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/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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.h"
#include "smi.h"
using namespace std;
namespace OpenBabel {
bool ReadMol2(istream &ifs,OBMol &mol,char *title)
{
bool foundAtomLine = false;
char buffer[BUFF_SIZE];
char *comment = NULL;
string str,str1;
vector<string> vstr;
mol.BeginModify();
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
if (EQn(buffer,"@<TRIPOS>MOLECULE",17)) break;
}
int lcount;
int natoms,nbonds;
for (lcount=0;;lcount++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
if (EQn(buffer,"@<TRIPOS>ATOM",13)) {foundAtomLine = true; break;}
if (lcount == 0)
{
tokenize(vstr,buffer);
if (!vstr.empty()) mol.SetTitle(buffer);
}
else if (lcount == 1)
sscanf(buffer,"%d%d",&natoms,&nbonds);
else if (lcount == 4) //energy
{
tokenize(vstr,buffer);
if (!vstr.empty() && vstr[0] == "Energy" && vstr.size() == 3)
mol.SetEnergy(atof(vstr[2].c_str()));
}
else if (lcount == 5) //comment
{
if (strlen(buffer) != 0)
{
comment = new char [strlen(buffer)+1];
strcpy(comment,buffer);
}
}
}
if (!foundAtomLine)
{
mol.EndModify();
mol.Clear();
ThrowError("Unable to read Mol2 format file");
return(false);
}
mol.ReserveAtoms(natoms);
int i;
Vector v;
OBAtom atom;
bool hasPartialCharges=false;
float x,y,z,pcharge;
char temp_type[BUFF_SIZE];
ttab.SetFromType("SYB");
for (i = 0;i < natoms;i++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
sscanf(buffer," %*s %*s %f %f %f %s %*s %*s %f",
&x,&y,&z,
temp_type,
&pcharge);
v.SetX(x);v.SetY(y);v.SetZ(z);
atom.SetVector(v);
str = temp_type;
ttab.SetToType("ATN"); ttab.Translate(str1,str);
atom.SetAtomicNum(atoi(str1.c_str()));
ttab.SetToType("INT"); ttab.Translate(str1,str);
atom.SetType(str1);
atom.SetPartialCharge(pcharge);
if (!mol.AddAtom(atom)) return(false);
if (pcharge != 0.0f) hasPartialCharges = true;
}
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
str = buffer;
if (EQn(buffer,"@<TRIPOS>BOND",13)) break;
}
int start,end,order;
for (i = 0; i < nbonds; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
sscanf(buffer,"%*d %d %d %s",&start,&end,temp_type);
str = temp_type;
order = 1;
if (str == "ar" || str == "AR" || str == "Ar") order = 5;
else
if (str == "AM" || str == "am" || str == "Am") order = 1;
else order = atoi(str.c_str());
mol.AddBond(start,end,order);
}
mol.EndModify();
//must add generic data after end modify - otherwise it will be blown away
if (comment)
{
OBCommentData *cd = new OBCommentData;
cd->SetData(comment);
mol.SetData(cd);
delete [] comment;
}
if (hasPartialCharges)
mol.SetPartialChargesPerceived();
return(true);
}
bool WriteMol2(ostream &ofs,OBMol &mol,char *dimension)
{
string str,str1;
char buffer[BUFF_SIZE],label[BUFF_SIZE];
char rnum[BUFF_SIZE],rlabel[BUFF_SIZE];
ofs << "@<TRIPOS>MOLECULE" << endl;
str = mol.GetTitle();
if (str.empty()) ofs << "*****" << endl;
else ofs << str << endl;
sprintf(buffer, " %d %d 0 0 0", mol.NumAtoms(),mol.NumBonds());
ofs << buffer << endl;
ofs << "SMALL" << endl;
//if (mol.HasPartialChargesPerceived()) ofs << "GASTEIGER" << endl;
// else ofs << "NO_CHARGES" << endl;
ofs << "GASTEIGER" << endl;
ofs << "Energy = " << mol.GetEnergy() << endl;
if (mol.HasData("Comment"))
{
OBCommentData *cd = (OBCommentData*)mol.GetData(obCommentData);
