RDKit: Pattern.h Source File

| RDKit Open-source cheminformatics and machine learning.

- Main Page
- Namespaces
- Classes
- Files

- File List
- File Members

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 #pragma once
11 #include "StructChecker.h"
12 #include "Utilites.h"
13
14 namespace RDKit {
15 namespace StructureCheck {
16
17 RDKit::Bond::BondType convertBondType(AABondType bt);
18 AABondType convertBondType(RDKit::Bond::BondType rdbt);
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
31 bool TransformAugmentedAtoms(
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 }
Utilites.h
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
RDKit::StructureCheck::Ligand
Definition: StructChecker.h:62
StructChecker.h
Contains the public API of the StructChecker.
RDKit::StructureCheck::AAMatch
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::getAtomicNumber
unsigned getAtomicNumber(const std::string symbol)
RDKit::Bond::BondType
BondType
the type of Bond
Definition: Bond.h:57
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
RDKit::StructureCheck::AtomSymbolMatch
bool AtomSymbolMatch(const std::string symbol, const std::string pattern)
RDKit::StructureCheck::AugmentedAtom
Definition: StructChecker.h:75
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::StructureCheck::convertBondType
RDKit::Bond::BondType convertBondType(AABondType bt)
RDKit::Bond
class for representing a bond
Definition: Bond.h:47
RDKit::StructureCheck::AABondType
AABondType
Definition: StructChecker.h:43
RDKit::StructureCheck::RecMatch
bool RecMatch(const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa, const std::vector< Neighbourhood > &nbp, bool verbose)
RDKit::StructureCheck::isBondTypeMatch
bool isBondTypeMatch(const RDKit::Bond &b, AABondType lbt)
RDKit::StructureCheck::TransformAugmentedAtoms
bool TransformAugmentedAtoms(RWMol &mol, const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &aapair, bool verbose)
RDKit::StructureCheck::CheckAtoms
bool CheckAtoms(const ROMol &mol, const std::vector< AugmentedAtom > &good_atoms, bool verbose)
RDKit::StructureCheck::LigandMatches
bool LigandMatches(const Atom &a, const Bond &b, const Ligand &l, bool use_charge=false)
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68