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a9477d2694
* use std::span for substruct match callbacks This removes a copy from every evaluation of potential matches * some cleanup/modernization * some modernization * deprecate chiralAtomCompat * small optimization * remove naked pointers * improve new_timings.py script * changes suggested in review * response to review * response to review
628 lines
20 KiB
C++
628 lines
20 KiB
C++
//
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// Copyright (C) 2021-2023 Greg Landrum and 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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#include <RDGeneral/export.h>
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#include <GraphMol/RWMol.h>
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#include <GraphMol/MolOps.h>
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#ifndef RD_GENERICGROUPS_H
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#define RD_GENERICGROUPS_H
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#include <vector>
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#include <functional>
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#include <map>
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#include <span>
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#include <boost/dynamic_bitset.hpp>
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namespace RDKit {
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class ROMol;
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class Atom;
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class Bond;
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namespace GenericGroups {
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// We'd like to be able to correctly interpret what's written by Marvin and
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// MarvinJS, so the conditions for these are adapted from the ChemAxon
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// documentation for homology groups
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// (https://docs.chemaxon.com/display/docs/homology-groups.md)
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//
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// If I had questions about what the queries should do, I ran example in Reaxys
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// with MarvinJS as the sketcher to see what that returns.
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//
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// I've tried to document deviations or surprises
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namespace Matchers {
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//! Matches any group as a side chain
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/*!
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Note: this is Reaxys query type G and matches any sidechain
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Conditions:
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- at least one non-hydrogen atom is in the sidechain
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*/
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RDKIT_GENERICGROUPS_EXPORT bool GroupAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches any group as a side chain including just an H atom
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/*!
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Note: this is Reaxys query type GH and matches any sidechain
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Conditions:
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- none
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*/
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RDKIT_GENERICGROUPS_EXPORT bool GroupHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches any group as a side chain
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/*!
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Note: this is Reaxys query type G* and matches any sidechain that has a ring
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closure
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Conditions:
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- at least one non-hydrogen atom is in the sidechain
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- at least one ring closure
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*/
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RDKIT_GENERICGROUPS_EXPORT bool GroupStarAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches any group as a side chain that has a ring closure or just an H atom
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/*!
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Note: this is Reaxys query type GH* and matches any sidechains
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Conditions:
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- at least one ring closure
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- OR
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- the entire group is just an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool GroupStarHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches alkyl side chains
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/*!
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Conditions:
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- side chain consists entirely of carbon or hydrogen
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- at least one carbon is present
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- all bonds are single
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- no ring bonds
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches alkyl side chains or an H atom
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/*!
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Conditions:
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- side chain consists entirely of carbon or hydrogen
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- all bonds are single
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- no ring bonds
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches alkenyl side chains
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/*!
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Conditions:
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- side chain consists entirely of carbon or hydrogen
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- contains at least one C=C
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- no ring bonds
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkenylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches alkenyl side chains or an H
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/*!
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Conditions:
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- side chain consists entirely of carbon or hydrogen
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- contains at least one C=C
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- no ring bonds
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkenylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches alkynyl side chains
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/*!
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Conditions:
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- side chain consists entirely of carbon or hydrogen
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- contains at least one C#C
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- no ring bonds
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkynylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches alkynyl side chains or an H
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/*!
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Conditions:
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- side chain consists entirely of carbon or hydrogen
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- contains at least one C#C
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- no ring bonds
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- OR
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- the whole group is an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkynylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches carbocyclic side chains
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/*!
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Note: this is Reaxys query type CBC and matches carbocycles
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Conditions:
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- atom is in at least one ring composed entirely of carbon
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches carbocyclic side chains or an H atom
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/*!
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Note: this is Reaxys query type CBC and matches carbocycles
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Conditions:
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- atom is in at least one ring composed entirely of carbon
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules
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- OR the entire group is just an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches cycloalkyl side chains
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/*!
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Note: this is Reaxys query type CAL and is directly equivalent to alkyl,
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except the immediate atom needs to be in a ring.
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Conditions:
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- atom is in at least one ring composed entirely of carbon and connected
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with single bonds
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- atoms in the ring do not have unsaturations (including exocyclic)
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules (i.e. all
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single bonds)
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches cycloalkyl side chains or an H atom
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/*!
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Note: this is Reaxys query type CAL and is directly equivalent to alkyl,
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except the immediate atom needs to be in a ring.
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Conditions:
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- atom is in at least one ring composed entirely of carbon and connected
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with single bonds
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- atoms in the ring do not have unsaturations (including exocyclic)
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules (i.e. all
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single bonds)
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- OR
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- the whole group is an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches cycloalkenyl side chains
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/*!
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Note: this is Reaxys query type CEL and matches carbocycles which have at
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least one double or aromatic bond.
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Conditions:
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- atom is in at least one ring composed entirely of carbon and with at least
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one double or aromatic bond
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules (including
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that each ring must have at least one double or aromatic bond)
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches cycloalkenyl side chains or an H atom
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/*!
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Note: this is Reaxys query type CEL and matches carbocycles which have at
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least one double or aromatic bond.
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Conditions:
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- atom is in at least one ring composed entirely of carbon and with at least
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one double or aromatic bond
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules (including
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that each ring must have at least one double or aromatic bond)
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches heterocyclic side chains
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/*!
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Note: this is Reaxys query type CHC and matches heterocycles
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Conditions:
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- atom is in at least one fused ring with a heteroatom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches heterocyclic side chains or an H atom
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/*!
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Note: this is Reaxys query type CHH and matches heterocycles or an H atom
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Conditions:
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- atom is in at least one fused ring with a heteroatom
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- or the entire group is a single H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches aryl side chains
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/*!
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Note: this is Reaxys query type ARY and matches carbocycles which are aromatic
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Conditions:
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- atom is in at least one aromatic ring composed entirely of carbon
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarboarylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches aryl side chains or an H atom
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/*!
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Note: this is Reaxys query type ARH and matches carbocycles which are aromatic
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or an H atom
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Conditions:
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- atom is in at least one aromatic ring composed entirely of carbon
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- atom is not in any rings not compatible with the above conditions
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- additional fused rings in the system must obey the same rules
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarboarylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches heteroaryl side chains
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/*!
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Note: this is Reaxys query type HAR and matches aromatic heterocycles
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Conditions:
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- atom is in at least one fused aromatic sytem with a heteroatom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool HeteroarylAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches heteroaryl side chains or an H atom
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/*!
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Note: this is Reaxys query type HAR and matches aromatic heterocycles
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Conditions:
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- atom is in at least one fused aromatic sytem with a heteroatom
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- or the entire group is an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool HeteroarylHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches cyclic side chains
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/*!
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Note: this is Reaxys query type CYC and matches cycles
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Conditions:
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- atom is in at least one ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches cyclic side chains or an H atom
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/*!
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Note: this is Reaxys query type CYH and matches cycles
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Conditions:
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- atom is in at least one ring
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- or the entire group is just an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches acyclic side chains
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/*!
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Note: this is Reaxys query type ACY and matches sidechains with no cycles
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Conditions:
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- no atom in the sidechain is in a ring and the group is NOT just an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AcyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches acyclic side chains or an H atom
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/*!
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Note: this is Reaxys query type ACY and matches sidechains with no cycles
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Conditions:
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- no atom in the sidechain is in a ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AcyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches all-carbon acyclic side chains
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/*!
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Note: this is Reaxys query type ABC and matches all-carbon sidechains with no
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cycles
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Conditions:
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- all atoms in the sidechain are carbon
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- no atom in the sidechain is in a ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarboacyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches all-carbon acyclic side chainsor or an H atom
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/*!
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Note: this is Reaxys query type ABH and matches all-carbon sidechains with no
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cycles or just a H atom
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Conditions:
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- all atoms in the sidechain are carbon or H
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- no atom in the sidechain is in a ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool CarboacyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches acyclic side chains with at least one heteroatom
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/*!
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Note: this is Reaxys query type AHC and matches sidechains with no cycles and
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at least one heteroatom
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Conditions:
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- at least one non-carbon, non-hydrogen atom is in the sidechain
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- no atom in the sidechain is in a ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool HeteroacyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches acyclic side chains with at least one heteroatom or an H atom
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/*!
