RDKit: SmilesParseOps.h Source File

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SmilesParseOps.h
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1 //
2 // Copyright (C) 2001-2008 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 #ifndef _RD_SMILESPARSEOPS_H
11 #define _RD_SMILESPARSEOPS_H
12 #include <GraphMol/Bond.h>
13
14 namespace RDKit {
15 class RWMol;
16 class Atom;
17 }
18 namespace SmilesParseOps {
19 void CheckRingClosureBranchStatus(RDKit::Atom *atom, RDKit::RWMol *mp);
20 void ReportParseError(const char *message, bool throwIt = true);
21 void CleanupAfterParseError(RDKit::RWMol *mol);
22 void AddFragToMol(RDKit::RWMol *mol, RDKit::RWMol *frag,
23 RDKit::Bond::BondType bondOrder = RDKit::Bond::UNSPECIFIED,
24 RDKit::Bond::BondDir bondDir = RDKit::Bond::NONE,
25 bool closeRings = false, bool doingQuery = false);
26 RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol,
27 const RDKit::Atom *atom1,
28 const RDKit::Atom *atom2);
29 void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials);
30 void AdjustAtomChiralityFlags(RDKit::RWMol *mol);
31 void CleanupAfterParsing(RDKit::RWMol *mol);
32 };
33
34 #endif
SmilesParseOps::CleanupAfterParsing
void CleanupAfterParsing(RDKit::RWMol *mol)
SmilesParseOps::CleanupAfterParseError
void CleanupAfterParseError(RDKit::RWMol *mol)
Definition: SLNParseOps.h:301
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
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)
RDKit::Bond::BondType
BondType
the type of Bond
Definition: Bond.h:56
SmilesParseOps::GetUnspecifiedBondType
RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
SmilesParseOps::CloseMolRings
void CloseMolRings(RDKit::RWMol *mol, bool toleratePartials)
Bond.h
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
SmilesParseOps
Definition: SmilesParseOps.h:18
SmilesParseOps::ReportParseError
void ReportParseError(const char *message, bool throwIt=true)
SmilesParseOps::CheckRingClosureBranchStatus
void CheckRingClosureBranchStatus(RDKit::Atom *atom, RDKit::RWMol *mp)
RDKit::Bond::BondDir
BondDir
the bond's direction (for chirality)
Definition: Bond.h:83
RDKit::Bond::UNSPECIFIED
Definition: Bond.h:57
RDKit::Bond::NONE
no special style
Definition: Bond.h:84
SmilesParseOps::AdjustAtomChiralityFlags
void AdjustAtomChiralityFlags(RDKit::RWMol *mol)
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:67