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/********************************************************************** |
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Copyright (C) 2005 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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#include "mol.hpp" |
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#include "obconversion.hpp" |
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#include "obmolecformat.hpp" |
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#include "fingerprint.hpp" |
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#include <vector> |
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#include <string> |
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#include <iomanip> |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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|
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/// \brief Constructs and displays fingerprints. For details see OBFingerprint class |
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class FingerprintFormat : public OBMoleculeFormat |
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{ |
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public: |
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//Register this format type ID |
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FingerprintFormat() {OBConversion::RegisterFormat("fpt",this);} |
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|
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virtual const char* Description() //required |
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{ return |
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"Fingerprint format\n \ |
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Constructs and displays fingerprints and (for multiple input objects)\n \ |
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the Tanimoto coefficient and whether a superstructure of the first object\n \ |
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Options e.g. -xfFP3 -xn128\n \ |
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f<id> fingerprint type\n \ |
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N# fold to specified number of bits, 32, 64, 128, etc.\n \ |
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h hex output when multiple molecules\n \ |
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F displays the available fingerprint types\n \ |
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"; |
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}; |
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|
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virtual unsigned int Flags(){return NOTREADABLE;}; |
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virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
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|
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private: |
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vector<unsigned int> firstfp; |
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string firstname; |
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bool IsPossibleSubstructure(vector<unsigned int>Mol, vector<unsigned int>Frag); |
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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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FingerprintFormat theFingerprintFormat; |
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|
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//******************************************************************* |
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bool FingerprintFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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ostream &ofs = *pConv->GetOutStream(); |
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|
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OBFingerprint* pFP; |
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string id; |
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if(pConv->IsOption("F")) |
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{ |
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while(OBFingerprint::GetNextFPrt(id, pFP)) |
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ofs << id << " -- " << pFP->Description() << endl; |
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return true; |
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} |
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|
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|
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bool hexoutput=false; |
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if(pConv->IsOption("h") || (pConv->GetOutputIndex()==1 && pConv->IsLast())) |
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hexoutput=true; |
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|
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string fpid; |
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int nbits=0; |
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const char* p=pConv->IsOption("f"); |
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if(p) |
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{ |
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fpid=p; |
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fpid = fpid.substr(0,fpid.find('"')); |
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} |
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|
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pFP = OBFingerprint::FindFingerprint(fpid); |
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if(!pFP) |
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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 << "Fingerprint type '" << fpid << "' not available" << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obError); |
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return false; |
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} |
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|
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p=pConv->IsOption("N"); |
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if(p) |
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nbits = atoi(p); |
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|
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vector<unsigned int> fptvec; |
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if(!pFP->GetFingerprint(pOb, fptvec, nbits)) |
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return false; |
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|
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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if(pmol) |
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ofs << ">" << pmol->GetTitle(); |
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|
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if(hexoutput) |
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{ |
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unsigned int i, bitsset=0; |
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for (i=0;i<fptvec.size();++i) |
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{ |
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int wd = fptvec[i]; |
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for(;wd;wd=wd<<1)//count bits set by shifting into sign bit until word==0 |
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if(wd<0) ++bitsset; |
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} |
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ofs << " " << bitsset << " bits set. "; |
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} |
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|
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if(pConv->GetOutputIndex()==1) |
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{ |
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//store the fingerprint and name of first molecule |
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firstfp=fptvec; |
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if(pmol) |
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firstname=pmol->GetTitle(); |
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if(firstname.empty()) |
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firstname = "first mol"; |
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} |
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else |
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{ |
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ofs << " Tanimoto from " << firstname << " = " << OBFingerprint::Tanimoto(firstfp, fptvec); |
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if(IsPossibleSubstructure(fptvec,firstfp)) |
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ofs << "\nPossible superstructure of " << firstname; |
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} |
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ofs << endl; |
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|
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int i; |
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|
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if(hexoutput) |
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{ |
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for(i=fptvec.size()-1;i>=0;i--) |
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{ |
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ofs << hex << setfill('0') << setw(8) << fptvec[i] << " " ; |
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if((fptvec.size()-i)%6==0) |
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ofs <<endl; |
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} |
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ofs << dec << endl; |
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} |
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return true; |
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} |
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|
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bool FingerprintFormat::IsPossibleSubstructure(vector<unsigned int>Mol, vector<unsigned int>Frag) |
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{ |
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//Returns false if Frag is definitely NOT a substructure of Mol |
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unsigned int i; |
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for (i=0;i<Mol.size();++i) |
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if((Mol[i] & Frag[i]) ^ Frag[i]) return false; |
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return true; |
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} |
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|
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} //namespace OpenBabel |
