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"
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());
    }

    WriteMDFile(mdMols, numMols);    

    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, 
    for (unsigned int i =0 ; i < frag1.size(); ++i)
    {
        if (strcmp(mol.GetAtom(frag1[i])->GetType(), mol.GetAtom(frag2[i])->GetType()) )
        {
            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)
{
    std::string identLevel1("\t");
    std::string identLevel2("\t\t");
    std::string molPrefix("MolName");
    ostream& ofs = std::cout;
    const int BUFFLEN = 1024;
    char buffer[BUFFLEN];
    
    for(unsigned int i = 0; i < mols.size(); ++i)
    {
        OBMol* pmol = mols[i];
        map<OBAtom*, int> atomMap;
        ofs << "molecule {\n";
        sprintf(buffer, "%d", i);
        ofs << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";

        
        //atom
        ofs << identLevel1 << "nAtoms = " << pmol->NumAtoms() << ";\n";
        int ai = 0;
        FOR_ATOMS_OF_MOL(atom, *pmol ) {
            ofs << identLevel1 << "atom[" << ai << "] {\n";
            ofs << identLevel2 << "type = " << "\"" << atom->GetType() << "\"" << ";\n";
            ofs << identLevel2 << "position(" << atom->GetX() << ", " << atom->GetY() << ", " << atom->GetZ() << ");\n";
            ofs << identLevel1 << "}\n";
            atomMap[&(*atom)] = ai++;
        }        

        //bond
        ofs << identLevel1 << "nBonds = " << pmol->NumBonds() << ";\n";
        int bi = 0;
        FOR_BONDS_OF_MOL(bond, *pmol ) {
            ofs << identLevel1 << "bond[" << bi++ << "] {\n";
            ofs << identLevel2 << "member(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << ");\n";
            ofs << identLevel1 << "}\n";
        }  
        /*
        //bend
        OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData);
        OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData);
        vector<OBAngle> angles = pAngleData->GetData();

        ofs << 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();
            ofs << identLevel1 << "bend[" << bendIndex++ << "] {\n";
            ofs << identLevel2 << "member(" << atomMap[bendAtoms.first] <<  ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n";
            ofs << 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());            
        }

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

    ofs << "nComponents = " << mols.size() << ";\n";
    
    for(unsigned int i =0; i < mols.size(); ++i)
    {
        ofs << "component{\n";
        sprintf(buffer, "%d", i);
        ofs << "type = " << molPrefix << buffer << ";\n";
        ofs << "nMol = " << numMols[i]<< ";\n";
        ofs << "}\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,"%15s%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",
                atom->GetType(),
                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:	2445
Committed:	Wed Nov 16 21:22:51 2005 UTC (18 years, 9 months ago) by tim
File size:	9551 byte(s)
Log Message:	adding more readers/writers
#	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	2440	namespace OpenBabel
18			{
19
20			bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
21			{
22			OBMol* pmol = dynamic_cast<OBMol*>(pOb);
23			if(pmol==NULL)
24			return false;
25
26			vector<vector<int> > fragmentLists;
27			pmol->ContigFragList(fragmentLists);
28			OBBitVec unused;
29			vector<bool> used(fragmentLists.size(), 0);
30			vector<vector<int> > molecules;
31			vector<int> indices;
32			for(int i =0; i < used.size(); ++i) {
33			if (used[i])
34			{
35			continue;
36			}
37			used[i] = true;
38			vector<int> sameMolTypes;
39			sameMolTypes.push_back(i);
40			indices.insert(indices.end(), fragmentLists[i].begin(), fragmentLists[i].end());
41			for (int j = i + 1;j < used.size(); ++j)
42			{
43			if (used[j])
44			{
45			continue;
46			}
47
48			if (AreSameFragments(*pmol, fragmentLists[i], fragmentLists[j]))
49			{
50			sameMolTypes.push_back(j);
51			indices.insert(indices.end(), fragmentLists[j].begin(), fragmentLists[j].end());
52			used[j]=true;
53			}
54			}
55			molecules.push_back(sameMolTypes);
56
57			}
58
59			//
60			vector<OBMol*> mdMols;
61			vector<int> numMols;
62			for(vector<vector<int> >::iterator i = molecules.begin(); i != molecules.end(); ++i)
63			{
64			mdMols.push_back(createMolFromFragment(*pmol, fragmentLists[i->front()]));
65			numMols.push_back((*i).size());
66			}
67
68			WriteMDFile(mdMols, numMols);
69
70			for(vector<OBMol*>::iterator i = mdMols.begin(); i != mdMols.end(); ++i)
71			{
72			delete *i;
73			}
74
75			//
76			WriteINFile(pmol, pConv->GetOutStream(), indices);
77
78
79
80			return(true);
81			}
82
83			bool OOPSEFormat::AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2)
84			{
85			if (frag1.size() != frag2.size())
86			{
87			return false;
88			}
89
90			//exact graph matching is a NP complete problem,
91			for (unsigned int i =0 ; i < frag1.size(); ++i)
92			{
93			if (strcmp(mol.GetAtom(frag1[i])->GetType(), mol.GetAtom(frag2[i])->GetType()) )
94			{
95			return false;
96			}
97			}
98			return true;
99			}
100
101			struct SameAngle
102			{
103			bool operator()(const triple<OBAtom,OBAtom,OBAtom> t1, const triple<OBAtom,OBAtom,OBAtom> t2) const
104			{
105			return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) \|\| (t1.first == t2.third && t1.third == t2.first));
106			}
107			};
108
109			void OOPSEFormat::findAngles(OBMol& mol)
110			{
111			/*
112			//if already has data return
113			if(mol.HasData(OBGenericDataType::AngleData))
114			return;
115
116			vector<OBEdgeBase*>::iterator bi1,bi2;
117			OBBond* bond;
118			OBAtom a,b,*c;
119
120			set<triple<OBAtom,OBAtom,OBAtom*>, SameAngle> uniqueAngles;
121			//loop through all bonds generating torsions
122			for(bond = mol.BeginBond(bi1);bond;bond = mol.NextBond(bi1))
123			{
124			b = bond->GetBeginAtom();
125			c = bond->GetEndAtom();
126			if(b->IsHydrogen())
127			continue;
128
129			for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2))
130			{
131			if(a == c)
132			continue;
133
134			uniqueAngles.insert(triple<OBAtom,OBAtom,OBAtom*>(a, b, c));
135			}
136			}
137
138			//get new data and attach it to molecule
139			OBAngleData *angles = new OBAngleData;
140			mol.SetData(angles);
141			set<triple<OBAtom,OBAtom,OBAtom*>, SameAngle>::iterator i;
142
143			for (i = uniqueAngles.begin(); i != uniqueAngles.end(); ++i) {
144			OBAngle angle;
145			angle.SetAtoms(i->first, i->second, i->second);
146			angles->SetData(angle);
147			}
148			*/
149			}
150			OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment)
151			{
152			OBMol* newMol = new OBMol();
153			newMol->ReserveAtoms(fragment.size());
154			newMol->BeginModify();
155			for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i)
156			{
157			OBAtom* newAtom = newMol->NewAtom();
158			newAtom = mol.GetAtom(*i);
159			}
160			newMol->EndModify();
