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//
// Copyright (C) 2001-2012 Greg Landrum and Rational Discovery LLC
// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <GraphMol/GraphMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Atom.h>
#include <GraphMol/AtomIterators.h>
#include <GraphMol/BondIterators.h>
#include <GraphMol/PeriodicTable.h>
#include <vector>
#include <algorithm>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/graph/connected_components.hpp>
#include <boost/graph/kruskal_min_spanning_tree.hpp>
#include <boost/graph/johnson_all_pairs_shortest.hpp>
#include <boost/version.hpp>
#if BOOST_VERSION >= 104000
#include <boost/property_map/property_map.hpp>
#else
#include <boost/property_map.hpp>
#endif
#include <RDGeneral/BoostEndInclude.h>
#include <boost/config.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <GraphMol/ROMol.h>
const int ci_LOCAL_INF = static_cast<int>(1e8);
namespace RDKit {
namespace MolOps {
namespace {
void nitrogenCleanup(RWMol &mol, Atom *atom) {
// conversions here:
// - neutral 5 coordinate Ns with double bonds to Os to the
// zwitterionic form. e.g.:
// CN(=O)=O -> C[N+](=O)[O-]
// and:
// C1=CC=CN(=O)=C1 -> C1=CC=C[N+]([O-])=C1
// - neutral 5 coordinate Ns with triple bonds to Ns to the
// zwitterionic form. e.g.:
// C-N=N#N -> C-N=[N+]=[N-]
PRECONDITION(atom, "bad atom");
bool aromHolder;
// we only want to do neutrals so that things like this don't get
// munged:
// O=[n+]1occcc1
// this was sf.net issue 1811276
if (atom->getFormalCharge())
return;
// we need to play this little aromaticity game because the
// explicit valence code modifies its results for aromatic
// atoms.
aromHolder = atom->getIsAromatic();
atom->setIsAromatic(0);
// NOTE that we are calling calcExplicitValence() here, we do
// this because we cannot be sure that it has already been
// called on the atom (cleanUp() gets called pretty early in
// the sanitization process):
if (atom->calcExplicitValence(false) == 5) {
unsigned int aid = atom->getIdx();
RWMol::ADJ_ITER nid1, end1;
boost::tie(nid1, end1) = mol.getAtomNeighbors(atom);
while (nid1 != end1) {
if ((mol.getAtomWithIdx(*nid1)->getAtomicNum() == 8) &&
(mol.getAtomWithIdx(*nid1)->getFormalCharge() == 0) &&
(mol.getBondBetweenAtoms(aid, *nid1)->getBondType() ==
Bond::DOUBLE)) {
// here's the double bonded oxygen
Bond *b = mol.getBondBetweenAtoms(aid, *nid1);
b->setBondType(Bond::SINGLE);
atom->setFormalCharge(1);
mol.getAtomWithIdx(*nid1)->setFormalCharge(-1);
break;
} else if ((mol.getAtomWithIdx(*nid1)->getAtomicNum() == 7) &&
(mol.getAtomWithIdx(*nid1)->getFormalCharge() == 0) &&
(mol.getBondBetweenAtoms(aid, *nid1)->getBondType() ==
Bond::TRIPLE)) {
// here's the triple bonded nitrogen
Bond *b = mol.getBondBetweenAtoms(aid, *nid1);
b->setBondType(Bond::DOUBLE);
atom->setFormalCharge(1);
mol.getAtomWithIdx(*nid1)->setFormalCharge(-1);
break;
}
++nid1;
} // end of loop over the first neigh
} // if this atom is 5 coordinate nitrogen
// force a recalculation of the explicit valence here
atom->setIsAromatic(aromHolder);
atom->calcExplicitValence(false);
}
}
void cleanUp(RWMol &mol) {
ROMol::AtomIterator ai;
for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ++ai) {
switch ((*ai)->getAtomicNum()) {
case 7:
nitrogenCleanup(mol, *ai);
break;
case 17:
// recognize perchlorate and convert it from:
// Cl(=O)(=O)(=O)[O-]
// to:
// [Cl+3]([O-])([O-])([O-])[O-]
if ((*ai)->calcExplicitValence(false) == 7 &&
(*ai)->getFormalCharge() == 0) {
unsigned int aid = (*ai)->getIdx();
bool neighborsAllO = true;
RWMol::ADJ_ITER nid1, end1;
boost::tie(nid1, end1) = mol.getAtomNeighbors(*ai);
while (nid1 != end1) {
if (mol.getAtomWithIdx(*nid1)->getAtomicNum() != 8) {
neighborsAllO = false;
break;
}
++nid1;
}
if (neighborsAllO) {
(*ai)->setFormalCharge(3);
boost::tie(nid1, end1) = mol.getAtomNeighbors(*ai);
while (nid1 != end1) {
Bond *b = mol.getBondBetweenAtoms(aid, *nid1);
if (b->getBondType() == Bond::DOUBLE) {
b->setBondType(Bond::SINGLE);
Atom *otherAtom = mol.getAtomWithIdx(*nid1);
otherAtom->setFormalCharge(-1);
otherAtom->calcExplicitValence(false);
}
++nid1;
}
(*ai)->calcExplicitValence(false);
}
}
break;
}
}
}
void adjustHs(RWMol &mol) {
//
// Go through and adjust the number of implicit and explicit Hs
// on each atom in the molecule.
