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553424d6b6
This reverts commit 040bdb61c7.
During testing of using this as a replacement for portions of
getTheFrags in getMolFrags, several issues came up regarding
how copies should actually work in practice. These are being
corrected in a new pr: https://github.com/rdkit/rdkit/pull/8811
Co-authored-by: Brian Kelley <bkelley@glysade.com>
157 lines
6.5 KiB
C++
157 lines
6.5 KiB
C++
//
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// Copyright (C) 2003-2022 Greg Landrum and other RDKit contributors
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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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/*! \file Subgraphs.h
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\brief functionality for finding subgraphs and paths in molecules
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Difference between _subgraphs_ and _paths_ :
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Subgraphs are potentially branched, whereas paths (in our
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terminology at least) cannot be. So, the following graph:
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\verbatim
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C--0--C--1--C--3--C
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2
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C
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\endverbatim
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has 3 _subgraphs_ of length 3: (0,1,2),(0,1,3),(2,1,3)
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but only 2 _paths_ of length 3: (0,1,3),(2,1,3)
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*/
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#include <RDGeneral/export.h>
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#ifndef RD_SUBGRAPHS_H
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#define RD_SUBGRAPHS_H
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#include <vector>
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#include <list>
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#include <map>
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#include <unordered_map>
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namespace RDKit {
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class ROMol;
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// NOTE: before replacing the defn of PATH_TYPE: be aware that
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// we do occasionally use reverse iterators on these things, so
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// replacing with a slist would probably be a bad idea.
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typedef std::vector<int> PATH_TYPE;
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typedef std::list<PATH_TYPE> PATH_LIST;
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typedef PATH_LIST::const_iterator PATH_LIST_CI;
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typedef std::map<int, PATH_LIST> INT_PATH_LIST_MAP;
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typedef INT_PATH_LIST_MAP::const_iterator INT_PATH_LIST_MAP_CI;
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typedef INT_PATH_LIST_MAP::iterator INT_PATH_LIST_MAP_I;
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// --- --- --- --- --- --- --- --- --- --- --- --- ---
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//
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//
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// --- --- --- --- --- --- --- --- --- --- --- --- ---
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//! \brief find all bond subgraphs in a range of sizes
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/*!
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* \param mol - the molecule to be considered
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* \param lowerLen - the minimum subgraph size to find
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* \param upperLen - the maximum subgraph size to find
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* \param useHs - if set, hydrogens in the graph will be considered
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* eligible to be in paths. NOTE: this will not add
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* Hs to the graph.
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* \param rootedAtAtom - if non-negative, only subgraphs that start at
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* this atom will be returned.
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*
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* The result is a map from subgraph size -> list of paths
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* (i.e. list of list of bond indices)
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*/
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RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP findAllSubgraphsOfLengthsMtoN(
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const ROMol &mol, unsigned int lowerLen, unsigned int upperLen,
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bool useHs = false, int rootedAtAtom = -1);
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//! \brief find all bond subgraphs of a particular size
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/*!
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* \param mol - the molecule to be considered
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* \param targetLen - the length of the subgraphs to be returned
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* \param useHs - if set, hydrogens in the graph will be considered
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* eligible to be in paths. NOTE: this will not add
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* Hs to the graph.
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* \param rootedAtAtom - if non-negative, only subgraphs that start at
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* this atom will be returned.
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*
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*
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* The result is a list of paths (i.e. list of list of bond indices)
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*/
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RDKIT_SUBGRAPHS_EXPORT PATH_LIST
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findAllSubgraphsOfLengthN(const ROMol &mol, unsigned int targetLen,
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bool useHs = false, int rootedAtAtom = -1);
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//! \brief find unique bond subgraphs of a particular size
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/*!
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* \param mol - the molecule to be considered
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* \param targetLen - the length of the subgraphs to be returned
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* \param useHs - if set, hydrogens in the graph will be considered
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* eligible to be in paths. NOTE: this will not add
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* Hs to the graph.
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* \param useBO - if set, bond orders will be considered when uniquifying
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* the paths
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* \param rootedAtAtom - if non-negative, only subgraphs that start at
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* this atom will be returned.
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*
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* The result is a list of paths (i.e. list of list of bond indices)
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*/
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RDKIT_SUBGRAPHS_EXPORT PATH_LIST findUniqueSubgraphsOfLengthN(
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const ROMol &mol, unsigned int targetLen, bool useHs = false,
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bool useBO = true, int rootedAtAtom = -1);
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//! \brief find all paths of a particular size
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/*!
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* \param mol - the molecule to be considered
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* \param targetLen - the length of the paths to be returned
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* \param useBonds - if set, the path indices will be bond indices,
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* not atom indices
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* \param useHs - if set, hydrogens in the graph will be considered
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* eligible to be in paths. NOTE: this will not add
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* Hs to the graph.
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* \param rootedAtAtom - if non-negative, only subgraphs that start at
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* this atom will be returned.
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* \param onlyShortestPaths - if set then only paths which are <= the shortest
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* path between the begin and end atoms will be
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* included in the results
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*
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* The result is a list of paths (i.e. list of list of bond indices)
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*/
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RDKIT_SUBGRAPHS_EXPORT PATH_LIST findAllPathsOfLengthN(
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const ROMol &mol, unsigned int targetLen, bool useBonds = true,
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bool useHs = false, int rootedAtAtom = -1, bool onlyShortestPaths = false);
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RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP findAllPathsOfLengthsMtoN(
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const ROMol &mol, unsigned int lowerLen, unsigned int upperLen,
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bool useBonds = true, bool useHs = false, int rootedAtAtom = -1,
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bool onlyShortestPaths = false);
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//! \brief Find bond subgraphs of a particular radius around an atom.
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//! Return empty result if there is no bond at the requested radius.
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/*!
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* \param mol - the molecule to be considered
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* \param radius - the radius of the subgraphs to be considered
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* \param rootedAtAtom - the atom to consider
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* \param useHs - if set, hydrogens in the graph will be considered
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* eligible to be in paths. NOTE: this will not add
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* Hs to the graph.
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* \param enforceSize - If false, all the bonds within the requested radius
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* (<= radius) is collected. Otherwise, at least one bond
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* located at the requested radius must be found and
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* added. \param atomMap - Optional: If provided, it will measure the minimum
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* distance of the atom from the rooted atom (start with 0 from the rooted
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* atom). The result is a pair of the atom ID and the distance. The result is a
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* path (a vector of bond indices)
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*/
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RDKIT_SUBGRAPHS_EXPORT PATH_TYPE findAtomEnvironmentOfRadiusN(
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const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom,
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bool useHs = false, bool enforceSize = true,
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std::unordered_map<unsigned int, unsigned int> *atomMap = nullptr);
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} // namespace RDKit
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#endif
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