GreenPolyProducts/openbabel
5
0
Fork 0
mirror of https://github.com/openbabel/openbabel.git synced 2026-08-11 05:24:42 -05:00
Code Issues Packages Projects Releases Wiki Activity

Use chiral_neighbors paramter in smiles writing...

Browse Source
This commit is contained in:
Tim Vandermeersch
2009-07-18 22:19:48 +00:00
parent a89af44140
commit 6156d63291
3 changed files with 26 additions and 112 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/formats/smilesformat.cpp
+25 -94
View File
@@ -828,7 +828,7 @@ namespace OpenBabel {
ChiralSearch = _tetrahedralMap.find(mol.GetAtom(_prev));
if (ChiralSearch != _tetrahedralMap.end() && ChiralSearch->second != NULL)
{
//cout << "Line 800: previous atom is chiral, adding reference: id = " << mol.NumAtoms() - 1 << endl;
cout << "Line 800: previous atom is chiral, adding reference: id = " << mol.NumAtoms() - 1 << endl;
ChiralSearch->second->refs.push_back(mol.NumAtoms() - 1);
}
}
@@ -1681,14 +1681,14 @@ namespace OpenBabel {
if(chiralWatch) // if chiral atom need to add its previous into atom4ref
{
assert( _tetrahedralMap[atom] );
//cout << "Line 1622: adding previous reference: id = " << mol.GetAtom(_prev)->GetId() << endl;
cout << "Line 1622: adding previous reference: id = " << mol.GetAtom(_prev)->GetId() << endl;
_tetrahedralMap[atom]->refs.push_back(mol.GetAtom(_prev)->GetId());
}
map<OBAtom*,TetrahedralStereo*>::iterator ChiralSearch;
ChiralSearch = _tetrahedralMap.find(mol.GetAtom(_prev));
if (ChiralSearch != _tetrahedralMap.end() && ChiralSearch->second != NULL)
{
//cout << "Line 1629: previous atom is chiral, adding this one to the refs: id = " << atom->GetId() << endl;
cout << "Line 1629: previous atom is chiral, adding this one to the refs: id = " << atom->GetId() << endl;
ChiralSearch->second->refs.push_back(atom->GetId());
}
}
@@ -1710,7 +1710,7 @@ namespace OpenBabel {
mol.AddBond(_prev,mol.NumAtoms(),1);
if(chiralWatch)
{
//cout << "Line 1652: explicit hydrogen on chiral atom, adding to the refs: id = " << atom->GetId() << endl;
cout << "Line 1652: explicit hydrogen on chiral atom, adding to the refs: id = " << atom->GetId() << endl;
_tetrahedralMap[mol.GetAtom(_prev)]->refs.push_back(atom->GetId());
}
}
@@ -1826,7 +1826,7 @@ namespace OpenBabel {
ChiralSearch = _tetrahedralMap.find(mol.GetAtom(_prev));
if (ChiralSearch != _tetrahedralMap.end() && ChiralSearch->second != NULL)
{
//cout << "previous atom is chiral, adding this one to the refs: id = " << (*j)[1] - 1 << endl;
cout << "previous atom is chiral, adding this one to the refs: id = " << (*j)[1] - 1 << endl;
ChiralSearch->second->refs.push_back((*j)[1] - 1);
}
@@ -1899,12 +1899,12 @@ namespace OpenBabel {
cs2 = _tetrahedralMap.find(mol.GetAtom((*j)[1]));
if (ChiralSearch != _tetrahedralMap.end() && ChiralSearch->second != NULL)
{
//cout << "ring closure bond to previous atom: id = " << (*j)[1] - 1 << endl;
cout << "ring closure bond to previous atom: id = " << (*j)[1] - 1 << endl;
ChiralSearch->second->refs.push_back((*j)[1] - 1);
}
if (cs2 != _tetrahedralMap.end() && cs2->second != NULL)
{
//cout << "ring opening bond to previous atom: id = " << (*j)[1] - 1 << endl;
cout << "ring opening bond to previous atom: id = " << (*j)[1] - 1 << endl;
//Ensure that the closure atom index is inserted at the position
//decided when the ring closure digit was encountered.