//
// Atoms that do not *need* explicit Hs
//
// Assumptions: this is called after the molecule has been
// sanitized, aromaticity has been perceived, and the implicit
// valence of everything has been calculated.
//
for (ROMol::AtomIterator ai = mol.beginAtoms(); ai != mol.endAtoms(); ++ai) {
int origImplicitV = (*ai)->getImplicitValence();
(*ai)->calcExplicitValence();
int origExplicitV = (*ai)->getNumExplicitHs();
int newImplicitV = (*ai)->calcImplicitValence();
//
// Case 1: The disappearing Hydrogen
// Smiles: O=C1NC=CC2=C1C=CC=C2
//
// after perception is done, the N atom has two aromatic
// bonds to it and a single implict H. When the Smiles is
// written, we get: n1ccc2ccccc2c1=O. Here the nitrogen has
// no implicit Hs (because there are two aromatic bonds to
// it, giving it a valence of 3). Also: this SMILES is bogus
// (un-kekulizable). The correct SMILES would be:
// [nH]1ccc2ccccc2c1=O. So we need to loop through the atoms
// and find those that have lost implicit H; we'll add those
// back as explict Hs.
//
// <phew> that takes way longer to comment than it does to
// write:
if (newImplicitV < origImplicitV) {
(*ai)->setNumExplicitHs(origExplicitV + (origImplicitV - newImplicitV));
(*ai)->calcExplicitValence();
}
}
}
void assignRadicals(RWMol &mol) {
for (ROMol::AtomIterator ai = mol.beginAtoms(); ai != mol.endAtoms(); ++ai) {
// we only put automatically assign radicals to things that
// don't have them already and don't have implicit Hs:
if (!(*ai)->getNoImplicit() || (*ai)->getNumRadicalElectrons() ||
!(*ai)->getAtomicNum()) {
continue;
}
double accum = 0.0;
RWMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(*ai);
while (beg != end) {
accum += mol[*beg]->getValenceContrib(*ai);
++beg;
}
accum += (*ai)->getNumExplicitHs();
int totalValence = static_cast<int>(accum + 0.1);
int chg = (*ai)->getFormalCharge();
int nOuter =
PeriodicTable::getTable()->getNouterElecs((*ai)->getAtomicNum());
int baseCount = 8;
if ((*ai)->getAtomicNum() == 1) {
baseCount = 2;
}
// applies to later (more electronegative) elements:
int numRadicals = baseCount - nOuter - totalValence + chg;
if (numRadicals < 0) {
numRadicals = 0;
// can the atom be "hypervalent"? (was github #447)
const INT_VECT &valens =
PeriodicTable::getTable()->getValenceList((*ai)->getAtomicNum());
if (valens.size() > 1) {
BOOST_FOREACH (int val, valens) {
if (val - totalValence + chg >= 0) {
numRadicals = val - totalValence + chg;
break;
}
}
}
}
// applies to earlier elements:
int numRadicals2 = nOuter - totalValence - chg;
if (numRadicals2 >= 0) {
numRadicals = std::min(numRadicals, numRadicals2);
}
(*ai)->setNumRadicalElectrons(numRadicals);
}
}
void sanitizeMol(RWMol &mol) {
unsigned int failedOp = 0;
sanitizeMol(mol, failedOp, SANITIZE_ALL);
}
void sanitizeMol(RWMol &mol, unsigned int &operationThatFailed,
unsigned int sanitizeOps) {
// clear out any cached properties
mol.clearComputedProps();
operationThatFailed = SANITIZE_CLEANUP;
if (sanitizeOps & operationThatFailed) {
// clean up things like nitro groups
cleanUp(mol);
}
// update computed properties on atoms and bonds:
operationThatFailed = SANITIZE_PROPERTIES;
if (sanitizeOps & operationThatFailed) {
mol.updatePropertyCache(true);
} else {
mol.updatePropertyCache(false);
}
operationThatFailed = SANITIZE_SYMMRINGS;
if (sanitizeOps & operationThatFailed) {
VECT_INT_VECT arings;
MolOps::symmetrizeSSSR(mol, arings);
}
// kekulizations
operationThatFailed = SANITIZE_KEKULIZE;
if (sanitizeOps & operationThatFailed) {
Kekulize(mol);
}
// look for radicals:
// We do this now because we need to know
// that the N in [N]1C=CC=C1 has a radical
// before we move into setAromaticity().
