adding scripts for struct params

meta_data_analysis/run_pdb_dssp.py

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+#!/usr/bin/python
+# Read a PDB and output DSSP to console
+import sys, os
+from Bio.PDB import PDBParser
+from Bio.PDB.DSSP import DSSP
+import pandas as pd
+import pprint as pp
+
+#%%
+# TASK: read a pdb file and generate a dssp output file
+# FIXME: Pending output dssp hasn't been generated
+# needs dssp exe on linux
+# may be easier to run the dssp exe locally
+#%%
+# my working dir
+os.getcwd()
+homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
+os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
+os.getcwd()
+#%%
+# specify variables for input and output paths and filenames
+drug = "pyrazinamide"
+#gene = "pnca"
+
+datadir = homedir + "/git/Data"
+basedir =  datadir + "/" + drug + "/input"
+
+# input
+inpath = "/original"
+
+# uncomment as necessary
+in_filename  = "/3pl1.pdb"
+
+infile = basedir + inpath + in_filename
+#print(infile)
+
+# output file 
+outpath = "/processed"
+outdir =   datadir + "/" + drug + outpath
+out_filename = "/3pl1.dssp"
+outfile =  outdir + out_filename
+#print(outdir)
+
+if not os.path.exists(datadir):
+    print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
+    os.makedirs(datadir)
+    exit()
+
+if not os.path.exists(outdir):
+    print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
+    exit()
+    
+else:
+    print('Dir exists: Carrying on')
+# end of variable assignment for input and output files
+#%%
+p = PDBParser()
+structure = p.get_structure("3pl1", infile)
+
+model = structure[0]
+dssp = DSSP(model, infile)
+#dssp = DSSP(model, infile, dssp='mkdssp') #incase you used DSSP2 exe
+pp.pprint(dssp)
+
+#DSSP data is accessed by a tuple - (chain id, residue id): RSA
+a_key = list(dssp.keys())[3]
+dssp[a_key]
+
+pp.pprint(dssp.keys())
+pp.pprint(dssp.property_dict)
+pp.pprint(dssp.property_keys)
+pp.pprint(dssp.property_list)