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// $Id$
//
// Copyright (C) 2001-2008 Greg Landrum and Rational Discovery LLC
//
// @@ 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 "ROMol.h"
#include "RWMol.h"
#include "Atom.h"
#include "Bond.h"
#include "MolOps.h"
#include "PeriodicTable.h"
#include "AtomIterators.h"
#include "BondIterators.h"
namespace RDKit {
// local utility namespace:
namespace {
bool isAtomConjugCand(const Atom *at) {
// the second check here is for Issue211, where the c-P bonds in
// Pc1ccccc1 were being marked as conjugated. This caused the P atom
// itself to be SP2 hybridized. This is wrong. For now we'll do a quick
// hack and forbid this check from adding conjugation to anything out of
// the first row of the periodic table. (Conjugation in aromatic rings
// has already been attended to, so this is safe.)
int nouter = PeriodicTable::getTable()->getNouterElecs(at->getAtomicNum());
if (((at->getAtomicNum() <= 10) || (nouter != 5 && nouter != 6) ||
(nouter == 6 && at->getTotalDegree() < 2)) &&
(MolOps::countAtomElec(at) > 0)) {
return true;
}
return false;
}
void markConjAtomBonds(Atom *at) {
if (!isAtomConjugCand(at)) return;
ROMol &mol = at->getOwningMol();
Atom *at2;
int atx = at->getIdx();
// make sure that have either 2 or 3 subtitutions on this atom
int sbo = at->getDegree() + at->getTotalNumHs();
if ((sbo < 2) || (sbo > 3)) {
return;
}
ROMol::OEDGE_ITER bnd1, end1, bnd2, end2;
boost::tie(bnd1, end1) = mol.getAtomBonds(at);
while (bnd1 != end1) {
if (mol[*bnd1]->getValenceContrib(at) < 1.5) {
bnd1++;
continue;
}
boost::tie(bnd2, end2) = mol.getAtomBonds(at);
while (bnd2 != end2) {
if (bnd1 == bnd2) {
bnd2++;
continue;
}
at2 = mol.getAtomWithIdx(mol[*bnd2]->getOtherAtomIdx(atx));
sbo = at2->getDegree() + at2->getTotalNumHs();
if (sbo > 3) {
bnd2++;
continue;
}
if (isAtomConjugCand(at2)) {
mol[*bnd1]->setIsConjugated(true);
mol[*bnd2]->setIsConjugated(true);
}
bnd2++;
}
bnd1++;
}
}
int numBondsPlusLonePairs(Atom *at) {
PRECONDITION(at, "bad atom");
int deg = at->getTotalDegree();
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at);
while (beg != end) {
Bond* bond = at->getOwningMol()[*beg];
if (bond->getBondType() == Bond::ZERO) --deg;
++beg;
}
if (at->getAtomicNum() <= 1) {
return deg;
}
int nouter = PeriodicTable::getTable()->getNouterElecs(at->getAtomicNum());
int totalValence = at->getExplicitValence() + at->getImplicitValence();
int chg = at->getFormalCharge();
int numFreeElectrons = nouter - (totalValence + chg);
if (totalValence + nouter - chg < 8) {
// we're below an octet, so we need to think
// about radicals:
int numRadicals = at->getNumRadicalElectrons();
int numLonePairs = (numFreeElectrons - numRadicals) / 2;
return deg + numLonePairs + numRadicals;
} else {
int numLonePairs = numFreeElectrons / 2;
return deg + numLonePairs;
}
}
} // end of utility namespace
namespace MolOps {
bool atomHasConjugatedBond(const Atom *at) {
PRECONDITION(at, "bad atom");
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at);
while (beg != end) {
if (at->getOwningMol()[*beg]->getIsConjugated()) return true;
beg++;
}
return false;
}
void setConjugation(ROMol &mol) {
// start with all bonds being marked unconjugated
// except for aromatic bonds
ROMol::BondIterator bi;
for (bi = mol.beginBonds(); bi != mol.endBonds(); bi++) {
if ((*bi)->getIsAromatic()) {
(*bi)->setIsConjugated(true);
} else {
(*bi)->setIsConjugated(false);
}
}
ROMol::AtomIterator ai;
// loop over each atom and check if the bonds connecting to it can
// be conjugated
for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ai++) {
markConjAtomBonds(*ai);
}
}
void setHybridization(ROMol &mol) {
ROMol::AtomIterator ai;
int norbs;
for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ai++) {
if ((*ai)->getAtomicNum() == 0) {
(*ai)->setHybridization(Atom::UNSPECIFIED);
} else {
norbs = numBondsPlusLonePairs(*ai);
switch (norbs) {
case 0:
// This occurs for things like Na+
(*ai)->setHybridization(Atom::S);
break;
case 1:
(*ai)->setHybridization(Atom::S);
break;
case 2:
(*ai)->setHybridization(Atom::SP);
break;
case 3:
(*ai)->setHybridization(Atom::SP2);
break;
case 4:
// potentially SP3, but we'll set it down to SP2
// if we have a conjugated bond (like the second O
// in O=CO)
// we'll also avoid setting the hybridization down to
// SP2 in the case of an atom with degree higher than 3
// (e.g. things like CP1(C)=CC=CN=C1C, where the P
// has norbs = 4, and a conjugated bond, but clearly should
// not be SP2)
// This is Issue276
if ((*ai)->getDegree() > 3 || !MolOps::atomHasConjugatedBond(*ai)) {
(*ai)->setHybridization(Atom::SP3);
} else {
(*ai)->setHybridization(Atom::SP2);
}
break;
case 5:
(*ai)->setHybridization(Atom::SP3D);
break;
case 6:
(*ai)->setHybridization(Atom::SP3D2);
break;
default:
(*ai)->setHybridization(Atom::UNSPECIFIED);
}
}
}
}
} // end of namespace MolOps
} // end of namespace RDKit
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