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Note: this is Reaxys query type AHC and matches sidechains with no cycles and
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at least one heteroatom
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Conditions:
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- at least one non-carbon, non-hydrogen atom is in the sidechain
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- no atom in the sidechain is in a ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool HeteroacyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches acyclic alkoxy side chains
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/*!
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Note: this is Reaxys query type AOX and matches alkoxy sidechains
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Conditions:
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- first atom is an O
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- all other atoms are C
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- all single bonds
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- no atom in the sidechain is in a ring
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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/*!
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Note: this is Reaxys query type AOH and matches alkoxy sidechains or a hydrogen
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Conditions:
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- first atom is an O
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- all other atoms are C
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- all single bonds
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- no atom in the sidechain is in a ring
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- OR
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- the whole group is just an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches rings without carbon
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/*!
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Note: this is Reaxys query type CXX and matches rings which contain no carbon
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Conditions:
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- a ring is present
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- none of the atoms in the fused ring system are carbon
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*/
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RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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//! Matches rings without carbon or just an H
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/*!
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Note: this is Reaxys query type CXH and matches rings which contain no carbon
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Conditions:
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- a ring is present
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- none of the atoms in the fused ring system are carbon
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- OR
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- the entire group is just an H atom
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*/
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RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingHAtomMatcher(
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const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
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} // namespace Matchers
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const static std::map<
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std::string,
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std::function<bool(const ROMol &, const Atom &, boost::dynamic_bitset<>)>>
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genericMatchers = {
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{"Group", Matchers::GroupAtomMatcher},
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{"G", Matchers::GroupAtomMatcher},
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{"GroupH", Matchers::GroupHAtomMatcher},
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{"GH", Matchers::GroupHAtomMatcher},
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{"Group*", Matchers::GroupStarAtomMatcher},
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{"G*", Matchers::GroupStarAtomMatcher},
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{"GroupH*", Matchers::GroupStarHAtomMatcher},
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{"GH*", Matchers::GroupStarHAtomMatcher},
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{"Alkyl", Matchers::AlkylAtomMatcher},
