API reference for UI submodule
API reference for UI submodule¶
User Interface module.
It contains functions used for the CLI mode and the one for the ‘module mode’.
- exception buildh.UI.BuildHError¶
Raised when BuildH returns a error.
This should be used when using BuildH as a module.
- buildh.UI.entry_point()¶
Correspond to the entry point buildH.
- buildh.UI.isfile(path)¶
Callback for checking file existence.
This function checks if path is an existing file. If not, raise an error. Else, return the path.
- Parameters
path (str) – The path to be checked.
- Returns
The validated path.
- Return type
str
- buildh.UI.launch(coord_file, def_file, lipid_type, traj_file=None, out_file='OP_buildH.out', prefix_traj_ouput=None, begin=None, end=None, lipid_jsons=None, ignore_CH3s=False)¶
Launch BuildH calculations.
This is the only function which can be called inside a Python script to use BuildH as a module. It checks the different arguments and call the main function.
- Parameters
coord_file (str) – Coordinate file. Only .pdb and .gro files are currently supported.
def_file (str) – Order parameter definition file.
lipid_type (str) – Combinaison of ForceField name and residue name for the lipid to calculate the OP on (e.g. Berger_POPC). It must match with the internal topology files or the one(s) supplied.
traj_file (str, optional) – Trajectory file (could be in XTC, TRR or DCD format), by default None.
out_file (str, optional) – Output file name for storing order parameters, by default “OP_buildH.out”.
prefix_traj_ouput (str, optional) – Base name for trajectory output with hydrogens. File extension will be automatically added. By default None.
begin (int, optional) – The first frame (ps) to read from the trajectory, by default None.
end (int, optional) – The last frame (ps) to read from the trajectory, by default None.
lipid_jsons (list, optional) – User topology lipid json file(s), by default None.
ignore_CH3s (bool, optional) – Ignore CH3s groups for the construction of hydrogens and the calculation of the OP.
- Raises
FileNotFoundError – When either coord_file, def_file or the traj_file is missing.
TypeError – When lipid_jsons is not a list.
BuildHError – When something went wront during calculation.
- buildh.UI.main(coord_file, traj_file, def_file, out_file, prefix_traj_ouput, dic_lipid, begin=None, end=None, ignore_CH3s=False)¶
Main function of BuildH.
- It takes care of all the necessary steps to compute the Order Parameter :
create MDAnalysis Universe
create internal dictionaries
Check topology
Reconstruct the hydrogens
Compute OP and write the result in the output file.
If asked, write the trajectory with the hydrogens.
Note
This function shouldn’t be called directly. Either it’s called by the entry point or by the launch function.
- Parameters
coord_file (str) – Coordinate file. Only .pdb and .gro files are currently supported.
traj_file (str) – Trajectory file (could be in XTC, TRR or DCD format). Can be None.
def_file (str) – Order parameter definition file.
out_file (str) – Output file name for storing order parameters.
prefix_traj_ouput (str) – Base name for trajectory output with hydrogens. File extension will be automatically added. Can be None.
dic_lipid (dict) – Lipid Topology for the reconstruction of the hydrogens.
begin (int) – The first frame (ps) to read from the trajectory, by default None.
end (int) – The last frame (ps) to read from the trajectory, by default None.
ignore_CH3s (bool) – Ignore CH3s groups for the construction of hydrogens and the calculation of the OP. By default, False.
- Raises
BuildHError – When something went wront during calculation.
- buildh.UI.parse_cli()¶
Handle the user parameters from the command line.