((OBBond*)*j)->IsUp()) |
| 2088 |
((OBBond*)*k)->SetUp(); |
| 2089 |
else |
| 2090 |
((OBBond*)*k)->SetDown(); |
| 2091 |
else |
| 2092 |
if (((OBBond*)*j)->IsUp()) |
| 2093 |
((OBBond*)*k)->SetDown(); |
| 2094 |
else |
| 2095 |
((OBBond*)*k)->SetUp(); |
| 2096 |
} |
| 2097 |
else //assign stereo to both ends |
| 2098 |
{ |
| 2099 |
((OBBond*)*j)->SetUp(); |
| 2100 |
if (fabs(CalcTorsionAngle(a->GetVector(),b->GetVector(), |
| 2101 |
c->GetVector(),d->GetVector())) > 10.0) |
| 2102 |
((OBBond*)*k)->SetUp(); |
| 2103 |
else |
| 2104 |
((OBBond*)*k)->SetDown(); |
| 2105 |
} |
| 2106 |
} |
| 2107 |
} |
| 2108 |
AssignCisTrans(node->GetNextNode(i)); |
| 2109 |
} |
| 2110 |
} |
| 2111 |
|
| 2112 |
void OBMol2Smi::Init(OBConversion* pconv) |
| 2113 |
{ |
| 2114 |
_vclose.clear(); |
| 2115 |
_atmorder.clear(); |
| 2116 |
_storder.clear(); |
| 2117 |
_aromNH.clear(); |
| 2118 |
_uatoms.Clear(); |
| 2119 |
_ubonds.Clear(); |
| 2120 |
_vopen.clear(); |
| 2121 |
_pconv = pconv; |
| 2122 |
} |
| 2123 |
|
| 2124 |
bool OBMol2Smi::GetSmilesElement(OBSmiNode *node,char *element) |
| 2125 |
{ |
| 2126 |
//***handle reference atom stuff here and return*** |
| 2127 |
char symbol[16]; |
| 2128 |
bool bracketElement = false; |
| 2129 |
bool normalValence = true; |
| 2130 |
|
| 2131 |
OBAtom *atom = node->GetAtom(); |
| 2132 |
|
| 2133 |
int bosum = atom->KBOSum(); |
| 2134 |
atom->BOSum(); //CM temp |
| 2135 |
switch (atom->GetAtomicNum()) |
| 2136 |
{ |
| 2137 |
case 0: |
| 2138 |
break; |
| 2139 |
case 5: /*bracketElement = !(normalValence = (bosum == 3)); break;*/ |
| 2140 |
break; |
| 2141 |
case 6: |
| 2142 |
break; |
| 2143 |
case 7: |
| 2144 |
if (atom->IsAromatic() && atom->GetHvyValence() == 2 && atom->GetImplicitValence() == 3) |
| 2145 |
{ |
| 2146 |
bracketElement = !(normalValence = false); |
| 2147 |
break; |
| 2148 |
} |
| 2149 |
else |
| 2150 |
bracketElement = !(normalValence = (bosum == 3 || bosum == 5)); |
| 2151 |
break; |
| 2152 |
case 8: |
| 2153 |
break; |
| 2154 |
case 9: |
| 2155 |
break; |
| 2156 |
case 15: |
| 2157 |
break; |
| 2158 |
case 16: |
| 2159 |
bracketElement = !(normalValence = (bosum == 2 || bosum == 4 || bosum == 6)); |
| 2160 |
break; |
| 2161 |
case 17: |
| 2162 |
break; |
| 2163 |
case 35: |
| 2164 |
break; |
| 2165 |
case 53: |
| 2166 |
break; |
| 2167 |
|
| 2168 |
default: |
| 2169 |
bracketElement = true; |
| 2170 |
} |
| 2171 |
|
| 2172 |
if (atom->GetHvyValence() > 2 && atom->IsChiral()) |
| 2173 |
if (((OBMol*)atom->GetParent())->HasNonZeroCoords() || atom->HasChiralitySpecified()) |
| 2174 |
bracketElement = true; |
| 2175 |
|
| 2176 |
if (atom->GetFormalCharge() != 0) //bracket charged elements |
| 2177 |
bracketElement = true; |
| 2178 |
|
| 2179 |
if(atom->GetIsotope()) //CM 19Mar05 |
