RDKit: Pattern.h Source File

| RDKit Open-source cheminformatics and machine learning.

Loading...
Searching...
No Matches
Pattern.h
Go to the documentation of this file.
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#include <RDGeneral/export.h>
11#pragma once
12#include "StructChecker.h"
13#include "Utilites.h"
14
15namespace RDKit {
16 namespace StructureCheck {
17
18 RDKIT_STRUCTCHECKER_EXPORT RDKit::Bond::BondType convertBondType(AABondType bt);
19 RDKIT_STRUCTCHECKER_EXPORT AABondType
20 convertBondType(RDKit::Bond::BondType rdbt);
21
22 RDKIT_STRUCTCHECKER_EXPORT unsigned getAtomicNumber(const std::string symbol);
23 RDKIT_STRUCTCHECKER_EXPORT bool AtomSymbolMatch(const std::string symbol,
24 const std::string pattern);
25 RDKIT_STRUCTCHECKER_EXPORT bool LigandMatches(const Atom &a, const Bond &b,
26 const Ligand &l,
27 bool use_charge = false);
28 RDKIT_STRUCTCHECKER_EXPORT bool isBondTypeMatch(const RDKit::Bond &b,
29 AABondType lbt);
30 RDKIT_STRUCTCHECKER_EXPORT bool RecMatch(const ROMol &mol, unsigned atomIdx,
31 const AugmentedAtom &aa,
32 const std::vector<Neighbourhood> &nbp,
33 bool verbose);
34 RDKIT_STRUCTCHECKER_EXPORT bool AAMatch(
35 const ROMol &mol, unsigned i, const AugmentedAtom &aa,
36 const std::vector<unsigned> &atom_ring_status,
37 const std::vector<Neighbourhood> &nbp, bool verbose);
38
39 RDKIT_STRUCTCHECKER_EXPORT bool TransformAugmentedAtoms(
40 RWMol &mol,
41 const std::vector<std::pair<AugmentedAtom, AugmentedAtom>> &aapair,
42 bool verbose);
43 RDKIT_STRUCTCHECKER_EXPORT bool CheckAtoms(
44 const ROMol &mol, const std::vector<AugmentedAtom> &good_atoms,
45 bool verbose);
46} // namespace StructureCheck
47} // namespace RDKit
StructChecker.h
Contains the public API of the StructChecker.
Utilites.h
RDKit::Atom
The class for representing atoms.
Definition Atom.h:74
RDKit::Bond
class for representing a bond
Definition Bond.h:46
RDKit::Bond::BondType
BondType
the type of Bond
Definition Bond.h:55
RDKit::ROMol
Definition ROMol.h:199
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
export.h
RDKIT_STRUCTCHECKER_EXPORT
#define RDKIT_STRUCTCHECKER_EXPORT
Definition export.h:545
symbol
static const char * symbol[119]
Definition mf.h:257
RDKit::StructureCheck
Definition Pattern.h:16
RDKit::StructureCheck::AtomSymbolMatch
RDKIT_STRUCTCHECKER_EXPORT bool AtomSymbolMatch(const std::string symbol, const std::string pattern)
RDKit::StructureCheck::convertBondType
RDKIT_STRUCTCHECKER_EXPORT RDKit::Bond::BondType convertBondType(AABondType bt)
RDKit::StructureCheck::LigandMatches
RDKIT_STRUCTCHECKER_EXPORT bool LigandMatches(const Atom &a, const Bond &b, const Ligand &l, bool use_charge=false)
RDKit::StructureCheck::TransformAugmentedAtoms
RDKIT_STRUCTCHECKER_EXPORT bool TransformAugmentedAtoms(RWMol &mol, const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &aapair, bool verbose)
RDKit::StructureCheck::CheckAtoms
RDKIT_STRUCTCHECKER_EXPORT bool CheckAtoms(const ROMol &mol, const std::vector< AugmentedAtom > &good_atoms, bool verbose)
RDKit::StructureCheck::AABondType
AABondType
Definition StructChecker.h:44
RDKit::StructureCheck::AAMatch
RDKIT_STRUCTCHECKER_EXPORT bool AAMatch(const ROMol &mol, unsigned i, const AugmentedAtom &aa, const std::vector< unsigned > &atom_ring_status, const std::vector< Neighbourhood > &nbp, bool verbose)
RDKit::StructureCheck::isBondTypeMatch
RDKIT_STRUCTCHECKER_EXPORT bool isBondTypeMatch(const RDKit::Bond &b, AABondType lbt)
RDKit::StructureCheck::RecMatch
RDKIT_STRUCTCHECKER_EXPORT bool RecMatch(const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa, const std::vector< Neighbourhood > &nbp, bool verbose)
RDKit::StructureCheck::getAtomicNumber
RDKIT_STRUCTCHECKER_EXPORT unsigned getAtomicNumber(const std::string symbol)
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::StructureCheck::AugmentedAtom
Definition StructChecker.h:76
RDKit::StructureCheck::Ligand
Definition StructChecker.h:63