Package generic_fns :: Module molmol
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Module molmol

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Module for interfacing with Molmol.

Classes [hide private]
  Molmol
The Molmol execution object.
Functions [hide private]
 
command(command)
Function for sending Molmol commands to the program pipe.
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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 Molmol commands.
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macro_apply(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None)
Execute a Molmol macro.
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macro_run(file=None, dir=None)
Execute the Molmol macro from the given text file.
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macro_write(data_type=None, style='classic', colour_start=None, colour_end=None, colour_list=None, file=None, dir=None, force=False)
Create a Molmol macro.
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ribbon()
Apply the Molmol ribbon style.
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tensor_pdb(file=None)
Display the diffusion tensor geometric structure.
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view()
Start Molmol.
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Variables [hide private]
  status = Status()
  molmol_obj = Molmol()
Molmol data container instance.
  __package__ = 'generic_fns'

Imports: sep, split, PIPE, Popen, sleep, exists_mol_res_spin_data, pipes, RelaxError, RelaxNoSequenceError, get_file_path, open_read_file, open_write_file, test_binary, get_specific_fn, Status


Function Details [hide private]

command(command)

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Function for sending Molmol commands to the program pipe.

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

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

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Create an array of Molmol 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 Molmol commands.

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

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Execute a Molmol 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)

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Execute the Molmol 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)

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Create a Molmol 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'.
  • 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 PDB file containing the tensor geometric object.