RDKit
Open-source cheminformatics and machine learning.
SmilesParseOps.h
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1 //
2 // Copyright (C) 2001-2016 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 void AddFragToMol(RDKit::RWMol *mol, RDKit::RWMol *frag,
26  bool closeRings = false, bool doingQuery = false);
28  const RDKit::Atom *atom1,
29  const RDKit::Atom *atom2);
30 void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials);
34 void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText,
35  std::string::const_iterator &pos);
36 //! removes formal charge, isotope, etc. Primarily useful for QueryAtoms
38 }; // namespace SmilesParseOps
39 
40 #endif
SmilesParseOps::ClearAtomChemicalProps
void ClearAtomChemicalProps(RDKit::Atom *atom)
removes formal charge, isotope, etc. Primarily useful for QueryAtoms
Bond.h
SmilesParseOps::GetUnspecifiedBondType
RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
SmilesParseOps::CheckRingClosureBranchStatus
void CheckRingClosureBranchStatus(RDKit::Atom *atom, RDKit::RWMol *mp)
SmilesParseOps::CleanupAfterParsing
void CleanupAfterParsing(RDKit::RWMol *mol)
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:31
RDKit::Bond::BondType
BondType
the type of Bond
Definition: Bond.h:56
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:69
SmilesParseOps::ReportParseError
void ReportParseError(const char *message, bool throwIt=true)
SmilesParseOps
Definition: SmilesParseOps.h:19
SmilesParseOps::AdjustAtomChiralityFlags
void AdjustAtomChiralityFlags(RDKit::RWMol *mol)
RDKit::Bond::NONE
@ NONE
no special style
Definition: Bond.h:84
RDKit
Std stuff.
Definition: Atom.h:30
SmilesParseOps::SetUnspecifiedBondTypes
void SetUnspecifiedBondTypes(RDKit::RWMol *mol)
RDKit::Bond::UNSPECIFIED
@ UNSPECIFIED
Definition: Bond.h:57
SmilesParseOps::CloseMolRings
void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials)
SmilesParseOps::AddFragToMol
void AddFragToMol(RDKit::RWMol *mol, RDKit::RWMol *frag, RDKit::Bond::BondType bondOrder=RDKit::Bond::UNSPECIFIED, RDKit::Bond::BondDir bondDir=RDKit::Bond::NONE, bool closeRings=false, bool doingQuery=false)
SmilesParseOps::parseCXExtensions
void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos)
SmilesParseOps::CleanupAfterParseError
void CleanupAfterParseError(RDKit::RWMol *mol)
RDKit::Bond::BondDir
BondDir
the bond's direction (for chirality)
Definition: Bond.h:83
export.h