RDKit
Open-source cheminformatics and machine learning.
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SmilesParseOps.h
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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;
18class QueryBond;
19} // namespace RDKit
20namespace SmilesParseOps {
22 RDKit::RWMol *mp);
24 bool throwIt = true);
26// This uses SMARTS semantics: unspecified bonds are treated as
27// aromatic or single.
29 RDKit::RWMol *mol, RDKit::RWMol *frag,
33 const RDKit::RWMol *mol, const RDKit::Atom *atom1,
34 const RDKit::Atom *atom2);
36 bool strict);
38 bool toleratePartials);
43 RDKit::RWMol &mol, const std::string &extText,
44 std::string::const_iterator &pos, unsigned int startAtomIdx = 0,
45 unsigned int startBondIdx = 0);
46inline void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText,
47 unsigned int startAtomIdx,
48 unsigned int startBondIdx) {
49 auto iter = extText.begin();
50 parseCXExtensions(mol, extText, iter, startAtomIdx, startBondIdx);
51};
52//! removes formal charge, isotope, etc. Primarily useful for QueryAtoms
54
55//! returns whether or not the combination of tag and permutation provided are
56//! legal
58 int permutation);
59
60//! this is a bit of a hack to try and get nicer "SMILES" from
61//! a SMARTS molecule
63 const RDKit::Atom *a1, const RDKit::Atom *a2);
64
65namespace detail {
66constexpr auto _needsDetectBondStereo = "_needsDetectBondStereo";
67constexpr auto _needsDetectAtomStereo = "_needsDetectAtomStereo";
68} // namespace detail
69} // namespace SmilesParseOps
70
71#endif
The class for representing atoms.
Definition Atom.h:75
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
Class for storing Bond queries.
Definition QueryBond.h:28
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
#define RDKIT_SMILESPARSE_EXPORT
Definition export.h:481
Std stuff.
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 RDKit::QueryBond * getUnspecifiedQueryBond(const RDKit::Atom *a1, const RDKit::Atom *a2)
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)