src/openbabel/fingerprintformat.cpp

/**********************************************************************
Copyright (C) 2005 by Chris Morley
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/
#include "mol.hpp"
#include "obconversion.hpp"
#include "obmolecformat.hpp"
#include "fingerprint.hpp"
#include <vector>
#include <string>
#include <iomanip>

using namespace std;
namespace OpenBabel
{

/// \brief Constructs and displays fingerprints. For details see OBFingerprint class
class FingerprintFormat : public OBMoleculeFormat
{
public:
        //Register this format type ID
        FingerprintFormat() {OBConversion::RegisterFormat("fpt",this);}

        virtual const char* Description() //required
        { return
"Fingerprint format\n \
Constructs and displays fingerprints and (for multiple input objects)\n \
the Tanimoto coefficient and whether a superstructure of the first object\n \
Options e.g. -xfFP3 -xn128\n \
 f<id> fingerprint type\n \
 N# fold to specified number of bits, 32, 64, 128, etc.\n \
 h  hex output when multiple molecules\n \
 F  displays the available fingerprint types\n \
";
        };

        virtual unsigned int Flags(){return NOTREADABLE;};
        virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);

private:
        vector<unsigned int> firstfp;
        string firstname;
        bool IsPossibleSubstructure(vector<unsigned int>Mol, vector<unsigned int>Frag);
};

////////////////////////////////////////////////////
//Make an instance of the format class
FingerprintFormat theFingerprintFormat;

//*******************************************************************
bool FingerprintFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
        ostream &ofs = *pConv->GetOutStream();

        OBFingerprint* pFP;
        string id;
        if(pConv->IsOption("F"))
        {
                while(OBFingerprint::GetNextFPrt(id, pFP))
                        ofs << id << " -- " << pFP->Description() << endl;
                return true;
        }


        bool hexoutput=false;
        if(pConv->IsOption("h") || (pConv->GetOutputIndex()==1 && pConv->IsLast()))
                hexoutput=true;

        string fpid;
        int nbits=0;
        const char* p=pConv->IsOption("f");
        if(p)
        {
                fpid=p;
                fpid = fpid.substr(0,fpid.find('"'));
        }

        pFP = OBFingerprint::FindFingerprint(fpid);
        if(!pFP)
        {
#ifdef HAVE_SSTREAM
          stringstream errorMsg;
#else
          strstream errorMsg;
#endif
                errorMsg << "Fingerprint type '" << fpid << "' not available" << endl;
                obErrorLog.ThrowError(__func__, errorMsg.str(), obError);
                return false;
        }

        p=pConv->IsOption("N");
        if(p)
                nbits = atoi(p);                

        vector<unsigned int> fptvec;
        if(!pFP->GetFingerprint(pOb, fptvec, nbits))
                return false;
        
        OBMol* pmol = dynamic_cast<OBMol*>(pOb);
        if(pmol)
                ofs << ">" << pmol->GetTitle();

        if(hexoutput)
        {
        unsigned int i, bitsset=0;
                for (i=0;i<fptvec.size();++i)
                {
                        int wd = fptvec[i];
                        for(;wd;wd=wd<<1)//count bits set by shifting into sign bit until word==0
                                if(wd<0) ++bitsset;
                }
                ofs  << "   " << bitsset << " bits set. "; 
        }

        if(pConv->GetOutputIndex()==1)
        {
                //store the fingerprint and name of first molecule
                firstfp=fptvec;
                if(pmol)
                        firstname=pmol->GetTitle();
                if(firstname.empty())
                        firstname = "first mol";
        }
        else
        {
                ofs << "   Tanimoto from " << firstname << " = " << OBFingerprint::Tanimoto(firstfp, fptvec);
                if(IsPossibleSubstructure(fptvec,firstfp))
                        ofs << "\nPossible superstructure of " << firstname;
        }
        ofs << endl;
        
        int i;

        if(hexoutput)
        {
                for(i=fptvec.size()-1;i>=0;i--)
                {
                        ofs << hex << setfill('0') << setw(8) << fptvec[i] << " " ;
                        if((fptvec.size()-i)%6==0)
                                ofs <<endl;
                }
                ofs << dec << endl;
        }
        return true;
}

bool FingerprintFormat::IsPossibleSubstructure(vector<unsigned int>Mol, vector<unsigned int>Frag)
{
        //Returns false if Frag is definitely NOT a substructure of Mol
    unsigned int i;
        for (i=0;i<Mol.size();++i)
                if((Mol[i] & Frag[i]) ^ Frag[i]) return false;
        return true;
}

