Avril Coghlan avrilcoghlan

## pdb_rest_example_get_uniprot_for_pdbidlist.py
#!/usr/bin/env python
# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
# edited to use the python 'requests' module, and to get the UniProt id. for particular PDBe entry ids

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

## pdb_rest_example_get_uniprot_for_pdbid.py
#!/usr/bin/env python
# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
# edited to use the python 'requests' module, and to get the UniProt id. for a particular PDBe entry id.

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

## "pdb_rest_example_get_pdbids_for_ligandidlist.py
#!/usr/bin/env python
# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
# edited to use the python 'requests' module, and to get the PDB ids. for an input list of PDB ligand ids.

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

## unichem_rest_example_get_pdbligandids_for_chemblidlist.py
#!/usr/bin/env python
# script to find out the PDB three-letter ligand id. for a ChEMBL id., using UniChem

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

if PY3:

## unichem_rest_example_get_pdbligandids_for_chemblid.py
#!/usr/bin/env python
# script to find out the PDB three-letter ligand id. for a ChEMBL id., using UniChem

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

if PY3:

## pdb_rest_example_get_pbids_with_ligand.py
#!/usr/bin/env python
# adapted example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
# edited to use the python 'requests' module

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

## retrieve_bioactivity_info_from_chembl.py
import pandas as pd # uses pandas python module to view and analyse data
import requests # this is used to access json files

#====================================================================#

# using a list of known targets, find compounds that are active on these targets:

def find_bioactivities_for_targets(targets):

    targets = ",".join(targets) # join the targets into a suitable string to fulfil the search conditions of the ChEMBL api

## Find_compounds_for_NTD_targets_and_filter_those_compounds.ipynb

      
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                avrilcoghlan
                / Find_compounds_for_NTD_targets_and_filter_those_compounds.ipynb
            
            
              Created
              May 29, 2019 09:56
            
              
                Python notebook to query ChEMBL, to retrieve compounds with bioactivities for certain targets, and obtain properties of those compounds
              
          
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## fix_embl_file_cds_error.py
import sys
import os
from collections import defaultdict

#====================================================================#

# read in the line numbers of dodgy CDS:

def read_error_file(error_file):

## list_dogdy_genes_in_embl_file.py
import sys
import os
from collections import defaultdict

#====================================================================#

# read in the set of lines with dodgy genes on them in the embl file:

def read_lines_with_dodgy_genes(input_error_file):
	#!/usr/bin/env python
	# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
	# edited to use the python 'requests' module, and to get the UniProt id. for particular PDBe entry ids

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'
	#!/usr/bin/env python
	# script to find out the PDB three-letter ligand id. for a ChEMBL id., using UniChem

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

	if PY3:
	#!/usr/bin/env python
	# adapted example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
	# edited to use the python 'requests' module

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'
	import pandas as pd # uses pandas python module to view and analyse data
	import requests # this is used to access json files

	#====================================================================#

	# using a list of known targets, find compounds that are active on these targets:

	def find_bioactivities_for_targets(targets):

	targets = ",".join(targets) # join the targets into a suitable string to fulfil the search conditions of the ChEMBL api
	import sys
	import os
	from collections import defaultdict

	#====================================================================#

	# read in the line numbers of dodgy CDS:

	def read_error_file(error_file):