src/openbabel/oopseformat.cpp

/**********************************************************************
Copyright (C) 2000 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
Some portions Copyright (C) 2004 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 "oopseformat.hpp"
#include <fstream>
namespace OpenBabel
{

bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
        return false;
    
    vector<vector<int> > fragmentLists;
    pmol->ContigFragList(fragmentLists);
    OBBitVec unused;
    vector<bool> used(fragmentLists.size(), 0);
    vector<vector<int> > molecules;
    vector<int> indices;
    for(int i =0; i < used.size(); ++i) {
        if (used[i])
        {
            continue;
        }
        used[i] = true;
        vector<int> sameMolTypes;
        sameMolTypes.push_back(i);
        indices.insert(indices.end(), fragmentLists[i].begin(), fragmentLists[i].end());
        for (int j = i + 1;j < used.size(); ++j)
        {
            if (used[j])
            {
                continue;
            }
            
            if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j]))
            {
                sameMolTypes.push_back(j);
                indices.insert(indices.end(), fragmentLists[j].begin(), fragmentLists[j].end());
                used[j]=true;
            }
        }
        molecules.push_back(sameMolTypes);
        
    }

    //
    vector<OBMol*> mdMols;    
    vector<int> numMols;
    for(vector<vector<int> >::iterator  i = molecules.begin(); i != molecules.end(); ++i) 
    {
        mdMols.push_back(createMolFromFragment(*pmol, fragmentLists[i->front()]));
        numMols.push_back((*i).size());
    }

    string OutputFileName = pConv->GetInFilename();
    unsigned int pos = OutputFileName.rfind(".");
    if(pos==string::npos)
        OutputFileName += ".md";
    else
        OutputFileName = OutputFileName.substr(0, pos) + ".md";       
    ofstream ofs(OutputFileName.c_str());
    if(!ofs)
    {
         cerr << "Cannot write to " << OutputFileName <<endl;
         return false;
    }
                
    WriteMDFile(mdMols, numMols, ofs);    

    for(vector<OBMol*>::iterator  i = mdMols.begin(); i != mdMols.end(); ++i) 
    {
        delete *i;
    }

    //    
    WriteINFile(*pmol, *pConv->GetOutStream(), indices);


    return(true);
}

bool OOPSEFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2)
{
    if (frag1.size() != frag2.size())
    {
        return false;
    }

    //exact graph matching is a NP complete problem
    /** @todo using sparse matrix to store the connectivities*/
    for (unsigned int i =0 ; i < frag1.size(); ++i)
    {
        OBAtom* atom1 = mol.GetAtom(frag1[i]);
        OBAtom* atom2 = mol.GetAtom(frag2[i]);
        
        if (atom1->GetAtomicNum() != atom2->GetAtomicNum())
        {
            return false;
        }
    }
    return true;
}

struct SameAngle
{
  bool operator()(const triple<OBAtom*,OBAtom*,OBAtom*> t1, const triple<OBAtom*,OBAtom*,OBAtom*> t2) const
  {
    return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) || (t1.first == t2.third && t1.third == t2.first));
  }
};

void OOPSEFormat::findAngles(OBMol& mol)
{
    /*
    //if already has data return
    if(mol.HasData(OBGenericDataType::AngleData))
        return;

    vector<OBEdgeBase*>::iterator bi1,bi2;
    OBBond* bond;
    OBAtom *a,*b,*c;

    set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle> uniqueAngles;
    //loop through all bonds generating torsions
    for(bond = mol.BeginBond(bi1);bond;bond = mol.NextBond(bi1))
    {
        b = bond->GetBeginAtom();
        c = bond->GetEndAtom();
        if(b->IsHydrogen())
            continue;

        for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2))
        {
            if(a == c)
                continue;          
            
