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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>
97 lines
1.7 KiB
C++
97 lines
1.7 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 <string>
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#include <stdexcept>
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namespace RDKit {
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namespace CIPLabeler {
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/**
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* Defines a descriptor which can be assigned to an atom to indicate the type of
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* chirality (if there is any). Each descriptor defines its general @{link
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* Type} which can be useful when comparing centres of different geometry.
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*
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*/
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enum class Descriptor {
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NONE, // Unspecified
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UNKNOWN,
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ns, // Other
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/**
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* Tetrahedral
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*/
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R,
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S,
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r,
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s,
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/**
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* Cis/Trans
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*/
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seqTrans,
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seqCis,
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E,
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Z,
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/* Axial */
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M,
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P,
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m,
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p,
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SP_4,
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TBPY_5,
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OC_6
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};
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static std::string to_string(const Descriptor &desc) {
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switch (desc) {
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case Descriptor::NONE:
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return "NONE";
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case Descriptor::UNKNOWN:
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return "UNKNOWN";
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case Descriptor::ns:
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return "ns";
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case Descriptor::R:
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return "R";
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case Descriptor::S:
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return "S";
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case Descriptor::r:
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return "r";
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case Descriptor::s:
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return "s";
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case Descriptor::seqTrans:
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return "e";
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case Descriptor::seqCis:
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return "z";
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case Descriptor::E:
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return "E";
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case Descriptor::Z:
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return "Z";
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case Descriptor::M:
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return "M";
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case Descriptor::P:
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return "P";
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case Descriptor::m:
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return "m";
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case Descriptor::p:
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return "p";
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case Descriptor::SP_4:
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return "SP_4";
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case Descriptor::TBPY_5:
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return "TBPY_5";
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case Descriptor::OC_6:
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return "OC_6";
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}
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throw std::runtime_error("Unknown descriptor");
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}
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} // namespace CIPLabeler
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} // namespace RDKit
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