diff --git a/pyScripts/get_pdb_structure.py b/pyScripts/get_pdb_structure.py
deleted file mode 100644
index d5dd27838698a9550b60550d5b1d87dab7252d36..0000000000000000000000000000000000000000
--- a/pyScripts/get_pdb_structure.py
+++ /dev/null
@@ -1,80 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: March 2018
-Version: 1
-
-
-DOWNLOAD PDB 3D STRUCTURE FILES FROM PDB
-
-
-Usage: [Script.py] [pdb_id]
-------------------------------------------------------------------
-Argument:
- [file]: list of PDB IDs (txt format)
-
-Return:
- [file]: PDB files, stored in 'PDB' folder
-"""
-
-# =============================================================================
-
-import os
-import argparse
-import logging
-import csv
-import Bio
-from Bio.PDB import PDBList
-
-# =============================================================================
-
-LOG = logging.getLogger("DOWNLOAD PDB 3D STRUCTURE FILES")
-
-FOLDER = 'PDB'
-
-# =============================================================================
-
-def main(pdb_id):
- get_pdb_file(get_pdbID(pdb_id))
- rename_pdb_file()
-
-
-def get_pdbID(txtfile):
- pdb_id = []
- with open(txtfile, 'rb') as pdb_txtfile:
- for line in csv.reader(pdb_txtfile):
- pdb_id.append(line[0].upper())
- return pdb_id
-
-
-def get_pdb_file(pdbID):
- for i in pdbID:
- PDBList().retrieve_pdb_file(i, pdir = FOLDER, file_format = 'pdb')
-
-
-def rename_pdb_file():
- working_dir = os.path.dirname(__file__)
- pdb_dir = os.path.abspath(os.path.join(working_dir, FOLDER))
- os.chdir(pdb_dir)
- for filename in os.listdir(pdb_dir):
- os.rename(filename, filename.replace('pdb', '').replace('ent', 'pdb'))
-
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-# =============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description =
- 'DOWNLOAD PDB 3D STRUCTURE FILES FROM PDB')
- parser.add_argument('pdb_id', help = 'Input [.txt file]: PDB IDs')
- options = parser.parse_args()
- setlogger()
- main(options.pdb_id)
diff --git a/pyScripts/get_ppc_V2.py b/pyScripts/get_ppc_V2.py
deleted file mode 100644
index 6d801b9c9a1e30ed70137e206681968e4bca6a66..0000000000000000000000000000000000000000
--- a/pyScripts/get_ppc_V2.py
+++ /dev/null
@@ -1,171 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: March 2018
-Version: 2
-
-
-
-IDENTIFY PROTEIN-PROTEIN COMPLEXES FROM PDBe
-
-
-Usage: [Script.py] [PDBe]
-------------------------------------------------------------------
-Argument:
- [PDBe]:
- Input (json format)
- PDBe (with [assembly_composition] and [assembly_type] information included)
-
-Return:
- [list(PPC)]:
- Output (txt format)
- Protein/protein complex PDB IDs
-
- [json(PPC)]:
- Output (json format)
- Protein/protein complex information
-
-
-Warning:
--------
-PDBs with unique and repeated assembly composition annotation are both included!
-[unique annotation: 'protein/protein complex']
-[repeated annotation: 'protein/protein complex, protein/protein complex']
-"""
-
-# =============================================================================
-
-import os
-import sys
-import argparse
-import logging
-import json
-
-# =============================================================================
-
-LOG = logging.getLogger('Get PPC PDB IDs from PDBe')
-FILENAME = 'PPC-DIMER_3-26-18PDBe'
-
-XRAY = ['X-ray diffraction', 'X-ray powder diffraction']
-
-RESOLUTION = 3.5
-DIFFR = 0.05
-
-# =============================================================================
-
-def main(pdbe):
- with open(pdbe) as infile:
- structure = json.load(infile)
- dimer = get_dimer(get_ppc(structure))
- dimer_filt = filter_rfactor(filter_resolution(filter_annotation(dimer)))
- to_json(dimer_filt, FILENAME)
- to_txt(get_id(dimer_filt), FILENAME)
-
- if os.path.exists('{}.txt'.format(FILENAME)):
- LOG.info('Finished!')
- else:
- LOG.error('Warning! [Output] Not found!')
- sys.exit(1)
-
-
-
-def get_ppc(pdbe):
- ppc_unique = []
- ppc_repeated = []
- for i in xrange(len(pdbe)):
- if 'assembly_composition' in pdbe[i].keys():
- assembly_composition = pdbe[i]['assembly_composition']
- if len(assembly_composition) == 1 and \
- assembly_composition == ['protein/protein complex']:
- ppc_unique.append(pdbe[i])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein/protein complex') >= 1 and \
- assembly_composition.count(
- assembly_composition[0]) == len(assembly_composition):
- ppc_repeated.append(pdbe[i])
- ppc_all = ppc_unique + ppc_repeated
- return ppc_all
-
-
-def get_dimer(pdbe):
- dimer_unique = []
- dimer_repeated = []
- for i in xrange(len(pdbe)):
- if 'assembly_type' in pdbe[i].keys():
- assembly_type = pdbe[i]['assembly_type']
- if len(assembly_type) == 1 and \
- assembly_type == ['dimer']:
- dimer_unique.append(pdbe[i])
- elif len(assembly_type) > 1:
- if assembly_type.count('dimer') >= 1 and \
- assembly_type.count(assembly_type[0]) == len(assembly_type):
- dimer_repeated.append(pdbe[i])
- dimer_all = dimer_unique + dimer_repeated
- return dimer_all
-
-
-def filter_annotation(pdbe):
- annotation = []
- for i in xrange(len(pdbe)):
- if len(pdbe[i]['experimental_method']) == 1:
- annotation.append(pdbe[i])
- return annotation
-
-def filter_resolution(pdbe):
- quality = []
- for i in xrange(len(pdbe)):
- if len([e for e in pdbe[i]['experimental_method'] if e in XRAY]) == 1:
- if 'resolution' in pdbe[i].keys() and \
- float(pdbe[i]['resolution']) <= RESOLUTION:
- quality.append(pdbe[i])
- return quality
-
-def filter_rfactor(pdbe):
- quality = []
- for i in xrange(len(pdbe)):
- if len([e for e in pdbe[i]['experimental_method'] if e in XRAY]) == 1:
- if 'r_free' in pdbe[i].keys() and 'r_factor' in pdbe[i].keys():
- if float(pdbe[i]['r_free'] - pdbe[i]['r_factor']) <= abs(DIFFR):
- quality.append(pdbe[i])
- return quality
-
-
-def get_id(pdbe):
- pdb_id = []
- for i in xrange(len(pdbe)):
- pdb_id.append(pdbe[i]['pdb_id'])
- return pdb_id
-
-
-def to_json(data, outfile):
- with open('{}.json'.format(outfile), 'wb') as jsonfile:
- json.dump(data, jsonfile)
-
-
-def to_txt(data, outfile):
- with open('{}.txt'.format(outfile), 'wb') as txtfile:
- for pdb_id in data:
- txtfile.write(pdb_id + '\n')
-
-
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - \
- %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-# =============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description = 'Get protein/protein \
- complex PDB IDs from PDBe')
- parser.add_argument('pdbe', help = 'Input [.json file]: \
- PBDe (with assembly and structure quality information included')
- options = parser.parse_args()
- setlogger()
- main(options.pdbe)
diff --git a/pyScripts/get_ppc_id_from_pdbe.py b/pyScripts/get_ppc_id_from_pdbe.py
deleted file mode 100644
index e41157a8c94a05634d5bcdfaea385670bb4a5abc..0000000000000000000000000000000000000000
--- a/pyScripts/get_ppc_id_from_pdbe.py
+++ /dev/null
@@ -1,121 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: February 2018
-Version: 1
-
-
-
-IDENTIFY PROTEIN-PROTEIN COMPLEXES FROM PDBe
-
-
-Usage: [Script.py] [PDBe]
-------------------------------------------------------------------
-Argument:
- [PDBe]:
- Input (json format)
- PDBe (with assembly information included)
-
-Return:
- [list(PPC)]:
- Output (txt format)
- Protein/protein complex PDB IDs
-
- [json(PPC)]:
- Output (json format)
- Protein/protein complex information
-
-
-Warning:
--------
-PDBs with unique and repeated assembly composition annotation are both included!