// It's important that this happen post-Kekulization
// because there's no way of telling what to do
// with the same molecule if it's in the form
// [n]1cccc1
operationThatFailed = SANITIZE_FINDRADICALS;
if (sanitizeOps & operationThatFailed) {
assignRadicals(mol);
}
// then do aromaticity perception
operationThatFailed = SANITIZE_SETAROMATICITY;
if (sanitizeOps & operationThatFailed) {
setAromaticity(mol);
}
// set conjugation
operationThatFailed = SANITIZE_SETCONJUGATION;
if (sanitizeOps & operationThatFailed) {
setConjugation(mol);
}
// set hybridization
operationThatFailed = SANITIZE_SETHYBRIDIZATION;
if (sanitizeOps & operationThatFailed) {
setHybridization(mol);
}
// remove bogus chirality specs:
operationThatFailed = SANITIZE_CLEANUPCHIRALITY;
if (sanitizeOps & operationThatFailed) {
cleanupChirality(mol);
}
// adjust Hydrogen counts:
operationThatFailed = SANITIZE_ADJUSTHS;
if (sanitizeOps & operationThatFailed) {
adjustHs(mol);
}
operationThatFailed = 0;
}
std::vector<ROMOL_SPTR> getMolFrags(const ROMol &mol, bool sanitizeFrags,
INT_VECT *frags,
VECT_INT_VECT *fragsMolAtomMapping,
bool copyConformers) {
bool ownIt = false;
INT_VECT *mapping;
if (frags) {
mapping = frags;
} else {
mapping = new INT_VECT;
ownIt = true;
}
unsigned int nFrags = getMolFrags(mol, *mapping);
std::vector<ROMOL_SPTR> res;
if (nFrags == 1) {
ROMol *tmp = new ROMol(mol);
ROMOL_SPTR sptr(tmp);
res.push_back(sptr);
if (fragsMolAtomMapping) {
INT_VECT comp;
for (unsigned int idx = 0; idx < mol.getNumAtoms(); ++idx) {
comp.push_back(idx);
}
(*fragsMolAtomMapping).push_back(comp);
}
} else {
std::vector<int> ids(mol.getNumAtoms(), -1);
boost::dynamic_bitset<> copiedAtoms(mol.getNumAtoms(), 0);
boost::dynamic_bitset<> copiedBonds(mol.getNumBonds(), 0);
res.reserve(nFrags);
for (unsigned int frag = 0; frag < nFrags; ++frag) {
ROMol *tmp = new ROMol();
ROMOL_SPTR sptr(tmp);
res.push_back(sptr);
}
// copy atoms
INT_INT_VECT_MAP comMap;
for (unsigned int idx = 0; idx < mol.getNumAtoms(); ++idx) {
RWMol *tmp = static_cast<RWMol *>(res[(*mapping)[idx]].get());
const Atom *oAtm = mol.getAtomWithIdx(idx);
ids[idx] = tmp->addAtom(oAtm->copy(), false, true);
copiedAtoms[idx] = 1;
if (fragsMolAtomMapping) {
if (comMap.find((*mapping)[idx]) == comMap.end()) {
INT_VECT comp;
comMap[(*mapping)[idx]] = comp;
}
comMap[(*mapping)[idx]].push_back(idx);
}
// loop over neighbors and add bonds in the fragment to all atoms
// that are already in the same fragment
ROMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(oAtm);
while (nbrIdx != endNbrs) {
if (copiedAtoms[*nbrIdx]) {
copiedBonds[mol.getBondBetweenAtoms(idx, *nbrIdx)->getIdx()] = 1;
}
++nbrIdx;
}
}
// update ring stereochemistry information
for (unsigned int idx = 0; idx < mol.getNumAtoms(); ++idx) {
const Atom *oAtm = mol.getAtomWithIdx(idx);
INT_VECT ringStereoAtomsMol;
if (oAtm->getPropIfPresent(common_properties::_ringStereoAtoms,
ringStereoAtomsMol)) {
INT_VECT ringStereoAtomsCopied;
for (unsigned rnbr = 0; rnbr < ringStereoAtomsMol.size(); ++rnbr) {