| 2180 |
bracketElement = true; |
| 2181 |
|
| 2182 |
//CM begin 18 Sept 2003 |
| 2183 |
|
| 2184 |
//This outputs form [CH3][CH3] rather than CC if -h option has been specified |
| 2185 |
if (((OBMol*)atom->GetParent())->HasHydrogensAdded()) |
| 2186 |
bracketElement = true; |
| 2187 |
else |
| 2188 |
{ |
| 2189 |
if (atom->GetSpinMultiplicity()) |
| 2190 |
{ |
| 2191 |
//For radicals output bracket form anyway unless r option specified |
| 2192 |
if(!(_pconv && _pconv->IsOption ("r"))) |
| 2193 |
bracketElement = true; |
| 2194 |
} |
| 2195 |
} |
| 2196 |
//CM end |
| 2197 |
|
| 2198 |
if (!bracketElement) |
| 2199 |
{ |
| 2200 |
if (!atom->GetAtomicNum()) |
| 2201 |
{ |
| 2202 |
bool external = false; |
| 2203 |
vector<pair<int,pair<OBAtom *,OBBond *> > > *externalBonds = |
| 2204 |
(vector<pair<int,pair<OBAtom *,OBBond *> > > *)((OBMol*)atom->GetParent())->GetData("extBonds"); |
| 2205 |
vector<pair<int,pair<OBAtom *,OBBond *> > >::iterator externalBond; |
| 2206 |
|
| 2207 |
if (externalBonds) |
| 2208 |
for(externalBond = externalBonds->begin();externalBond != externalBonds->end();externalBond++) |
| 2209 |
{ |
| 2210 |
if (externalBond->second.first == atom) |
| 2211 |
{ |
| 2212 |
external = true; |
| 2213 |
strcpy(symbol,"&"); |
| 2214 |
OBBond *bond = externalBond->second.second; |
| 2215 |
if (bond->IsUp()) |
| 2216 |
{ |
| 2217 |
if ( (bond->GetBeginAtom())->HasDoubleBond() || |
| 2218 |
(bond->GetEndAtom())->HasDoubleBond() ) |
| 2219 |
strcat(symbol,"/"); |
| 2220 |
} |
| 2221 |
if (bond->IsDown()) |
| 2222 |
{ |
| 2223 |
if ( (bond->GetBeginAtom())->HasDoubleBond() || |
| 2224 |
(bond->GetEndAtom())->HasDoubleBond() ) |
| 2225 |
strcat(symbol,"\\"); |
| 2226 |
} |
| 2227 |
#ifndef KEKULE |
| 2228 |
|
| 2229 |
if (bond->GetBO() == 2 && !bond->IsAromatic()) |
| 2230 |
strcat(symbol,"="); |
| 2231 |
if (bond->GetBO() == 2 && bond->IsAromatic()) |
| 2232 |
strcat(symbol,";"); |
| 2233 |
#else |
| 2234 |
|
| 2235 |
if (bond->GetBO() == 2) |
| 2236 |
strcat(symbol,"="); |
| 2237 |
#endif |
| 2238 |
|
| 2239 |
if (bond->GetBO() == 3) |
| 2240 |
strcat(symbol,"#"); |
| 2241 |
sprintf(symbol,"%s%d",symbol,externalBond->first); |
| 2242 |
break; |
| 2243 |
} |
| 2244 |
} |
| 2245 |
|
| 2246 |
if(!external) |
| 2247 |
strcpy(symbol,"*"); |
| 2248 |
} |
| 2249 |
else |
| 2250 |
{ |
| 2251 |
strcpy(symbol,etab.GetSymbol(atom->GetAtomicNum())); |
| 2252 |
#ifndef KEKULE |
| 2253 |
if (atom->IsAromatic()) |
| 2254 |
symbol[0] = tolower(symbol[0]); |
| 2255 |
#endif |
| 2256 |
|
| 2257 |
//Radical centres lc if r option set |
| 2258 |
if(atom->GetSpinMultiplicity() && _pconv && _pconv->IsOption ("r")) |
| 2259 |
symbol[0] = tolower(symbol[0]); |
| 2260 |
} |
| 2261 |
strcpy(element,symbol); |
| 2262 |
|
| 2263 |