            uniqueAngles.insert(triple<OBAtom*,OBAtom*,OBAtom*>(a, b, c));
        }
    }

    //get new data and attach it to molecule
    OBAngleData *angles = new OBAngleData;
    mol.SetData(angles);
    set<triple<OBAtom*,OBAtom*,OBAtom*>, SameAngle>::iterator i;

    for (i = uniqueAngles.begin(); i != uniqueAngles.end(); ++i) {
        OBAngle angle;
        angle.SetAtoms(i->first, i->second, i->second);
        angles->SetData(angle);
    }
    */
}
OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment)
{
    OBMol* newMol = new OBMol();
    newMol->ReserveAtoms(fragment.size());
    newMol->BeginModify();
    for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i)
    {
        OBAtom* newAtom = newMol->NewAtom();
        *newAtom = *mol.GetAtom(*i);
    }
    newMol->EndModify();
    newMol->ConnectTheDots();
    findAngles(*newMol);
    newMol->FindTorsions();
    return newMol;
}
void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os)
{
    std::string identLevel1("\t");
    std::string identLevel2("\t\t");
    std::string molPrefix("MolName");
    const int BUFFLEN = 1024;
    char buffer[BUFFLEN];
    
    for(unsigned int i = 0; i < mols.size(); ++i)
    {
        OBMol* pmol = mols[i];
        map<OBAtom*, int> atomMap;
        os << "molecule {\n";
        sprintf(buffer, "%d", i);
        os << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";

        
        //atom
        int ai = 0;
        FOR_ATOMS_OF_MOL(atom, *pmol ) {
            os << identLevel1 << "atom[" << ai << "] {\n";
            os << identLevel2 << "type = " << "\"" << etab.GetSymbol(atom->GetAtomicNum()) << "\"" << ";\n";
            os << identLevel1 << "}\n";
            atomMap[&(*atom)] = ai++;
        }        
        os << "\n";

        //bond
        FOR_BONDS_OF_MOL(bond, *pmol ) {
            os << identLevel1 << "bond {\n";
            os << identLevel2 << "members(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << ");\n";
            os << identLevel1 << "}\n";
        }  
        /*
        //bend
        OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData);
        OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData);
        vector<OBAngle> angles = pAngleData->GetData();

        os << identLevel1 << "nBends = " << angles.size() << ";\n";        
        int bendIndex = 0;
        for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti)
        {
            triple<OBAtom*, OBAtom*, OBAtom*> bendAtoms = ti->getAtoms();
            os << identLevel1 << "bend[" << bendIndex++ << "] {\n";
            os << identLevel2 << "member(" << atomMap[bendAtoms.first] <<  ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n";
            os << identLevel1 << "}\n";            
        }
        
        //torsion
        pGenericData = pmol->GetData(OBGenericDataType::TorsionData);
        OBTorsionData* pTorsionData = dynamic_cast<OBTorsionData*>(pGenericData);
        vector<OBTorsion> torsions = pTorsionData->GetData();
        vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > torsionArray;
        for (vector<OBTorsion>::iterator ti = torsions.begin(); ti != torsions.end(); ++ti)
        {
            vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> > tmpTorsions = ti->getTorsions();
            torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end());            
        }

        os << identLevel1 << "nTorsions = " << torsionArray.size() << ";\n";
        int torsionIndex = 0;
        for (vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti)
        {
            os << identLevel1 << "torsion[" << torsionIndex++ << "] {\n";
            os << identLevel2 << "member(" << atomMap[ti->first] <<  ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n";
            os << identLevel1 << "}\n";          
        }
        */
        os << "}\n";
        os << "\n";

    }

    os << "\n";
    os << "nComponents = " << mols.size() << ";\n";
    
    for(unsigned int i =0; i < mols.size(); ++i)
    {
        os << "component{\n";
        sprintf(buffer, "%d", i);
        os << "type = " << molPrefix << buffer << ";\n";
        os << "nMol = " << numMols[i]<< ";\n";
        os << "}\n";
    }
}
void OOPSEFormat::WriteINFile(OBMol& mol, ostream& ofs, vector<int>& indices)
{
    unsigned int i;
    char buffer[BUFF_SIZE];
    
    sprintf(buffer,"%d", mol.NumAtoms());
    ofs << buffer << endl;
    //sprintf(buffer,"0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", boxx, boxy, boxz);
    sprintf(buffer, "0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", 100.0, 100.0, 100.0);
    ofs << buffer << endl;