-[unique annotation: 'protein/protein complex']
-[repeated annotation: 'protein/protein complex, protein/protein complex']
-"""
-
-# =============================================================================
-
-import argparse
-import logging
-import json
-import pandas as pd
-
-# =============================================================================
-
-LOG = logging.getLogger('Get protein/protein complex PDB IDs from PDBe')
-
-# =============================================================================
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-
-
-def main(pdbe):
- structure = pd.read_json(pdbe, orient = 'columns')
- ppc_to_txt(get_ppc_id(structure))
- ppc_to_json(get_ppc_data(structure))
-
-
-
-def get_ppc_id(pdbe):
- ppc_unique = []
- ppc_repeated = []
- for i in xrange(len(pdbe['grouped']['pdb_id']['groups'])):
- assembly_composition = pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['assembly_composition']
- if len(assembly_composition) == 1 and assembly_composition == ['protein/protein complex']:
- ppc_unique.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['pdb_id'])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein/protein complex') >= 1 and \
- assembly_composition.count(assembly_composition[0]) == len(assembly_composition):
- ppc_repeated.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['pdb_id'])
- ppc_all = ppc_unique + ppc_repeated
- return ppc_all
-
-
-
-def get_ppc_data(pdbe):
- ppc_unique_data = []
- ppc_repeated_data = []
- for i in xrange(len(pdbe['grouped']['pdb_id']['groups'])):
- assembly_composition = pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['assembly_composition']
- if len(assembly_composition) == 1 and assembly_composition == ['protein/protein complex']:
- ppc_unique_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein/protein complex') >= 1 and \
- assembly_composition.count(assembly_composition[0]) == len(assembly_composition):
- ppc_repeated_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- ppc_all_data = ppc_unique_data + ppc_repeated_data
- return ppc_all_data
-
-
-
-def ppc_to_txt(ppc):
- with open('PPC_2-20-18PDBe.txt', 'wb') as txtfile:
- for pdb_id in ppc:
- txtfile.write(pdb_id + '\n')
-
-
-
-def ppc_to_json(ppc):
- with open('PPC_2-20-18PDBe.json', 'wb') as jsonfile:
- json.dump(ppc, jsonfile)
-
-
-
-# ==============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description =
- 'Get protein/protein complex PDB IDs from PDBe')
- parser.add_argument('pdbe', help = 'Input [.json file]: \
- PBDe (with assembly information included')
- options = parser.parse_args()
- setlogger()
- main(options.pdbe)
diff --git a/pyScripts/get_ppc_ligand_V2.py b/pyScripts/get_ppc_ligand_V2.py
deleted file mode 100644
index ed1f1576c33a4f3be066d1a2326152198654130b..0000000000000000000000000000000000000000
--- a/pyScripts/get_ppc_ligand_V2.py
+++ /dev/null
@@ -1,268 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: March 2018
-Version: 3
-
-
-
-IDENTIFY PROTEIN STRUCTURE WITH COMPOUNDS (with or without including ions)
-INVOLVED IN PROTEIN-PROTEIN INTERACTION FROM PDBe
-
-
-Usage: [Script.py] [PDBe] [IONS]
-------------------------------------------------------------------
-Arguments:
- [PDBe]:
- Input (json format)
- PDBe (with [assembly_composition], [compound_id] and [uniprot_id] included)
-
- [IONS]:
- Input (txt format)
- Compounds considered as ions
-
-Return:
- [list(protein)]:
- Output (txt format)
- Proteins with compounds associated with a protein/protein complex PDB IDs
-
- [json(protein)]:
- Output (json format)
- Proteins with compounds associated with a protein/protein complex dataset
-
- Compounds:
- ---------
- ** EXAMPLE: [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID']
- or [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID', u'FE : FE (III) ION']
-
-
- [list(protein)]:
- Output (txt format)
- Proteins with compounds associated with a protein/protein complex PDB IDs
- IONS ONLY EXCLUDED
-
- [json(protein)]:
- Output (json format)
- Proteins with compounds associated with a protein/protein complex dataset
- IONS ONLY EXCLUDED
-
- Compounds:
- ---------
- ** EXAMPLE: [u'FE : FE (III) ION']
-
-
-
-!Warning!:
--------
-PDBs with unique and repeated assembly composition annotation are both included!
-[unique annotation: 'protein/protein complex']
-[repeated annotation: 'protein/protein complex, protein/protein complex']
-"""
-
-# =============================================================================
-
-import os
-import sys
-import argparse
-import logging
-import json
-
-# =============================================================================
-
-LOG = logging.getLogger('Get PPC PDB IDs with ligand')
-FILENAME_with_ions = 'PPC-PROT-COMPOUNDS_3-26-18PDBe'
-FILENAME_without_ions = 'PPC-PROT-COMPOUNDS_noIONS_3-26-18PDBe'
-
-XRAY = ['X-ray diffraction', 'X-ray powder diffraction']
-
-RESOLUTION = 3.5
-DIFFR = 0.05
-
-# =============================================================================
-
-def main(pdbe, ion):
- with open(pdbe) as infile:
- structure = json.load(infile)
-
- # Get protein/protein complex (PPC)
- ppc = filter_rfactor(filter_resolution(filter_annotation(
- get_ppc(structure))))
- to_txt(get_id(ppc), 'PPC_3-26-18PDBe')
-
- # Get protein structure with [compounds]
- prot_compound = filter_rfactor(filter_resolution(filter_annotation(
- get_with_compound(get_prot(structure)))))
-
- # Collect PPC UniProt
- ppc_uniprot = get_uniprot(ppc)
-
- # Get PPC-associated proteins with compounds
- ppc_ligand = get_prot_compound_ppc(prot_compound, ppc_uniprot)
- to_json(ppc_ligand, FILENAME_with_ions)
- to_txt(get_id(ppc_ligand), FILENAME_with_ions)
-
- # Get PPC-associated proteins with compounds (ions only not included)
- ions = []
- with open(ion, 'r') as ion_file:
- for i in ion_file:
- ions.append(i.strip().upper())
-
- prot_compound_without_ions = get_without_ions(prot_compound, ions)
- ppc_ligand_without_ions = get_prot_compound_ppc(prot_compound_without_ions, ppc_uniprot)
- to_json(ppc_ligand_without_ions, FILENAME_without_ions)
- to_txt(get_id(ppc_ligand_without_ions), FILENAME_without_ions)
-
-
- if os.path.exists('{}.txt'.format(FILENAME_with_ions)) and \
- os.path.exists('{}.txt'.format(FILENAME_without_ions)):
- LOG.info('Finished!')
- else:
- LOG.error('Warning! [Outputs] Not found!')
