mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
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>
126 lines
2.4 KiB
C++
126 lines
2.4 KiB
C++
//
|
|
//
|
|
// Copyright (C) 2020 Schrödinger, LLC
|
|
//
|
|
// @@ 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.
|
|
//
|
|
#pragma once
|
|
|
|
#include <vector>
|
|
|
|
#include "Descriptor.h"
|
|
#include "Mancude.h"
|
|
#include "Edge.h"
|
|
|
|
namespace RDKit {
|
|
|
|
class Atom;
|
|
|
|
namespace CIPLabeler {
|
|
|
|
class Digraph;
|
|
|
|
class Node {
|
|
public:
|
|
/**
|
|
* Flag indicates whether the node has been expanded.
|
|
*/
|
|
static const int EXPANDED = 0x1;
|
|
|
|
/**
|
|
* Flag indicates whether the node was duplicated
|
|
* at a ring closure.
|
|
*/
|
|
static const int RING_DUPLICATE = 0x2;
|
|
|
|
/**
|
|
* Flag indicates whether the node was duplicated
|
|
* at a bond with order > 1.
|
|
*/
|
|
static const int BOND_DUPLICATE = 0x4;
|
|
|
|
/**
|
|
* Mask to check if a node is duplicated.
|
|
*/
|
|
static const int DUPLICATE = 0x6;
|
|
|
|
/**
|
|
* Node was created for an implicit hydrogen,
|
|
* the 'atom' value will be null.
|
|
*/
|
|
static const int IMPL_HYDROGEN = 0x8;
|
|
|
|
Node() = delete;
|
|
Node(const Node &) = delete;
|
|
Node &operator=(const Node &) = delete;
|
|
|
|
Node(Digraph *g, std::vector<char> &&visit, Atom *atom,
|
|
boost::rational<int> &&frac, int dist, int flags);
|
|
|
|
Digraph *getDigraph() const;
|
|
|
|
Atom *getAtom() const;
|
|
|
|
int getDistance() const;
|
|
|
|
boost::rational<int> getAtomicNumFraction() const;
|
|
|
|
int getAtomicNum() const;
|
|
|
|
unsigned getMassNum() const;
|
|
|
|
double getAtomicMass() const;
|
|
|
|
Descriptor getAux() const;
|
|
|
|
bool isSet(int mask) const;
|
|
|
|
bool isDuplicate() const;
|
|
|
|
bool isTerminal() const;
|
|
|
|
bool isExpanded() const;
|
|
|
|
bool isVisited(int idx) const;
|
|
|
|
Node *newChild(int idx, Atom *atom) const;
|
|
|
|
Node *newBondDuplicateChild(int idx, Atom *atom) const;
|
|
|
|
Node *newRingDuplicateChild(int idx, Atom *atom) const;
|
|
|
|
Node *newImplicitHydrogenChild() const;
|
|
|
|
void add(Edge *e);
|
|
|
|
void setAux(Descriptor desc);
|
|
|
|
const std::vector<Edge *> &getEdges() const;
|
|
|
|
std::vector<Edge *> getEdges(Atom *end) const;
|
|
|
|
std::vector<Edge *> getNonTerminalOutEdges() const;
|
|
|
|
private:
|
|
Digraph *dp_g;
|
|
Atom *dp_atom;
|
|
int d_dist;
|
|
boost::rational<int> d_atomic_num;
|
|
double d_atomic_mass;
|
|
Descriptor d_aux = Descriptor::NONE;
|
|
int d_flags = 0x0;
|
|
|
|
std::vector<Edge *> d_edges;
|
|
|
|
std::vector<char> d_visit;
|
|
|
|
Node *newTerminalChild(int idx, Atom *atom, int flags) const;
|
|
};
|
|
|
|
} // namespace CIPLabeler
|
|
} // namespace RDKit
|