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 ‘#’.

  • filename (string) – The name of the input file.

  • delimiter (str) – 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']}