From 2911678177abf2a27ed5f40fcfe43ba1164a1e09 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 17 Nov 2020 13:55:16 +0000
Subject: [PATCH] updating notes to running_scripts.py as running for another
 drug-target

---
 foldx/runFoldx.py       | 2 +-
 scripts/dssp_df.py      | 1 +
 scripts/running_scripts | 7 ++++---
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/foldx/runFoldx.py b/foldx/runFoldx.py
index ffd24e8..219f421 100755
--- a/foldx/runFoldx.py
+++ b/foldx/runFoldx.py
@@ -82,7 +82,7 @@ if not outdir:
 # FIXME: this is a temporary directory and should be correctly handled
 process_dir = datadir + '/' + drug +'/' + 'processing'
 
-os.mkdir(process_dir)
+#os.mkdir(process_dir)
 #=======
 # input
 #=======
diff --git a/scripts/dssp_df.py b/scripts/dssp_df.py
index 966acaf..7afe39e 100755
--- a/scripts/dssp_df.py
+++ b/scripts/dssp_df.py
@@ -156,6 +156,7 @@ def extract_chain_dssp(inputpdbfile):
     return pdbchainlist
 #=======================================================================
 #%% write csv of processed dssp output
+# FIXME specify chain as cmd option!
 def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']):
     """
     Create a df from a dssp file containing ASA, RSA, SS for all chains
diff --git a/scripts/running_scripts b/scripts/running_scripts
index 465a3a2..646c654 100644
--- a/scripts/running_scripts
+++ b/scripts/running_scripts
@@ -9,9 +9,9 @@
 ./runFoldx.py -d pyrazinamide -g pncA
 
 #========
-# mcsm
+# mcsm: specify chain if default is NOT 'A'
 #========
-./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA
+./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA --debug
 ./run_mcsm.py -d pyrazinamide -g pncA -s get
 ./run_mcsm.py -d pyrazinamide -g pncA -s format
 
@@ -19,7 +19,8 @@
 # other struct params
 #====================
 ./dssp_df.py -d pyrazinamide -g pncA
-./kd_df.py -d pyrazinamide -g pncA # fixme: NO of cols says 2,but is actually 3
+# Errors on matplot.lib warn=, so just comment it out for the timebeing!: MONKEY PATCH
+./kd_df.py -d pyrazinamide -g pncA  -fasta # fixme: NO of cols says 2, but is actually 3
 ./rd_df.py -d pyrazinamide -g pncA # fixme: input tsv file is sourced manually from website!
 
 #==============================