} //namespace OpenBabel
Revision:	1081
Committed:	Thu Oct 19 20:49:05 2006 UTC (19 years ago) by gezelter
File size:	4262 byte(s)
Log Message:	updated OpenBabel to version 2.0.2
#	User	Rev	Content
1	tim	746	/**********************************************************************
2			Copyright (C) 2005 by Chris Morley
3
4			This program is free software; you can redistribute it and/or modify
5			it under the terms of the GNU General Public License as published by
6			the Free Software Foundation version 2 of the License.
7
8			This program is distributed in the hope that it will be useful,
9			but WITHOUT ANY WARRANTY; without even the implied warranty of
10			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11			GNU General Public License for more details.
12			***********************************************************************/
13	gezelter	1081	#include "mol.hpp"
14			#include "obconversion.hpp"
15			#include "obmolecformat.hpp"
16			#include "fingerprint.hpp"
17			#include <vector>
18			#include <string>
19			#include <iomanip>
20	tim	746
21			using namespace std;
22	gezelter	1081	namespace OpenBabel
23			{
24	tim	746
25	gezelter	1081	/// \brief Constructs and displays fingerprints. For details see OBFingerprint class
26			class FingerprintFormat : public OBMoleculeFormat
27			{
28			public:
29			//Register this format type ID
30			FingerprintFormat() {OBConversion::RegisterFormat("fpt",this);}
31
32			virtual const char* Description() //required
33			{ return
34			"Fingerprint format\n \
35			Constructs and displays fingerprints and (for multiple input objects)\n \
36			the Tanimoto coefficient and whether a superstructure of the first object\n \
37			Options e.g. -xfFP3 -xn128\n \
38			f<id> fingerprint type\n \
39			N# fold to specified number of bits, 32, 64, 128, etc.\n \
40			h hex output when multiple molecules\n \
41			F displays the available fingerprint types\n \
42			";
43			};
44
45			virtual unsigned int Flags(){return NOTREADABLE;};
46			virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
47
48			private:
49			vector<unsigned int> firstfp;
50			string firstname;
51			bool IsPossibleSubstructure(vector<unsigned int>Mol, vector<unsigned int>Frag);
52			};
53
54			////////////////////////////////////////////////////
55			//Make an instance of the format class
56			FingerprintFormat theFingerprintFormat;
57
58			//*******************************************************************
59	tim	746	bool FingerprintFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
60			{
61			ostream &ofs = *pConv->GetOutStream();
62
63			OBFingerprint* pFP;
64			string id;
65			if(pConv->IsOption("F"))
66			{
67			while(OBFingerprint::GetNextFPrt(id, pFP))
68			ofs << id << " -- " << pFP->Description() << endl;
69			return true;
70			}
71
72
73			bool hexoutput=false;
74			if(pConv->IsOption("h") \|\| (pConv->GetOutputIndex()==1 && pConv->IsLast()))
75			hexoutput=true;
76
77			string fpid;
78			int nbits=0;
79			const char* p=pConv->IsOption("f");
80			if(p)
81			{
82			fpid=p;
83			fpid = fpid.substr(0,fpid.find('"'));
84			}
85
86			pFP = OBFingerprint::FindFingerprint(fpid);
87			if(!pFP)
88			{
89			#ifdef HAVE_SSTREAM
90			stringstream errorMsg;
91			#else
92			strstream errorMsg;
93			#endif
94			errorMsg << "Fingerprint type '" << fpid << "' not available" << endl;
95	tim	819	obErrorLog.ThrowError(__func__, errorMsg.str(), obError);
96	tim	746	return false;
97			}
98
99			p=pConv->IsOption("N");
100			if(p)
101			nbits = atoi(p);
102
103			vector<unsigned int> fptvec;
104			if(!pFP->GetFingerprint(pOb, fptvec, nbits))
105			return false;
106
107			OBMol* pmol = dynamic_cast<OBMol*>(pOb);
108			if(pmol)
109			ofs << ">" << pmol->GetTitle();
110
111			if(hexoutput)
112			{
113	gezelter	1081	unsigned int i, bitsset=0;
114	tim	746	for (i=0;i<fptvec.size();++i)
115			{
116			int wd = fptvec[i];
117			for(;wd;wd=wd<<1)//count bits set by shifting into sign bit until word==0
118			if(wd<0) ++bitsset;
119			}
120			ofs << " " << bitsset << " bits set. ";
121			}
122
123			if(pConv->GetOutputIndex()==1)
124			{
125			//store the fingerprint and name of first molecule
126			firstfp=fptvec;
127			if(pmol)
128			firstname=pmol->GetTitle();
129			if(firstname.empty())
130			firstname = "first mol";
131			}
132			else
133			{
134			ofs << " Tanimoto from " << firstname << " = " << OBFingerprint::Tanimoto(firstfp, fptvec);
135			if(IsPossibleSubstructure(fptvec,firstfp))
136			ofs << "\nPossible superstructure of " << firstname;
137			}
138			ofs << endl;
139
140			int i;
141
142			if(hexoutput)
143			{
144			for(i=fptvec.size()-1;i>=0;i--)
145			{
146			ofs << hex << setfill('0') << setw(8) << fptvec[i] << " " ;
147			if((fptvec.size()-i)%6==0)
148			ofs <<endl;
149			}
150			ofs << dec << endl;
151			}
152			return true;
153			}
154
155			bool FingerprintFormat::IsPossibleSubstructure(vector<unsigned int>Mol, vector<unsigned int>Frag)
156			{
157			//Returns false if Frag is definitely NOT a substructure of Mol
158	gezelter	1081	unsigned int i;
159	tim	746	for (i=0;i<Mol.size();++i)
160			if((Mol[i] & Frag[i]) ^ Frag[i]) return false;
161			return true;
162			}
163
164			} //namespace OpenBabel