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, or GRO 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.