bool ReportFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
char buffer[BUFF_SIZE];
ofs << "FILENAME: " << mol.GetTitle() << "\n";
ofs << "FORMULA: " << mol.GetFormula() << "\n";
ofs << "MASS: ";
snprintf(buffer, BUFF_SIZE, "%5.4f\n", mol.GetMolWt());
ofs << buffer;
ofs << "EXACT MASS: ";
snprintf(buffer, BUFF_SIZE, "%5.7f", mol.GetExactMass());
ofs << buffer << "\n";
if (mol.GetTotalCharge() != 0)
{
ofs << "TOTAL CHARGE: ";
snprintf(buffer, BUFF_SIZE, "%d", mol.GetTotalCharge());
ofs << buffer << "\n";
}
if (mol.GetTotalSpinMultiplicity() != 1)
{
ofs << "TOTAL SPIN: ";
snprintf(buffer, BUFF_SIZE, "%d", mol.GetTotalSpinMultiplicity());
ofs << buffer << "\n";
}
ofs << "INTERATOMIC DISTANCES" << "\n";
WriteDistanceMatrix(ofs, mol);
ofs << "\n" << "\n" << "ATOMIC CHARGES" << "\n";
WriteCharges(ofs, mol);
ofs << "\n" << "\n" << "BOND ANGLES" << "\n";
WriteAngles(ofs, mol);
ofs << "\n" << "\n" << "TORSION ANGLES" << "\n";
WriteTorsions(ofs, mol);
if (OldIsChiral(mol)) // TODO: Replace with this current stereo approach
{
ofs << "\n" << "\n" << "CHIRAL ATOMS" << "\n";
WriteChiral(ofs, mol);
}
if (mol.HasData(OBGenericDataType::CommentData))
{
ofs << "\n" << "\n" << "COMMENTS" << "\n";
OBCommentData *cd = (OBCommentData*)mol.GetData(OBGenericDataType::CommentData);
ofs << cd->GetData() << "\n";
}
ofs << "\n" << "\n";
return(true);
}
bool WriteReport(ostream &ofs,OBMol &mol)
{
char buffer[BUFF_SIZE];
ofs << "FILENAME: " << mol.GetTitle() << endl;
ofs << "MASS: ";
sprintf(buffer, "%5.4f", mol.GetMolWt());
ofs << buffer << endl;
ofs << "EXACT MASS: ";
sprintf(buffer, "%5.7f", mol.GetExactMass());
ofs << buffer << endl;
if (mol.GetTotalCharge() != 0)
{
ofs << "TOTAL CHARGE: ";
sprintf(buffer, "%d", mol.GetTotalCharge());
ofs << buffer << endl;
}
if (mol.GetTotalSpinMultiplicity() != 1)
{
ofs << "TOTAL SPIN: ";
sprintf(buffer, "%d", mol.GetTotalSpinMultiplicity());
ofs << buffer << endl;
}
ofs << "INTERATOMIC DISTANCES" << endl;
WriteDistanceMatrix(ofs, mol);
ofs << endl << endl << "ATOMIC CHARGES" << endl;
WriteCharges(ofs, mol);
ofs << endl << endl << "BOND ANGLES" << endl;
WriteAngles(ofs, mol);
ofs << endl << endl << "TORSION ANGLES" << endl;
WriteTorsions(ofs, mol);
if (mol.IsChiral())
{
ofs << endl << endl << "CHIRAL ATOMS" << endl;
WriteChiral(ofs, mol);
}
if (mol.HasData(obCommentData)) {
ofs << endl << endl << "COMMENTS" << endl;
OBCommentData *cd = (OBCommentData*)mol.GetData(obCommentData);
ofs << cd->GetData() << endl;
}
ofs << endl << endl;
return(true);
}
bool MOL2Format::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool ligandsOnly = pConv->IsOption("l", OBConversion::OUTOPTIONS)!=NULL;
//The old code follows....
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;
snprintf(buffer, BUFF_SIZE," %d %d 0 0 0", mol.NumAtoms(),mol.NumBonds());
ofs << buffer << endl;
ofs << "SMALL" << endl;
OBPairData *dp = (OBPairData*)mol.GetData("PartialCharges");
if (dp != NULL) {
// Tripos spec says:
// NO_CHARGES, DEL_RE, GASTEIGER, GAST_HUCK, HUCKEL, PULLMAN,
// GAUSS80_CHARGES, AMPAC_CHARGES, MULLIKEN_CHARGES, DICT_ CHARGES,
// MMFF94_CHARGES, USER_CHARGES
if (dp->GetValue() == "Mulliken")
ofs << "MULLIKEN_CHARGES" << endl;
else // should pick from the Tripos types
ofs << "GASTEIGER" << endl;
}
else { // No idea what these charges are... all our code sets "PartialCharges"
ofs << "GASTEIGER" << endl;
}
ofs << "Energy = " << mol.GetEnergy() << endl;
if (mol.HasData(OBGenericDataType::CommentData))
{
OBCommentData *cd = (OBCommentData*)mol.GetData(OBGenericDataType::CommentData);
ofs << cd->GetData();
}
ofs << endl;
ofs << "@<TRIPOS>ATOM" << endl;
OBAtom *atom;
OBResidue *res;
vector<OBAtom*>::iterator i;
vector<int> labelcount;
labelcount.resize( etab.GetNumberOfElements() );
ttab.SetFromType("INT");
ttab.SetToType("SYB");
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
//
// Use sequentially numbered atom names if no residues
//
snprintf(label,BUFF_SIZE, "%s%d",
etab.GetSymbol(atom->GetAtomicNum()),
++labelcount[atom->GetAtomicNum()]);
strcpy(rlabel,"<1>");
strcpy(rnum,"1");
str = atom->GetType();
ttab.Translate(str1,str);
//
// Use original atom names if there are residues
//
if (!ligandsOnly && (res = atom->GetResidue()) )
{
// use original atom names defined by residue
snprintf(label,BUFF_SIZE,"%s",(char*)res->GetAtomID(atom).c_str());
// make sure that residue name includes its number
snprintf(rlabel,BUFF_SIZE,"%s%d",res->GetName().c_str(), res->GetNum());
snprintf(rnum,BUFF_SIZE,"%d",res->GetNum());
}
snprintf(buffer,BUFF_SIZE,"%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<OBBond*>::iterator j;
OBSmartsPattern pat;
string s1, s2;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
s1 = bond->GetBeginAtom()->GetType();
s2 = bond->GetEndAtom()->GetType();
if (bond->IsAromatic() || s1 == "O.co2" || s2 == "O.co2")
strcpy(label,"ar");
else if (bond->IsAmide())
strcpy(label,"am");
else
snprintf(label,BUFF_SIZE,"%d",bond->GetBO());
snprintf(buffer, BUFF_SIZE,"%6d%6d%6d%3s%2s",
bond->GetIdx()+1,bond->GetBeginAtomIdx(),bond->GetEndAtomIdx(),
"",label);
ofs << buffer << endl;
}
// NO trailing blank line (PR#1868929).
// ofs << endl;
return(true);
}
