trajectory2saxs¶
Calculate a set of SAXS curves (.dat) from a trajectory file (.xtc).
Functions¶
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Calculate a set of theoretical SAXS curves from a trajectory file using Pepsi-SAXS. |
Module Contents¶
- ensemblify.conversion.trajectory2saxs.traj2saxs(trajectory, topology, trajectory_id, exp_saxs_file, pepsi_saxs_opt)¶
Calculate a set of theoretical SAXS curves from a trajectory file using Pepsi-SAXS.
Calculation is done in chunks distributed across available processor cores. A Universe object is created with the given trajectory and topology, which allows for writing of temporary individual .pdb files from trajectory frames that are then used for SAXS curve calculation at every frame.
- Parameters:
trajectory (
str) – Path to trajectory file used in Universe object creation.topology (
str) – Path to topology file used in Universe object creation.trajectory_id (
str) – Prefix identifier for created files.exp_saxs_file (
str) – Path to the experimental SAXS data for this protein. Used in Pepsi-SAXS for SAXS curve calculation, as an indication of the number of experimental data points that should be calculated for each frame of the trajectory.pepsi_saxs_opt (
str) – This string will be passed onto Pepsi-SAXS as additional command line options. If None, default Pepsi-SAXS options are used instead.
- Returns:
- str:
Path to the file containing the set of calculated SAXS curves, one for every frame of the trajectory.
- str:
Path to the file containing the average SAXS curve of the trajectory.
- str:
Path to the file containing the fitting of the average SAXS curve to the experimental SAXS data, including the chi-square value and residuals.
- Return type:
tuple[str, str, str]