return(true); |
| 2264 |
} |
| 2265 |
|
| 2266 |
strcpy(element,"["); |
| 2267 |
if(atom->GetIsotope()) //CM 19Mar05 |
| 2268 |
{ |
| 2269 |
char iso[4]; |
| 2270 |
sprintf(iso,"%d",atom->GetIsotope()); |
| 2271 |
strcat(element,iso); |
| 2272 |
} |
| 2273 |
if (!atom->GetAtomicNum()) |
| 2274 |
strcpy(symbol,"*"); |
| 2275 |
else |
| 2276 |
{ |
| 2277 |
strcpy(symbol,etab.GetSymbol(atom->GetAtomicNum())); |
| 2278 |
#ifndef KEKULE |
| 2279 |
if (atom->IsAromatic()) |
| 2280 |
symbol[0] = tolower(symbol[0]); |
| 2281 |
#endif |
| 2282 |
|
| 2283 |
} |
| 2284 |
strcat(element,symbol); |
| 2285 |
|
| 2286 |
//if (atom->IsCarbon() && atom->GetHvyValence() > 2 && atom->IsChiral()) |
| 2287 |
if (atom->GetHvyValence() > 2 && atom->IsChiral()) |
| 2288 |
{ |
| 2289 |
char stereo[5]; |
| 2290 |
if (GetChiralStereo(node,stereo)) |
| 2291 |
strcat(element,stereo); |
| 2292 |
} |
| 2293 |
|
| 2294 |
//add extra hydrogens |
| 2295 |
if (!atom->IsHydrogen()) |
| 2296 |
{ |
| 2297 |
int hcount = atom->ImplicitHydrogenCount() + atom->ExplicitHydrogenCount(); |
| 2298 |
if (hcount != 0) |
| 2299 |
{ |
| 2300 |
strcat(element,"H"); |
| 2301 |
if (hcount > 1) |
| 2302 |
{ |
| 2303 |
char tcount[10]; |
| 2304 |
sprintf(tcount,"%d", hcount); |
| 2305 |
strcat(element,tcount); |
| 2306 |
} |
| 2307 |
} |
| 2308 |
} |
| 2309 |
|
| 2310 |
//cat charge on the end |
| 2311 |
if (atom->GetFormalCharge() != 0) |
| 2312 |
{ |
| 2313 |
|
| 2314 |
/* |
| 2315 |
if (atom->ImplicitHydrogenCount()) |
| 2316 |
{ |
| 2317 |
cerr << "imp = " << atom->GetAtomicNum() << ' ' << atom->GetImplicitValence() << endl; |
| 2318 |
strcat(element,"H"); |
| 2319 |
if (atom->ImplicitHydrogenCount() > 1) |
| 2320 |
{ |
| 2321 |
char tcount[10]; |
| 2322 |
sprintf(tcount,"%d",atom->ImplicitHydrogenCount()); |
| 2323 |
strcat(element,tcount); |
| 2324 |
} |
| 2325 |
} |
| 2326 |
*/ |
| 2327 |
if (atom->GetFormalCharge() > 0) |
| 2328 |
strcat(element,"+"); |
| 2329 |
else |
| 2330 |
strcat(element,"-"); |
| 2331 |
|
| 2332 |
if (abs(atom->GetFormalCharge()) > 1) |
| 2333 |
{ |
| 2334 |
char tcharge[10]; |
| 2335 |
sprintf(tcharge,"%d",abs(atom->GetFormalCharge())); |
| 2336 |
strcat(element,tcharge); |
| 2337 |
} |
| 2338 |
} |
| 2339 |
|
| 2340 |
strcat(element,"]"); |
| 2341 |
|
| 2342 |
return(true); |
| 2343 |
} |
| 2344 |
|
| 2345 |
bool OBMol2Smi::GetChiralStereo(OBSmiNode *node,char *stereo) |
| 2346 |
{ |
| 2347 |
bool is2D=false; |
| 2348 |
double torsion; |
| 2349 |
OBAtom *a,*b,*c,*d,hydrogen; |
| 2350 |
|
| 2351 |
b = node->GetAtom(); |
| 2352 |
OBMol *mol = (OBMol*)b->GetParent(); |
| 2353 |
|
| 2354 |
if (!mol->HasNonZeroCoords()) //must have come in from smiles string |
| 2355 |
{ |
| 2356 |
if (!b->HasChiralitySpecified()) |
| 2357 |
return(false); |
