rdkit.Chem.rdtrajectory module — The RDKit 2025.09.6 documentation

# 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((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg1, (list)coordList[, (float)energy=0.0]) → object :

  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__( (rdkit.Chem.rdMolDescriptors.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) → rdkit.Geometry.rdGeometry.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) → rdkit.Geometry.rdGeometry.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((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg1, (int)dimension, (int)numPoints[, (list)snapshotList=[]]) → object :

  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__( (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg1, (Trajectory)other) -> object :

    Copy constructor

    C++ signature :

      void* __init__(boost::python::api::object,RDKit::Trajectory*)

  AddConformersToMol((Trajectory)self, (rdkit.Chem.rdchem.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)