    OBAtom *atom;
    string str,str1;
    
    for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i)
    {
        atom = mol.GetAtom(*i);
        sprintf(buffer,"%-10s%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f",
                etab.GetSymbol(atom->GetAtomicNum()),
                atom->GetX(), atom->GetY(), atom->GetZ(),
                0.0, 0.0, 0.0,
                0.0, 0.0, 0.0, 0.0,
                0.0, 0.0, 0.0
                );
        ofs << buffer << endl;
    }
    
}

} //namespace OpenBabel

Revision:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 9 months ago) by tim
File size:	9888 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	User	Rev	Content
1	tim	2440	/**********************************************************************
2			Copyright (C) 2000 by OpenEye Scientific Software, Inc.
3			Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
4			Some portions Copyright (C) 2004 by Chris Morley
5
6			This program is free software; you can redistribute it and/or modify
7			it under the terms of the GNU General Public License as published by
8			the Free Software Foundation version 2 of the License.
9
10			This program is distributed in the hope that it will be useful,
11			but WITHOUT ANY WARRANTY; without even the implied warranty of
12			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13			GNU General Public License for more details.
14			***********************************************************************/
15
16	tim	2445	#include "oopseformat.hpp"
17	tim	2455	#include <fstream>
18	tim	2440	namespace OpenBabel
19			{
20
21			bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
22			{
23			OBMol* pmol = dynamic_cast<OBMol*>(pOb);
24			if(pmol==NULL)
25			return false;
26
27			vector<vector<int> > fragmentLists;
28			pmol->ContigFragList(fragmentLists);
29			OBBitVec unused;
30			vector<bool> used(fragmentLists.size(), 0);
31			vector<vector<int> > molecules;
32			vector<int> indices;
33			for(int i =0; i < used.size(); ++i) {
34			if (used[i])
35			{
36			continue;
37			}
38			used[i] = true;
39			vector<int> sameMolTypes;
40			sameMolTypes.push_back(i);
41			indices.insert(indices.end(), fragmentLists[i].begin(), fragmentLists[i].end());
42			for (int j = i + 1;j < used.size(); ++j)
43			{
44			if (used[j])
45			{
46			continue;
47			}
48
49			if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j]))
50			{
51			sameMolTypes.push_back(j);
52			indices.insert(indices.end(), fragmentLists[j].begin(), fragmentLists[j].end());
53			used[j]=true;
54			}
55			}
56			molecules.push_back(sameMolTypes);
57
58			}
59
60			//
61			vector<OBMol*> mdMols;
62			vector<int> numMols;
63			for(vector<vector<int> >::iterator i = molecules.begin(); i != molecules.end(); ++i)
64			{
65			mdMols.push_back(createMolFromFragment(*pmol, fragmentLists[i->front()]));
66			numMols.push_back((*i).size());
67			}
68
69	tim	2455	string OutputFileName = pConv->GetInFilename();
70			unsigned int pos = OutputFileName.rfind(".");
71			if(pos==string::npos)
72			OutputFileName += ".md";
73			else
74			OutputFileName = OutputFileName.substr(0, pos) + ".md";
75			ofstream ofs(OutputFileName.c_str());
76			if(!ofs)
77			{
78			cerr << "Cannot write to " << OutputFileName <<endl;
79			return false;
80			}
81
82			WriteMDFile(mdMols, numMols, ofs);
83	tim	2440
84			for(vector<OBMol*>::iterator i = mdMols.begin(); i != mdMols.end(); ++i)
85			{
86			delete *i;
87			}
88
89			//
