RDKit
Open-source cheminformatics and machine learning.
SLNAttribs.h
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32 // Created by Greg Landrum, September 2006
33 //
34 #ifndef __RD_SLNATTRIBS_H__
35 #define __RD_SLNATTRIBS_H__
36 
37 #include <string>
38 #include <vector>
39 #include <boost/smart_ptr.hpp>
40 
41 namespace RDKit{
42  class Atom;
43  class Bond;
44 
45  namespace SLNParse {
46  typedef enum {
52 
53  class AttribType {
54  public:
55  AttribType() :first(""),second(""),op(""),negated(false),structQuery(0) {};
56  std::string first;
57  std::string second;
58  std::string op;
59  bool negated;
60  void *structQuery;
61  };
62 
63  typedef std::vector< std::pair<AttribCombineOp,boost::shared_ptr<AttribType> > > AttribListType;
64 
65  //! parses the attributes provided for an atom and sets
66  // the appropriate RD properties/queries.
67  // NOTES:
68  // 1) Some SLN query values cannot be properly set until the molecule is fully/
69  // initialized. These are handled by parseFinalAtomAttribs()
70  //
71  void parseAtomAttribs(Atom *atom,AttribListType attribs,bool doingQuery);
72  void parseFinalAtomAttribs(Atom *atom,bool doingQuery);
73 
74  //! parses the attributes provided for a bond and sets
75  // the appropriate RD properties/queries.
76  // NOTES:
77  // 1) Some SLN query values cannot be properly set until the molecule is fully/
78  // initialized. These are handled by parseFinalBondAttribs()
79  void parseBondAttribs(Bond *bond,AttribListType attribs,bool doingQuery);
80  void parseFinalBondAttribs(Bond *bond,bool doingQuery);
81 
82  //! parses the attributes provided for a ctab and sets
83  // the appropriate RD properties/queries.
84  void parseMolAttribs(ROMol *mol,AttribListType attribs);
85 
86  void adjustAtomChiralities(RWMol *mol);
87  }
88 }
89 #endif
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery)
parses the attributes provided for an atom and sets
void parseBondAttribs(Bond *bond, AttribListType attribs, bool doingQuery)
parses the attributes provided for a bond and sets
void parseMolAttribs(ROMol *mol, AttribListType attribs)
parses the attributes provided for a ctab and sets
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:105
void adjustAtomChiralities(RWMol *mol)
void parseFinalBondAttribs(Bond *bond, bool doingQuery)
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
class for representing a bond
Definition: Bond.h:46
std::vector< std::pair< AttribCombineOp, boost::shared_ptr< AttribType > > > AttribListType
Definition: SLNAttribs.h:63
The class for representing atoms.
Definition: Atom.h:67
void parseFinalAtomAttribs(Atom *atom, bool doingQuery)