Open-source cheminformatics and machine learning.
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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 //
12 #include <GraphMol/Bond.h>
14 namespace RDKit {
15 class RWMol;
16 class Atom;
17 }
18 namespace SmilesParseOps {
20 void ReportParseError(const char *message, bool throwIt = true);
22 void AddFragToMol(RDKit::RWMol *mol, RDKit::RWMol *frag,
25  bool closeRings = false, bool doingQuery = false);
27  const RDKit::Atom *atom1,
28  const RDKit::Atom *atom2);
29 void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials);
32 void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos);
33 };
35 #endif
void parseCXExtensions(RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos)
void CleanupAfterParsing(RDKit::RWMol *mol)
void CleanupAfterParseError(RDKit::RWMol *mol)
Definition: SLNParseOps.h:303
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
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)
the type of Bond
Definition: Bond.h:57
RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials)
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29
void ReportParseError(const char *message, bool throwIt=true)
void CheckRingClosureBranchStatus(RDKit::Atom *atom, RDKit::RWMol *mp)
the bond&#39;s direction (for chirality)
Definition: Bond.h:84
no special style
Definition: Bond.h:85
void AdjustAtomChiralityFlags(RDKit::RWMol *mol)
The class for representing atoms.
Definition: Atom.h:68