Package pipe_control :: Module pymol_control

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Module pymol_control

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Module for interfacing with PyMOL.

Classes

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Pymol
The PyMOL execution object.

Functions

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

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

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

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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. source code

frame_order(ave_pos_file='ave_pos.pdb', rep_file='frame_order.pdb', dist_file='domain_distribution.pdb', dir=None)
Display the frame order results (the geometric object, average position and distribution). source code

frame_order_ave_pos(file=None)
Display the PDB structure for the frame order average domain position.

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frame_order_distribution(file=None)
Display the PDB structure for the frame order distribution of domain positions.

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frame_order_geometric(file=None)
Display the frame order geometric object.

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macro_apply(data_type=None, style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None)
Execute a PyMOL macro. source code

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

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macro_write(data_type=None, style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir=None, force=False)
Create a PyMOL macro file. source code

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

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

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view()
Start PyMOL.

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Variables

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status = Status()

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

__package__ = 'pipe_control'

Imports: dep_check, pymol, F_OK, access, pardir, sep, PIPE, Popen, mktemp, sleep, warn, RelaxError, RelaxNoPdbError, RelaxNoSequenceError, RelaxWarning, delete, file_root, get_file_path, open_read_file, open_write_file, test_binary, exists_mol_res_spin_data, check_pipe, add_result_file, return_api, Status

Function Details

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command(command)

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Function for sending PyMOL commands to the program pipe.

Parameters:

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

cone_pdb(file=None)

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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)

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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.

frame_order(ave_pos_file=`'ave_pos.pdb'`, rep_file=`'frame_order.pdb'`, dist_file=`'domain_distribution.pdb'`, dir=None)

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Display the frame order results (the geometric object, average position and distribution).

Parameters:

ave_pos_file (str or None) - The name of the file for the average molecule structure.
rep_file (str or None) - The name of the file of the PDB representation of the frame order dynamics to create.
dist_file (str or None) - The name of the file which will contain multiple models spanning the full dynamics distribution of the frame order model.
dir (str or None) - The name of the directory to place the PDB file into.

frame_order_ave_pos(file=None)

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Display the PDB structure for the frame order average domain position.

Parameters:

file (str) - The name of the PDB file containing the frame order average structure.

frame_order_distribution(file=None)

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Display the PDB structure for the frame order distribution of domain positions.

Parameters:

file (str) - The name of the PDB file containing the frame order distribution of domain positions.

frame_order_geometric(file=None)

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Display the frame order geometric object.

Parameters:

file (str) - The name of the PDB file containing the frame order geometric object.

macro_apply(data_type=None, style=`'classic'`, colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None)

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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_name (str) - The name of the starting colour of the linear gradient.
colour_start_rgb (RBG colour array (len 3 with vals from 0 to 1)) - The RGB array starting colour of the linear gradient.
colour_end_name (str) - The name of the ending colour of the linear gradient.
colour_end_rgb (RBG colour array (len 3 with vals from 0 to 1)) - The RGB array 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)

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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_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir=None, force=False)

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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_name (str) - The name of the starting colour of the linear gradient.
colour_start_rgb (RBG colour array (len 3 with vals from 0 to 1)) - The RGB array starting colour of the linear gradient.
colour_end_name (str) - The name of the ending colour of the linear gradient.
colour_end_rgb (RBG colour array (len 3 with vals from 0 to 1)) - The RGB array 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)

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Display the diffusion tensor geometric structure.

Parameters:

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

vector_dist(file=None)

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Display the XH bond vector distribution.

Parameters:

file (str) - The vector distribution PDB file.

Module pymol_control

command(command)

cone_pdb(file=None)

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

frame_order(ave_pos_file='ave_pos.pdb', rep_file='frame_order.pdb', dist_file='domain_distribution.pdb', dir=None)

frame_order_ave_pos(file=None)

frame_order_distribution(file=None)

frame_order_geometric(file=None)

macro_apply(data_type=None, style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None)

macro_run(file=None, dir=None)

macro_write(data_type=None, style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir=None, force=False)

tensor_pdb(file=None)

vector_dist(file=None)

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

frame_order(ave_pos_file=`'ave_pos.pdb'`, rep_file=`'frame_order.pdb'`, dist_file=`'domain_distribution.pdb'`, dir=None)

macro_apply(data_type=None, style=`'classic'`, colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None)

macro_write(data_type=None, style=`'classic'`, colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir=None, force=False)