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* CIPLabeler performance: Store vector of bonds CIPLabelling refers to bonds by index over and over again. This causes a measurable hit in performance in findConfigs() because we iterate over a bitset of "allowed" bonds. For very large molecules with many bonds, this can be a rate-limiting step! This affects many PDB-sized structures. 2J3N goes from 0.7s to 0.25s with this change. I had another example for which the findBondWithIdx() call was taking 500ms of a 700ms call (after the performance update in #9171 was implemented) * yikes, XXL reserve thanks, greg Co-authored-by: Greg Landrum <greg.landrum@gmail.com> --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
105 lines
2.2 KiB
C++
105 lines
2.2 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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#pragma once
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#include <memory>
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#include <GraphMol/RDKitBase.h>
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#include "Descriptor.h"
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#include "Mancude.h"
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namespace RDKit {
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namespace CIPLabeler {
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template <typename T, typename U>
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class CIPMolSpan {
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public:
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class CIPMolIter {
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public:
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CIPMolIter() = delete;
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CIPMolIter(ROMol &mol, U pos) : d_mol{mol}, d_pos{std::move(pos)} {}
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T &operator*() {
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d_current = d_mol[*d_pos];
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return d_current;
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}
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CIPMolIter &operator++() {
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++d_pos;
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return *this;
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}
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bool operator!=(const CIPMolIter &it) const { return d_pos != it.d_pos; }
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private:
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ROMol &d_mol;
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U d_pos;
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T d_current = nullptr;
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};
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public:
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CIPMolSpan() = delete;
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CIPMolSpan(ROMol &mol, std::pair<U, U> &&itr)
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: d_mol{mol},
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d_istart{std::move(itr.first)},
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d_iend{std::move(itr.second)} {}
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CIPMolIter begin() { return {d_mol, d_istart}; }
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CIPMolIter end() { return {d_mol, d_iend}; }
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private:
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ROMol &d_mol;
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const U d_istart;
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const U d_iend;
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};
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class CIPMol {
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public:
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CIPMol() = delete;
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explicit CIPMol(ROMol &mol);
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// Average atomic number with other atoms that are in an
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// aromatic ring with this one.
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boost::rational<int> getFractionalAtomicNum(Atom *atom) const;
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unsigned getNumAtoms() const;
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unsigned getNumBonds() const;
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Atom *getAtom(int idx) const;
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CXXAtomIterator<MolGraph, Atom *> atoms() const;
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Bond *getBond(int idx) const;
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CIPMolSpan<Bond *, ROMol::OEDGE_ITER> getBonds(Atom *atom) const;
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CIPMolSpan<Atom *, ROMol::ADJ_ITER> getNeighbors(Atom *atom) const;
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bool isInRing(Bond *bond) const;
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// Integer bond order of a kekulized molecule
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// Dative bonds get bond order 0.
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int getBondOrder(Bond *bond) const;
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private:
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ROMol &d_mol;
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std::vector<RDKit::Bond::BondType> d_kekulized_bonds;
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std::vector<boost::rational<int>> d_atomnums;
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std::vector<RDKit::Bond* > d_bonds;
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};
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} // namespace CIPLabeler
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} // namespace RDKit
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