ofs << cd->GetData();
}
ofs << endl;
ofs << "@<TRIPOS>ATOM" << endl;
ttab.SetFromType("INT");ttab.SetToType("SYB");
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
vector<int> labelcount;labelcount.resize(105); //Number of elements
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
sprintf(label,"%s%d",
etab.GetSymbol(atom->GetAtomicNum()),
++labelcount[atom->GetAtomicNum()]);
str = atom->GetType();
ttab.Translate(str1,str);
strcpy(rlabel,"<1>");
strcpy(rnum,"1");
sprintf(buffer,"%7d%1s%-6s%12.4f%10.4f%10.4f%1s%-5s%4s%1s %-8s%10.4f",
atom->GetIdx(),"",label,
atom->GetX(),atom->GetY(),atom->GetZ(),
"",str1.c_str(),
rnum,"",rlabel,
atom->GetPartialCharge());
ofs << buffer << endl;
}
ofs << "@<TRIPOS>BOND" << endl;
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
if (bond->GetBO() == 5) strcpy(label,"ar");
else if (bond->IsAmide()) strcpy(label,"am");
else sprintf(label,"%d",bond->GetBO());
sprintf(buffer, "%6d%6d%6d%3s%2s",
bond->GetIdx()+1,bond->GetBeginAtomIdx(),bond->GetEndAtomIdx(),
"",label);
ofs << buffer << endl;
}
ofs << endl;
return(true);
}
bool WriteSmiOrderedMol2(ostream &ofs,OBMol &mol,char *dimension)
{
string str,str1;
char buffer[BUFF_SIZE],label[BUFF_SIZE];
char rnum[BUFF_SIZE],rlabel[BUFF_SIZE];
ofs << "@<TRIPOS>MOLECULE" << endl;
str = mol.GetTitle();
if (str.empty()) ofs << "*****" << endl;
else ofs << str << endl;
sprintf(buffer, " %d %d 0 0 0", mol.NumAtoms(),mol.NumBonds());
ofs << buffer << endl;
ofs << "SMALL" << endl;
//if (mol.HasPartialChargesPerceived()) ofs << "GASTEIGER" << endl;
// else ofs << "NO_CHARGES" << endl;
ofs << "GASTEIGER" << endl;
ofs << "Energy = " << mol.GetEnergy() << endl;
if (mol.HasData("Comment"))
ofs << (char*)mol.GetData("Comment");
ofs << endl;
ofs << "@<TRIPOS>ATOM" << endl;
ttab.SetFromType("INT");ttab.SetToType("SYB");
//get smiles order
OBMol2Smi m2s;
char smibuffer[BUFF_SIZE];
m2s.Init();
m2s.CorrectAromaticAmineCharge(mol);
m2s.CreateSmiString(mol,smibuffer);
vector<int>::iterator idx;
vector<int> smiorder;
int *backmap = new int[mol.NumAtoms()];
smiorder = m2s.GetOutputOrder();
int ct;
OBAtom *atom;
// vector<OBNodeBase*>::iterator i;
vector<int> labelcount;labelcount.resize(105); //Number of elements
// for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
for(ct = 1,idx = smiorder.begin();idx != smiorder.end();idx++,ct++) //loop over smiles order
{
cerr << (*idx) << " ";
atom = mol.GetAtom(*idx); //set atom for .mol2 files
backmap[atom->GetIdx()] = ct;
sprintf(label,"%s%d",
etab.GetSymbol(atom->GetAtomicNum()),
++labelcount[atom->GetAtomicNum()]);
str = atom->GetType();
ttab.Translate(str1,str);
strcpy(rlabel,"<1>");
strcpy(rnum,"1");
sprintf(buffer,"%7d%1s%-6s%12.4f%10.4f%10.4f%1s%-5s%4s%1s %-8s%10.4f",
ct,"",label,
atom->GetX(),atom->GetY(),atom->GetZ(),
"",str1.c_str(),
rnum,"",rlabel,
atom->GetPartialCharge());
ofs << buffer << endl;
}
cerr << endl;
ofs << "@<TRIPOS>BOND" << endl;
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
if (bond->GetBO() == 5) strcpy(label,"ar");
else if (bond->IsAmide()) strcpy(label,"am");
else sprintf(label,"%d",bond->GetBO());
sprintf(buffer, "%6d%6d%6d%3s%2s",
bond->GetIdx()+1,backmap[bond->GetBeginAtomIdx()],backmap[bond->GetEndAtomIdx()],
"",label);
ofs << buffer << endl;
}
ofs << endl;
return(true);
}
}
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