pyxmolpp2 module

Pure-python part of pyxmolpp2

Reference
- Classes
- Functions
- Data

Classes

class AmberNetCDF: Amber trajectory file
class AngleValue: Angular value
class Atom: Atom reference
class AtomPredicate: Atom Preidcate
class AtomSelection: Ordered set of atom references
class AtomSpan: Continuous span of atom references
class CoordSelection: Ordered set of atomic coordinate references
class CoordSelectionSizeMismatchError
class CoordSpan: Continuous span of atomic coordinate references
class DeadFrameAccessError
class DeadObserverAccessError
class Frame: Molecular frame
class GeomError
class GromacsXtcFile: Gromacs binary .xtc input file
class Molecule: Molecule reference
class MoleculePredicate: Molecule Predicate
class MoleculeSelection: Ordered set of molecule references
class MoleculeSpan: Continuous span of molecule references
class MultipleFramesSelectionError
class PdbFile: PDB file
class Residue: Residue reference
class ResidueId: Residue id
class ResiduePredicate: Residue Predicate
class ResidueSelection: Ordered set of residue references
class ResidueSpan: Continuous span of residue references
class Rotation: Rotational transformation
class SpanSplitError
class TorsionAngle: Torsion angle
class TorsionAngleFactory: Generates torsion angles for standard residues
class Trajectory: Trajectory of frames
class TrajectoryDoubleTraverseError
class TrajectoryInputFile: Trajectory input file ABC
class Transformation: Generic transformation
class Translation: Translational transformation
class TrjtoolDatFile: Trajtool trajectory file
class UniformScale: Uniform scale transformation
class UnitCell: Unit cell
class XYZ: 3D Vector
class XtcReadError
class XtcWriteError
class XtcWriter: Writes frames in .xtc binary format

Functions

def Degrees(degrees: float) -> AngleValue
def Radians(radians: float) -> AngleValue
def calc_alignment(ref: numpy.ndarray[numpy.float64[m, 3]], var: numpy.ndarray[numpy.float64[m, 3]]) -> Transformation
def calc_autocorr_order_2(vectors: numpy.ndarray[numpy.float64], limit: int = -1) -> numpy.ndarray[numpy.float64]
def calc_autocorr_order_2_PRE(vectors: numpy.ndarray[numpy.float64], limit: int = -1) -> numpy.ndarray[numpy.float64]
def calc_inertia_tensor(coords: numpy.ndarray[numpy.float64[m, 3]]) -> numpy.ndarray[numpy.float64[3, 3]]
def calc_rmsd(ref: numpy.ndarray[numpy.float64[m, 3]], var: numpy.ndarray[numpy.float64[m, 3]]) -> float
def calc_sasa(coordinates: numpy.ndarray[numpy.float64], vdw_radii: numpy.ndarray[numpy.float64], solvent_radius: float, indices_of_interest: typing.Optional[numpy.ndarray[numpy.int32]] = None, n_samples: int = 20) -> numpy.ndarray[numpy.float64]
def degrees_to_radians(degrees: float) -> float
def radians_to_degrees(radians: float) -> float

pyxmolpp2 module

Contents

Classes

Functions

Data