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