| 2358 |
if (b->IsClockwise()) |
| 2359 |
strcpy(stereo,"@@"); |
| 2360 |
else if (b->IsAntiClockwise()) |
| 2361 |
strcpy(stereo,"@"); |
| 2362 |
else |
| 2363 |
return(false); |
| 2364 |
//if (b->GetHvyValence() == 3) strcat(stereo,"H"); |
| 2365 |
return(true); |
| 2366 |
} |
| 2367 |
|
| 2368 |
//give peudo Z coords if mol is 2D |
| 2369 |
if (!mol->Has3D()) |
| 2370 |
{ |
| 2371 |
vector3 v,vz(0.0,0.0,1.0); |
| 2372 |
is2D = true; |
| 2373 |
OBAtom *nbr; |
| 2374 |
OBBond *bond; |
| 2375 |
vector<OBEdgeBase*>::iterator i; |
| 2376 |
for (bond = b->BeginBond(i);bond;bond = b->NextBond(i)) |
| 2377 |
{ |
| 2378 |
nbr = bond->GetEndAtom(); |
| 2379 |
if (nbr != b) |
| 2380 |
{ |
| 2381 |
v = nbr->GetVector(); |
| 2382 |
if (bond->IsWedge()) |
| 2383 |
v += vz; |
| 2384 |
else if (bond->IsHash()) |
| 2385 |
v -= vz; |
| 2386 |
|
| 2387 |
nbr->SetVector(v); |
| 2388 |
} |
| 2389 |
else |
| 2390 |
{ |
| 2391 |
nbr = bond->GetBeginAtom(); |
| 2392 |
v = nbr->GetVector(); |
| 2393 |
if (bond->IsWedge()) |
| 2394 |
v -= vz; |
| 2395 |
else if (bond->IsHash()) |
| 2396 |
v += vz; |
| 2397 |
|
| 2398 |
nbr->SetVector(v); |
| 2399 |
} |
| 2400 |
} |
| 2401 |
} |
| 2402 |
|
| 2403 |
c = d = NULL; |
| 2404 |
a = node->GetParent(); |
| 2405 |
// obAssert(a); //chiral atom can't be used as root node - must have parent |
| 2406 |
|
| 2407 |
if (b->GetHvyValence() == 3) //must have attached hydrogen |
| 2408 |
{ |
| 2409 |
if (b->GetValence() == 4) //has explicit hydrogen |
| 2410 |
{ |
| 2411 |
vector<OBEdgeBase*>::iterator i; |
| 2412 |
for (c = b->BeginNbrAtom(i);c;c = b->NextNbrAtom(i)) |
| 2413 |
if (c->IsHydrogen()) |
| 2414 |
break; |
| 2415 |
// obAssert(c); |
| 2416 |
} |
| 2417 |
else //implicit hydrogen |
| 2418 |
{ |
| 2419 |
vector3 v; |
| 2420 |
b->GetNewBondVector(v,1.0); |
| 2421 |
hydrogen.SetVector(v); |
| 2422 |
c = &hydrogen; |
| 2423 |
} |
| 2424 |
} |
| 2425 |
|
| 2426 |
//get connected atoms in order |
| 2427 |
OBAtom *nbr; |
| 2428 |
vector<int>::iterator j; |
| 2429 |
|
| 2430 |
//try to get neighbors that are closure atoms in the order they appear in the string |
| 2431 |
vector<OBNodeBase*> va; |
| 2432 |
GetClosureAtoms(b,va); |
| 2433 |
if (!va.empty()) |
| 2434 |
{ |
| 2435 |
vector<OBNodeBase*>::iterator k; |
| 2436 |
for (k = va.begin();k != va.end();k++) |
| 2437 |
if (*k != a) |
| 2438 |
{ |
| 2439 |
if (!c) |
| 2440 |
c = (OBAtom*)*k; |
| 2441 |
else if (!d) |
| 2442 |
d = (OBAtom*)*k; |
| 2443 |
} |
| 2444 |
} |
| 2445 |
|
| 2446 |
for (j = _storder.begin();j != _storder.end();j++) |
| 2447 |
{ |
| 2448 |
nbr = mol->GetAtom(*j); |
| 2449 |
if (!b->IsConnected(nbr)) |
| 2450 |
continue; |
| 2451 |
if (nbr == a || nbr == b || nbr == c) |
| 2452 |
continue; |
| 2453 |
if (!c) |
| 2454 |
c = nbr; |