int ori_ridx = abs(ringStereoAtomsMol[rnbr]) - 1;
int ridx = ids[ori_ridx] + 1;
if (ringStereoAtomsMol[rnbr] < 0) {
ridx *= (-1);
}
ringStereoAtomsCopied.push_back(ridx);
}
RWMol *tmp = static_cast<RWMol *>(res[(*mapping)[idx]].get());
tmp->getAtomWithIdx(ids[idx])->setProp(
common_properties::_ringStereoAtoms, ringStereoAtomsCopied);
}
}
// copy bonds and bond stereochemistry information
ROMol::EDGE_ITER beg, end;
boost::tie(beg, end) = mol.getEdges();
while (beg != end) {
Bond* bond = (mol)[*beg];
++beg;
if (!copiedBonds[bond->getIdx()]) {
continue;
}
Bond *nBond = bond->copy();
RWMol *tmp =
static_cast<RWMol *>(res[(*mapping)[nBond->getBeginAtomIdx()]].get());
nBond->setOwningMol(static_cast<ROMol *>(tmp));
nBond->setBeginAtomIdx(ids[nBond->getBeginAtomIdx()]);
nBond->setEndAtomIdx(ids[nBond->getEndAtomIdx()]);
nBond->getStereoAtoms().clear();
INT_VECT stereoAtoms = bond->getStereoAtoms();
for (unsigned i = 0; i < stereoAtoms.size(); ++i) {
nBond->getStereoAtoms().push_back(ids[stereoAtoms[i]]);
}
tmp->addBond(nBond, true);
}
// copy RingInfo
if (mol.getRingInfo()->isInitialized()) {
for (unsigned i = 0; i < mol.getRingInfo()->atomRings().size(); ++i) {
INT_VECT aids;
RWMol *tmp = static_cast<RWMol *>(
res[(*mapping)[mol.getRingInfo()->atomRings()[i][0]]].get());
if (!tmp->getRingInfo()->isInitialized()) {
tmp->getRingInfo()->initialize();
}
for (unsigned j = 0; j < mol.getRingInfo()->atomRings()[i].size();
++j) {
aids.push_back(ids[mol.getRingInfo()->atomRings()[i][j]]);
}
INT_VECT bids;
INT_VECT_CI lastRai;
for (INT_VECT_CI rai = aids.begin(); rai != aids.end(); rai++) {
if (rai != aids.begin()) {
const Bond *bnd = tmp->getBondBetweenAtoms(*rai, *lastRai);
if (!bnd)
throw ValueErrorException("expected bond not found");
bids.push_back(bnd->getIdx());
}
lastRai = rai;
}
const Bond *bnd = tmp->getBondBetweenAtoms(*lastRai, *(aids.begin()));
if (!bnd)
throw ValueErrorException("expected bond not found");
bids.push_back(bnd->getIdx());
tmp->getRingInfo()->addRing(aids, bids);
}
}
if (copyConformers) {
// copy conformers
for (ROMol::ConstConformerIterator cit = mol.beginConformers();
cit != mol.endConformers(); ++cit) {
for (std::vector<ROMOL_SPTR>::iterator iter = res.begin();
iter != res.end(); ++iter) {
ROMol *newM = iter->get();
Conformer *conf = new Conformer(newM->getNumAtoms());
conf->setId((*cit)->getId());
conf->set3D((*cit)->is3D());
newM->addConformer(conf);
}
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
if (ids[i] < 0)
continue;
res[(*mapping)[i]]
->getConformer((*cit)->getId())
.setAtomPos(ids[i], (*cit)->getAtomPos(i));
}
}
}
if (fragsMolAtomMapping) {
for (INT_INT_VECT_MAP_CI mci = comMap.begin(); mci != comMap.end();
mci++) {
(*fragsMolAtomMapping).push_back((*mci).second);
}
}
}
if (sanitizeFrags) {
for (std::vector<ROMOL_SPTR>::iterator iter = res.begin();
iter != res.end(); ++iter) {
sanitizeMol(*static_cast<RWMol *>(iter->get()));
}
}
if (ownIt) {
delete mapping;
}
return res;
}
unsigned int getMolFrags(const ROMol &mol, INT_VECT &mapping) {
