/**
@since version 2.3
Adds an OBPairData object to each atom and bond in a substructure.
The substructure's atoms are specified in an input parameter, a
vector of atom indx; the bonds are those in the molecule that join
these atoms. The attribute and value of the OBPairObject (the same
for all the added objects) are specified as parameters.
**/
bool AddDataToSubstruct(OBMol* pmol,
const std::vector<int>& atomIdxs,
const std::string& attribute,
const std::string& value)
{
//Add data to atoms
for(unsigned int j=0; j<atomIdxs.size(); ++j)
{
OBAtom* pAtom = pmol->GetAtom(atomIdxs[j]);
if(!pAtom)
continue;
OBPairData* dp = new OBPairData;
dp->SetAttribute(attribute);
dp->SetValue(value);
pAtom->SetData(dp);
}
OBBond* pBond;
vector<OBBond*>::iterator i;
for(pBond = pmol->BeginBond(i); pBond; pBond = pmol->NextBond(i))
{
//Add data to bond if it joins two atoms in list
if(count(atomIdxs.begin(), atomIdxs.end(), pBond->GetBeginAtomIdx())
&& count(atomIdxs.begin(), atomIdxs.end(), pBond->GetEndAtomIdx()))
{
OBPairData* dp = new OBPairData;
dp->SetAttribute(attribute);
dp->SetValue(value);
pBond->SetData(dp);
}
}
return true;
}
static int DetermineFRJ(OBMol &mol)
{
vector<vector<int> >::iterator i;
vector<vector<int> > cfl;
//find all continuous graphs in the mol area
mol.ContigFragList(cfl);
if (cfl.empty())
return(0);
if (cfl.size() == 1)
return(mol.NumBonds() - mol.NumAtoms() + 1);
//count up the atoms and bonds belonging to each graph
OBBond *bond;
vector<OBBond*>::iterator j;
int numatoms,numbonds,frj=0;
OBBitVec frag;
for (i = cfl.begin();i != cfl.end();++i)
{
frag.Clear();
frag.FromVecInt(*i);
numatoms = (*i).size();
numbonds=0;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
if (frag.BitIsOn(bond->GetBeginAtomIdx()) &&
frag.BitIsOn(bond->GetEndAtomIdx()))
numbonds++;
frj += numbonds - numatoms + 1;
}
return(frj);
}
bool OBRotorList::FindRotors(OBMol &mol, bool sampleRingBonds)
{
// Find ring atoms & bonds
// This function will set OBBond::IsRotor().
mol.FindRingAtomsAndBonds();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::FindRotors", obAuditMsg);
//
// Score the bonds using the graph theoretical distance (GTD).
// The GTD is the distance from atom i to every other atom j.
// Atoms on the "inside" of the molecule will have a lower GTD
// value than atoms on the "outside"
//
// The scoring will rank "inside" bonds first.
//
vector<int> gtd;
mol.GetGTDVector(gtd);
// compute the scores
vector<OBBond*>::iterator i;
vector<pair<OBBond*,int> > vtmp;
for (OBBond *bond = mol.BeginBond(i);bond;bond = mol.NextBond(i)) {
// check if the bond is "rotatable"
if (bond->IsRotor(sampleRingBonds)) {
// check if the bond is fixed (using deprecated fixed atoms or new fixed bonds)
if ((HasFixedAtoms() || HasFixedBonds()) && IsFixedBond(bond))
continue;
if (bond->IsInRing()) {
//otherwise mark that we have them and add it to the pile
_ringRotors = true;
}
int score = gtd[bond->GetBeginAtomIdx()-1] + gtd[bond->GetEndAtomIdx()-1];
// compute the GTD bond score as sum of atom GTD scores
vtmp.push_back(pair<OBBond*,int> (bond,score));
}
}
// sort the rotatable bonds by GTD score
sort(vtmp.begin(),vtmp.end(),CompareRotor);
// create rotors for the bonds
int count = 0;
vector<pair<OBBond*,int> >::iterator j;
for (j = vtmp.begin(); j != vtmp.end(); ++j, ++count) {
OBRotor *rotor = new OBRotor;
rotor->SetBond((*j).first);
rotor->SetIdx(count);
rotor->SetNumCoords(mol.NumAtoms()*3);
_rotor.push_back(rotor);
}
return true;
}
bool WriteAlchemy(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
char bond_string[10];
snprintf(buffer, BUFF_SIZE, "%5d ATOMS, %5d BONDS, 0 CHARGES",
mol.NumAtoms(),
mol.NumBonds());
ofs << buffer << endl;
ttab.SetFromType("INT"); ttab.SetToType("ALC");
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.Translate(str1,str);
snprintf(buffer, BUFF_SIZE, "%5d %-6s%8.4f %8.4f %8.4f 0.0000",
i,
(char*)str1.c_str(),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
switch(bond->GetBO())
{
case 1 : strcpy(bond_string,"SINGLE"); break;
case 2 : strcpy(bond_string,"DOUBLE"); break;
case 3 : strcpy(bond_string,"TRIPLE"); break;
case 5 : strcpy(bond_string,"AROMATIC"); break;
default : strcpy(bond_string,"SINGLE");
}
snprintf(buffer, BUFF_SIZE, "%5d %4d %4d %s",
bond->GetIdx()+1,
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx(),
bond_string);
ofs << buffer << 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);
}
bool AlchemyFormat::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;
unsigned int i;
char buffer[BUFF_SIZE];
char bond_string[10];
snprintf(buffer, BUFF_SIZE, "%5d ATOMS, %5d BONDS, 0 CHARGES",
mol.NumAtoms(),
mol.NumBonds());
ofs << buffer << endl;
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.SetFromType("INT");
ttab.SetToType("ALC");
ttab.Translate(str1,str);
snprintf(buffer, BUFF_SIZE, "%5d %-6s%8.4f %8.4f %8.4f 0.0000",
i,
(char*)str1.c_str(),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
OBBond *bond;
vector<OBBond*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
switch(bond->GetBO())
{
case 1 :
strcpy(bond_string,"SINGLE");
break;
case 2 :
strcpy(bond_string,"DOUBLE");
break;
case 3 :
strcpy(bond_string,"TRIPLE");
break;
case 5 :
strcpy(bond_string,"AROMATIC");
break;
default :
strcpy(bond_string,"SINGLE");
}
snprintf(buffer, BUFF_SIZE, "%5d %4d %4d %s",
bond->GetIdx()+1,
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx(),
bond_string);
ofs << buffer << endl;
}
return(true);
}
