ensemble2trajectory¶
Create a trajectory (.xtc) file from an ensemble of .pdb files.
Functions¶
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Create a trajectory (.xtc) file from an ensemble of .pdb files. |
Module Contents¶
- ensemblify.conversion.ensemble2trajectory.ensemble2traj(ensemble_dir=None, trajectory_dir=None, trajectory_id='', trajectory_size=None)¶
Create a trajectory (.xtc) file from an ensemble of .pdb files.
Additionally, one of the .pdb files used to create this trajectory is kept as a .pdb topology file. Uses GROMACS for trajectory conversion if installed, else uses MDAnalysis.
- Parameters:
ensemble_dir (
str, optional) – Path to directory where all the .pdb files are stored. Defaults to current working directory.trajectory_dir (
str, optional) – Path to directory where trajectory .xtc file will be created. Will be created if it does not exist. Defaults to current working directory.trajectory_id (
str, optional) – Prefix identifier for any created files.trajectory_size (
int, optional) – Number of randomly sampled .pdb files to use for trajectory creation. Defaults to all .pdb files in the ensemble directory.
- Returns:
- trajectory_path (str):
Path to created trajectory .xtc file.
- topology_path (str):
Path to created topology .pdb file.
- Return type:
tuple[str,str]