- sys.exit(1)
-
-
-
-def get_ppc(pdbe):
- ppc_unique = []
- ppc_repeated = []
- for i in xrange(len(pdbe)):
- if 'assembly_composition' in pdbe[i].keys():
- assembly_composition = pdbe[i]['assembly_composition']
- if len(assembly_composition) == 1 and \
- assembly_composition == ['protein/protein complex']:
- ppc_unique.append(pdbe[i])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein/protein complex') >= 1 and \
- assembly_composition.count(
- assembly_composition[0]) == len(assembly_composition):
- ppc_repeated.append(pdbe[i])
- ppc_all = ppc_unique + ppc_repeated
- return ppc_all
-
-
-def get_prot(pdbe):
- prot_unique = []
- prot_repeated = []
- for i in xrange(len(pdbe)):
- if 'assembly_composition' in pdbe[i].keys():
- assembly_composition = pdbe[i]['assembly_composition']
- if len(assembly_composition) == 1 and \
- assembly_composition == ['protein structure']:
- prot_unique.append(pdbe[i])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein structure') >= 1 and \
- assembly_composition.count(
- assembly_composition[0]) == len(assembly_composition):
- prot_repeated.append(pdbe[i])
- prot_all = prot_unique + prot_repeated
- return prot_all
-
-
-def filter_annotation(pdbe):
- annotation = []
- for i in xrange(len(pdbe)):
- if len(pdbe[i]['experimental_method']) == 1:
- annotation.append(pdbe[i])
- return annotation
-
-def filter_resolution(pdbe):
- quality = []
- for i in xrange(len(pdbe)):
- if len([e for e in pdbe[i]['experimental_method'] if e in XRAY]) == 1:
- if 'resolution' in pdbe[i].keys() and \
- float(pdbe[i]['resolution']) <= RESOLUTION:
- quality.append(pdbe[i])
- return quality
-
-def filter_rfactor(pdbe):
- quality = []
- for i in xrange(len(pdbe)):
- if len([e for e in pdbe[i]['experimental_method'] if e in XRAY]) == 1:
- if 'r_free' in pdbe[i].keys() and 'r_factor' in pdbe[i].keys():
- if float(pdbe[i]['r_free'] - pdbe[i]['r_factor']) <= abs(DIFFR):
- quality.append(pdbe[i])
- return quality
-
-
-def get_with_compound(pdbe):
- compound = []
- for i in xrange(len(pdbe)):
- if 'compound_id' in pdbe[i].keys():
- compound.append(pdbe[i])
- return compound
-
-
-def get_uniprot(pdbe):
- uniprot = []
- for i in xrange(len(pdbe)):
- if 'uniprot_id' in pdbe[i].keys():
- uniprot.extend(pdbe[i]['uniprot_id'])
- return uniprot
-
-
-def get_prot_compound_ppc(protein, uniprot):
- prot_compound_ppc = []
- for i in xrange(len(protein)):
- if 'uniprot_id' in protein[i].keys():
- if len([e for e in protein[i]['uniprot_id'] if e in uniprot]) >= 1:
- prot_compound_ppc.append(protein[i])
- return prot_compound_ppc
-
-
-def get_without_ions(protein, ions):
- without_ions = []
- with_ions_not_only = []
- for i in xrange(len(protein)):
- if 'compound_id' in protein[i].keys():
- if len([e for e in protein[i]['compound_id'] if e in ions]) == 0:
- without_ions.append(protein[i])
- elif len([e for e in protein[i]['compound_id'] if e in ions]) >= 1:
- if len([e for e in protein[i]['compound_id'] if e in ions]) \
- != len(protein[i]['compound_id']):
- with_ions_not_only.append(protein[i])
- print len(without_ions), len(with_ions_not_only)
- compound_ions = without_ions + with_ions_not_only
- return compound_ions
-
-
-def get_id(pdbe):
- pdb_id = []
- for i in xrange(len(pdbe)):
- pdb_id.append(pdbe[i]['pdb_id'])
- return pdb_id
-
-
-def to_json(data, outfile):
- with open('{}.json'.format(outfile), 'wb') as jsonfile:
- json.dump(data, jsonfile)
-
-
-def to_txt(data, outfile):
- with open('{}.txt'.format(outfile), 'wb') as txtfile:
- for pdb_id in data:
- txtfile.write(pdb_id + '\n')
-
-
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - \
- %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-# =============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description = 'Get protein/protein \
- complex PDB IDs from PDBe')
- parser.add_argument('pdbe', help = 'Input [.json file]: \
- PBDe (with assembly and structure quality information included')
- parser.add_argument('ion', help = 'Input [.txt file]: Compounds considered \
- as ions')
- options = parser.parse_args()
- setlogger()
- main(options.pdbe, options.ion)
diff --git a/pyScripts/get_ppc_ligand_compound_from_pdbe.py b/pyScripts/get_ppc_ligand_compound_from_pdbe.py
deleted file mode 100644
index a91caa2d8a00c3559d5e14213294b8308dff1b43..0000000000000000000000000000000000000000
--- a/pyScripts/get_ppc_ligand_compound_from_pdbe.py
+++ /dev/null
@@ -1,131 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: February 2018
-Version: 2
-
-
-
-IDENTIFY INTERACTING LIGANDS AND COMPOUNDS OF PROTEIN-PROTEIN COMPLEXES FROM PDBe
-
-
-Usage: [Script.py] [PDBe]
-------------------------------------------------------------------
-Argument:
- [PDBe]:
- Input (json format)
- PDBe (with assembly information included)
-
-Return:
- [list(ligands)]:
- Output (txt format)
- Interacting ligands of protein/protein complexes
-
- [list(compounds)]:
- Output (txt format)
- Compounds of protein/protein complexes
-
-
-Warning:
--------
-PDBs with unique and repeated assembly composition annotation are both included!
-[unique annotation: 'protein/protein complex']
-[repeated annotation: 'protein/protein complex, protein/protein complex']
-"""
-
-# =============================================================================
-
-import argparse
-import logging
-import json
-import pandas as pd
-
-# =============================================================================
-
-LOG = logging.getLogger('Get ligands and compounds of protein/protein complexes from PDBe')
-
-# =============================================================================
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-
-
-def main(pdbe):
- structure = pd.read_json(pdbe, orient = 'columns')
- ligand_to_txt(get_ligand(get_ppc_data(structure)))
- compound_to_txt(get_compound(get_ppc_data(structure)))
-
-def get_ppc_data(pdbe):
- ppc_unique_data = []
- ppc_repeated_data = []
- for i in xrange(len(pdbe['grouped']['pdb_id']['groups'])):
- assembly_composition = pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['assembly_composition']
- if len(assembly_composition) == 1 and assembly_composition == ['protein/protein complex']:
- ppc_unique_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein/protein complex') >= 1 and \
- assembly_composition.count(assembly_composition[0]) == len(assembly_composition):
- ppc_repeated_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- ppc_all_data = ppc_unique_data + ppc_repeated_data
- return ppc_all_data
-
-
-
-def get_ligand(ppc):
- ppc_ligand = []
- unique_ligand = []
- for i in xrange(len(ppc)):
- if 'interacting_ligands' in ppc[i].keys():
- ppc_ligand.append(ppc[i]['interacting_ligands'][0].split(' :')[0])
-
- for j in ppc_ligand:
- if j not in unique_ligand:
- unique_ligand.append(j)
-
- #print len(unique_ligand)
- return unique_ligand
-
-
-
-def get_compound(ppc):
- ppc_compound = []
- unique_compound = []
- for i in xrange(len(ppc)):
- if 'compound_id' in ppc[i].keys():
- ppc_compound.extend(ppc[i]['compound_id'])
-
- for j in ppc_compound:
- if j not in unique_compound:
- unique_compound.append(j)
-
- #print len(unique_compound)
- return unique_compound
-
-
-def ligand_to_txt(ligand):
- with open('PPC_LIGANDS_2-20-18PDBe.txt', 'wb') as txtfile:
- for lig in ligand:
- txtfile.write(lig + '\n')
-
-def compound_to_txt(compound):
- with open('PPC_COMPOUNDS_2-20-18PDBe.txt', 'wb') as txtfile:
- for c in compound:
- txtfile.write(c + '\n')
-
-# ==============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description =
- 'Get ligands and compounds of protein/protein complexes from PDBe')
- parser.add_argument('pdbe', help = 'Input [.json file]: \
- PBDe (with interacting ligand and compound information included')
- options = parser.parse_args()
- setlogger()
- main(options.pdbe)
diff --git a/pyScripts/get_ppc_protcomp-ion_ppc_from_pdbe.py b/pyScripts/get_ppc_protcomp-ion_ppc_from_pdbe.py
deleted file mode 100644
index 59a2c0ac99f63241860924a3b5001e069f73a7ac..0000000000000000000000000000000000000000
--- a/pyScripts/get_ppc_protcomp-ion_ppc_from_pdbe.py
+++ /dev/null
@@ -1,321 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: February 2018
-Version: 2
-
-
-
-IDENTIFY PROTEIN STRUCTURE WITH COMPOUNDS (with or without including ions)
-INVOLVED IN PROTEIN-PROTEIN INTERACTION FROM PDBe
-
-
-Usage: [Script.py] [PDBe]
-------------------------------------------------------------------
-Argument:
- [PDBe]:
- Input (json format)
- PDBe (with [assembly_composition], [compound_id] and [uniprot_id] included)
-
-Return:
- [list(protein)]:
- Output (txt format)
- Proteins with compounds associated with a protein/protein complex PDB IDs
-
- [json(protein)]:
- Output (json format)
- Proteins with compounds associated with a protein/protein complex dataset
-
- Compounds:
- ---------
- ** EXAMPLE: [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID']
- or [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID', u'FE : FE (III) ION']
-
-
-
- [list(protein)]:
- Output (txt format)
- Proteins with compounds associated with a protein/protein complex PDB IDs
- IONS ONLY EXCLUDED
-
- [json(protein)]:
- Output (json format)
- Proteins with compounds associated with a protein/protein complex dataset
- IONS ONLY EXCLUDED
-
- Compounds:
- ---------
- ** EXAMPLE: [u'FE : FE (III) ION']
-
-
-
-!Warning!:
--------
-PDBs with unique and repeated assembly composition annotation are both included!
