RDKit
Open-source cheminformatics and machine learning.
MolBundle.h
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1 //
2 // Copyright (C) 2017 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 /*! \file MolBundle.h
11 
12  \brief Defines a class for managing bundles of molecules
13 
14 */
15 
16 #ifndef RD_MOLBUNDLE_AUG2017
17 #define RD_MOLBUNDLE_AUG2017
18 
19 /// Std stuff
20 #include <vector>
21 
22 // boost stuff
24 #include <boost/smart_ptr.hpp>
26 
27 // our stuff
28 #include <RDGeneral/Exceptions.h>
29 
30 namespace RDKit {
31 class ROMol;
32 
33 //! MolBundle contains (conceptually) a collection of ROMols with the same
34 //! topology
35 /*!
36  This is designed to allow handling things like enhanced stereochemistry,
37  but can no doubt be (ab)used in other ways.
38 */
39 class MolBundle : public RDProps {
40  public:
41  MolBundle() : RDProps(){};
42 
43  //! copy constructor
44  MolBundle(const MolBundle &other) : RDProps(other) { d_mols = other.d_mols; };
45  // FIX: need serialization/deserialization
46 
47  virtual ~MolBundle(){};
48 
49  //! returns our molecules
50  virtual const std::vector<boost::shared_ptr<ROMol> > &getMols() const {
51  return d_mols;
52  };
53 
54  //! adds a new molecule and returns the total number of molecules
55  //! enforces that the new molecule has the same number of atoms and bonds
56  //! as the molecules that are already there.
57  virtual size_t addMol(boost::shared_ptr<ROMol> nmol) {
58  PRECONDITION(nmol.get(), "bad mol pointer");
59  if (d_mols.size()) {
60  if (nmol->getNumAtoms() != d_mols[0]->getNumAtoms())
61  throw ValueErrorException(
62  "all molecules in a bundle must have the same number of atoms");
63  // REVIEW: should we allow different numbers of bonds?
64  if (nmol->getNumBonds() != d_mols[0]->getNumBonds())
65  throw ValueErrorException(
66  "all molecules in a bundle must have the same number of bonds");
67  }
68  d_mols.push_back(nmol);
69  return (d_mols.size());
70  }
71  //! returns the number of molecules from the bundle
72  virtual size_t size() const { return d_mols.size(); };
73  //! returns a particular molecule in the bundle
74  virtual const boost::shared_ptr<ROMol> getMol(size_t idx) const {
75  if (idx >= d_mols.size()) throw IndexErrorException(idx);
76  return d_mols[idx];
77  };
78  //! returns a particular molecule from the bundle
79  virtual const boost::shared_ptr<ROMol> operator[](size_t idx) const {
80  return getMol(idx);
81  };
82 
83  private:
84  std::vector<boost::shared_ptr<ROMol> > d_mols;
85 };
86 
87 }; // end of RDKit namespace
88 #endif
virtual size_t addMol(boost::shared_ptr< ROMol > nmol)
Definition: MolBundle.h:57
virtual ~MolBundle()
Definition: MolBundle.h:47
virtual const std::vector< boost::shared_ptr< ROMol > > & getMols() const
returns our molecules
Definition: MolBundle.h:50
virtual size_t size() const
returns the number of molecules from the bundle
Definition: MolBundle.h:72
virtual const boost::shared_ptr< ROMol > getMol(size_t idx) const
returns a particular molecule in the bundle
Definition: MolBundle.h:74
Std stuff.
Definition: Atom.h:29
Class to allow us to throw an IndexError from C++ and have it make it back to Python.
Definition: Exceptions.h:18
#define PRECONDITION(expr, mess)
Definition: Invariant.h:107
virtual const boost::shared_ptr< ROMol > operator[](size_t idx) const
returns a particular molecule from the bundle
Definition: MolBundle.h:79
Class to allow us to throw a ValueError from C++ and have it make it back to Python.
Definition: Exceptions.h:32
MolBundle(const MolBundle &other)
copy constructor
Definition: MolBundle.h:44