RDKit
Open-source cheminformatics and machine learning.
Trajectory.h
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1 //
2 // Copyright (C) 2003-2016 Sereina Riniker, Paolo Tosco
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 
11 #include <RDGeneral/export.h>
12 #ifndef RD_TRAJECTORY_H
13 #define RD_TRAJECTORY_H
14 #include <vector>
15 #include "Snapshot.h"
16 
17 namespace RDKit {
18 
19 class ROMol;
20 
22  public:
23  /*! \brief Constructor
24  \param dimension represents the dimensionality of this Trajectory's
25  coordinate tuples; this is normally 2 (2D coordinates) or 3 (3D
26  coordinates) \param numPoints is the number of coordinate tuples associated
27  to each Snapshot \param snapshotVect (optional, defaults to NULL) is a
28  pointer to a SnapshotVect used to initialize the Trajectory; if not NULL,
29  the Trajectory takes ownership of the SnapshotVect
30  */
31  Trajectory(unsigned int dimension, unsigned int numPoints,
32  SnapshotVect *snapshotVect = NULL);
33  /*! \brief Copy constructor
34  */
35  Trajectory(const Trajectory &other);
36  /*! \return the dimensionality of this Trajectory's coordinate tuples
37  */
38  unsigned int dimension() const { return d_dimension; }
39  /*! \return the number of coordinate tuples associated to each Snapshot
40  */
41  unsigned int numPoints() const { return d_numPoints; }
42  /*! \return the number of Snapshots associated to this Trajectory
43  */
44  size_t size() const { return d_snapshotVect->size(); }
45  /*! \brief Appends a Snapshot to this Trajectory
46  \param s is the Snapshot to be added; the Trajectory
47  takes ownership of the snapshot coordinates
48  \return the zero-based index position of the added Snapshot
49  */
50  unsigned int addSnapshot(const Snapshot &s);
51  /*! \param snapshotNum is the zero-based index of the retrieved Snapshot
52  \return a const reference to the relevant Snapshot in the Trajectory
53  */
54  const Snapshot &getSnapshot(unsigned int snapshotNum) const;
55  /*! \brief Inserts a Snapshot into this Trajectory
56  \param snapshotNum is the zero-based index of the Trajectory's Snapshot
57  before which the Snapshot s will be inserted
58  \param s is the Snapshot to be inserted; the Trajectory
59  takes ownership of the snapshot coordinates
60  \return the zero-based index position of the inserted Snapshot
61  */
62  unsigned int insertSnapshot(unsigned int snapshotNum, Snapshot s);
63  /*! \brief Removes a Snapshot from this Trajectory
64  \param snapshotNum is the zero-based index of Snapshot to be removed
65  \return the zero-based index position of the Snapshot after the
66  removed one; if the last Snapshot was removed, it returns the
67  size of the trajectory
68  */
69  unsigned int removeSnapshot(unsigned int snapshotNum);
70  //! Clear all Snapshots from a Trajectory
71  void clear() { d_snapshotVect->clear(); };
72  //! Add conformations from the Trajectory to a molecule
73  /*!
74  \param mol - ROMol to which Conformers with coordinates from the Trajectory
75  will be added; the Trajectory must have numPoints() == mol.getNumAtoms()
76  \param from - the first Snapshot that will be added as a Conformer; defaults
77  to -1 (first available) \param to - the last Snapshot that will be added as
78  a Conformer; defaults to -1 (all) \return the number of conformations added
79  */
80  unsigned int addConformersToMol(ROMol &mol, int from = -1, int to = -1);
81 
82  private:
83  // dimensionality of this Trajectory's coordinates;
84  // this is normally 2 (2D coordinates) or 3 (3D coordinates)
85  const unsigned int d_dimension;
86  // number of coordinate tuples associated to each Snapshot
87  const unsigned int d_numPoints;
88  // smart_ptr to vector holding the Snapshots for this Trajectory
89  boost::shared_ptr<SnapshotVect> d_snapshotVect;
90 };
91 /*! \brief Reads coordinates from an AMBER trajectory file
92  into the traj Trajectory object
93  \return the number of Snapshot objects read in
94  */
96  const std::string &fName, Trajectory &traj);
97 /*! \brief Reads coordinates from a GROMOS trajectory file
98  into the traj Trajectory object
99  \return the number of Snapshot objects read in
100  */
102  const std::string &fName, Trajectory &traj);
103 
104 } // namespace RDKit
105 #endif
RDKit::Trajectory::size
size_t size() const
Definition: Trajectory.h:44
RDKit::Trajectory::clear
void clear()
Clear all Snapshots from a Trajectory.
Definition: Trajectory.h:71
Snapshot.h
RDKit::readAmberTrajectory
RDKIT_TRAJECTORY_EXPORT unsigned int readAmberTrajectory(const std::string &fName, Trajectory &traj)
Reads coordinates from an AMBER trajectory file into the traj Trajectory object.
RDKit::Trajectory::numPoints
unsigned int numPoints() const
Definition: Trajectory.h:41
RDKit::Trajectory::dimension
unsigned int dimension() const
Definition: Trajectory.h:38
RDKit::Trajectory
Definition: Trajectory.h:21
RDKit::ROMol
Definition: ROMol.h:171
RDKit::SnapshotVect
std::vector< Snapshot > SnapshotVect
Definition: Snapshot.h:19
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::Snapshot
Definition: Snapshot.h:25
RDKIT_TRAJECTORY_EXPORT
#define RDKIT_TRAJECTORY_EXPORT
Definition: export.h:697
RDKit::readGromosTrajectory
RDKIT_TRAJECTORY_EXPORT unsigned int readGromosTrajectory(const std::string &fName, Trajectory &traj)
Reads coordinates from a GROMOS trajectory file into the traj Trajectory object.
export.h