Module pymol_control

Module for interfacing with PyMOL.

Classes

Pymol
The PyMOL execution object.

Functions

cartoon()
Apply the PyMOL cartoon style and colour by secondary structure.

command(command)
Function for sending PyMOL commands to the program pipe.

cone_pdb(file=None)
Display the cone geometric object.

list of str create_macro(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None)
Create an array of PyMOL commands.

macro_apply(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None)
Execute a PyMOL macro.

macro_run(file=None, dir=None)
Execute the PyMOL macro from the given text file.

macro_write(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None, file=None, dir=None, force=False)
Create a PyMOL macro file.

tensor_pdb(file=None)
Display the diffusion tensor geometric structure.

vector_dist(file=None)
Display the XH bond vector distribution.

view()
Start PyMOL.

Variables

status = Status()

pymol_obj = Pymol('external')
Pymol data container instance.

__package__ = 'generic_fns'

Imports: dep_check, pymol, pi, float64, transpose, zeros, sep, PIPE, Popen, mktemp, sleep, exists_mol_res_spin_data, pipes, euler_to_R_zyz, R_to_axis_angle, RelaxError, RelaxNoPdbError, RelaxNoSequenceError, delete, file_root, get_file_path, open_read_file, open_write_file, test_binary, get_specific_fn, Status

Function Details

command(command)

Function for sending PyMOL commands to the program pipe.

Parameters:

• command (str) - The command to send into the program.

cone_pdb(file=None)

Display the cone geometric object.

Parameters:

• file (str) - The name of the file containing the cone geometric object.

create_macro(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None)

Create an array of PyMOL commands.

Parameters:

• data_type (str) - The data type to map to the structure.
• style (str) - The style of the macro.
• colour_start (str or RBG colour array (len 3 with vals from 0 to 1)) - The starting colour of the linear gradient.
• colour_end (str or RBG colour array (len 3 with vals from 0 to 1)) - The ending colour of the linear gradient.
• colour_list (str or None) - The colour list to search for the colour names. Can be either 'molmol' or 'x11'.

Returns: list of str

The list of PyMOL commands.

macro_apply(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None)

Execute a PyMOL macro.

Parameters:

• data_type (str) - The data type to map to the structure.
• style (str) - The style of the macro.
• colour_start (str or RBG colour array (len 3 with vals from 0 to 1)) - The starting colour of the linear gradient.
• colour_end (str or RBG colour array (len 3 with vals from 0 to 1)) - The ending colour of the linear gradient.
• colour_list (str or None) - The colour list to search for the colour names. Can be either 'molmol' or 'x11'.

macro_run(file=None, dir=None)

Execute the PyMOL macro from the given text file.

Parameters:

• file (str) - The name of the macro file to execute.
• dir (str) - The name of the directory where the macro file is located.

macro_write(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None, file=None, dir=None, force=False)

Create a PyMOL macro file.

Parameters:

• data_type (str) - The data type to map to the structure.
• style (str) - The style of the macro.
• colour_start (str or RBG colour array (len 3 with vals from 0 to 1)) - The starting colour of the linear gradient.
• colour_end (str or RBG colour array (len 3 with vals from 0 to 1)) - The ending colour of the linear gradient.
• colour_list (str or None) - The colour list to search for the colour names. Can be either 'molmol' or 'x11'.
• file (str) - The name of the macro file to create.
• dir (str) - The name of the directory to place the macro file into.
• force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.

tensor_pdb(file=None)

Display the diffusion tensor geometric structure.

Parameters:

• file (str) - The name of the file containing the diffusion tensor geometric object.

vector_dist(file=None)

Display the XH bond vector distribution.

Parameters:

• file (str) - The vector distribution PDB file.