-[unique annotation: 'protein/protein complex']
-[repeated annotation: 'protein/protein complex, protein/protein complex']
-"""
-
-# =============================================================================
-
-import argparse
-import logging
-import json
-import pandas as pd
-
-# =============================================================================
-
-LOG = logging.getLogger('Proteins associated with a PPC - Compounds')
-
-# =============================================================================
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-
-def main(pdbe):
- structure = pd.read_json(pdbe, orient = 'columns')
-
- # Get protein/protein complex [assembly_composition]
- ppc = get_ppc_data(structure)
-
- # Get protein structure [assembly_composition] with 'compounds'
- prot_compound = get_compound_id(get_prot_data(structure))
-
- # Collect PPC UniProt
- ppc_uniprot = get_uniprot(ppc)
-
- # Identify protein structure with compounds associated to PPC
- to_txt(get_id_prot_compound_ppc(prot_compound, ppc_uniprot))
- to_json(get_data_prot_compound_ppc(prot_compound, ppc_uniprot))
-
-
- # Get protein structure [assembly_composition] with compounds (ions only not included)
- ion = get_ion(get_compound_name(prot_compound))
- prot_compound_without_ions = get_compound_without_ion(prot_compound, ion)
- to_txt_ion(get_id_prot_compound_ppc(prot_compound_without_ions, ppc_uniprot))
- to_json_ion(get_data_prot_compound_ppc(prot_compound_without_ions, ppc_uniprot))
-
-
-
-
-def get_ppc_data(pdbe):
- ppc_unique_data = []
- ppc_repeated_data = []
- for i in xrange(len(pdbe['grouped']['pdb_id']['groups'])):
- assembly_composition = pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['assembly_composition']
- if len(assembly_composition) == 1 and assembly_composition == ['protein/protein complex']:
- ppc_unique_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein/protein complex') >= 1 and \
- assembly_composition.count(assembly_composition[0]) == len(assembly_composition):
- ppc_repeated_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- ppc_all_data = ppc_unique_data + ppc_repeated_data
- return ppc_all_data
-
-
-
-def get_prot_data(pdbe):
- prot_unique_data = []
- prot_repeated_data = []
- for i in xrange(len(pdbe['grouped']['pdb_id']['groups'])):
- assembly_composition = pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0]['assembly_composition']
- if len(assembly_composition) == 1 and assembly_composition == ['protein structure']:
- prot_unique_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- elif len(assembly_composition) > 1:
- if assembly_composition.count('protein structure') >= 1 and \
- assembly_composition.count(assembly_composition[0]) == len(assembly_composition):
- prot_repeated_data.append(pdbe['grouped']['pdb_id']['groups'][i]['doclist']['docs'][0])
- prot_all_data = prot_unique_data + prot_repeated_data
- return prot_all_data
-
-
-
-def get_compound_id(data):
- '''
- Get 3D structure with compound [compound_id]
- --------------------------------------------------
- Argument:
- [json]: protein structures (dataset)
-
- Return:
- [json]: protein structures with compounds (dataset)
- '''
- compound = []
- for i in xrange(len(data)):
- if 'compound_id' in data[i].keys():
- compound.append(data[i])
- return compound
-
-
-
-def get_uniprot(data):
- '''
- Get UniProt
- -------------------------------------------------
- Argument:
- [json]: protein/protein complexes (dataset)
-
- Return:
- [list]: protein/protein complexes Uniprot IDs
- '''
- uniprot = []
- for i in xrange(len(data)):
- if 'uniprot_id' in data[i].keys():
- uniprot.extend(data[i]['uniprot_id'])
- return uniprot
-
-
-def get_id_prot_compound_ppc(data, uniprot):
- '''
- Get PDB IDs only of protein structure with compounds associated with a protein/protein complex
- -----------------------------------------------------------------------------------------------
- Arguments:
- [json]: protein structures with compounds (dataset)
- [list]: protein/protein complex uniprot id
-
- Return:
- [list]: protein structure with compounds associated with a protein/protein complex PDB IDs
- '''
- prot_compound_pcc = []
- for i in xrange(len(data)):
- if 'uniprot_id' in data[i].keys():
- if len([e for e in data[i]['uniprot_id'] if e in uniprot]) >= 1:
- prot_compound_pcc.append(data[i]['pdb_id'])
- return prot_compound_pcc
-
-
-
-def get_data_prot_compound_ppc(data, uniprot):
- '''
- Get data only of protein structure with compounds associated with a protein/protein complex
- -----------------------------------------------------------------------------------------------
- Arguments:
- [json]: protein structures with compounds (dataset)
- [list]: protein/protein complex uniprot id
-
- Return:
- [json]: protein structure with compounds associated with a protein/protein complex (dataset)
- '''
- prot_compound_pcc_data = []
- for i in xrange(len(data)):
- if 'uniprot_id' in data[i].keys():
- if len([e for e in data[i]['uniprot_id'] if e in uniprot]) >= 1:
- prot_compound_pcc_data.append(data[i])
- return prot_compound_pcc_data
-
-
-
-
-def get_compound_name(data):
- '''
- Get protein compound names
- --------------------------------------------------
- Argument:
- [json]: protein structures with compounds (dataset)
-
- Return:
- [list]: compound names
- ** EXAMPLE: [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID', u'FE : FE (III) ION']
- '''
- compound = []
- for i in xrange(len(data)):
- if 'compound_name' in data[i].keys():
- compound.extend(data[i]['compound_name'])
- return compound
-
-
-
-def get_ion(compound_name):
- '''
- Get protein ions
- --------------------------------------------------
- Argument:
- [list]: compound names
- ** EXAMPLE: [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID', u'FE : FE (III) ION']
-
- Return:
- [list]: ions
- ** EXAMPLE: ['FE']
- '''
- ion = []
- ion_unique = []
- for i in xrange(len(compound_name)):
- if 'ION' in compound_name[i].split(' :')[1].split(' '):
- ion.append(compound_name[i].split(' :')[0])
- for j in ion:
- if j not in ion_unique:
- ion_unique.append(j)
- print ion_unique
- return ion_unique
-
-
-
-def get_compound_without_ion(data, ions):
- '''
- Get 3D structure with compound [compound_id], ion excluded
- ----------------------------------------------------------
- Arguments:
- [json]: protein structures (dataset)
- [list]: ions
-
- Return:
- [json]: protein structures with compounds != ions (dataset)
-
- !Warning!
- ---------
- Protein structures either with only compounds, or compounds and ions are included
- ** EXAMPLE: [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID']
- or [u'FHB : 3-FLUORO-4-HYDROXYBENZOIC ACID', u'FE : FE (III) ION']
-
- Only protein structures with only ions are excluded
- ** EXAMPLE: [u'FE : FE (III) ION']
- '''
- compound_without_ion = []
- compound_with_ion = []
- for i in xrange(len(data)):
- if 'compound_id' in data[i].keys():
- if len([e for e in data[i]['compound_id'] if e in ions]) == 0:
- compound_without_ion.append(data[i])
- elif len([e for e in data[i]['compound_id'] if e in ions]) >= 1:
- if len([e for e in data[i]['compound_id'] if e in ions]) != len(data[i]['compound_id']):
- compound_with_ion.append(data[i])
- compound_ion = compound_without_ion + compound_with_ion
- return compound_ion
-
-
-
-def to_txt(index):
- with open('PROT-COMPOUNDS_PPC_2-20-18PDBe.txt', 'wb') as txtfile:
- for i in index:
- txtfile.write(i + '\n')
-
-def to_json(index):
- with open('PROT-COMPOUNDS_PPC_2-20-18PDBe.json', 'wb') as jsonfile:
- json.dump(index, jsonfile)
-
-def to_txt_ion(index):
- with open('PROT-COMPOUNDS-noIONS_PPC_2-20-18PDBe.txt', 'wb') as txtfile:
- for i in index:
- txtfile.write(i + '\n')
-
-def to_json_ion(index):
- with open('PROT-COMPOUNDS-noIONS_PPC_2-20-18PDBe.json', 'wb') as jsonfile:
- json.dump(index, jsonfile)
-
-# ==============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description =
- 'IDENTIFY PROTEIN STRUCTURE WITH COMPOUNDS INVOLVED IN PROTEIN-PROTEIN INTERACTION FROM PDBe')
- parser.add_argument('pdbe', help = 'Input [.json file]: \
- PBDe (with [assembly_composition], [compound_id] and [uniprot_id] included)')
- options = parser.parse_args()
- setlogger()
- main(options.pdbe)
diff --git a/pyScripts/iPPI-DB_descriptors_V2.py b/pyScripts/iPPI-DB_descriptors_V2.py
deleted file mode 100644
index ef516ce6ee41b26aecaada0d83730c0d57572e08..0000000000000000000000000000000000000000
--- a/pyScripts/iPPI-DB_descriptors_V2.py
+++ /dev/null
@@ -1,320 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: January 2018
-Version: 2
-
-
-
-CALCULATE 2D/3D POCKET DESCRIPTORS FROM VOLSITE
-
-
-Usage: [Script.py] [PDB_descriptor.txt] [PDB_2D-3Ddescriptors.csv]
-------------------------------------------------------------------
-
-[PDB_descriptor.txt]:
- Input (txt format)
- Pocket descriptors calculated by VolSite
-
-[PDB_2D-3Ddescriptors.csv]:
- Output (csv format)
- Pocket descriptors including:
- * 89 descriptors from VolSite
- * 10 descriptors using a linear combination of VolSite descriptors
- (Kuenemann, 2016 Scientific Reports)
- * 10 geometric descriptors from RDKit toolkit
- (http://www.rdkit.org/docs/Overview.html, version 2017.09.1)
-"""
-
-# =============================================================================
-
-import os
-import sys
-import argparse
-import logging
-import csv
-import pandas as pd
-from rdkit import Chem
-from rdkit.Chem import Descriptors3D
-
-# =============================================================================
-
-LOG = logging.getLogger("CALCULATE 2D/3D POCKET DESCRIPTORS FROM VOLSITE")
-
-
-VOLSITE_HEADER = [
- 'Volume', 'CZ', 'CA', 'O', 'OD1', 'OG', 'N', 'NZ', 'DU',
- 'CZ40', 'CZ40-50', 'CZ50-60', 'CZ60-70', 'CZ70-80', 'CZ80-90', 'CZ90-100', 'CZ100-110', 'CZ110-120', 'CZ120',
- 'CA40', 'CA40-50', 'CA50-60', 'CA60-70', 'CA70-80', 'CA80-90', 'CA90-100', 'CA100-110', 'CA110-120', 'CA120',
- 'O40', 'O40-50', 'O50-60', 'O60-70', 'O70-80', 'O80-90', 'O90-100', 'O100-110', 'O110-120', 'O120',
- 'OD140', 'OD140-50', 'OD150-60', 'OD160-70', 'OD170-80', 'OD180-90', 'OD190-100', 'OD1100-110', 'OD1110-120',
- 'OD1120',
- 'OG40', 'OG40-50', 'OG50-60', 'OG60-70', 'OG70-80', 'OG80-90', 'OG90-100', 'OG100-110', 'OG110-120', 'OG120',
- 'N40', 'N40-50', 'N50-60', 'N60-70', 'N70-80', 'N80-90', 'N90-100', 'N100-110', 'N110-120', 'N120',
- 'NZ40', 'NZ40-50', 'NZ50-60', 'NZ60-70', 'NZ70-80', 'NZ80-90', 'NZ90-100', 'NZ100-110', 'NZ110-120', 'NZ120',
- 'DU40', 'DU40-50', 'DU50-60', 'DU60-70', 'DU70-80', 'DU80-90', 'DU90-100', 'DU100-110', 'DU110-120', 'DU120',
- 'POCKET'
-]
-
-DESC_COMBINATION = {
- 'T40': ['CZ40', 'CA40', 'O40', 'OD140', 'OG40', 'N40', 'NZ40', 'DU40'],
- 'T40-50': ['CZ40-50', 'CA40-50', 'O40-50', 'OD140-50', 'OG40-50', 'N40-50', 'NZ40-50', 'DU40-50'],
- 'T50-60': ['CZ50-60', 'CA50-60', 'O50-60', 'OD150-60', 'OG50-60', 'N50-60', 'NZ50-60', 'DU50-60'],
- 'T60-70': ['CZ60-70', 'CA60-70', 'O60-70', 'OD160-70', 'OG60-70', 'N60-70', 'NZ60-70', 'DU60-70'],
- 'T70-80': ['CZ70-80', 'CA70-80', 'O70-80', 'OD170-80', 'OG70-80', 'N70-80', 'NZ70-80', 'DU70-80'],
- 'T80-90': ['CZ80-90', 'CA80-90', 'O80-90', 'OD180-90', 'OG80-90', 'N80-90', 'NZ80-90', 'DU80-90'],
- 'T90-100': ['CZ90-100', 'CA90-100', 'O90-100', 'OD190-100', 'OG90-100', 'N90-100', 'NZ90-100', 'DU90-100'],
- 'T100-110': ['CZ100-110', 'CA100-110', 'O100-110', 'OD1100-110', 'OG100-110', 'N100-110', 'NZ100-110', 'DU100-110'],
- 'T110-120': ['CZ110-120', 'CA110-120', 'O110-120', 'OD1110-120', 'OG110-120', 'N110-120', 'NZ110-120', 'DU110-120'],
-}
-
-DESC_GEOM = [
- 'PMI1', 'PMI2', 'PMI3', 'NPR1', 'NPR2', 'Rgyr',
- 'Asphericity', 'SpherocityIndex', 'Eccentricity', 'InertialShapeFactor'
-]
-
-# =============================================================================
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - \
- %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-
-def main(volsitedescriptor, pocketdescriptor):
- volsite_csv = descriptor_volsite(volsitedescriptor)
- combination_csv = descriptor_combination(volsite_csv)
- volsite_combination_csv = "{}volsite+combinaison.csv".format(
- volsite_csv.rsplit("volsite.csv")[0])
- merge_csv(volsite_csv, combination_csv, volsite_combination_csv)
- geometric_csv = descriptor_geometric(volsitedescriptor)
- merge_csv(volsite_combination_csv, geometric_csv, pocketdescriptor)
-
- if os.path.exists(pocketdescriptor):
- os.remove(volsite_csv)
- os.remove(combination_csv)
- os.remove(volsite_combination_csv)
- os.remove(geometric_csv)
- LOG.info('Finished!')
