RDKit
Open-source cheminformatics and machine learning.
Pattern.h
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1 //
2 // Copyright (C) 2016 Novartis Institutes for BioMedical Research
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #pragma once
11 #include "StructChecker.h"
12 #include "Utilites.h"
13 
14 namespace RDKit {
15 namespace StructureCheck {
16 
19 
20 unsigned getAtomicNumber(const std::string symbol);
21 bool AtomSymbolMatch(const std::string symbol, const std::string pattern);
22 bool LigandMatches(const Atom &a, const Bond &b, const Ligand &l,
23  bool use_charge = false);
24 bool isBondTypeMatch(const RDKit::Bond &b, AABondType lbt);
25 bool RecMatch(const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa,
26  const std::vector<Neighbourhood> &nbp, bool verbose);
27 bool AAMatch(const ROMol &mol, unsigned i, const AugmentedAtom &aa,
28  const std::vector<unsigned> &atom_ring_status,
29  const std::vector<Neighbourhood> &nbp, bool verbose);
30 
32  RWMol &mol,
33  const std::vector<std::pair<AugmentedAtom, AugmentedAtom> > &aapair, bool verbose);
34 bool CheckAtoms(const ROMol &mol, const std::vector<AugmentedAtom> &good_atoms,
35  bool verbose);
36 }
37 }
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
Contains the public API of the StructChecker.
bool AAMatch(const ROMol &mol, unsigned i, const AugmentedAtom &aa, const std::vector< unsigned > &atom_ring_status, const std::vector< Neighbourhood > &nbp, bool verbose)
unsigned getAtomicNumber(const std::string symbol)
BondType
the type of Bond
Definition: Bond.h:57
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
bool AtomSymbolMatch(const std::string symbol, const std::string pattern)
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29
RDKit::Bond::BondType convertBondType(AABondType bt)
class for representing a bond
Definition: Bond.h:47
bool RecMatch(const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa, const std::vector< Neighbourhood > &nbp, bool verbose)
bool isBondTypeMatch(const RDKit::Bond &b, AABondType lbt)
bool TransformAugmentedAtoms(RWMol &mol, const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &aapair, bool verbose)
bool CheckAtoms(const ROMol &mol, const std::vector< AugmentedAtom > &good_atoms, bool verbose)
bool LigandMatches(const Atom &a, const Bond &b, const Ligand &l, bool use_charge=false)
The class for representing atoms.
Definition: Atom.h:68