RDKit
Open-source cheminformatics and machine learning.
SmilesParseOps.h
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1 //
2 // Copyright (C) 2001-2019 Greg Landrum and Rational Discovery LLC
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 
15 namespace RDKit {
16 class RWMol;
17 class Atom;
18 } // namespace RDKit
19 namespace SmilesParseOps {
21 void ReportParseError(const char *message, bool throwIt = true);
23 // This uses SMARTS semantics: unspecified bonds are treated as
24 // aromatic or single.
29  const RDKit::Atom *atom1,
30  const RDKit::Atom *atom2);
31 void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials);
35 void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText,
36  std::string::const_iterator &pos);
37 //! removes formal charge, isotope, etc. Primarily useful for QueryAtoms
39 }; // namespace SmilesParseOps
40 
41 #endif
The class for representing atoms.
Definition: Atom.h:69
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:31
Std stuff.
Definition: Abbreviations.h:17
void ReportParseError(const char *message, bool throwIt=true)
void CleanupAfterParseError(RDKit::RWMol *mol)
RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials)
void CheckRingClosureBranchStatus(RDKit::Atom *atom, RDKit::RWMol *mp)
void AdjustAtomChiralityFlags(RDKit::RWMol *mol)
void CleanupAfterParsing(RDKit::RWMol *mol)
void SetUnspecifiedBondTypes(RDKit::RWMol *mol)
void ClearAtomChemicalProps(RDKit::Atom *atom)
removes formal charge, isotope, etc. Primarily useful for QueryAtoms
void AddFragToMol(RDKit::RWMol *mol, RDKit::RWMol *frag, RDKit::Bond::BondType bondOrder=RDKit::Bond::UNSPECIFIED, RDKit::Bond::BondDir bondDir=RDKit::Bond::NONE)
void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos)