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c1de3aefb5
For example, PDB ID 2ZP8 goes from 133s to 53s on my M3 laptop. Boost graph edges (our bonds) cannot be accessed by index, they must be searched for - linearly. This protein only has 27,000 bonds (after addition of explicit hydrogens), but that's still a lot.
111 lines
2.9 KiB
C++
111 lines
2.9 KiB
C++
//
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//
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// Copyright (C) 2020 Schrödinger, LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <GraphMol/MolOps.h>
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#include "CIPMol.h"
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namespace RDKit {
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namespace CIPLabeler {
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CIPMol::CIPMol(ROMol &mol) : d_mol{mol} {}
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boost::rational<int> CIPMol::getFractionalAtomicNum(Atom *atom) const {
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PRECONDITION(atom, "bad atom")
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if (d_atomnums.empty()) {
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const_cast<CIPMol *>(this)->d_atomnums = calcFracAtomNums(*this);
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}
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return d_atomnums[atom->getIdx()];
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}
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unsigned CIPMol::getNumAtoms() const { return d_mol.getNumAtoms(); }
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unsigned CIPMol::getNumBonds() const { return d_mol.getNumBonds(); };
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Atom *CIPMol::getAtom(int idx) const { return d_mol.getAtomWithIdx(idx); };
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CXXAtomIterator<MolGraph, Atom *> CIPMol::atoms() const {
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return d_mol.atoms();
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}
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Bond *CIPMol::getBond(int idx) const { return d_mol.getBondWithIdx(idx); };
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CIPMolSpan<Bond *, ROMol::OEDGE_ITER> CIPMol::getBonds(Atom *atom) const {
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PRECONDITION(atom, "bad atom")
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return {d_mol, d_mol.getAtomBonds(atom)};
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}
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CIPMolSpan<Atom *, ROMol::ADJ_ITER> CIPMol::getNeighbors(Atom *atom) const {
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PRECONDITION(atom, "bad atom")
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return {d_mol, d_mol.getAtomNeighbors(atom)};
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}
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bool CIPMol::isInRing(Bond *bond) const {
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PRECONDITION(bond, "bad bond")
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const auto rings = d_mol.getRingInfo();
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if (!rings->isFindFastOrBetter()) {
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MolOps::fastFindRings(d_mol);
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}
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return rings->numBondRings(bond->getIdx()) != 0u;
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};
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int CIPMol::getBondOrder(Bond *bond) const {
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PRECONDITION(bond, "bad bond")
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if (d_kekulized_bonds.empty()) {
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RWMol tmp{d_mol};
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try {
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MolOps::Kekulize(tmp);
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} catch (const MolSanitizeException &) {
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}
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auto& bonds = const_cast<std::vector<RDKit::Bond::BondType>&>(d_kekulized_bonds);
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bonds.reserve(d_mol.getNumBonds());
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for (const auto &b : tmp.bonds()) {
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bonds.push_back(b->getBondType());
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}
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}
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const auto bond_type = d_kekulized_bonds.at(bond->getIdx());
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// Dative bonds might need to be considered with a different bond order
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// for the end atom at the end of the bond.
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switch (bond_type) {
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case Bond::ZERO:
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case Bond::HYDROGEN:
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case Bond::DATIVE:
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case Bond::DATIVEL:
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case Bond::DATIVER:
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return 0;
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case Bond::SINGLE:
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return 1;
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case Bond::AROMATIC:
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BOOST_LOG(rdWarningLog)
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<< "non kekulizable aromatic bond being treated as bond order 1"
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<< std::endl;
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return 1;
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case Bond::DOUBLE:
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return 2;
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case Bond::TRIPLE:
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return 3;
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case Bond::QUADRUPLE:
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return 4;
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case Bond::QUINTUPLE:
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return 5;
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case Bond::HEXTUPLE:
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return 6;
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default:
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throw std::runtime_error("Non integer-order bonds are not allowed.");
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}
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};
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} // namespace CIPLabeler
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} // namespace RDKit
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