bool ReadFeat(istream &ifs,OBMol &mol, const char *title)
{
char buffer[BUFF_SIZE];
int i,natoms;
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%d",&natoms);
mol.ReserveAtoms(natoms);
mol.BeginModify();
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
mol.SetTitle(buffer);
double x,y,z;
char type[20];
OBAtom *atom;
for (i = 0; i < natoms;i++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
sscanf(buffer,"%s %lf %lf %lf",
type,
&x,
&y,
&z);
CleanAtomType(type);
atom = mol.NewAtom();
atom->SetVector(x,y,z);
atom->SetAtomicNum(etab.GetAtomicNum(type));
}
mol.EndModify();
return(true);
}
bool BGFFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
mol.SetTitle( pConv->GetTitle()); //default title is the filename
mol.BeginModify();
char buffer[BUFF_SIZE];
char tmp[16],tmptyp[16];
vector<string> vs;
while (ifs.getline(buffer,BUFF_SIZE)) {
if (EQn(buffer,"CRYSTX",6)) {
// Parse unit cell
tokenize(vs,buffer," \n\t,");
if (vs.size() != 7)
continue; // something strange
double A, B, C, Alpha, Beta, Gamma;
A = atof(vs[1].c_str());
B = atof(vs[2].c_str());
C = atof(vs[3].c_str());
Alpha = atof(vs[4].c_str());
Beta = atof(vs[5].c_str());
Gamma = atof(vs[6].c_str());
OBUnitCell *uc = new OBUnitCell;
uc->SetOrigin(fileformatInput);
uc->SetData(A, B, C, Alpha, Beta, Gamma);
mol.SetData(uc);
} else if (EQn(buffer,"FORMAT",6))
break;
}
ttab.SetFromType("DRE");
ttab.SetToType("INT");
OBAtom *atom;
double x,y,z,chrg;
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE))
break;
if (EQn(buffer,"FORMAT",6))
break;
sscanf(buffer,"%*s %*s %*s %*s %*s %*s %lf %lf %lf %15s %*s %*s %lf",
&x,&y,&z,
tmptyp,
&chrg);
atom = mol.NewAtom();
ttab.Translate(tmp,tmptyp);
atom->SetType(tmp);
CleanAtomType(tmptyp);
atom->SetAtomicNum(etab.GetAtomicNum(tmptyp));
atom->SetVector(x,y,z);
}
unsigned int i;
vector<int> vtmp;
vector<vector<int> > vcon;
vector<vector<int> > vord;
for (i = 0; i < mol.NumAtoms();i++)
{
vcon.push_back(vtmp);
vord.push_back(vtmp);
}
unsigned int bgn;
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE) || EQn(buffer,"END",3))
break;
tokenize(vs,buffer);
if (vs.empty() || vs.size() < 3 || vs.size() > 10)
continue;
if (EQn(buffer,"CONECT",6))
{
bgn = atoi((char*)vs[1].c_str()) - 1;
if (bgn < 1 || bgn > mol.NumAtoms())
continue;
for (i = 2;i < vs.size();i++)
{
vcon[bgn].push_back(atoi((char*)vs[i].c_str()));
vord[bgn].push_back(1);
}
}
else
if (EQn(buffer,"ORDER",5))
{
bgn = atoi((char*)vs[1].c_str()) - 1;
if (bgn < 1 || bgn > mol.NumAtoms())
continue;
if (vs.size() > vord[bgn].size()+2)
continue;
for (i = 2;i < vs.size();i++)
vord[bgn][i-2] = atoi((char*)vs[i].c_str());
}
}
unsigned int j;
for (i = 1;i <= mol.NumAtoms();i++)
if (!vcon[i - 1].empty())
for (j = 0;j < vcon[i - 1].size();j++)
{
mol.AddBond(i,vcon[i - 1][j],vord[i - 1][j]);
}
//load up the next line after the END marker
ifs.getline(buffer,BUFF_SIZE);
mol.EndModify();
return(true);
}
