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https://github.com/rdkit/rdkit.git
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d5d4d194ec
* atropisomer handling added * fixed non-used variables, linking directives * BOOST LIB start/stop fixes, linking fix * Fixes for RDKIT CI errors * minimalLib fix * changed vector<enum> for java builds * check for extra chars in CIP labeling * removed wrong deprecated message * fix ostrstream output error? * restored _ChiralAtomRank to lowercase first letter * changes for merged master * Fixed catch label for new Catch package * update expected psql results * get swig wrappers building * restore MolFileStereochem to FileParsers * fix java wrapper for reapplyMolBlockWedging * some suggestions * move a couple functions out of Bond * Merge branch 'master' into pr/atropisomers2 * merged master * Renamed setStereoanyFromSquiggleBond * atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol * fix for CI build * attempt to fix java build in CI * attempt to fix java build in CI #2 * New routine to remove non-explicit 3D-geneated chirality * changed to use pair for atrop atoms and related bonds * Changes as per PR reviews * PR review respnses * PR review reponse - more * Fix merge from master * fixing java ci after merge * Updated the help doc for atripisomers * update the atropisomer docs * improve the images * add the source CXSMILES --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
121 lines
2.8 KiB
C++
121 lines
2.8 KiB
C++
//
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// Digraph is the core data structure for determining
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// Cahn–Ingold–Prelog (CIP) chirality of a molecule.
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//
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// It's a "directed graph" - meaning that each bond
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// has a start and an end. For CIP determination,
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// the start points back towards the atom that is
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// being labelled.
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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 <list>
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#include <vector>
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#include <boost/rational.hpp>
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#include "TooManyNodesException.h"
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namespace RDKit {
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class Atom;
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class Bond;
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namespace CIPLabeler {
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class Node;
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class Edge;
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class CIPMol;
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/**
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* A class to hold directed acyclic graphs representing the molecule.
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*
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* The root of the DAG is one of the foci of the configuration for
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* which the label is being calculated. The tmproot may be set to
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* other nodes that may become relevant in the calculation.
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*
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*/
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class Digraph {
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public:
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Digraph() = delete;
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Digraph(const Digraph &) = delete;
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Digraph &operator=(const Digraph &) = delete;
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Digraph(const CIPMol &mol, Atom *atom, bool atropsomerMode = false);
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const CIPMol &getMol() const;
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Node *getOriginalRoot() const;
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Node *getCurrentRoot() const;
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int getNumNodes() const;
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/**
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* Get all nodes which refer to `atom` in order of
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* distance from the root.
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*/
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std::vector<Node *> getNodes(Atom *atom) const;
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/**
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* Access the reference atom for Rule 6 (if one is set).
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*/
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Atom *getRule6Ref() const;
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/**
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* Used exclusively for Rule 6, we set one atom as the reference.
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* @param ref reference atom
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*/
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void setRule6Ref(Atom *ref);
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/**
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* Sets the root node of this digraph by flipping the directions
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* of edges as required.
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*
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* This is more efficient than building a new Digraph, but is
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* only valid for neighboring Nodes.
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*
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* @param newroot the new root
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*/
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void changeRoot(Node *newroot);
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void expand(Node *beg);
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Node &addNode(std::vector<char> &&visit, Atom *atom,
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boost::rational<int> &&frac, int dist, int flags);
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private:
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const CIPMol &d_mol;
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// The node from which the Digraph is first initialized.
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// It matches the atom that is being labeled.
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Node *dp_origin = nullptr;
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// in atropisomer mode, we expand the two atoms of the atrop bond
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bool d_atropisomerMode = false;
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// The current root of the Digraph
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Node *dp_root = nullptr;
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Atom *dp_rule6Ref = nullptr;
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// We can't store these in a vector, as adding new items will
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// cause it to reallocate and invalidate the references
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std::list<Node> d_nodes;
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std::list<Edge> d_edges;
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void addEdge(Node *beg, Bond *bond, Node *end);
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};
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} // namespace CIPLabeler
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} // namespace RDKit
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