| 2455 |
else if (!d) |
| 2456 |
d = nbr; |
| 2457 |
} |
| 2458 |
|
| 2459 |
torsion = CalcTorsionAngle(a->GetVector(),b->GetVector(), |
| 2460 |
c->GetVector(),d->GetVector()); |
| 2461 |
|
| 2462 |
// if we have a 2D structure with marked unspecified chirality |
| 2463 |
// we should leave it blank and return false |
| 2464 |
bool success = false; |
| 2465 |
if ( !(is2D && b->IsChiral() && !b->HasChiralitySpecified()) ) |
| 2466 |
{ |
| 2467 |
strcpy(stereo,(torsion<0.0)?"@":"@@"); |
| 2468 |
success = true; |
| 2469 |
} |
| 2470 |
//if (b->GetHvyValence() == 3) strcat(stereo,"H"); |
| 2471 |
|
| 2472 |
//re-zero psuedo-coords |
| 2473 |
if (is2D) |
| 2474 |
{ |
| 2475 |
vector3 v; |
| 2476 |
OBAtom *atom; |
| 2477 |
vector<OBNodeBase*>::iterator k; |
| 2478 |
for (atom = mol->BeginAtom(k);atom;atom = mol->NextAtom(k)) |
| 2479 |
{ |
| 2480 |
v = atom->GetVector(); |
| 2481 |
v.SetZ(0.0); |
| 2482 |
atom->SetVector(v); |
| 2483 |
} |
| 2484 |
} |
| 2485 |
|
| 2486 |
return(success); |
| 2487 |
} |
| 2488 |
//******************************************************** |
| 2489 |
class FIXFormat : public OBFormat |
| 2490 |
{ |
| 2491 |
public: |
| 2492 |
//Register this format type ID |
| 2493 |
FIXFormat() |
| 2494 |
{ |
| 2495 |
OBConversion::RegisterFormat("fix",this); |
| 2496 |
} |
| 2497 |
|
| 2498 |
virtual const char* Description() //required |
| 2499 |
{ |
| 2500 |
return |
| 2501 |
"SMILES FIX format\n \ |
| 2502 |
No comments yet\n \ |
| 2503 |
"; |
| 2504 |
}; |
| 2505 |
|
| 2506 |
virtual const char* SpecificationURL(){return "";}; //optional |
| 2507 |
|
| 2508 |
//Flags() can return be any the following combined by | or be omitted if none apply |
| 2509 |
// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY |
| 2510 |
virtual unsigned int Flags() |
| 2511 |
{ |
| 2512 |
return NOTREADABLE; |
| 2513 |
}; |
| 2514 |
|
| 2515 |
//////////////////////////////////////////////////// |
| 2516 |
/// The "API" interface functions |
| 2517 |
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
| 2518 |
|
| 2519 |
//////////////////////////////////////////////////// |
| 2520 |
/// The "Convert" interface functions |
| 2521 |
virtual bool WriteChemObject(OBConversion* pConv) |
| 2522 |
{ |
| 2523 |
//Retrieve the target OBMol |
| 2524 |
OBBase* pOb = pConv->GetChemObject(); |
| 2525 |
OBMol* pmol = dynamic_cast<OBMol*> (pOb); |
| 2526 |
bool ret=false; |
| 2527 |
if(pmol) |
| 2528 |
ret=WriteMolecule(pmol,pConv); |
| 2529 |
delete pOb; |
| 2530 |
return ret; |
| 2531 |
}; |
| 2532 |
}; |
| 2533 |
|
| 2534 |
//Make an instance of the format class |
| 2535 |
FIXFormat theFIXFormat; |
| 2536 |
|
| 2537 |
///////////////////////////////////////////////////////////////// |
| 2538 |
|
| 2539 |