90			WriteINFile(pmol, pConv->GetOutStream(), indices);
91
92
93
94			return(true);
95			}
96
97			bool OOPSEFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2)
98			{
99			if (frag1.size() != frag2.size())
100			{
101			return false;
102			}
103
104	tim	2469	//exact graph matching is a NP complete problem
105			/** @todo using sparse matrix to store the connectivities*/
106	tim	2440	for (unsigned int i =0 ; i < frag1.size(); ++i)
107			{
108	tim	2469	OBAtom* atom1 = mol.GetAtom(frag1[i]);
109			OBAtom* atom2 = mol.GetAtom(frag2[i]);
110
111			if (atom1->GetAtomicNum() != atom2->GetAtomicNum())
112	tim	2440	{
113			return false;
114			}
115			}
116			return true;
117			}
118
119			struct SameAngle
120			{
121			bool operator()(const triple<OBAtom,OBAtom,OBAtom> t1, const triple<OBAtom,OBAtom,OBAtom> t2) const
122			{
123			return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) \|\| (t1.first == t2.third && t1.third == t2.first));
124			}
125			};
126
127			void OOPSEFormat::findAngles(OBMol& mol)
128			{
129			/*
130			//if already has data return
131			if(mol.HasData(OBGenericDataType::AngleData))
132			return;
133
134			vector<OBEdgeBase*>::iterator bi1,bi2;
135			OBBond* bond;
136			OBAtom a,b,*c;
137
138			set<triple<OBAtom,OBAtom,OBAtom*>, SameAngle> uniqueAngles;
139			//loop through all bonds generating torsions
140			for(bond = mol.BeginBond(bi1);bond;bond = mol.NextBond(bi1))
141			{
142			b = bond->GetBeginAtom();
143			c = bond->GetEndAtom();
144			if(b->IsHydrogen())
145			continue;
146
147			for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2))
148			{
149			if(a == c)
150			continue;
151
152			uniqueAngles.insert(triple<OBAtom,OBAtom,OBAtom*>(a, b, c));
153			}
154			}
155
156			//get new data and attach it to molecule
157			OBAngleData *angles = new OBAngleData;
158			mol.SetData(angles);
159			set<triple<OBAtom,OBAtom,OBAtom*>, SameAngle>::iterator i;
160
161			for (i = uniqueAngles.begin(); i != uniqueAngles.end(); ++i) {
162			OBAngle angle;
163			angle.SetAtoms(i->first, i->second, i->second);
164			angles->SetData(angle);
165			}
166			*/
167			}
168			OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment)
169			{
170			OBMol* newMol = new OBMol();
171			newMol->ReserveAtoms(fragment.size());
172			newMol->BeginModify();
173			for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i)
174			{
175			OBAtom* newAtom = newMol->NewAtom();
176			newAtom = mol.GetAtom(*i);
177			}
178			newMol->EndModify();
179			newMol->ConnectTheDots();
180			findAngles(*newMol);
181			newMol->FindTorsions();
182			return newMol;
183			}
184	tim	2455	void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os)
185	tim	2440	{
186			std::string identLevel1("\t");
187			std::string identLevel2("\t\t");
188			std::string molPrefix("MolName");
189			const int BUFFLEN = 1024;
190			char buffer[BUFFLEN];
191
192			for(unsigned int i = 0; i < mols.size(); ++i)
193			{
194			OBMol* pmol = mols[i];
195			map<OBAtom*, int> atomMap;
196	tim	2455	os << "molecule {\n";
197	tim	2440	sprintf(buffer, "%d", i);
198	tim	2455	os << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";
199	tim	2440
200
201			//atom
202			int ai = 0;
203			FOR_ATOMS_OF_MOL(atom, *pmol ) {
204	tim	2455	os << identLevel1 << "atom[" << ai << "] {\n";
205	tim	2469	os << identLevel2 << "type = " << "\"" << etab.GetSymbol(atom->GetAtomicNum()) << "\"" << ";\n";
206	tim	2455	os << identLevel1 << "}\n";
207	tim	2440	atomMap[&(*atom)] = ai++;
