Loading...
Searching...
No Matches
Digraph.h
Go to the documentation of this file.
//
// Digraph is the core data structure for determining
// Cahn–Ingold–Prelog (CIP) chirality of a molecule.
//
// It's a "directed graph" - meaning that each bond
// has a start and an end. For CIP determination,
// the start points back towards the atom that is
// being labelled.
//
// 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 <list>
#include <vector>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/rational.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include "TooManyNodesException.h"
namespace RDKit {
class Atom;
class Bond;
namespace CIPLabeler {
class Node;
class Edge;
class CIPMol;
/**
* A class to hold directed acyclic graphs representing the molecule.
*
* The root of the DAG is one of the foci of the configuration for
* which the label is being calculated. The tmproot may be set to
* other nodes that may become relevant in the calculation.
*
*/
class Digraph {
public:
Digraph() = delete;
Digraph(const Digraph &) = delete;
Digraph &operator=(const Digraph &) = delete;
Digraph(const CIPMol &mol, Atom *atom, bool atropsomerMode = false);
const CIPMol &getMol() const;
Node *getOriginalRoot() const;
Node *getCurrentRoot() const;
int getNumNodes() const;
/**
* Get all nodes which refer to `atom` in order of
* distance from the root.
*/
std::vector<Node *> getNodes(Atom *atom) const;
/**
* Access the reference atom for Rule 6 (if one is set).
*/
Atom *getRule6Ref() const;
/**
* Used exclusively for Rule 6, we set one atom as the reference.
* @param ref reference atom
*/
void setRule6Ref(Atom *ref);
/**
* Sets the root node of this digraph by flipping the directions
* of edges as required.
*
* This is more efficient than building a new Digraph, but is
* only valid for neighboring Nodes.
*
* @param newroot the new root
*/
void changeRoot(Node *newroot);
void expand(Node *beg);
Node &addNode(std::vector<char> &&visit, Atom *atom,
boost::rational<int> &&frac, int dist, int flags);
private:
const CIPMol &d_mol;
// The node from which the Digraph is first initialized.
// It matches the atom that is being labeled.
Node *dp_origin = nullptr;
// in atropisomer mode, we expand the two atoms of the atrop bond
bool d_atropisomerMode = false;
// The current root of the Digraph
Node *dp_root = nullptr;
Atom *dp_rule6Ref = nullptr;
// We can't store these in a vector, as adding new items will
// cause it to reallocate and invalidate the references
std::list<Node> d_nodes;
std::list<Edge> d_edges;
void addEdge(Node *beg, Bond *bond, Node *end);
};
} // namespace CIPLabeler
} // namespace RDKit
BoostEndInclude.h
BoostStartInclude.h
TooManyNodesException.h
RDKit::Atom
The class for representing atoms.
Definition Atom.h:74
RDKit::Bond
class for representing a bond
Definition Bond.h:46
RDKit::CIPLabeler::CIPMol
Definition CIPMol.h:66
RDKit::CIPLabeler::Digraph::Digraph
Digraph(const CIPMol &mol, Atom *atom, bool atropsomerMode=false)
RDKit::CIPLabeler::Digraph::operator=
Digraph & operator=(const Digraph &)=delete
RDKit::CIPLabeler::Digraph::changeRoot
void changeRoot(Node *newroot)
RDKit::CIPLabeler::Digraph::getOriginalRoot
Node * getOriginalRoot() const
RDKit::CIPLabeler::Digraph::addNode
Node & addNode(std::vector< char > &&visit, Atom *atom, boost::rational< int > &&frac, int dist, int flags)
RDKit::CIPLabeler::Digraph::setRule6Ref
void setRule6Ref(Atom *ref)
RDKit::CIPLabeler::Digraph::getRule6Ref
Atom * getRule6Ref() const
RDKit::CIPLabeler::Digraph::expand
void expand(Node *beg)
RDKit::CIPLabeler::Digraph::getMol
const CIPMol & getMol() const
RDKit::CIPLabeler::Digraph::getCurrentRoot
Node * getCurrentRoot() const
RDKit::CIPLabeler::Digraph::Digraph
Digraph(const Digraph &)=delete
RDKit::CIPLabeler::Digraph::Digraph
Digraph()=delete
RDKit::CIPLabeler::Digraph::getNumNodes
int getNumNodes() const
RDKit::CIPLabeler::Digraph::getNodes
std::vector< Node * > getNodes(Atom *atom) const
RDKit::CIPLabeler::Edge
Definition Edge.h:23
RDKit::CIPLabeler::Node
Definition Node.h:27
RDKit::CIPLabeler
Definition CIPLabeler.h:27
RDKit
Std stuff.
Definition Abbreviations.h:19