schrodinger.application.combiglide.utils module

This module contains the utility functions for CombiGlide.

schrodinger.application.combiglide.utils.get_spec_dict(filename, delimiter=':', pat_replace={}, ignore_case=True)

Reads the file, tokenizes the each line with delimiter, and returns the dict. It ignores the lines which start with ‘#’.

Parameters:

• filename (string) – The name of the input file.
• delimiter (string) – line is divided from delimiter to create the <key,value> of dict.
• pat_replace (dict) –

  this dict can be used to replace pattern, if specified. For example: pat_replace={‘#.*’:’‘, ‘s+’:’ ‘} would do… - replace all characters starting from ‘#’ to end of the line

  with ‘’ and

  • replace multiple spaces with one space.
• ignore_case (bool) – it is used to create the lowercase keys to make case insensitive search

A call to get_spec_dict(filename, pat_replace={‘#.*’:’‘, ‘s+’:’ ‘}) with following file.. file content = “

#CombGen input file

#Core molecule Core: cg_singledock_run1_tproj38171a23586-core.mae

#Attachment AcCl Chain: AcCl 1 1 1f 1t Frag: AcCl 1 cg_acid_chlorides_Acid_Cl_C_C

#Attachment Hyd Chain: Hyd 1 1 2f 2t Frag: Hyd 1 cg_hydrazines_Hydrazine_C_N

#Attachment NCO Chain: NCO 1 1 3f 3t Frag: NCO 1 cg_isocyanates_Isocyanate_C_N

” would return spec_dict as follow… {‘frag’: [‘AcCl’, ‘1’, ‘cg_acid_chlorides_Acid_Cl_C_C’,

‘Hyd’, ‘1’, ‘cg_hydrazines_Hydrazine_C_N’, ‘NCO’, ‘1’, ‘cg_isocyanates_Isocyanate_C_N’],

‘core’: [‘cg_singledock_run1_tproj38171a23586-core.mae’], ‘chain’: [‘AcCl’, ‘1’, ‘1’, ‘1f’, ‘1t’,

‘Hyd’, ‘1’, ‘1’, ‘2f’, ‘2t’, ‘NCO’, ‘1’, ‘1’, ‘3f’, ‘3t’]}