unsigned int natms = mol.getNumAtoms();
mapping.resize(natms);
return natms ? boost::connected_components(mol.getTopology(), &mapping[0])
: 0;
};
unsigned int getMolFrags(const ROMol &mol, VECT_INT_VECT &frags) {
frags.clear();
INT_VECT mapping;
getMolFrags(mol, mapping);
INT_INT_VECT_MAP comMap;
for (unsigned int i = 0; i < mol.getNumAtoms(); i++) {
int mi = mapping[i];
if (comMap.find(mi) == comMap.end()) {
INT_VECT comp;
comMap[mi] = comp;
}
comMap[mi].push_back(i);
}
for (INT_INT_VECT_MAP_CI mci = comMap.begin(); mci != comMap.end(); mci++) {
frags.push_back((*mci).second);
}
return frags.size();
}
template <typename T>
std::map<T, boost::shared_ptr<ROMol>>
getMolFragsWithQuery(const ROMol &mol, T (*query)(const ROMol &, const Atom *),
bool sanitizeFrags, const std::vector<T> *whiteList,
bool negateList) {
PRECONDITION(query, "no query");
std::vector<T> assignments(mol.getNumAtoms());
std::vector<int> ids(mol.getNumAtoms(), -1);
std::map<T, boost::shared_ptr<ROMol>> res;
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
T where = query(mol, mol.getAtomWithIdx(i));
if (whiteList) {
bool found = std::find(whiteList->begin(), whiteList->end(), where) !=
whiteList->end();
if (!found && !negateList)
continue;
else if (found && negateList)
continue;
}
assignments[i] = where;
if (res.find(where) == res.end()) {
res[where] = boost::shared_ptr<ROMol>(new ROMol());
}
RWMol *frag = static_cast<RWMol *>(res[where].get());
ids[i] = frag->addAtom(mol.getAtomWithIdx(i)->copy(), false, true);
// loop over neighbors and add bonds in the fragment to all atoms
// that are already in the same fragment
ROMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(mol.getAtomWithIdx(i));
while (nbrIdx != endNbrs) {
if (*nbrIdx < i && assignments[*nbrIdx] == where) {
Bond *nBond = mol.getBondBetweenAtoms(i, *nbrIdx)->copy();
nBond->setOwningMol(static_cast<ROMol *>(frag));
nBond->setBeginAtomIdx(ids[nBond->getBeginAtomIdx()]);
nBond->setEndAtomIdx(ids[nBond->getEndAtomIdx()]);
frag->addBond(nBond, true);
}
++nbrIdx;
}
}
// update conformers
for (ROMol::ConstConformerIterator cit = mol.beginConformers();
cit != mol.endConformers(); ++cit) {
for (typename std::map<T, boost::shared_ptr<ROMol>>::iterator iter =
res.begin();
iter != res.end(); ++iter) {
ROMol *newM = iter->second.get();
Conformer *conf = new Conformer(newM->getNumAtoms());
conf->setId((*cit)->getId());
conf->set3D((*cit)->is3D());
newM->addConformer(conf);
}
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
if (ids[i] < 0)
continue;
res[assignments[i]]
->getConformer((*cit)->getId())
.setAtomPos(ids[i], (*cit)->getAtomPos(i));
}
}
if (sanitizeFrags) {
for (typename std::map<T, boost::shared_ptr<ROMol>>::iterator iter =
res.begin();
iter != res.end(); ++iter) {
sanitizeMol(*static_cast<RWMol *>(iter->second.get()));
}
}
return res;
}
template std::map<std::string, boost::shared_ptr<ROMol>> getMolFragsWithQuery(
const ROMol &mol, std::string (*query)(const ROMol &, const Atom *),
bool sanitizeFrags, const std::vector<std::string> *, bool);
