From e38fcd7abcc9af854fe3afb167cc519dc604f751 Mon Sep 17 00:00:00 2001
From: Fabien Mareuil <fmareuil@pasteur.fr>
Date: Thu, 12 Apr 2018 14:45:08 +0200
Subject: [PATCH] method get_molecules
Former-commit-id: be15bd63263293acf0dbbe23e7ad4965ef7b4b10
---
...nterface_residues_ppc_dimer_IN_PROGRESS.py | 31 +++++++++----------
1 file changed, 14 insertions(+), 17 deletions(-)
diff --git a/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py b/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py
index 66883850..1f5e103b 100644
--- a/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py
+++ b/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py
@@ -48,12 +48,12 @@ Return:
import os
import sys
import argparse
-import textwrap
import logging
import time
from Bio.PDB import Select, PDBIO
from Bio.PDB.PDBParser import PDBParser
+from argparse import RawTextHelpFormatter
import itertools
# =============================================================================
@@ -140,10 +140,10 @@ def main(pdb, distance):
# Save each chain in different file
- for chain in target_partner_chain:
- io = PDBIO()
- io.set_structure(model)
- io.save('{}_{}.pdb'.format(pdb_code, chain), select = ChainSelection(chain),
+ #for chain in target_partner_chain:
+ io = PDBIO()
+ io.set_structure(model)
+ io.save('{}_{}.pdb'.format(pdb_code, chain), select = ChainSelection(target_partner_chain),
preserve_atom_numbering = True)
@@ -153,11 +153,11 @@ def main(pdb, distance):
class ChainSelection(Select):
- def __init__(self, chain):
- self.chain = chain
+ def __init__(self, chains):
+ self.chains = chains
def accept_chain(self, chain):
- if chain.get_id() == self.chain:
+ if chain.get_id() in self.chains:
return 1
else:
return 0
@@ -297,21 +297,18 @@ def setlogger():
# =============================================================================
if __name__ == '__main__':
- parser = argparse.ArgumentParser(description =
- textwrap.dedent('''
+ parser = argparse.ArgumentParser(description = '''
1) Format protein/protein complex PDB structure (no ligand)
1.a) Number of models
1.b) Alternative atomic locations
1.c) Heteroatoms
2) Identify protein/protein interface residues
(for combinations of first chain of each protein)
- 3) Save each chain in separate files'''))
- parser.add_argument('pdb', help =
- textwrap.dedent(''' Input [.pdb file]: PBD 3D structure
- (with HEADER included)'''))
- parser.add_argument('-d', dest = 'distance', help =
- textwrap.dedent('''Input [float or integer]: distance threshold
- {by default, 6 Angstroms}'''))
+ 3) Save each chain in separate files''', formatter_class=RawTextHelpFormatter)
+ parser.add_argument('pdb', help = '''Input [.pdb file]: PBD 3D structure
+ (with HEADER included)''')
+ parser.add_argument('-d', dest = 'distance', help = '''Input [float or integer]: distance threshold
+ {by default, 6 Angstroms}''')
options = parser.parse_args()
if options.distance is None:
--
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