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d54e77e375
* add port of centres
* Several changes:
- Added a test based on RDKit issue 2984
(default RDKit fails it, this gets it right)
- Use bond directions for bond stereo (label is no longer required)
- Fix bugs in rules 4b and 5new
- Fix some mem errors
- clang-formatted
- some other minor cleanups
* Several changes and some improvements:
- Added LGPL license, as well as a mention in the doc.
- Fix/update/add some comments
- Fix typo/bug in Mancude calculation
- Fix bug in rules 4b, 5New
- Fix Sp2 Bond dir reference
- Re clang-format
- other minor changes suggested by Dan
* Another bunch of changes:
- require integer-order bonds; kekulize when required
- fix fraction comparison
- rename sq Cis/Trans e/z
- replace queues with vectors
- update copyright notices
- revert LGPL changes
- fix Asymmetric typo
* move to separate lib/mod, add python validation test
* Moving away from the original implementation:
- Rename to CIPLabeler
- Remove the abstraction layer
- Remove some stats stuff
- Push some CIPMol functions down to Node
- Use RDKit's isotope info
* Another bundle of changes. The most relevant ones:
- fix parity translation
- use cis trans as bond reference -- breaks #2984 test
- kill a lot of unused code
- use lists for queues
- store nodes and edges in digraph
- add prefixes to class data member names
- update changeRoot() test
- use fastFindRings() for mancude rings
- update docs
- add references to the scientific paper
- Document the Mancude functions
- Fix Mancude atom types and their comments
- remove mol data member from SequenceRule
- replace Fraction with boost::rational
- update comments, docstrings and the doc
* fix building the test
* Changes here include:
- adding bitset overload for the labeling function
- python wrap of the overload
- handling trigonal pyramids with implicit H
- setting bond labels sets stereo atoms, cis/trans
- nix LEFT/RIGHT/TOGETHER/OPPOSITE constants
- don't use GLOB in cmake
- a decent amount of refactoring
* Minor edits to new_CIP_labeling (#6)
* Some changes for clarity
Added some documentation and changed some variable names to match
my understanding. Also a ran clang-tidy to ensure that all blocks
were brace-enclosed.
* Return a reference instead of a copy for performance
This is called many times and showed up after some light
profiling. This change bumped throughput by about 20%
* move out of Graphmol
* move .hpp headers to .h
* update documentation; add label set of atoms test
* Address comments:
- Added references to centres to CIPLabeler.h and Python Wrap.
- Update validation test to skip sanitization.
- Document mancude fractional atomic number calculation.
- Use unittest assertions in python test.
- Update mancude docstrings to 'resonance' instad of 'tautomers'.
- Rename prioritise() to prioritize().
- Add postcondition to check carriers size in Tetrahedral.cpp.
- Use getNeighbors() in Tetrahedral.cpp.
- Move findStereoAtoms to Chirality namespace.
- Move code back into GraphMol.
- Fix typos and reformat doc.
* More comments:
- Mention why we use boost's unordered map rather than the std one.
- Fix include in Python wrapper.
* Addressed second batch of comments:
- fix the bug in rule 4b
- fix docstring for rule 2
- move atomic mass calculation from rule 2 to node
- addressed some build warnings
- simplify sp2bond::label(comp)
- add start/end atoms to Sp2Bond constructor
- update system/local includes
Co-authored-by: Dan N <dan.nealschneider@schrodinger.com>
98 lines
2.5 KiB
C++
98 lines
2.5 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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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->isInitialized()) {
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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 (dp_kekulized_mol == nullptr) {
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auto tmp = new RWMol(d_mol);
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MolOps::Kekulize(*tmp);
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const_cast<CIPMol *>(this)->dp_kekulized_mol.reset(tmp);
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}
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const auto kekulized_bond = dp_kekulized_mol->getBondWithIdx(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 (kekulized_bond->getBondType()) {
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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::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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