208			}
209	tim	2458	os << "\n";
210	tim	2440
211			//bond
212			FOR_BONDS_OF_MOL(bond, *pmol ) {
213	tim	2455	os << identLevel1 << "bond {\n";
214			os << identLevel2 << "members(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << ");\n";
215			os << identLevel1 << "}\n";
216	tim	2440	}
217			/*
218			//bend
219			OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData);
220			OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData);
221			vector<OBAngle> angles = pAngleData->GetData();
222
223	tim	2455	os << identLevel1 << "nBends = " << angles.size() << ";\n";
224	tim	2440	int bendIndex = 0;
225			for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti)
226			{
227			triple<OBAtom, OBAtom, OBAtom*> bendAtoms = ti->getAtoms();
228	tim	2455	os << identLevel1 << "bend[" << bendIndex++ << "] {\n";
229			os << identLevel2 << "member(" << atomMap[bendAtoms.first] << ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n";
230			os << identLevel1 << "}\n";
231	tim	2440	}
232
233			//torsion
234			pGenericData = pmol->GetData(OBGenericDataType::TorsionData);
235			OBTorsionData* pTorsionData = dynamic_cast<OBTorsionData*>(pGenericData);
236			vector<OBTorsion> torsions = pTorsionData->GetData();
237			vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> > torsionArray;
238			for (vector<OBTorsion>::iterator ti = torsions.begin(); ti != torsions.end(); ++ti)
239			{
240			vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> > tmpTorsions = ti->getTorsions();
241			torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end());
242			}
243
244	tim	2455	os << identLevel1 << "nTorsions = " << torsionArray.size() << ";\n";
245	tim	2440	int torsionIndex = 0;
246			for (vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti)
247			{
248	tim	2455	os << identLevel1 << "torsion[" << torsionIndex++ << "] {\n";
249			os << identLevel2 << "member(" << atomMap[ti->first] << ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n";
250			os << identLevel1 << "}\n";
251	tim	2440	}
252			*/
253	tim	2455	os << "}\n";
254	tim	2458	os << "\n";
255
256	tim	2440	}
257
258	tim	2458	os << "\n";
259	tim	2455	os << "nComponents = " << mols.size() << ";\n";
260	tim	2440
261			for(unsigned int i =0; i < mols.size(); ++i)
262			{
263	tim	2455	os << "component{\n";
264	tim	2440	sprintf(buffer, "%d", i);
265	tim	2455	os << "type = " << molPrefix << buffer << ";\n";
266			os << "nMol = " << numMols[i]<< ";\n";
267			os << "}\n";
268	tim	2440	}
269			}
270			void OOPSEFormat::WriteINFile(OBMol& mol, ostream& ofs, vector<int>& indices)
271			{
272			unsigned int i;
273			char buffer[BUFF_SIZE];
274
275			sprintf(buffer,"%d", mol.NumAtoms());
276			ofs << buffer << endl;
277			//sprintf(buffer,"0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", boxx, boxy, boxz);
278			sprintf(buffer, "0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", 100.0, 100.0, 100.0);
279			ofs << buffer << endl;
280
281			OBAtom *atom;
282			string str,str1;
283
284			for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i)
285			{
286			atom = mol.GetAtom(*i);
287	tim	2469	sprintf(buffer,"%-10s%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f%-15.5f",
288			etab.GetSymbol(atom->GetAtomicNum()),
289	tim	2440	atom->GetX(), atom->GetY(), atom->GetZ(),
290			0.0, 0.0, 0.0,
291			0.0, 0.0, 0.0, 0.0,
292			0.0, 0.0, 0.0
293			);
294			ofs << buffer << endl;
295			}
296
297			}
298
299			} //namespace OpenBabel
300