Module molmol
source code
Module for interfacing with Molmol.
Molmol
The Molmol execution object.
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list of str
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create_macro(data_type=None,
style='classic',
colour_start=None,
colour_end=None,
colour_list=None)
Create an array of Molmol commands. |
source code
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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 Molmol macro. |
source code
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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 Molmol macro. |
source code
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status = Status()
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molmol_obj = Molmol()
Molmol data container instance.
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__package__ = 'pipe_control' |
Imports:
dep_check,
F_OK,
access,
sep,
PIPE,
Popen,
sleep,
RelaxError,
RelaxNoSequenceError,
get_file_path,
open_read_file,
open_write_file,
test_binary,
exists_mol_res_spin_data,
check_pipe,
add_result_file,
return_api,
Status
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Function for sending Molmol commands to the program pipe.
- Parameters:
command (str) - The command to send into the program.
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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.
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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)
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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_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'.
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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.
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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)
| source code
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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_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.
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Display the diffusion tensor geometric structure.
- Parameters:
file (str) - The name of the PDB file containing the tensor geometric object.
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