Performing the analysis
- class gorder.Analysis(structure, trajectory, analysis_type, bonds=None, index=None, output_yaml=None, output_tab=None, output_xvg=None, output_csv=None, membrane_normal=None, begin=None, end=None, step=None, min_samples=None, n_threads=None, leaflets=None, ordermap=None, estimate_error=None, geometry=None, handle_pbc=None, silent=None, overwrite=None)
Class describing all the parameters of the analysis.
- structure
Path to a TPR (recommended), PDB, GRO, or PQR file containing the structure and topology of the system.
- Type:
str
- trajectory
Path to an XTC (recommended), TRR, GRO, PDB, Amber NetCDF, DCD, or LAMMPSTRJ trajectory file to be analyzed. You can provide multiple XTC or TRR trajectories and these will be seamlessly concatenated.
- Type:
Union[str, list[str]]
- analysis_type
Type of analysis to perform (e.g., AAOrder or CGOrder).
- bonds
Path to a file containing bonding information. If specified, this overrides bonds from the structure file.
- Type:
Optional[str], default=None
- index
Path to an NDX file specifying groups in the system.
- Type:
Optional[str], default=None
- output_yaml
Path to an output YAML file containing the full analysis results.
- Type:
Optional[str], default=None
- output_tab
Path to an output TABLE file with human-readable results.
- Type:
Optional[str], default=None
- output_xvg
Filename pattern for output XVG files storing results. Each molecule type gets a separate file.
- Type:
Optional[str], default=None
- output_csv
Path to an output CSV file containing analysis results.
- Type:
Optional[str], default=None
- membrane_normal
Direction of the membrane normal. Allowed values are x, y, z, path to file, dictionary specifying manual membrane normals or an instance of DynamicNormal. Defaults to the z-axis if not specified.
- Type:
Optional[Union[str, dict, DynamicNormal]], default=None
- begin
Starting time of the trajectory analysis in picoseconds (ps). Defaults to the beginning of the trajectory.
- Type:
Optional[float], default=None
- end
Ending time of the trajectory analysis in picoseconds (ps). Defaults to the end of the trajectory.
- Type:
Optional[float], default=None
- step
Step size for analysis. Every Nth frame will be analyzed. Defaults to 1.
- Type:
Optional[int], default=None
- min_samples
Minimum number of samples required for each heavy atom or bond type to compute its order parameter. Defaults to 1.
- Type:
Optional[int], default=None
- n_threads
Number of threads to use for analysis. Defaults to 1.
- Type:
Optional[int], default=None
- leaflets
Defines how lipids are assigned to membrane leaflets. If provided, order parameters are calculated per leaflet.
- Type:
Optional[Union[GlobalClassification, LocalClassification, IndividualClassification, ManualClassification, NdxClassification]], default=None
- ordermap
Specifies parameters for ordermap calculations. If not provided, ordermaps are not generated.
- Type:
Optional[OrderMap], default=None
- estimate_error
Enables error estimation for each bond if specified.
- Type:
Optional[EstimateError], default=None
- geometry
Defines a specific region in the simulation box for order parameter calculations. Defaults to the entire system.
- handle_pbc
If False, ignores periodic boundary conditions (PBC). Defaults to True.
- Type:
Optional[bool], default=True
- silent
If True, suppresses standard output messages during analysis.
- Type:
Optional[bool], default=False
- overwrite
If True, overwrites existing output files and directories without backups.
- Type:
Optional[bool], default=False
- static from_file(file)
Read the options for the analysis from a config YAML file.
- run()
Perform the analysis.