@@ -2732,6 +2732,9 @@ namespace OpenBabel {
return false;
if (atom->IsNitrogen())
return false;
// Added by timvdm 18 march 2009
if (atom->HasData(OBGenericDataType::StereoData))
return true;
// Added by ghutchis 2007-06-04 -- make sure to check for 3D molecules
// Fixes PR#1699418
if (atom->GetParent()->GetDimension() == 3)
@@ -2762,6 +2765,11 @@ namespace OpenBabel {
OBAtom *atom = node->GetAtom();
OBMol *mol = (OBMol*) atom->GetParent();
// If no chiral neighbors were passed in, we're done
if (chiral_neighbors.size() < 4)
return false;
// If the molecule has no coordinates but DOES have chirality specified, it
// must have come from a SMILES. In this case, the atoms' GetIdx() values
// will be in the same order they appeared in the original SMILES, so we
@@ -2779,37 +2787,21 @@ namespace OpenBabel {
//
if (!mol->HasNonZeroCoords()) { // no coordinates?
// NOTE: THIS SECTION IS WRONG. IT'S JUST A COPY OF THE ORIGINAL OPENBABEL
// CODE, AND DOESN'T ACCOUNT FOR THE FACT THAT THE CANONICAL SMILES IS REORDERED.
// NEEDS TO BE REWRITTEN, BUT IN COORDINATION WITH A REWRITE OF CHIRALITY IN
// THE smilesformat.cpp FILE. -- CJ
if (!atom->HasData(OBGenericDataType::StereoData))
return false; // no chirality on this atom
// use & for now, will be replaced by @ or @@, we don't know yet...
strcpy(stereo, "@");
return true;
/*
if (!atom->HasChiralitySpecified()) // and no chirality on this atom?
return(false); // not a chiral atom -- all done.
// Ok, it's a chiral atom, so we need to get the A, B, C, D atoms, in the order in
// which they appeared in the original SMILES. (NYI!!)
if (atom->IsClockwise())
strcpy(stereo,"@@");
else if (atom->IsAntiClockwise())
strcpy(stereo,"@");
OBTetrahedralStereo *ts = (OBTetrahedralStereo*) atom->GetData(OBGenericDataType::StereoData);
OBStereo::Refs canonRefs = OBStereo::MakeRefs(chiral_neighbors[1]->GetId(),
chiral_neighbors[2]->GetId(),
chiral_neighbors[3]->GetId());
if (ts->Compare(canonRefs, chiral_neighbors[0]->GetId(), OBStereo::Clockwise, OBStereo::ViewFrom))
strcpy(stereo, "@@");
else
return(false);
return(true);
*/
strcpy(stereo, "@");
return true;
}
// If no chiral neighbors were passed in, we're done
if (chiral_neighbors.size() < 4)
return false;
// If any of the neighbors have the same symmetry class, we're done.
for (int i = 0; i < chiral_neighbors.size(); i++) {
int idxI = chiral_neighbors[i]->GetIdx();
@@ -3191,6 +3183,7 @@ namespace OpenBabel {
}
}
// Write the current atom to the string
GetSmilesElement(node, chiral_neighbors, symmetry_classes, buffer+strlen(buffer), isomeric);
@@ -3398,65 +3391,6 @@ namespace OpenBabel {
delete root;
}
// timvdm: Fix chiral atoms.
