rdkit.Chem.rdtrajectory module¶
Module containing Trajectory and Snapshot objects
- rdkit.Chem.rdtrajectory.ReadAmberTrajectory((str)fName, (Trajectory)traj) int : ¶
reads coordinates from an AMBER trajectory file into the Trajectory object; returns the number of Snapshot objects read in
- C++ signature :
unsigned int ReadAmberTrajectory(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,RDKit::Trajectory {lvalue})
- rdkit.Chem.rdtrajectory.ReadGromosTrajectory((str)fName, (Trajectory)traj) int : ¶
reads coordinates from a GROMOS trajectory file into the Trajectory object; returns the number of Snapshot objects read in
- C++ signature :
unsigned int ReadGromosTrajectory(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,RDKit::Trajectory {lvalue})
- class rdkit.Chem.rdtrajectory.Snapshot((AtomPairsParameters)arg1, (list)coordList[, (float)energy=0.0])¶
Bases:
instance
A class which allows storing coordinates from a trajectory
- Constructor;
coordList: list of floats containing the coordinates for this Snapshot; energy: the energy for this Snapshot.
- C++ signature :
void* __init__(boost::python::api::object,boost::python::list {lvalue} [,double=0.0])
- __init__( (AtomPairsParameters)arg1, (Snapshot)other) -> object :
Copy constructor
- C++ signature :
void* __init__(boost::python::api::object,RDKit::Snapshot*)
- GetEnergy((Snapshot)self) float : ¶
returns the energy for this Snapshot
- C++ signature :
double GetEnergy(RDKit::Snapshot {lvalue})
- GetPoint2D((Snapshot)self, (int)pointNum) Point2D : ¶
return the coordinates at pointNum as a Point2D object; requires the Trajectory dimension to be == 2
- C++ signature :
RDGeom::Point2D GetPoint2D(RDKit::Snapshot {lvalue},unsigned int)
- GetPoint3D((Snapshot)self, (int)pointNum) Point3D : ¶
return the coordinates at pointNum as a Point3D object; requires the Trajectory dimension to be >= 2
- C++ signature :
RDGeom::Point3D GetPoint3D(RDKit::Snapshot {lvalue},unsigned int)
- SetEnergy((Snapshot)self, (float)energy) None : ¶
sets the energy for this Snapshot
- C++ signature :
void SetEnergy(RDKit::Snapshot {lvalue},double)
- class rdkit.Chem.rdtrajectory.Trajectory((AtomPairsParameters)arg1, (int)dimension, (int)numPoints[, (list)snapshotList=[]])¶
Bases:
instance
A class which allows storing Snapshots from a trajectory
- Constructor;
dimension: dimensionality of this Trajectory’s coordinate tuples; numPoints: number of coordinate tuples associated to each Snapshot; snapshotList: list of Snapshot objects used to initialize the Trajectory (optional; defaults to []).
- C++ signature :
void* __init__(boost::python::api::object,unsigned int,unsigned int [,boost::python::list=[]])
- __init__( (AtomPairsParameters)arg1, (Trajectory)other) -> object :
Copy constructor
- C++ signature :
void* __init__(boost::python::api::object,RDKit::Trajectory*)
- AddConformersToMol((Trajectory)self, (Mol)mol[, (int)fromCid=-1[, (int)toCid=-1]]) int : ¶
adds conformations from the Trajectory to mol fromCid is the first Snapshot that will be added as a Conformer; defaults to -1 (first available) toCid is the last Snapshot that will be added as a Conformer; defaults to -1 (all)
- C++ signature :
unsigned int AddConformersToMol(RDKit::Trajectory {lvalue},RDKit::ROMol {lvalue} [,int=-1 [,int=-1]])
- AddSnapshot((Trajectory)self, (Snapshot)s) int : ¶
appends Snapshot s to this Trajectory; returns the zero-based index position of the added snapshot
- C++ signature :
unsigned int AddSnapshot(RDKit::Trajectory {lvalue},RDKit::Snapshot)
- Clear((Trajectory)self) None : ¶
removes all Snapshots from the Trajectory
- C++ signature :
void Clear(RDKit::Trajectory {lvalue})
- Dimension((Trajectory)self) int : ¶
returns the dimensionality of this Trajectory’s coordinate tuples
- C++ signature :
unsigned int Dimension(RDKit::Trajectory {lvalue})
- GetSnapshot((Trajectory)self, (int)snapshotNum) Snapshot : ¶
returns the Snapshot snapshotNum, where the latter is the zero-based index of the retrieved Snapshot
- C++ signature :
RDKit::Snapshot* GetSnapshot(RDKit::Trajectory*,unsigned int)
- InsertSnapshot((Trajectory)self, (int)snapshotNum, (Snapshot)s) int : ¶
inserts Snapshot s into the Trajectory at the position snapshotNum, where the latter is the zero-based index of the Trajectory’s Snapshot before which the Snapshot s will be inserted; returns the zero-based index position of the inserted snapshot
- C++ signature :
unsigned int InsertSnapshot(RDKit::Trajectory {lvalue},unsigned int,RDKit::Snapshot)
- NumPoints((Trajectory)self) int : ¶
returns the number of coordinate tuples associated to each Snapshot
- C++ signature :
unsigned int NumPoints(RDKit::Trajectory {lvalue})
- RemoveSnapshot((Trajectory)self, (int)snapshotNum) int : ¶
removes Snapshot snapshotNum from the Trajectory, where snapshotNum is the zero-based index of Snapshot to be removed
- C++ signature :
unsigned int RemoveSnapshot(RDKit::Trajectory {lvalue},unsigned int)