From 58b5b635953bc49583bc4f5a08d7f978a2201da9 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Mon, 14 Jun 2021 13:22:56 +0100 Subject: [PATCH] changed aa_prop_water to 3 categ according to KD, updated ref dict --- scripts/mut_electrostatic_changes.py | 8 +++++--- scripts/reference_dict.py | 10 ++++++---- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/scripts/mut_electrostatic_changes.py b/scripts/mut_electrostatic_changes.py index 243ff93..5e74b7c 100755 --- a/scripts/mut_electrostatic_changes.py +++ b/scripts/mut_electrostatic_changes.py @@ -5,13 +5,15 @@ Created on Tue Aug 6 12:56:03 2019 @author: tanu ''' - # FIXME: import dirs.py to get the basic dir paths available #======================================================================= # TASK: calculate how many mutations result in # electrostatic changes wrt wt -# Input: merged_df3 +# Input: mCSM-normalised file or any file containing one-letter aa code +# of wt and mut +# Note: this can be easily modified into 3-letter code +# TODO: turn to a function # Output: mut_elec_changes_results.txt #======================================================================= @@ -215,4 +217,4 @@ print('Total no. of mutations: ', total_muts , '\nTotal no. of unchanged muts: ', no_change_muts.mut_count.sum() , '\n=======================================================') #%% end of script -#======================================================================= +#======================================================================= \ No newline at end of file diff --git a/scripts/reference_dict.py b/scripts/reference_dict.py index ee431c3..41aeaf8 100755 --- a/scripts/reference_dict.py +++ b/scripts/reference_dict.py @@ -132,9 +132,11 @@ qualities_taylor = { ('R', 'H', 'K'): 'Basic' , ('C', 'G', 'P'): 'Special' } -# binary classification: hydrophilic or hydrophobic -qualities_water = { ('D', 'E', 'N', 'P', 'Q', 'R', 'S'): 'hydrophilic' - , ('A', 'C', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'T', 'V', 'W', 'X', 'Y'): 'hydrophobic' +# ternary classification: hydrophobic --> neutral --> hydrophilic (KD scale) +#http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html +qualities_water = { ('I','V','L','F','C','M','A','W'): 'hydrophobic' + , ('G','T','S','Y','P','H'): 'neutral' + , ('N','D','Q','E','K','R'): 'hydrophilic' } # polarity: no overlap @@ -232,4 +234,4 @@ for k, v in oneletter_aa_dict.items(): # COMMENT:VOILA! two different keytypes set for dicts containinga all # associated aa properties #============================================================================== -#%% end of script \ No newline at end of file +#%% end of script