bool MacroModFormat::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;
const char* defaultTitle = pConv->GetTitle();
// Get Title
char buffer[BUFF_SIZE];
int natoms;
vector<vector<pair<int,int> > > connections;
if (ifs.getline(buffer,BUFF_SIZE))
{
vector<string> vs;
tokenize(vs,buffer," \n");
if ( !vs.empty() && vs.size() > 0)
sscanf(buffer,"%i%*s",&natoms);
if (natoms == 0)
return false;
if ( !vs.empty() && vs.size() > 1)
mol.SetTitle(vs[1]);
else
{
string s = defaultTitle;
mol.SetTitle(defaultTitle);
}
}
else
return(false);
mol.BeginModify();
mol.ReserveAtoms(natoms);
connections.resize(natoms+1);
/***********************************************************************/
// Get Type Bonds, BondOrder, X, Y, Z
double x,y,z;
vector3 v;
char temp_type[10];
int i,j;
double charge;
OBAtom atom;
ttab.SetFromType("MMD");
for (i = 1; i <= natoms; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
break;
int end[6], order[6];
sscanf(buffer,"%9s%d%d%d%d%d%d%d%d%d%d%d%d%lf%lf%lf",
temp_type,&end[0],&order[0],&end[1],&order[1],&end[2],&order[2],
&end[3], &order[3], &end[4], &order[4], &end[5], &order[5],
&x, &y, &z);
pair<int,int> tmp;
for ( j = 0 ; j <=5 ; j++ )
{
if ( end[j] > 0 && end[j] > i)
{
tmp.first = end[j];
tmp.second = order[j];
connections[i].push_back(tmp);
}
}
v.SetX(x);
v.SetY(y);
v.SetZ(z);
atom.SetVector(v);
string str = temp_type,str1;
ttab.SetToType("ATN");
ttab.Translate(str1,str);
atom.SetAtomicNum(atoi(str1.c_str()));
ttab.SetToType("INT");
ttab.Translate(str1,str);
atom.SetType(str1);
// stuff for optional fields
buffer[109]='\0';
sscanf(&buffer[101],"%lf", &charge);
atom.SetPartialCharge(charge);
mol.AddAtom(atom);
}
for (i = 1; i <= natoms; i++)
for (j = 0; j < (signed)connections[i].size(); j++)
mol.AddBond(i, connections[i][j].first, connections[i][j].second);
mol.EndModify();
OBBond *bond;
vector<OBBond*>::iterator bi;
for (bond = mol.BeginBond(bi);bond;bond = mol.NextBond(bi))
if (bond->GetBO() == 5 && !bond->IsInRing())
bond->SetBO(1);
if ( natoms != (signed)mol.NumAtoms() )
return(false);
// clean out remaining blank lines
while(ifs.peek() != EOF && ifs.good() &&
(ifs.peek() == '\n' || ifs.peek() == '\r'))
ifs.getline(buffer,BUFF_SIZE);
return(true);
}
bool OBChemTsfm::Apply(OBMol &mol)
{
if (!_bgn.Match(mol))
return(false);
vector<vector<int> > mlist = _bgn.GetUMapList();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::OBChemTransform", obAuditMsg);
if (!_vchrg.empty()) //modify charges
{
vector<vector<int> >::iterator i;
vector<pair<int,int> >::iterator j;
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vchrg.begin();j != _vchrg.end();++j)
if (j->first < (signed)i->size()) //goof proofing
mol.GetAtom((*i)[j->first])->SetFormalCharge(j->second);
mol.UnsetImplicitValencePerceived();
}
if (!_vbond.empty()) //modify bond orders
{
OBBond *bond;
vector<vector<int> >::iterator i;
vector<pair<pair<int,int>,int> >::iterator j;
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vbond.begin();j != _vbond.end();++j)
{
bond = mol.GetBond((*i)[j->first.first],(*i)[j->first.second]);
if (!bond)
{
obErrorLog.ThrowError(__FUNCTION__, "unable to find bond", obDebug);
continue;
}
bond->SetBO(j->second);
}
}
if (!_vadel.empty() || !_vele.empty()) //delete atoms and change elements
{
vector<int>::iterator j;
vector<vector<int> >::iterator i;
if (!_vele.empty())
{
vector<pair<int,int> >::iterator k;
for (i = mlist.begin();i != mlist.end();++i)
for (k = _vele.begin();k != _vele.end();++k)
mol.GetAtom((*i)[k->first])->SetAtomicNum(k->second);
}
//make sure same atom isn't deleted twice
vector<bool> vda;
vector<OBAtom*> vdel;
vda.resize(mol.NumAtoms()+1,false);
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vadel.begin();j != _vadel.end();++j)
if (!vda[(*i)[*j]])
{
vda[(*i)[*j]] = true;
vdel.push_back(mol.GetAtom((*i)[*j]));
}
vector<OBAtom*>::iterator k;
for (k = vdel.begin();k != vdel.end();++k)
mol.DeleteAtom((OBAtom*)*k);
}
return(true);
}