- else:
- LOG.error('Error: 2D/3D Pocket Descriptor file not found')
- sys.exit(1)
-
-
-def descriptor_volsite(txtfile):
- """
- Convert VolSite output file from txt format to csv format
- (descriptor headers added)
- ---------------------------------------------------------
- Argument:
- [file]: VolSite descriptors (txt format)
-
- Return:
- [file]: VolSite descriptors (csv format)
- with descriptor headers
- """
- try:
- with open(txtfile, 'rb') as infile:
- volsite_csv = "{}_volsite.csv".format(os.path.splitext(txtfile)[0])
- with open(volsite_csv, 'wb') as outfile:
- in_text = csv.reader(infile, delimiter=' ')
- out_csv = csv.writer(outfile)
- out_csv.writerow(VOLSITE_HEADER)
- for line in in_text:
- out_csv.writerow(line)
- except IOError, e:
- LOG.error('{}'.format(e))
- sys.exit(1)
- return volsite_csv
-
-
-def descriptor_combination(volsite_descriptor_csv):
- """
- Calculate and write linear combinations of VolSite descriptors to csv file
- (Kuenemann, 2016 Scientific Reports)
- ---------------------------------------------------------------------------
- Argument:
- [file]: VolSite descriptors (csv format)
-
- Return:
- [file]: linear combinations of VolSite descriptors (csv format)
- """
- with open(volsite_descriptor_csv, 'rb') as infile:
- volsite = csv.reader(infile, delimiter = ',')
- descriptors = volsite.next()
-
- # Create a dictionnary
- # key(descriptor): values(list of all pocket values)
- data = {}
- # Count the number of pockets
- numbpocket = 0
- for header in descriptors:
- data[header] = []
- for pocket in volsite:
- numbpocket += + 1
- for header, value in zip(descriptors, pocket):
- data[header].append(value)
- combination_csv = "{}combination.csv".format(
- volsite_descriptor_csv.rsplit("volsite.csv")[0])
- with open(combination_csv, 'wb') as outfile:
- combivolsite = csv.writer(outfile, delimiter = ',',
- lineterminator = '\n')
- # Descriptor headers and values have to be in variables
- # to write them in a new file column by column (sep = comma)
- descname = []
- cdata = []
- for dch in DESC_COMBINATION.keys():
- # dch = descriptor combination header (column)
- bsum = []
- for p in range(numbpocket):
- # p = pocket (row)
- buriedness_values = []
- for colname in DESC_COMBINATION[dch]:
- # Get buriedness value by descriptors
- buriedness_values.append(float(data[colname][p]))
- # Get sum of buriedness value by descriptor combinations
- bsum.append(sum(buriedness_values))
- descname.append(dch)
- cdata.append(bsum)
- combivolsite.writerow(descname)
- datatransposed = zip(*cdata)
- for row in datatransposed:
- combivolsite.writerow(row)
- return combination_csv
-
-
-def descriptor_geometric(txtfile):
- """
- Write geometric descriptor from the negative image of binding pockets
- detected by VolSite to csv file
- ---------------------------------------------------------------------------
- Argument:
- [file]: VolSite descriptors (txt format)
-
- Return:
- [file]: shape descriptors (csv format)
- """
- with open(txtfile, 'rb') as infile:
- pocketvolsite = csv.reader(infile, delimiter = ',')
- # Get the number of pockets
- numbpocket = 0
- for pocket in pocketvolsite:
- numbpocket += + 1
- geometric_csv = "{}geometric.csv".format(os.path.splitext(txtfile)[0])
- with open(geometric_csv, 'wb') as outfile:
- shape = csv.writer(outfile, delimiter = ',', lineterminator = '\n')
- shape.writerow(DESC_GEOM)
- # Calculate geometric descriptors pocket by pockets
- for cavity in range(1, numbpocket + 1):
- pocket_mol2 = "{}_CAVITY_N{}_ALL.mol2".format(
- geometric_csv.rsplit("_")[0], cavity)
- replace_mol2atom(pocket_mol2)
- shape.writerow(calculate_shape_descriptor(
- "temp_{}_CAVITY_N{}_ALL.mol2".format(
- geometric_csv.rsplit("_")[0], cavity)))
- os.remove("temp_{}_CAVITY_N{}_ALL.mol2".format(
- geometric_csv.rsplit("_")[0], cavity))
- return geometric_csv
-
-
-def replace_mol2atom(cavity):
- """
- Replace the atom name assigned by VolSite to the probes by 'C' (carbone)
-
- Warning 1
- Fixing the RDKit error: 'atom' with a degree > 1
-
- Warning 2
- RDKit needs the output file [PDB_CAVITY_Nx_ALL_temp.mol2]
- NOT the link
- ------------------------------------------------------------------
- Argument:
- [file]: negative image of a binding pocket (mol2 format)
-
- Return:
- [file]: negative image of a binding pocket with carbone as atom name
- (mol2 format, temporary file used as input by RDKit)
- """
- header = True
- parsing = False
- with open(cavity, 'rb') as infile:
- with open("temp_{}.mol2".format(cavity.rsplit('.')[0]), 'wb') as tempf:
- for line in infile:
- if line.startswith('@<TRIPOS>ATOM'):
- tempf.write(line)# + '\n')
- header = False
- parsing = True
- continue
- elif line.startswith('@<TRIPOS>BOND'):
- parsing = False
-
- if header:
- tempf.write(line)
- if parsing:
- tempf.write(line.replace(line.split()[5], 'C'))
- #return tempf
-
-
-def calculate_shape_descriptor(cavity):
- """
- Calculate geometric descriptors with RDKit
- ------------------------------------------
- Geometric descriptor details:
- http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors3D-module.html
-
- Argument:
- [file]: negative image of a binding pocket (mol2 format)
-
- Return:
- [list]: geometric descriptors
- """
- mol2file = Chem.MolFromMol2File(cavity, sanitize = False, removeHs = False)
- geom_val = []
- geom_val.append(Descriptors3D.PMI1(mol2file))
- geom_val.append(Descriptors3D.PMI2(mol2file))
- geom_val.append(Descriptors3D.PMI3(mol2file))
- geom_val.append(Descriptors3D.NPR1(mol2file))
- geom_val.append(Descriptors3D.NPR2(mol2file))
- geom_val.append(Descriptors3D.RadiusOfGyration(mol2file))
- geom_val.append(Descriptors3D.Asphericity(mol2file))
- geom_val.append(Descriptors3D.SpherocityIndex(mol2file))
- geom_val.append(Descriptors3D.Eccentricity(mol2file))
- geom_val.append(Descriptors3D.InertialShapeFactor(mol2file))
- return geom_val
-
-
-def merge_csv(csv_infile1, csv_infile2, csv_outfile):
- """
- Concatenate two csv files
- -------------------------
- Arguments:
- [file]: input (csv format)
- [file]: input (csv format)
- [file]: output filename (csv format)
- """
- csv1 = pd.read_csv(csv_infile1)
- csv2 = pd.read_csv(csv_infile2)
- csv3 = pd.concat([csv1, csv2], axis = 1)
- return csv3.to_csv(csv_outfile, sep = ',', index = False)
-
-# ==============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description =
- 'Calculate 2D/3D Pocket Descriptors from VolSite')
- parser.add_argument('volsitedescriptor', help = 'Input [.txt file]: \
- Pocket descriptors calculated by VolSite')
- parser.add_argument('pocketdescriptor', help = 'Output [.csv filename]: \
- Pocket descriptors including \
- 89 descriptors from VolSite, \
- 10 descriptors using a combination of VolSite descriptors \
- and 10 geometric descriptors')
-
- options = parser.parse_args()
- setlogger()
- main(options.volsitedescriptor, options.pocketdescriptor)
diff --git a/pyScripts/ion.pdf b/pyScripts/ion.pdf
deleted file mode 100644
index 46ecfa3582acda4ea7252068a70a9f9a1259d6f8..0000000000000000000000000000000000000000
Binary files a/pyScripts/ion.pdf and /dev/null differ
diff --git a/pyScripts/ion.txt b/pyScripts/ion.txt
deleted file mode 100644
index c2ec67982891e76539ee9654375ae4c8acb73de8..0000000000000000000000000000000000000000
--- a/pyScripts/ion.txt
+++ /dev/null
@@ -1,63 +0,0 @@
-
-3NI
-4MO
-4PU
-4TI
-6MO
-AG
-AL
-AU
-AU3
-AUC
-BA
-BR
-BS3
-CA
-CD
-CE
-CF
-CL
-CO
-CR
-CS
-CU
-CU1
-ER3
-EU
-EU3
-F
-FE
-FE2
-GA
-HG
-IOD
-IR
-IR3
-K
-LA
-LI
-LU
-MG
-MN
-MN3
-MOO
-NA
-NI
-PD
-PR
-PT
-PT4
-RB
-RU
-SB
-SE4
-SM
-SR
-TB
-TH
-THE
-TL
-W
-ZN
-ZR
-
diff --git a/pyScripts/ppiinterface_dist.py b/pyScripts/ppiinterface_dist.py
deleted file mode 100644
index e79e69ac85a5c9070b319f5dfa89d29c2570756f..0000000000000000000000000000000000000000
--- a/pyScripts/ppiinterface_dist.py
+++ /dev/null
@@ -1,335 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-Author: Alexandra Moine-Franel
-Date: February 2018
-Version: 4
-
-
-IDENTIFY PROTEIN INTERFACE / POCKET RESIDUES
-
-Determine protein residues at a specific distance either from protein partner,
-ligand (small molecule) or negative image of the pocket generated by VolSite.
-
-
-
-Usage: [Script.py] [TARGET] [PARTNER] -d (DISTANCE)
--------------------------------------------------------------------------------
-[TARGET]:
- Input (.mol2 or .pdb format)
- Protein CHAIN
-
-[PARTNER]:
- Input (.mol2 or .pdb format)
- Negative image of the pocket generated by VolSite (.mol2 format)
- OR Ligand (.pdb format)
- OR Protein (.pdb format)
-
-(DISTANCE)- optionnal
- Input (float or integer)
- Distance threshold between the target and the partner
- * Distance target-protein/ligand = 5 angstroms - by defaut
- * Distance target-cavity = 3.5 angstroms - by default
-
-------------------
-
-[POCKET_RESIDUES]:
- Output (.txt format)
- 'PDB-targetchain-partnerchain_distance.txt' (target-protein/ligand)
- OR 'PDB-targetchain-CAVITY_Nx_ALL_distance.txt' (target-cavity)
-"""
-
-# =============================================================================
-
-import csv
-import os
-import sys
-import argparse
-import logging
-#import time
-from biopandas.mol2 import PandasMol2
-from biopandas.pdb import PandasPdb
-
-# =============================================================================
-
-LOG = logging.getLogger("IDENTIFY PROTEIN INTERFACE / POCKET RESIDUES")
-
-# =============================================================================
-
-def main(target, partner, distance):
- #start = time.time()
- if target and partner:
- if os.path.splitext(target)[-1] == '.mol2' and \
- os.path.splitext(partner)[-1] == '.mol2':
- mol2target = parse_mol2(target)
- mol2partner = parse_mol2(partner)
- mol2_respocket(mol2target, mol2partner, distance)
- if os.path.exists('{}-{}_{}.txt'.format( \
- mol2target.code, mol2partner.code.rsplit('.mol2')[0], \
- distance)):
- LOG.info('Finished!')
- #end = time.time()
- #print(end - start)
- else:
- LOG.error('Warning! [Output] Not found!')
- sys.exit(1)
- elif os.path.splitext(target)[-1] == '.pdb' and \
- os.path.splitext(partner)[-1] == '.pdb':
- pdbtarget = parse_pdb(target)
- pdbpartner = parse_pdb(partner)
- if pdbpartner.df['ATOM'].empty == True:
- pdb_resinterfacePL(pdbtarget, pdbpartner, distance)
- if os.path.exists('{}-{}-{}_{}.txt'.format(pdbtarget.code, \
- pdbtarget.df['ATOM']['chain_id'][0], pdbpartner.df['HETATM']['residue_name'][0], \
- distance)):
- LOG.info('Finished!')
- #end = time.time()
- #print(end - start)
- else:
- LOG.error('Warning! [Output] Not found!')
- sys.exit(1)
- else:
- pdb_resinterfacePP(pdbtarget, pdbpartner, distance)
- if os.path.exists('{}-{}-{}_{}.txt'.format(pdbtarget.code, \
- pdbtarget.df['ATOM']['chain_id'][0], pdbpartner.df['ATOM']['chain_id'][0], \
- distance)):
- LOG.info('Finished!')
- #end = time.time()
- #print(end - start)
- else:
- LOG.error('Warning! [Output] Not found!')
- sys.exit(1)
- else:
- LOG.error('Error! [TARGET] or [PARTNER] file not in .mol2 or .pdb format')
- sys.exit(1)
- elif target and not partner:
- parser.error('Error: [PARTNER: protein, ligand or cavity] is required')
-
-
-
-
-def parse_mol2(mol2file):
- """
- Parse .mol2 file
- ---------------------------------------------------------------------------
- Argument: [file]: .mol2 format
- Return: [dataframe]
- """
- try:
- pmol = PandasMol2().read_mol2(mol2file)
- except(IOError), e:
- LOG.error('{}'.format(e))
- sys.exit(1)
- else:
- return pmol
-
-
-def parse_pdb(pdbfile):
- """
- Parse .pdb file
- ---------------------------------------------------------------------------
- Argument: [file]: .pdb format
- Return: [dataframe]
- """
- try:
- ppdb = PandasPdb().read_pdb(pdbfile)
- except(IOError), e:
- LOG.error('{}'.format(e))
- sys.exit(1)
- else:
- return ppdb
-
-
-def mol2_respocket(mol2target, mol2partner, distance):
- """
- Identify protein target residues at a specified distance from its partner
- (i.e. the cavity negative image generated by VolSite).
- ---------------------------------------------------------------------------
- Arguments:
- [file]: protein target (.mol2 format)
- [file]: negative image of the binding pocket (.mol2 format)
- [float]: distance threshold (by default, 3.5 angstroms)
- Return:
- [file]: pocket residues (.txt format)
- """
- ppires = []
- with open('{}-{}_{}.txt'.format(mol2target.code, \
- mol2partner.code.rsplit('.mol2')[0], \
- distance), 'wb') as outfile:
- for probe in xrange(len(mol2partner.df.atom_id)):
- for atom in xrange(len(mol2target.df.atom_id)):
- if mol2target.df.subst_name[atom] not in ppires:
- xp = mol2target.df['x'][atom]
- xc = mol2partner.df['x'][probe]
- distX = x_dist(xp, xc)
- if distX < float(distance):
- yp = mol2target.df['y'][atom]
- yc = mol2partner.df['y'][probe]
- distXY = xy_dist(xp, yp, xc, yc)
- if distXY < float(distance):
- zp = mol2target.df['z'][atom]
- zc = mol2partner.df['z'][probe]
- distXYZ = euclidian_dist(xp, yp, zp, xc, yc, zc)
- if distXYZ < float(distance):
- ppires.append(mol2target.df.subst_name[atom])
- for resp in ppires:
- outfile.write(resp + '\n')
-
-
-def pdb_resinterfacePP(pdbtarget, pdbpartner, distance):
- """
- Identify protein target residues at a specified distance from its partner
- (i.e. protein)
- ---------------------------------------------------------------------------
- Arguments:
- [file]: protein target (.pdb format)
- [file]: protein partner (.pdb format)
- [float]: distance threshold (by default, 5 angstroms)
- Return:
- [file]: interface residues (.txt format)
- """
- ppires = []
- with open('{}-{}-{}_{}.txt'.format(pdbtarget.code, \
- pdbtarget.df['ATOM']['chain_id'][0], pdbpartner.df['ATOM']['chain_id'][0], \
- distance), 'wb') as outfile:
- for atomt in xrange(len(pdbpartner.df['ATOM']['atom_number'])):
- for atomp in xrange(len(pdbtarget.df['ATOM']['atom_number'])):
- if ''.join(map(str, (pdbtarget.df['ATOM']['residue_name'][atomp], \
- pdbtarget.df['ATOM']['residue_number'][atomp]))) not in ppires:
- xp = pdbtarget.df['ATOM']['x_coord'][atomp]
- xc = pdbpartner.df['ATOM']['x_coord'][atomt]
- distX = x_dist(xp, xc)
- if distX < float(distance):
- yp = pdbtarget.df['ATOM']['y_coord'][atomp]
- yc = pdbpartner.df['ATOM']['y_coord'][atomt]
- distXY = xy_dist(xp, yp, xc, yc)
- if distXY < float(distance):
- zp = pdbtarget.df['ATOM']['z_coord'][atomp]
- zc = pdbpartner.df['ATOM']['z_coord'][atomt]
- distXYZ = euclidian_dist(xp, yp, zp, xc, yc, zc)
- if distXYZ < float(distance):
- ppires.append(''.join(map(str, \
- (pdbtarget.df['ATOM']['residue_name'][atomp], \
- pdbtarget.df['ATOM']['residue_number'][atomp]))))
- for resp in ppires:
- outfile.write(resp + '\n')
-
-
-def pdb_resinterfacePL(pdbtarget, pdbpartner, distance):
- """
- Identify protein target residues at a specified distance from its partner
- (i.e. ligand)
- ---------------------------------------------------------------------------
- Arguments:
- [file]: protein target (.pdb format)
- [file]: ligand (.pdb format)
- [float]: distance threshold (by default, 5 angstroms)
- Return:
- [file]: pocket residues (.txt format)
- """
- ppires = []
- with open('{}-{}-{}_{}.txt'.format(pdbtarget.code, \
- pdbtarget.df['ATOM']['chain_id'][0], pdbpartner.df['HETATM']['residue_name'][0], \
- distance), 'wb') as outfile:
- for atomt in xrange(len(pdbpartner.df['HETATM']['atom_number'])):
- for atomp in xrange(len(pdbtarget.df['ATOM']['atom_number'])):
- if ''.join(map(str, (pdbtarget.df['ATOM']['residue_name'][atomp], \
- pdbtarget.df['ATOM']['residue_number'][atomp]))) not in ppires:
- xp = pdbtarget.df['ATOM']['x_coord'][atomp]
- xc = pdbpartner.df['HETATM']['x_coord'][atomt]
- distX = x_dist(xp, xc)
- if distX < float(distance):
- yp = pdbtarget.df['ATOM']['y_coord'][atomp]
- yc = pdbpartner.df['HETATM']['y_coord'][atomt]
-
- distXY = xy_dist(xp, yp, xc, yc)
- if distXY < float(distance):
- zp = pdbtarget.df['ATOM']['z_coord'][atomp]
- zc = pdbpartner.df['HETATM']['z_coord'][atomt]
- distXYZ = euclidian_dist(xp, yp, zp, xc, yc, zc)
- if distXYZ < float(distance):
- ppires.append(''.join(map(str, \
- (pdbtarget.df['ATOM']['residue_name'][atomp], \
- pdbtarget.df['ATOM']['residue_number'][atomp]))))
- for resp in ppires:
- outfile.write(resp + '\n')
-
-
-def x_dist(x1, x2):
- """
- Calculate the distance x between two 1D points
- ----------------------------------------------------------------------
- Arguments:
- [float]: coordinate x of target atom
- coordinate x of partnet atom
- Return:
- [float]: distance
- """
- dist = ((x1-x2)**2) ** 0.5
- return dist
-
-
-def xy_dist(x1, y1, x2, y2):
- """
- Calculate the distance xy between two 2D points
- ----------------------------------------------------------------------
- Arguments:
- [float]: coordinates xy of target atom
- coordinates xy of partnet atom
- Return:
- [float]: distance
- """
- dist = ((x1-x2)**2 + (y1-y2)**2) ** 0.5
- return dist
-
-
-def euclidian_dist(x1, y1, z1, x2, y2, z2):
- """
- Calculate the euclidian distance xyz between two 3D points
- ----------------------------------------------------------------------
- Arguments:
- [float]: coordinates xyz of target atom
- coordinates xyz of partnet atom
- Return:
- [float]: distance
- """
- dist = ((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2) ** 0.5
- return dist
-
-
-
-def setlogger():
- LOG.setLevel(logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- formatter = logging.Formatter('%(asctime)s - %(name)s - %(funcName)s - \
- %(levelname)s - %(message)s')
- ch.setFormatter(formatter)
- LOG.addHandler(ch)
-
-
-def default_distance(options):
- if os.path.splitext(options.partner)[-1] == '.mol2':
- options.distance = 3.5
- elif os.path.splitext(options.partner)[-1] == '.pdb':
- options.distance = 5.0
- return options.distance
-
-# ==============================================================================
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description = 'Identify interface/pocket residues')
- parser.add_argument('target', \
- help = 'Input [.mol2 or .pdb file]: protein target')
- parser.add_argument('partner', \
- help = 'Input [.pdb file]: protein partner or ligand; OR [.mol2 file]: cavity')
- parser.add_argument('-d', dest = 'distance', type = float, \
- help = 'Input [float or integer]: distance threshold \
- {by default, target-protein/ligand = 5A; target-cavity = 3.5A}')
- options = parser.parse_args()
-
- if options.distance is None:
- default_distance(options)
-
- setlogger()
- main(options.target, options.partner, options.distance)