template std::map<int, boost::shared_ptr<ROMol>>
getMolFragsWithQuery(const ROMol &mol,
int (*query)(const ROMol &, const Atom *),
bool sanitizeFrags, const std::vector<int> *, bool);
template std::map<unsigned int, boost::shared_ptr<ROMol>> getMolFragsWithQuery(
const ROMol &mol, unsigned int (*query)(const ROMol &, const Atom *),
bool sanitizeFrags, const std::vector<unsigned int> *, bool);
#if 0
void findSpanningTree(const ROMol &mol,INT_VECT &mst){
//
// The BGL provides Prim's and Kruskal's algorithms for finding
// the MST of a graph. Prim's is O(n2) (n=# of atoms) while
// Kruskal's is O(e log e) (e=# of bonds). For molecules, where
// e << n2, Kruskal's should be a win.
//
const MolGraph *mgraph = &mol.getTopology();
MolGraph *molGraph = const_cast<MolGraph *> (mgraph);
std::vector<MolGraph::edge_descriptor> treeEdges;
treeEdges.reserve(boost::num_vertices(*molGraph));
boost::property_map < MolGraph, edge_wght_t >::type w = boost::get(edge_wght_t(), *molGraph);
boost::property_map < MolGraph, edge_bond_t>::type bps = boost::get(edge_bond_t(), *molGraph);
boost::graph_traits < MolGraph >::edge_iterator e, e_end;
Bond* bnd;
for (boost::tie(e, e_end) = boost::edges(*molGraph); e != e_end; ++e) {
bnd = bps[*e];
if(!bnd->getIsAromatic()){
w[*e] = (bnd->getBondTypeAsDouble());
} else {
w[*e] = 3.0/2.0;
}
}
// FIX: this is a hack due to problems with MSVC++
#if 1
typedef boost::graph_traits<MolGraph>::vertices_size_type size_type;
typedef boost::graph_traits<MolGraph>::vertex_descriptor vertex_t;
typedef boost::property_map<MolGraph,boost::vertex_index_t>::type index_map_t;
boost::graph_traits<MolGraph>::vertices_size_type
n = boost::num_vertices(*molGraph);
std::vector<size_type> rank_map(n);
std::vector<vertex_t> pred_map(n);
boost::detail::kruskal_mst_impl
(*molGraph, std::back_inserter(treeEdges),
boost::make_iterator_property_map(rank_map.begin(),
boost::get(boost::vertex_index, *molGraph),
rank_map[0]),
boost::make_iterator_property_map(pred_map.begin(),
boost::get(boost::vertex_index, *molGraph),
pred_map[0]),
w);
#else
boost::kruskal_minimum_spanning_tree(*molGraph,std::back_inserter(treeEdges),
w, *molGraph);
//boost::weight_map(static_cast<boost::property_map<MolGraph,edge_wght_t>::const_type>(boost::get(edge_wght_t(),*molGraph))));
#endif
mst.resize(0);
for(std::vector<MolGraph::edge_descriptor>::iterator edgeIt=treeEdges.begin();
edgeIt!=treeEdges.end();edgeIt++){
mst.push_back(mol[*edgeIt]->getIdx());
}
}
#endif
int getFormalCharge(const ROMol &mol) {
int accum = 0;
for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
atomIt != mol.endAtoms(); ++atomIt) {
accum += (*atomIt)->getFormalCharge();
}
return accum;
};
unsigned getNumAtomsWithDistinctProperty(const ROMol &mol, std::string prop) {
unsigned numPropAtoms = 0;
for (ROMol::ConstAtomIterator ai = mol.beginAtoms(); ai != mol.endAtoms();
++ai) {
if ((*ai)->hasProp(prop)) {
++numPropAtoms;
}
}
return numPropAtoms;
}
}; // end of namespace MolOps
}; // end of namespace RDKit
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