std::string::size_type pos = 0;
for (int index = 0; index < _atmorder.size(); ++index) {
OBAtom *a = mol.GetAtom(_atmorder.at(index));
assert( a );
if (a->HasData(OBGenericDataType::StereoData)) {
unsigned long fromId = mol.GetAtom(_atmorder.at(index-1))->GetId();
//cout << "fromId = " << fromId << endl;
OBTetrahedralStereo *ts = (OBTetrahedralStereo*) a->GetData(OBGenericDataType::StereoData);
//cout << "ts->GetCenter() = " << ts->GetCenter() << endl;
// get clockwise, viewing from previous atom
OBStereo::Refs refs = ts->GetRefs(fromId);
/*
cout << "refs = ";
for (OBStereo::RefIter j = refs.begin(); j != refs.end(); ++j)
cout << " " << *j;
cout << endl;
*/
// find the canonical refs
OBStereo::Refs canonRefs;
for (OBStereo::RefIter j = refs.begin(); j != refs.end(); ++j) {
OBAtom *b = mol.GetAtomById(*j);
if (b->IsHydrogen())
canonRefs.push_back(*j);
}
for (int k = 0; k < _atmorder.size(); ++k) {
OBAtom *c = mol.GetAtom(_atmorder.at(k));
for (OBStereo::RefIter j = refs.begin(); j != refs.end(); ++j) {
OBAtom *b = mol.GetAtomById(*j);
if (b->GetId() == c->GetId()) {
canonRefs.push_back(*j);
}
}
}
/*
cout << "canonRefs = ";
for (OBStereo::RefIter j = canonRefs.begin(); j != canonRefs.end(); ++j)
cout << " " << *j;
cout << endl;
*/
if (ts->Compare(canonRefs, fromId, OBStereo::Clockwise, OBStereo::ViewFrom)) {
std::string smiles(buffer);
pos = smiles.find("@", pos);
smiles.insert(pos, "@");
strncpy(buffer, smiles.c_str(), BUFF_SIZE);
pos += 2;
}
}
}
// save the canonical order as a space-separated string
// which will be returned by GetOutputOrder() for incorporation
// into an OBPairData keyed "canonical order"
@@ -3467,13 +3401,10 @@ namespace OpenBabel {
temp << (*can_iter++);
}
//cout << "_atmorder =";
for (; can_iter != _atmorder.end(); ++can_iter) {
if (*can_iter <= mol.NumAtoms())
temp << " " << (*can_iter);
//cout << " " << (*can_iter);
}
//cout << endl;
_canorder = temp.str(); // returned by GetOutputOrder()
}
}
src/mol.cpp
-2
View File
@@ -1182,8 +1182,6 @@ namespace OpenBabel
OBAtom *atom;
OBBond *bond;
cout << "OBMol::operator=" << endl;
Clear();
BeginModify();
src/stereo/tetrahedral.cpp
+1 -16
View File
@@ -56,25 +56,10 @@ namespace OpenBabel {
return false;
std::vector<unsigned long> clockwiseFrom1 = OBTetraNonPlanarStereo::ToInternal(refs, id, winding, view);
int Ni1 = OBTetraNonPlanarStereo::NumInversions(refs);
cout << "Ni1 = " << Ni1 << endl;
int Ni1 = OBTetraNonPlanarStereo::NumInversions(m_refs);
int Ni2 = OBTetraNonPlanarStereo::NumInversions(clockwiseFrom1);
cout << "Ni2 = " << Ni2 << endl;
return ((Ni1 + Ni2) % 2 == 0);
/*
if (m_refs.at(0) == clockwiseFrom1.at(1)) {
clockwiseFrom1[1] = clockwiseFrom1.at(2);
clockwiseFrom1[2] = clockwiseFrom1.at(0);
clockwiseFrom1[0] = m_refs.at(0); // use m_refs[0] rather than tmp var since it's got what we need
} else if (m_refs.at(0) == clockwiseFrom1.at(2)) {
clockwiseFrom1[2] = clockwiseFrom1.at(1);
clockwiseFrom1[1] = clockwiseFrom1.at(0);
clockwiseFrom1[0] = m_refs.at(0); // ditto re tmp usage
}
return (m_refs.at(2) == clockwiseFrom1.at(2));
*/
}
OBGenericData* OBTetrahedralStereo::Clone(OBBase *mol) const