RDKit
Open-source cheminformatics and machine learning.
RDKit::Trajectory Class Reference

#include <Trajectory.h>

Public Member Functions

 Trajectory (unsigned int dimension, unsigned int numPoints, SnapshotVect *snapshotVect=NULL)
 Constructor. More...
 
 Trajectory (const Trajectory &other)
 Copy constructor. More...
 
unsigned int dimension () const
 
unsigned int numPoints () const
 
size_t size () const
 
unsigned int addSnapshot (const Snapshot &s)
 Appends a Snapshot to this Trajectory. More...
 
const SnapshotgetSnapshot (unsigned int snapshotNum) const
 
unsigned int insertSnapshot (unsigned int snapshotNum, Snapshot s)
 Inserts a Snapshot into this Trajectory. More...
 
unsigned int removeSnapshot (unsigned int snapshotNum)
 Removes a Snapshot from this Trajectory. More...
 
void clear ()
 Clear all Snapshots from a Trajectory. More...
 
unsigned int addConformersToMol (ROMol &mol, int from=-1, int to=-1)
 Add conformations from the Trajectory to a molecule. More...
 

Detailed Description

Definition at line 20 of file Trajectory.h.

Constructor & Destructor Documentation

RDKit::Trajectory::Trajectory ( unsigned int  dimension,
unsigned int  numPoints,
SnapshotVect snapshotVect = NULL 
)

Constructor.

Parameters
dimensionrepresents the dimensionality of this Trajectory's coordinate tuples; this is normally 2 (2D coordinates) or 3 (3D coordinates)
numPointsis the number of coordinate tuples associated to each Snapshot
snapshotVect(optional, defaults to NULL) is a pointer to a SnapshotVect used to initialize the Trajectory; if not NULL, the Trajectory takes ownership of the SnapshotVect
RDKit::Trajectory::Trajectory ( const Trajectory other)

Copy constructor.

Member Function Documentation

unsigned int RDKit::Trajectory::addConformersToMol ( ROMol mol,
int  from = -1,
int  to = -1 
)

Add conformations from the Trajectory to a molecule.

Parameters
mol- ROMol to which Conformers with coordinates from the Trajectory will be added; the Trajectory must have numPoints() == mol.getNumAtoms()
from- the first Snapshot that will be added as a Conformer; defaults to -1 (first available)
to- the last Snapshot that will be added as a Conformer; defaults to -1 (all)
Returns
the number of conformations added

Referenced by clear().

unsigned int RDKit::Trajectory::addSnapshot ( const Snapshot s)

Appends a Snapshot to this Trajectory.

Parameters
sis the Snapshot to be added; the Trajectory takes ownership of the snapshot coordinates
Returns
the zero-based index position of the added Snapshot

Referenced by size().

void RDKit::Trajectory::clear ( )
inline

Clear all Snapshots from a Trajectory.

Definition at line 75 of file Trajectory.h.

References addConformersToMol(), RDKit::readAmberTrajectory(), and RDKit::readGromosTrajectory().

unsigned int RDKit::Trajectory::dimension ( ) const
inline
Returns
the dimensionality of this Trajectory's coordinate tuples

Definition at line 36 of file Trajectory.h.

const Snapshot& RDKit::Trajectory::getSnapshot ( unsigned int  snapshotNum) const
Parameters
snapshotNumis the zero-based index of the retrieved Snapshot
Returns
a const reference to the relevant Snapshot in the Trajectory

Referenced by size().

unsigned int RDKit::Trajectory::insertSnapshot ( unsigned int  snapshotNum,
Snapshot  s 
)

Inserts a Snapshot into this Trajectory.

Parameters
snapshotNumis the zero-based index of the Trajectory's Snapshot before which the Snapshot s will be inserted
sis the Snapshot to be inserted; the Trajectory takes ownership of the snapshot coordinates
Returns
the zero-based index position of the inserted Snapshot

Referenced by size().

unsigned int RDKit::Trajectory::numPoints ( ) const
inline
Returns
the number of coordinate tuples associated to each Snapshot

Definition at line 41 of file Trajectory.h.

unsigned int RDKit::Trajectory::removeSnapshot ( unsigned int  snapshotNum)

Removes a Snapshot from this Trajectory.

Parameters
snapshotNumis the zero-based index of Snapshot to be removed
Returns
the zero-based index position of the Snapshot after the removed one; if the last Snapshot was removed, it returns the size of the trajectory

Referenced by size().

size_t RDKit::Trajectory::size ( ) const
inline
Returns
the number of Snapshots associated to this Trajectory

Definition at line 46 of file Trajectory.h.

References addSnapshot(), getSnapshot(), insertSnapshot(), and removeSnapshot().


The documentation for this class was generated from the following file: