adding scripts for struct params

meta_data_analysis/RD.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Feb  6 12:18:24 2020
+
+@author: tanu
+"""
+#http://foldxsuite.crg.eu/faq-page#
+# after fold x downlaoded, extract and run it from 
+#https://biopython.org/DIST/docs/api/Bio.PDB.ResidueDepth%27-module.html
+#proDepth: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007072
+#Depth server: http://cospi.iiserpune.ac.in/depth/htdocs/index.html
+# needs biopython and msms
+
+# load libraries 
+import sys, os
+import pandas as pd
+from Bio.PDB.ResidueDepth import ResidueDepth
+from Bio.PDB.PDBParser import PDBParser
+from Bio.PDB.ResidueDepth import get_surface
+
+#%%
+homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
+os.getcwd()
+os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis/struct_params')
+os.getcwd()
+#%%
+parser = PDBParser()
+structure = parser.get_structure("3pl1", "/home/tanu/git/3pl1.pdb")
+model = structure[0]
+surface = get_surface(model)
+
+rd = ResidueDepth(model)
+print(rd['A',(' ', 152, ' ')])
+rd.keys()
+foo = rd.property_dict
+rd.property_keys
+baz = rd.property_list
+
+
+#To calculate the residue depth (average atom depth of the atoms in a residue):
+from Bio.PDB.ResidueDepth import residue_depth
+chain = model['A']
+res152 = chain[152]
+rd2 = residue_depth(res152, surface)
+
+# df from dict
+foo1 = pd.DataFrame.from_dict(baz, orient='index', columns = ['res_depth', 'surface'])
+test = pd.Series(foo, name = "test")
+
+# df from list
+foo2 = pd.DataFrame(baz, columns = ['residue', 'residue depth'])
+
+
+### iterate
+for i in range(185):
+    print(i)
+    rd3 = residue_depth(res+i, surface)
+    print(rd3)