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{"ALK", Matchers::AlkylAtomMatcher},
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{"AlkylH", Matchers::AlkylHAtomMatcher},
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{"ALH", Matchers::AlkylHAtomMatcher},
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{"Alkenyl", Matchers::AlkenylAtomMatcher},
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{"AEL", Matchers::AlkenylAtomMatcher},
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{"AlkenylH", Matchers::AlkenylHAtomMatcher},
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{"AEH", Matchers::AlkenylHAtomMatcher},
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{"Alkynyl", Matchers::AlkynylAtomMatcher},
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{"AYL", Matchers::AlkynylAtomMatcher},
|
|
{"AlkynylH", Matchers::AlkynylHAtomMatcher},
|
|
{"AYH", Matchers::AlkynylHAtomMatcher},
|
|
{"Carbocyclic", Matchers::CarbocyclicAtomMatcher},
|
|
{"CBC", Matchers::CarbocyclicAtomMatcher},
|
|
{"CarbocyclicH", Matchers::CarbocyclicHAtomMatcher},
|
|
{"CBH", Matchers::CarbocyclicHAtomMatcher},
|
|
{"Carbocycloalkyl", Matchers::CarbocycloalkylAtomMatcher},
|
|
{"CAL", Matchers::CarbocycloalkylAtomMatcher},
|
|
{"CarbocycloalkylH", Matchers::CarbocycloalkylHAtomMatcher},
|
|
{"CAH", Matchers::CarbocycloalkylHAtomMatcher},
|
|
{"Carbocycloalkenyl", Matchers::CarbocycloalkenylAtomMatcher},
|
|
{"CEL", Matchers::CarbocycloalkenylAtomMatcher},
|
|
{"CarbocycloalkenylH", Matchers::CarbocycloalkenylHAtomMatcher},
|
|
{"CEH", Matchers::CarbocycloalkenylHAtomMatcher},
|
|
{"Carboaryl", Matchers::CarboarylAtomMatcher},
|
|
{"ARY", Matchers::CarboarylAtomMatcher},
|
|
{"CarboarylH", Matchers::CarboarylHAtomMatcher},
|
|
{"ARH", Matchers::CarboarylHAtomMatcher},
|
|
{"Cyclic", Matchers::CyclicAtomMatcher},
|
|
{"CYC", Matchers::CyclicAtomMatcher},
|
|
{"CyclicH", Matchers::CyclicHAtomMatcher},
|
|
{"CYH", Matchers::CyclicHAtomMatcher},
|
|
{"Acyclic", Matchers::AcyclicAtomMatcher},
|
|
{"ACY", Matchers::AcyclicAtomMatcher},
|
|
{"AcyclicH", Matchers::AcyclicHAtomMatcher},
|
|
{"ACH", Matchers::AcyclicHAtomMatcher},
|
|
{"Carboacyclic", Matchers::CarboacyclicAtomMatcher},
|
|
{"ABC", Matchers::CarboacyclicAtomMatcher},
|
|
{"CarboacyclicH", Matchers::CarboacyclicHAtomMatcher},
|
|
{"ABH", Matchers::CarboacyclicHAtomMatcher},
|
|
{"Heteroacyclic", Matchers::HeteroacyclicAtomMatcher},
|
|
{"AHC", Matchers::HeteroacyclicAtomMatcher},
|
|
{"HeteroacyclicH", Matchers::HeteroacyclicHAtomMatcher},
|
|
{"AHH", Matchers::HeteroacyclicHAtomMatcher},
|
|
{"Alkoxy", Matchers::AlkoxyacyclicAtomMatcher},
|
|
{"AOX", Matchers::AlkoxyacyclicAtomMatcher},
|
|
{"AlkoxyH", Matchers::AlkoxyacyclicHAtomMatcher},
|
|
{"AOH", Matchers::AlkoxyacyclicHAtomMatcher},
|
|
{"Heterocyclic", Matchers::HeterocyclicAtomMatcher},
|
|
{"CHC", Matchers::HeterocyclicAtomMatcher},
|
|
{"HeterocyclicH", Matchers::HeterocyclicHAtomMatcher},
|
|
{"CHH", Matchers::HeterocyclicHAtomMatcher},
|
|
{"Heteroaryl", Matchers::HeteroarylAtomMatcher},
|
|
{"HAR", Matchers::HeteroarylAtomMatcher},
|
|
{"HeteroarylH", Matchers::HeteroarylHAtomMatcher},
|
|
{"HAH", Matchers::HeteroarylHAtomMatcher},
|
|
{"NoCarbonRing", Matchers::NoCarbonRingAtomMatcher},
|
|
{"CXX", Matchers::NoCarbonRingAtomMatcher},
|
|
{"NoCarbonRingH", Matchers::NoCarbonRingHAtomMatcher},
|
|
{"CXH", Matchers::NoCarbonRingHAtomMatcher}};
|
|
|
|
// This is an extension of adjustQueryProperties from GraphMol that allows the
|
|
// search of generic groups
|
|
RDKIT_GENERICGROUPS_EXPORT ROMol *adjustQueryPropertiesWithGenericGroups(
|
|
const ROMol &mol, const MolOps::AdjustQueryParameters *inParams = nullptr);
|
|
|
|
//! returns false if any of the molecule's generic atoms are not satisfied in
|
|
/// the current match
|
|
RDKIT_GENERICGROUPS_EXPORT bool genericAtomMatcher(
|
|
const ROMol &mol, const ROMol &query,
|
|
const std::span<const unsigned int> &match);
|
|
//! sets the apropriate generic query tags based on atom labels and/or SGroups
|
|
/*
|
|
|
|
- Generic query tags found in the atom labels/SGroups will be overwrite existing
|
|
generic query tags (if there are any present).
|
|
- only SUP SGroups are considered
|
|
- Any atom labels or SGroups which are converted will be removed
|
|
- If both atom labels and SGroups are being used and an atom has generic
|
|
query tags in both, the one from the SGroup will be used.
|
|
- Generic query tags not found in GenericGroups::genericMatchers will be ignored
|
|
|
|
*/
|
|
RDKIT_GENERICGROUPS_EXPORT void setGenericQueriesFromProperties(
|
|
ROMol &mol, bool useAtomLabels = true, bool useSGroups = true);
|
|
RDKIT_GENERICGROUPS_EXPORT void convertGenericQueriesToSubstanceGroups(
|
|
ROMol &mol);
|
|
} // namespace GenericGroups
|
|
} // namespace RDKit
|
|
|
|
#endif
|