// Seems to make a vector chirality become filled with array of +/- 1 for chiral atoms.
void GetChirality(OBMol &mol, std::vector<int> &chirality)
{
chirality.resize(mol.NumAtoms()+1);
fill(chirality.begin(),chirality.end(),0);
OBAtom *atom;
vector<OBAtom*>::iterator i;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
if (atom->IsChiral())
{
if (!atom->HasChiralVolume())
{
double sv = CalcSignedVolume(mol,atom);
if (sv < 0.0)
{
chirality[atom->GetIdx()-1] = -1;
atom->SetNegativeStereo();
}
else if (sv > 0.0)
{
chirality[atom->GetIdx()-1] = 1;
atom->SetPositiveStereo();
}
}
else // already calculated signed volume (e.g., imported from somewhere)
{
if (atom ->IsPositiveStereo())
chirality[atom->GetIdx()-1] = 1;
else
chirality[atom->GetIdx()-1] = -1;
}
}
}
void WriteChiral(ostream &ofs,OBMol &mol)
{
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
char buffer[BUFF_SIZE];
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (atom->IsChiral())
{
sprintf(buffer,"%4s %5d is chiral: %s",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetIdx(),
(atom->IsClockwise() ? "clockwise" : "counterclockwise"));
ofs << buffer << endl;
}
}
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
char *FileIn = NULL;
if (argc != 2)
{
cout << "Usage: " << program_name << " <filename>" << endl;
exit(-1);
}
else
{
FileIn = argv[1];
// const char* p = strrchr(FileIn,'.');
}
// Find Input filetype
OBConversion conv;
OBFormat *format = conv.FormatFromExt(FileIn);
if (!format || !conv.SetInAndOutFormats(format, format))
{
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs)
{
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBAtom *atom;
for (int c=1;;++c) // big for loop (replace with do while?)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
cout << "Molecule "<< c << ": " << mol.GetTitle() << endl;
//mol.FindChiralCenters(); // labels all chiral atoms
vector<OBAtom*>::iterator i; // iterate over all atoms
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if(!atom->IsChiral())continue; // aborts if atom isn't chiral
cout << "Atom " << atom->GetIdx() << " Is Chiral ";
cout << atom->GetType()<<endl;
OBChiralData* cd = (OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
if (cd){
vector<unsigned int> x=cd->GetAtom4Refs(input);
size_t n=0;
cout <<"Atom4refs:";
for (n=0;n<x.size();++n)
cout <<" "<<x[n];
cout <<endl;
}
else{cd=new OBChiralData;atom->SetData(cd);}
vector<unsigned int> _output;
unsigned int n;
for(n=1;n<5;++n) _output.push_back(n);
cd->SetAtom4Refs(_output,output);
/* // MOLV3000 uses 1234 unless an H then 123H
if (atom->GetHvyValence()==3)
{
OBAtom *nbr;
int Hid=1000;// max Atom ID +1 should be used here
vector<unsigned int> nbr_atms;
vector<OBBond*>::iterator i;
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
{
if (nbr->IsHydrogen()){Hid=nbr->GetIdx();continue;}
nbr_atms.push_back(nbr->GetIdx());
}
sort(nbr_atms.begin(),nbr_atms.end());
nbr_atms.push_back(Hid);
OBChiralData* cd=(OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
cd->SetAtom4Refs(nbr_atms,output);
}
else if (atom->GetHvyValence()==4)
{
OBChiralData* cd=(OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
vector<unsigned int> nbr_atms;
int n;
for(n=1;n<5;++n)nbr_atms.push_back(n);
cd->SetAtom4Refs(nbr_atms,output);
} */
/* FIXME
if (!mol.HasNonZeroCoords())
{
cout << "Calcing 0D chirality "<< CorrectChirality(mol,atom)<<endl;
}
else {
cout << "Volume= "<< CalcSignedVolume(mol,atom) << endl;
OBChiralData* cd=(OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
size_t n;
vector<unsigned int> refs=cd->GetAtom4Refs(output);
cout<<"Atom refs=";
for(n=0;n<refs.size();++n)cout<<" "<<refs[n];
cout<<endl;
}
cout << "Clockwise? " << atom->IsClockwise() << endl;
*/
} // end iterating over atoms
} // end big for loop
return(0);
} // end main
