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//
// Copyright (C) 2001-2024 Greg Landrum and other RDKit contributors
//
// @@ 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) {
PRECONDITION(at, "bad atom");
// return false for neutral atoms where the current valence exceeds the
// minimal valence for the atom. logic: if we're hypervalent we aren't
// conjugated
const auto &vals =
PeriodicTable::getTable()->getValenceList(at->getAtomicNum());
if (!at->getFormalCharge() && vals.front() >= 0 &&
at->getTotalValence() > static_cast<unsigned int>(vals.front())) {
return false;
}
// 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());
auto res = ((at->getAtomicNum() <= 10) || (nouter != 5 && nouter != 6) ||
(nouter == 6 && at->getTotalDegree() < 2u)) &&
MolOps::countAtomElec(at) > 0;
return res;
}
void markConjAtomBonds(Atom *at) {
PRECONDITION(at, "bad atom");
if (!isAtomConjugCand(at)) {
return;
}
auto &mol = at->getOwningMol();
int atx = at->getIdx();
// make sure that have either 2 or 3 substitutions on this atom
int sbo = at->getDegree() + at->getTotalNumHs();
if ((sbo < 2) || (sbo > 3)) {
return;
}
for (const auto bnd1 : mol.atomBonds(at)) {
if (bnd1->getValenceContrib(at) < 1.5 ||
!isAtomConjugCand(bnd1->getOtherAtom(at))) {
continue;
}
for (const auto bnd2 : mol.atomBonds(at)) {
if (bnd1 == bnd2) {
continue;
}
auto at2 = mol.getAtomWithIdx(bnd2->getOtherAtomIdx(atx));
sbo = at2->getDegree() + at2->getTotalNumHs();
if (sbo > 3) {
continue;
}
if (isAtomConjugCand(at2)) {
bnd1->setIsConjugated(true);
bnd2->setIsConjugated(true);
}
}
}
}
int numBondsPlusLonePairs(Atom *at) {
PRECONDITION(at, "bad atom");
int deg = at->getTotalDegree();
auto &mol = at->getOwningMol();
for (const auto bond : mol.atomBonds(at)) {
if (bond->getBondType() == Bond::ZERO ||
(isDative(*bond) && at->getIdx() != bond->getEndAtomIdx())) {
--deg;
}
}
if (at->getAtomicNum() <= 1) {
return deg;
}
int nouter = PeriodicTable::getTable()->getNouterElecs(at->getAtomicNum());
int totalValence = at->getTotalValence();
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;
}
}
} // namespace
namespace MolOps {
bool atomHasConjugatedBond(const Atom *at) {
PRECONDITION(at, "bad atom");
auto &mol = at->getOwningMol();
for (const auto bnd : mol.atomBonds(at)) {
if (bnd->getIsConjugated()) {
return true;
}
}
return false;
}
void setConjugation(ROMol &mol) {
// start with all bonds being marked unconjugated
// except for aromatic bonds
for (auto bond : mol.bonds()) {
bond->setIsConjugated(bond->getIsAromatic());
}
// loop over each atom and check if the bonds connecting to it can
// be conjugated
for (auto atom : mol.atoms()) {
markConjAtomBonds(atom);
}
}
void setHybridization(ROMol &mol) {
for (auto atom : mol.atoms()) {
if (atom->getAtomicNum() == 0) {
atom->setHybridization(Atom::UNSPECIFIED);
} else {
// if the stereo spec matches the coordination number, this is easy
switch (atom->getChiralTag()) {
case Atom::ChiralType::CHI_TETRAHEDRAL:
case Atom::ChiralType::CHI_TETRAHEDRAL_CW:
case Atom::ChiralType::CHI_TETRAHEDRAL_CCW:
if (atom->getTotalDegree() == 4) {
atom->setHybridization(Atom::HybridizationType::SP3);
continue;
}
break;
case Atom::ChiralType::CHI_SQUAREPLANAR:
if (atom->getTotalDegree() <= 4 && atom->getTotalDegree() >= 2) {
atom->setHybridization(Atom::HybridizationType::SP2D);
continue;
}
break;
case Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL:
if (atom->getTotalDegree() <= 5 && atom->getTotalDegree() >= 2) {
atom->setHybridization(Atom::HybridizationType::SP3D);
continue;
}
break;
case Atom::ChiralType::CHI_OCTAHEDRAL:
if (atom->getTotalDegree() <= 6 && atom->getTotalDegree() >= 2) {
atom->setHybridization(Atom::HybridizationType::SP3D2);
continue;
}
break;
default:
break;
}
// otherwise we have to do some work
int norbs;
// try to be smart for early elements, but for later
// ones just use the degree
// FIX: we should probably also be using the degree for metals
if (atom->getAtomicNum() < 89) {
norbs = numBondsPlusLonePairs(atom);
} else {
norbs = atom->getTotalDegree();
}
switch (norbs) {
case 0:
// This occurs for things like Na+
atom->setHybridization(Atom::S);
break;
case 1:
atom->setHybridization(Atom::S);
break;
case 2:
atom->setHybridization(Atom::SP);
break;
case 3:
atom->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 (atom->getTotalDegree() > 3 ||
!MolOps::atomHasConjugatedBond(atom)) {
atom->setHybridization(Atom::SP3);
} else {
atom->setHybridization(Atom::SP2);
}
break;
case 5:
atom->setHybridization(Atom::SP3D);
break;
case 6:
atom->setHybridization(Atom::SP3D2);
break;
default:
atom->setHybridization(Atom::UNSPECIFIED);
}
}
}
}
} // end of namespace MolOps
} // end of namespace RDKit
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