161			newMol->ConnectTheDots();
162			findAngles(*newMol);
163			newMol->FindTorsions();
164			return newMol;
165			}
166			void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols)
167			{
168			std::string identLevel1("\t");
169			std::string identLevel2("\t\t");
170			std::string molPrefix("MolName");
171			ostream& ofs = std::cout;
172			const int BUFFLEN = 1024;
173			char buffer[BUFFLEN];
174
175			for(unsigned int i = 0; i < mols.size(); ++i)
176			{
177			OBMol* pmol = mols[i];
178			map<OBAtom*, int> atomMap;
179			ofs << "molecule {\n";
180			sprintf(buffer, "%d", i);
181			ofs << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";
182
183
184			//atom
185			ofs << identLevel1 << "nAtoms = " << pmol->NumAtoms() << ";\n";
186			int ai = 0;
187			FOR_ATOMS_OF_MOL(atom, *pmol ) {
188			ofs << identLevel1 << "atom[" << ai << "] {\n";
189			ofs << identLevel2 << "type = " << "\"" << atom->GetType() << "\"" << ";\n";
190			ofs << identLevel2 << "position(" << atom->GetX() << ", " << atom->GetY() << ", " << atom->GetZ() << ");\n";
191			ofs << identLevel1 << "}\n";
192			atomMap[&(*atom)] = ai++;
193			}
194
195			//bond
196			ofs << identLevel1 << "nBonds = " << pmol->NumBonds() << ";\n";
197			int bi = 0;
198			FOR_BONDS_OF_MOL(bond, *pmol ) {
199			ofs << identLevel1 << "bond[" << bi++ << "] {\n";
200			ofs << identLevel2 << "member(" << atomMap[bond->GetBeginAtom()] << ", " << atomMap[bond->GetEndAtom()] << ");\n";
201			ofs << identLevel1 << "}\n";
202			}
203			/*
204			//bend
205			OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData);
206			OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData);
207			vector<OBAngle> angles = pAngleData->GetData();
208
209			ofs << identLevel1 << "nBends = " << angles.size() << ";\n";
210			int bendIndex = 0;
211			for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti)
212			{
213			triple<OBAtom, OBAtom, OBAtom*> bendAtoms = ti->getAtoms();
214			ofs << identLevel1 << "bend[" << bendIndex++ << "] {\n";
215			ofs << identLevel2 << "member(" << atomMap[bendAtoms.first] << ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n";
216			ofs << identLevel1 << "}\n";
217			}
218
219			//torsion
220			pGenericData = pmol->GetData(OBGenericDataType::TorsionData);
221			OBTorsionData* pTorsionData = dynamic_cast<OBTorsionData*>(pGenericData);
222			vector<OBTorsion> torsions = pTorsionData->GetData();
223			vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> > torsionArray;
224			for (vector<OBTorsion>::iterator ti = torsions.begin(); ti != torsions.end(); ++ti)
225			{
226			vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> > tmpTorsions = ti->getTorsions();
227			torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end());
228			}
229
230			ofs << identLevel1 << "nTorsions = " << torsionArray.size() << ";\n";
231			int torsionIndex = 0;
232			for (vector<quad<OBAtom,OBAtom,OBAtom,OBAtom> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti)
233			{
234			ofs << identLevel1 << "torsion[" << torsionIndex++ << "] {\n";
235			ofs << identLevel2 << "member(" << atomMap[ti->first] << ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n";
236			ofs << identLevel1 << "}\n";
237			}
238			*/
239			ofs << "}\n";
240			}
241
242			ofs << "nComponents = " << mols.size() << ";\n";
243
244			for(unsigned int i =0; i < mols.size(); ++i)
245			{
246			ofs << "component{\n";
247			sprintf(buffer, "%d", i);
248			ofs << "type = " << molPrefix << buffer << ";\n";
249			ofs << "nMol = " << numMols[i]<< ";\n";
250			ofs << "}\n";
251			}
252			}
253			void OOPSEFormat::WriteINFile(OBMol& mol, ostream& ofs, vector<int>& indices)
254			{
255			unsigned int i;
256			char buffer[BUFF_SIZE];
257
258			sprintf(buffer,"%d", mol.NumAtoms());
259			ofs << buffer << endl;
260			//sprintf(buffer,"0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", boxx, boxy, boxz);
261			sprintf(buffer, "0;%f, 0, 0; 0, %15.7f, 0; 0, 0, %15.7f;", 100.0, 100.0, 100.0);
262			ofs << buffer << endl;
263
264			OBAtom *atom;
265			string str,str1;
266
267			for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i)
268			{
269			atom = mol.GetAtom(*i);
270			sprintf(buffer,"%15s%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",
271			atom->GetType(),
272			atom->GetX(), atom->GetY(), atom->GetZ(),
273			0.0, 0.0, 0.0,
274			0.0, 0.0, 0.0, 0.0,
275			0.0, 0.0, 0.0
276			);
277			ofs << buffer << endl;
278			}
279
280			}
281
282			} //namespace OpenBabel
283