RDKit
Open-source cheminformatics and machine learning.
MolFragmenter.h
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1 //
2 // Copyright (C) 2013 Greg Landrum
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_MOLFRAGMENTER_H__
11 #define _RD_MOLFRAGMENTER_H__
12 
13 #include <istream>
14 #include <GraphMol/ROMol.h>
15 
16 namespace RDKit {
17 namespace MolFragmenter {
19  unsigned int atom1Label, atom2Label;
20  unsigned int atom1Type, atom2Type;
23 };
24 
25 //! \brief Fragments a molecule by breaking a set of bonds
26 //!
27 /*!
28 
29  \param mol - the molecule to be modified
30  \param bondIndices - indices of the bonds to be broken
31 
32  optional:
33  \param addDummies - toggles addition of dummy atoms to indicate where
34  bonds were broken
35  \param dummyLabels - used to provide the labels to be used for the dummies.
36  the first element in each pair is the label for the dummy
37  that replaces the bond's beginAtom, the second is for the
38  dummy that replaces the bond's endAtom. If not provided, the
39  dummies are labeled with atom indices.
40  \param bondTypes - used to provide the bond type to use between the
41  fragments and the dummy atoms. If not provided, defaults to single.
42  \param nCutsPerAtom - used to return the number of bonds that were
43  cut at each atom. Should be nAtoms long.
44 
45  \return a new ROMol with the modifications
46  The client is responsible for deleting this molecule.
47 
48 */
50  const ROMol &mol, const std::vector<unsigned int> &bondIndices,
51  bool addDummies = true,
52  const std::vector<std::pair<unsigned int, unsigned int> > *dummyLabels = 0,
53  const std::vector<Bond::BondType> *bondTypes = 0,
54  std::vector<unsigned int> *nCutsPerAtom = 0);
55 //! \overload
57  const ROMol &mol, const std::vector<FragmenterBondType> &bondPatterns,
58  const std::map<unsigned int, ROMOL_SPTR> *atomEnvirons = 0,
59  std::vector<unsigned int> *nCutsPerAtom = 0);
61  const ROMol &mol, const std::vector<unsigned int> &bondIndices,
62  std::vector<ROMOL_SPTR> &resMols, unsigned int maxToCut = 1,
63  bool addDummies = true,
64  const std::vector<std::pair<unsigned int, unsigned int> > *dummyLabels = 0,
65  const std::vector<Bond::BondType> *bondTypes = 0,
66  std::vector<std::vector<unsigned int> > *nCutsPerAtom = 0);
67 
68 //! \brief Fragments a molecule by breaking all BRICS bonds
69 /*!
70  \return a new ROMol with the modifications
71  The client is responsible for deleting this molecule.
72 
73 */
74 ROMol *fragmentOnBRICSBonds(const ROMol &mol);
75 
77  std::istream *inStream, std::map<unsigned int, std::string> &defs,
78  const std::string &comment = "//", bool validate = true,
79  std::map<unsigned int, ROMOL_SPTR> *environs = 0);
81  const std::string &str, std::map<unsigned int, std::string> &defs,
82  const std::string &comment = "//", bool validate = true,
83  std::map<unsigned int, ROMOL_SPTR> *environs = 0);
84 void constructBRICSAtomTypes(std::map<unsigned int, std::string> &defs,
85  std::map<unsigned int, ROMOL_SPTR> *environs = 0);
87  std::istream *inStream,
88  const std::map<unsigned int, std::string> &atomTypes,
89  std::vector<FragmenterBondType> &defs, const std::string &comment = "//",
90  bool validate = true, bool labelByConnector = true);
92  const std::string &str,
93  const std::map<unsigned int, std::string> &atomTypes,
94  std::vector<FragmenterBondType> &defs, const std::string &comment = "//",
95  bool validate = true, bool labelByConnector = true);
96 void constructBRICSBondTypes(std::vector<FragmenterBondType> &defs);
97 }
98 }
99 #endif
ROMol * fragmentOnBRICSBonds(const ROMol &mol)
Fragments a molecule by breaking all BRICS bonds.
void fragmentOnSomeBonds(const ROMol &mol, const std::vector< unsigned int > &bondIndices, std::vector< ROMOL_SPTR > &resMols, unsigned int maxToCut=1, bool addDummies=true, const std::vector< std::pair< unsigned int, unsigned int > > *dummyLabels=0, const std::vector< Bond::BondType > *bondTypes=0, std::vector< std::vector< unsigned int > > *nCutsPerAtom=0)
Defines the primary molecule class ROMol as well as associated typedefs.
BondType
the type of Bond
Definition: Bond.h:57
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
void constructBRICSBondTypes(std::vector< FragmenterBondType > &defs)
ROMol * fragmentOnBonds(const ROMol &mol, const std::vector< unsigned int > &bondIndices, bool addDummies=true, const std::vector< std::pair< unsigned int, unsigned int > > *dummyLabels=0, const std::vector< Bond::BondType > *bondTypes=0, std::vector< unsigned int > *nCutsPerAtom=0)
Fragments a molecule by breaking a set of bonds.
void constructFragmenterAtomTypes(std::istream *inStream, std::map< unsigned int, std::string > &defs, const std::string &comment="//", bool validate=true, std::map< unsigned int, ROMOL_SPTR > *environs=0)
void constructBRICSAtomTypes(std::map< unsigned int, std::string > &defs, std::map< unsigned int, ROMOL_SPTR > *environs=0)
boost::shared_ptr< ROMol > ROMOL_SPTR
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29
void constructFragmenterBondTypes(std::istream *inStream, const std::map< unsigned int, std::string > &atomTypes, std::vector< FragmenterBondType > &defs, const std::string &comment="//", bool validate=true, bool labelByConnector=true)