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106 lines
4.3 KiB
C++
106 lines
4.3 KiB
C++
//
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// Copyright (C) 2003-2016 Sereina Riniker, Paolo Tosco
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef RD_TRAJECTORY_H
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#define RD_TRAJECTORY_H
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#include <vector>
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#include "Snapshot.h"
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namespace RDKit {
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class ROMol;
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class RDKIT_TRAJECTORY_EXPORT Trajectory {
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public:
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/*! \brief Constructor
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\param dimension represents the dimensionality of this Trajectory's
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coordinate tuples; this is normally 2 (2D coordinates) or 3 (3D
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coordinates) \param numPoints is the number of coordinate tuples associated
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to each Snapshot \param snapshotVect (optional, defaults to NULL) is a
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pointer to a SnapshotVect used to initialize the Trajectory; if not NULL,
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the Trajectory takes ownership of the SnapshotVect
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*/
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Trajectory(unsigned int dimension, unsigned int numPoints,
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SnapshotVect *snapshotVect = nullptr);
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/*! \brief Copy constructor
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*/
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Trajectory(const Trajectory &other);
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/*! \return the dimensionality of this Trajectory's coordinate tuples
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*/
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unsigned int dimension() const { return d_dimension; }
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/*! \return the number of coordinate tuples associated to each Snapshot
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*/
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unsigned int numPoints() const { return d_numPoints; }
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/*! \return the number of Snapshots associated to this Trajectory
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*/
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size_t size() const { return d_snapshotVect->size(); }
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/*! \brief Appends a Snapshot to this Trajectory
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\param s is the Snapshot to be added; the Trajectory
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takes ownership of the snapshot coordinates
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\return the zero-based index position of the added Snapshot
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*/
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unsigned int addSnapshot(const Snapshot &s);
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/*! \param snapshotNum is the zero-based index of the retrieved Snapshot
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\return a const reference to the relevant Snapshot in the Trajectory
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*/
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const Snapshot &getSnapshot(unsigned int snapshotNum) const;
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/*! \brief Inserts a Snapshot into this Trajectory
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\param snapshotNum is the zero-based index of the Trajectory's Snapshot
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before which the Snapshot s will be inserted
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\param s is the Snapshot to be inserted; the Trajectory
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takes ownership of the snapshot coordinates
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\return the zero-based index position of the inserted Snapshot
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*/
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unsigned int insertSnapshot(unsigned int snapshotNum, Snapshot s);
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/*! \brief Removes a Snapshot from this Trajectory
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\param snapshotNum is the zero-based index of Snapshot to be removed
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\return the zero-based index position of the Snapshot after the
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removed one; if the last Snapshot was removed, it returns the
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size of the trajectory
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*/
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unsigned int removeSnapshot(unsigned int snapshotNum);
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//! Clear all Snapshots from a Trajectory
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void clear() { d_snapshotVect->clear(); }
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//! Add conformations from the Trajectory to a molecule
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/*!
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\param mol - ROMol to which Conformers with coordinates from the Trajectory
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will be added; the Trajectory must have numPoints() == mol.getNumAtoms()
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\param from - the first Snapshot that will be added as a Conformer; defaults
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to -1 (first available) \param to - the last Snapshot that will be added as
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a Conformer; defaults to -1 (all) \return the number of conformations added
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*/
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unsigned int addConformersToMol(ROMol &mol, int from = -1, int to = -1);
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private:
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// dimensionality of this Trajectory's coordinates;
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// this is normally 2 (2D coordinates) or 3 (3D coordinates)
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const unsigned int d_dimension;
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// number of coordinate tuples associated to each Snapshot
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const unsigned int d_numPoints;
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// smart_ptr to vector holding the Snapshots for this Trajectory
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boost::shared_ptr<SnapshotVect> d_snapshotVect;
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};
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/*! \brief Reads coordinates from an AMBER trajectory file
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into the traj Trajectory object
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\return the number of Snapshot objects read in
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*/
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RDKIT_TRAJECTORY_EXPORT unsigned int readAmberTrajectory(
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const std::string &fName, Trajectory &traj);
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/*! \brief Reads coordinates from a GROMOS trajectory file
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into the traj Trajectory object
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\return the number of Snapshot objects read in
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*/
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RDKIT_TRAJECTORY_EXPORT unsigned int readGromosTrajectory(
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const std::string &fName, Trajectory &traj);
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} // namespace RDKit
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#endif
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