RDKit
Open-source cheminformatics and machine learning.
SmilesParseOps.h
Go to the documentation of this file.
1//
2// Copyright (C) 2001-2022 Greg Landrum and other RDKit contributors
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#ifndef RD_SMILESPARSEOPS_H
12#define RD_SMILESPARSEOPS_H
13#include <GraphMol/Bond.h>
14
15namespace RDKit {
16class RWMol;
17class Atom;
18} // namespace RDKit
19namespace SmilesParseOps {
21 RDKit::RWMol *mp);
23 bool throwIt = true);
25// This uses SMARTS semantics: unspecified bonds are treated as
26// aromatic or single.
28 RDKit::RWMol *mol, RDKit::RWMol *frag,
32 const RDKit::RWMol *mol, const RDKit::Atom *atom1,
33 const RDKit::Atom *atom2);
35 bool strict);
37 bool toleratePartials);
42 RDKit::RWMol &mol, const std::string &extText,
43 std::string::const_iterator &pos, unsigned int startAtomIdx = 0,
44 unsigned int startBondIdx = 0);
45inline void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText,
46 unsigned int startAtomIdx,
47 unsigned int startBondIdx) {
48 auto iter = extText.begin();
49 parseCXExtensions(mol, extText, iter, startAtomIdx, startBondIdx);
50};
51//! removes formal charge, isotope, etc. Primarily useful for QueryAtoms
53
54//! returns whether or not the combination of tag and permutation provided are
55//! legal
57 int permutation);
58namespace detail {
59constexpr auto _needsDetectBondStereo = "_needsDetectBondStereo";
60constexpr auto _needsDetectAtomStereo = "_needsDetectAtomStereo";
61} // namespace detail
62} // namespace SmilesParseOps
63
64#endif
The class for representing atoms.
Definition: Atom.h:68
BondType
the type of Bond
Definition: Bond.h:56
@ UNSPECIFIED
Definition: Bond.h:57
BondDir
the bond's direction (for chirality)
Definition: Bond.h:83
@ NONE
no special style
Definition: Bond.h:84
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_SMILESPARSE_EXPORT
Definition: export.h:457
Std stuff.
Definition: Abbreviations.h:19
constexpr auto _needsDetectBondStereo
constexpr auto _needsDetectAtomStereo
RDKIT_SMILESPARSE_EXPORT void CheckChiralitySpecifications(RDKit::RWMol *mol, bool strict)
RDKIT_SMILESPARSE_EXPORT void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials)
RDKIT_SMILESPARSE_EXPORT bool checkChiralPermutation(int chiralTag, int permutation)
RDKIT_SMILESPARSE_EXPORT void ClearAtomChemicalProps(RDKit::Atom *atom)
removes formal charge, isotope, etc. Primarily useful for QueryAtoms
RDKIT_SMILESPARSE_EXPORT void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos, unsigned int startAtomIdx=0, unsigned int startBondIdx=0)
RDKIT_SMILESPARSE_EXPORT void ReportParseError(const char *message, bool throwIt=true)
RDKIT_SMILESPARSE_EXPORT void SetUnspecifiedBondTypes(RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void AddFragToMol(RDKit::RWMol *mol, RDKit::RWMol *frag, RDKit::Bond::BondType bondOrder=RDKit::Bond::UNSPECIFIED, RDKit::Bond::BondDir bondDir=RDKit::Bond::NONE)
RDKIT_SMILESPARSE_EXPORT void CleanupAfterParseError(RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void AdjustAtomChiralityFlags(RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void CheckRingClosureBranchStatus(RDKit::Atom *atom, RDKit::RWMol *mp)
RDKIT_SMILESPARSE_EXPORT RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
RDKIT_SMILESPARSE_EXPORT void CleanupAfterParsing(RDKit::RWMol *mol)