RDKit: Trajectory.h Source File

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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 #ifndef RD_TRAJECTORY_H
12 #define RD_TRAJECTORY_H
13 #include <vector>
14 #include "Snapshot.h"
15
16 namespace RDKit {
17
18 class ROMol;
19
20 class Trajectory {
21 public:
22 /*! \brief Constructor
23 \param dimension represents the dimensionality of this Trajectory's coordinate tuples;
24 this is normally 2 (2D coordinates) or 3 (3D coordinates)
25 \param numPoints is the number of coordinate tuples associated to each Snapshot
26 \param snapshotVect (optional, defaults to NULL) is a pointer to a SnapshotVect
27 used to initialize the Trajectory; if not NULL, the Trajectory takes ownership
28 of the SnapshotVect
29 */
30 Trajectory(unsigned int dimension, unsigned int numPoints, SnapshotVect *snapshotVect = NULL);
31 /*! \brief Copy constructor
32 */
33 Trajectory(const Trajectory &other);
34 /*! \return the dimensionality of this Trajectory's coordinate tuples
35 */
36 unsigned int dimension() const {
37 return d_dimension;
38 }
39 /*! \return the number of coordinate tuples associated to each Snapshot
40 */
41 unsigned int numPoints() const {
42 return d_numPoints;
43 }
44 /*! \return the number of Snapshots associated to this Trajectory
45 */
46 size_t size() const {
47 return d_snapshotVect->size();
48 }
49 /*! \brief Appends a Snapshot to this Trajectory
50 \param s is the Snapshot to be added; the Trajectory
51 takes ownership of the snapshot coordinates
52 \return the zero-based index position of the added Snapshot
53 */
54 unsigned int addSnapshot(const Snapshot &s);
55 /*! \param snapshotNum is the zero-based index of the retrieved Snapshot
56 \return a const reference to the relevant Snapshot in the Trajectory
57 */
58 const Snapshot &getSnapshot(unsigned int snapshotNum) const;
59 /*! \brief Inserts a Snapshot into this Trajectory
60 \param snapshotNum is the zero-based index of the Trajectory's Snapshot
61 before which the Snapshot s will be inserted
62 \param s is the Snapshot to be inserted; the Trajectory
63 takes ownership of the snapshot coordinates
64 \return the zero-based index position of the inserted Snapshot
65 */
66 unsigned int insertSnapshot(unsigned int snapshotNum, Snapshot s);
67 /*! \brief Removes a Snapshot from this Trajectory
68 \param snapshotNum is the zero-based index of Snapshot to be removed
69 \return the zero-based index position of the Snapshot after the
70 removed one; if the last Snapshot was removed, it returns the
71 size of the trajectory
72 */
73 unsigned int removeSnapshot(unsigned int snapshotNum);
74 //! Clear all Snapshots from a Trajectory
75 void clear() {
76 d_snapshotVect->clear();
77 };
78 //! Add conformations from the Trajectory to a molecule
79 /*!
80 \param mol - ROMol to which Conformers with coordinates from the Trajectory will be added;
81 the Trajectory must have numPoints() == mol.getNumAtoms()
82 \param from - the first Snapshot that will be added as a Conformer; defaults to -1 (first available)
83 \param to - the last Snapshot that will be added as a Conformer; defaults to -1 (all)
84 \return the number of conformations added
85 */
86 unsigned int addConformersToMol(ROMol &mol, int from = -1, int to = -1);
87 private:
88 // dimensionality of this Trajectory's coordinates;
89 // this is normally 2 (2D coordinates) or 3 (3D coordinates)
90 const unsigned int d_dimension;
91 // number of coordinate tuples associated to each Snapshot
92 const unsigned int d_numPoints;
93 // smart_ptr to vector holding the Snapshots for this Trajectory
94 boost::shared_ptr<SnapshotVect> d_snapshotVect;
95 };
96 /*! \brief Reads coordinates from an AMBER trajectory file
97 into the traj Trajectory object
98 \return the number of Snapshot objects read in
99 */
100 unsigned int readAmberTrajectory(const std::string &fName, Trajectory &traj);
101 /*! \brief Reads coordinates from a GROMOS trajectory file
102 into the traj Trajectory object
103 \return the number of Snapshot objects read in
104 */
105 unsigned int readGromosTrajectory(const std::string &fName, Trajectory &traj);
106
107 }
108 #endif
RDKit::readAmberTrajectory
unsigned int readAmberTrajectory(const std::string &fName, Trajectory &traj)
Reads coordinates from an AMBER trajectory file into the traj Trajectory object.
RDKit::Trajectory::addConformersToMol
unsigned int addConformersToMol(ROMol &mol, int from=-1, int to=-1)
Add conformations from the Trajectory to a molecule.
RDKit::Snapshot
Definition: Snapshot.h:24
Snapshot.h
RDKit::Trajectory::size
size_t size() const
Definition: Trajectory.h:46
RDKit::readGromosTrajectory
unsigned int readGromosTrajectory(const std::string &fName, Trajectory &traj)
Reads coordinates from a GROMOS trajectory file into the traj Trajectory object.
RDKit::Trajectory::addSnapshot
unsigned int addSnapshot(const Snapshot &s)
Appends a Snapshot to this Trajectory.
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
RDKit::Trajectory::removeSnapshot
unsigned int removeSnapshot(unsigned int snapshotNum)
Removes a Snapshot from this Trajectory.
RDKit::Trajectory::numPoints
unsigned int numPoints() const
Definition: Trajectory.h:41
RDKit::Trajectory::Trajectory
Trajectory(unsigned int dimension, unsigned int numPoints, SnapshotVect *snapshotVect=NULL)
Constructor.
RDKit::Trajectory::clear
void clear()
Clear all Snapshots from a Trajectory.
Definition: Trajectory.h:75
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::SnapshotVect
std::vector< Snapshot > SnapshotVect
Definition: Snapshot.h:18
RDKit::Trajectory::insertSnapshot
unsigned int insertSnapshot(unsigned int snapshotNum, Snapshot s)
Inserts a Snapshot into this Trajectory.
RDKit::Trajectory::dimension
unsigned int dimension() const
Definition: Trajectory.h:36
RDKit::Trajectory::getSnapshot
const Snapshot & getSnapshot(unsigned int snapshotNum) const
RDKit::Trajectory
Definition: Trajectory.h:20