bool FIXFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
| 2540 |
{ |
| 2541 |
OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
| 2542 |
if(pmol==NULL) |
| 2543 |
return false; |
| 2544 |
|
| 2545 |
//Define some references so we can use the old parameter names |
| 2546 |
ostream &ofs = *pConv->GetOutStream(); |
| 2547 |
OBMol &mol = *pmol; |
| 2548 |
|
| 2549 |
char buffer[BUFF_SIZE]; |
| 2550 |
OBMol2Smi m2s; |
| 2551 |
|
| 2552 |
// This is a hack to prevent recursion problems. |
| 2553 |
// we still need to fix the underlying problem -GRH |
| 2554 |
if (mol.NumAtoms() > 1000) |
| 2555 |
{ |
| 2556 |
#ifdef HAVE_SSTREAM |
| 2557 |
stringstream errorMsg; |
| 2558 |
#else |
| 2559 |
strstream errorMsg; |
| 2560 |
#endif |
| 2561 |
errorMsg << "SMILES Conversion failed: Molecule is too large to convert. Open Babel is currently limited to 1000 atoms." << endl; |
| 2562 |
errorMsg << " Molecule size: " << mol.NumAtoms() << " atoms " << endl; |
| 2563 |
obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo); |
| 2564 |
return(false); |
| 2565 |
} |
| 2566 |
|
| 2567 |
m2s.Init(); |
| 2568 |
//m2s.AssignCisTrans(mol); |
| 2569 |
m2s.CorrectAromaticAmineCharge(mol); |
| 2570 |
m2s.CreateSmiString(mol,buffer); |
| 2571 |
|
| 2572 |
OBAtom *atom; |
| 2573 |
vector<int>::iterator i; |
| 2574 |
vector<int> order = m2s.GetOutputOrder(); |
| 2575 |
ofs << buffer << endl; |
| 2576 |
|
| 2577 |
int j; |
| 2578 |
for (j = 0;j < mol.NumConformers();j++) |
| 2579 |
{ |
| 2580 |
mol.SetConformer(j); |
| 2581 |
for (i = order.begin();i != order.end();i++) |
| 2582 |
{ |
| 2583 |
atom = mol.GetAtom(*i); |
| 2584 |
sprintf(buffer,"%9.3f %9.3f %9.3f",atom->GetX(),atom->GetY(),atom->GetZ()); |
| 2585 |
ofs << buffer<< endl; |
| 2586 |
} |
| 2587 |
} |
| 2588 |
return(true); |
| 2589 |
} |
| 2590 |
|
| 2591 |
OBSmiNode::OBSmiNode(OBAtom *atom) |
| 2592 |
{ |
| 2593 |
_atom = atom; |
| 2594 |
_parent = NULL; |
| 2595 |
_nextnode.clear(); |
| 2596 |
_nextbond.clear(); |
| 2597 |
} |
| 2598 |
|
| 2599 |
void OBSmiNode::SetNextNode(OBSmiNode *node,OBBond *bond) |
| 2600 |
{ |
| 2601 |
_nextnode.push_back(node); |
| 2602 |
_nextbond.push_back(bond); |
| 2603 |
} |
| 2604 |
|
| 2605 |
OBSmiNode::~OBSmiNode() |
| 2606 |
{ |
| 2607 |
vector<OBSmiNode*>::iterator i; |
| 2608 |
for (i = _nextnode.begin();i != _nextnode.end();i++) |
| 2609 |
delete (*i); |
| 2610 |
} |
| 2611 |
|
| 2612 |
|
| 2613 |
bool WriteTheSmiles(OBMol & mol,char *out) |
| 2614 |
{ |
| 2615 |
char buffer[2*BUFF_SIZE]; |
| 2616 |
|
| 2617 |
OBMol2Smi m2s; |
| 2618 |
|
| 2619 |
m2s.Init(); |
| 2620 |
m2s.CorrectAromaticAmineCharge(mol); |
| 2621 |
m2s.CreateSmiString(mol,buffer); |
| 2622 |
|
| 2623 |
strcpy(out,buffer); |
| 2624 |
return(true); |
| 2625 |
|
| 2626 |
} |
| 2627 |
} |
