pycgtool.frame
¶
This module contains classes for storing atomic data.
The Frame class may contain multiple Residues which may each contain multiple Atoms. Both Frame and Residue are iterable. Residue is indexable with either atom numbers or names.
Module Contents¶
Functions¶
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Load a trajectory, if a PDB fails with zero box volume disable volume check and try again. |
Attributes¶
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pycgtool.frame.
logger
¶
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pycgtool.frame.
PathLike
¶
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exception
pycgtool.frame.
UnsupportedFormatException
(msg=None)[source]¶ Bases:
Exception
Exception raised when a topology/trajectory format cannot be parsed.
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exception
pycgtool.frame.
NonMatchingSystemError
(msg=None)[source]¶ Bases:
ValueError
Exception raised when topology and trajectory do not match.
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pycgtool.frame.
load_traj
(filepath: PathLike, **kwargs) → mdtraj.Trajectory[source]¶ Load a trajectory, if a PDB fails with zero box volume disable volume check and try again.
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class
pycgtool.frame.
Frame
(topology_file: Optional[PathLike] = None, trajectory_file: Optional[PathLike] = None, frame_start: int = 0, frame_end: Optional[int] = None)[source]¶ Load and store data from a simulation trajectory.
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_slice_trajectory
(self, frame_start: int = 0, frame_end: Optional[int] = None) → mdtraj.Trajectory[source]¶ Slice input simulation trajectory to a subset of frames.
- Parameters
frame_start – First frame of trajectory to use
frame_end – Last frame of trajectory to use
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property
residues
(self)¶ Residues in the frame topology.
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residue
(self, *args, **kwargs) → mdtraj.core.topology.Residue[source]¶ Get a residue from the frame topology by name or id.
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property
atoms
(self)¶ Atoms in the frame topology.
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atom
(self, *args, **kwargs) → mdtraj.core.topology.Atom[source]¶ Get an atom from the frame topology by name or id.
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property
natoms
(self) → int¶ Number of atoms in the frame topology.
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property
n_frames
(self) → int¶ Number of frames in the trajectory.
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add_residue
(self, name, chain: Optional[mdtraj.core.topology.Residue] = None, **kwargs) → mdtraj.core.topology.Residue[source]¶ Add a residue to the frame topology.
- Parameters
name – Name of residue
chain – MDTraj chain of residue
- Returns
New residue
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add_atom
(self, name: str, element: Optional[mdtraj.element.Element], residue: mdtraj.core.topology.Residue) → mdtraj.core.topology.Atom[source]¶ Add an atom or CG bead to the frame topology.
- Parameters
name – Name of atom
element – MDTraj element of atom
residue – MDTraj residue of atom
- Returns
New atom
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