RDKit
Open-source cheminformatics and machine learning.
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;
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 toleratePartials);
40 RDKit::RWMol &mol, const std::string &extText,
41 std::string::const_iterator &pos, unsigned int startAtomIdx = 0,
42 unsigned int startBondIdx = 0);
43inline void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText,
44 unsigned int startAtomIdx,
45 unsigned int startBondIdx) {
46 auto iter = extText.begin();
47 parseCXExtensions(mol, extText, iter, startAtomIdx, startBondIdx);
48};
49//! removes formal charge, isotope, etc. Primarily useful for QueryAtoms
51}; // namespace SmilesParseOps
52
53#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:449
Std stuff.
Definition: Abbreviations.h:18
RDKIT_SMILESPARSE_EXPORT void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials)
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)