From 1e790032d20d60f9bcb0492853c825dc6c22c77a Mon Sep 17 00:00:00 2001
From: Fabien Mareuil <fmareuil@pasteur.fr>
Date: Thu, 12 Apr 2018 11:03:39 +0200
Subject: [PATCH] reformat
Former-commit-id: dbc51f36f32ea66e9d4c7f9ceda01e300ca1db4a
---
...nterface_residues_ppc_dimer_IN_PROGRESS.py | 445 +++++++++---------
1 file changed, 221 insertions(+), 224 deletions(-)
diff --git a/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py b/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py
index a2f7eb30..66883850 100644
--- a/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py
+++ b/pyScripts/get_interface_residues_ppc_dimer_IN_PROGRESS.py
@@ -10,37 +10,37 @@ Version: 2
1) IDENTIFY PROTEIN/PROTEIN INTERFACE RESIDUES
2) SAVE EACH PROTEIN FIRST CHAIN IN SEPARATE FILE (after cleaning)
- - Number of models
- - Alternative atomic locations
- - Heteroatoms
+ - Number of models
+ - Alternative atomic locations
+ - Heteroatoms
-Usage: [Script.py] [PROTEIN/PROTEIN COMPLEX] -d (DISTANCE)
+Usage: [Script.py] [PROTEIN/PROTEIN COMPLEX] -d (DISTANCE)
-------------------------------------------------------------------------------
Arguments:
------------
[PROTEIN/PROTEIN COMPLEX]:
- Input (.pdb format)
- Protein/protein complex
+ Input (.pdb format)
+ Protein/protein complex
(DISTANCE)- optionnal
- Input (float or integer)
- Distance threshold between the target and the partner
- (6 angstroms - by defaut)
+ Input (float or integer)
+ Distance threshold between the target and the partner
+ (6 angstroms - by defaut)
Return:
------------
[PROTEIN/PROTEIN INTERFACE RESIDUES]:
- Output (.txt format) "PDB_Chain1-Chain2_distance.txt"
- (chain ID, residue name and residue ID included)
+ Output (.txt format) "PDB_Chain1-Chain2_distance.txt"
+ (chain ID, residue name and residue ID included)
[PROTEIN CHAIN]:
- Output (.pdb format) "PDB_Chain1.pdb"
- (heteroatom not included)
+ Output (.pdb format) "PDB_Chain1.pdb"
+ (heteroatom not included)
"""
# =============================================================================
@@ -67,258 +67,255 @@ NODIMER_FILENAME = 'pdb_not_dimer'
# =============================================================================
def main(pdb, distance):
- start = time.time()
-
- pdb_code = file.strip().split('.pdb')[:-1]
- structure = PDBParser().get_structure(pdb_code, file)
- model = structure[0]
-
- # Check if multiple models available
- if len(list(structure.get_models())) != 0:
- try:
- if not os.path.exists('{}.txt'.format(MODEL_FILENAME)):
- with open('{}.txt'.format(MODEL_FILENAME), 'w') as outfile:
- outfile.write(pdb_code)
- else:
- with open('{}.txt'.format(MODEL_FILENAME), 'a') as outfile:
- outfile.write(str(pdb_code) + '\n')
- except IOError, e:
- LOG.error('{}'.format(e))
- sys.exit(1)
-
- # Check if 3D structure contains alternative atomic locations
- if get_altloc(model) != 0:
- try:
- if not os.path.exists('{}.txt'.format(ALTLOC_FILENAME)):
- with open('{}.txt'.format(ALTLOC_FILENAME), 'w') as outfile:
- outfile.write(str(pdb_code) + '\n')
- else:
- with open('{}.txt'.format(ALTLOC_FILENAME), 'a') as outfile:
- outfile.write(str(pdb_code) + '\n')
- except IOError, e:
- LOG.error('{}'.format(e))
- sys.exit(1)
- else:
-
- # Get the first copy of each chain
- target_partner_chain = select_first_chain(get_protein_assembly(structure))
- print(target_partner_chain)
-
- # Check if 3D structure contains more than two molecule IDs
- if len(target_partner_chain) > 2:
- try:
- if not os.path.exists('{}.txt'.format(NODIMER_FILENAME_FILENAME)):
- with open('{}.txt'.format(NODIMER_FILENAME_FILENAME), 'w') as outfile:
- outfile.write(pdb_code)
- else:
- with open('{}.txt'.format(NODIMER_FILENAME_FILENAME), 'a') as outfile:
- outfile.write(str(pdb_code) + '\n')
- except IOError, e:
- LOG.error('{}'.format(e))
- sys.exit(1)
-
-
- # Remove heteroatom (protein/protein complex, no ligand)
- for chain in target_partner_chain:
- residue_to_remove = remove_hetatm(model, chain)
- for residue in residue_to_remove:
- model[chain].detach_child(residue[1])
-
-
- # Get all chain-chain combinations
- subset = permutation(target_partner_chain)
-
-
- # Calculate chain-chain distance (interaction patch)
- for chain_pair in subset:
- target = chain_pair[0]
- partner = chain_pair[1]
-
- if len(model[target].get_list()) > 3 and \
- len(model[partner].get_list()) > 3:
-
- get_interface_residues(target, partner, model, 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), \
- preserve_atom_numbering = True)
-
-
-
- end = time.time()
- print('TIME: {}'.format(end - start))
+ start = time.time()
+
+ pdb_code = pdb.strip().split('.pdb')[:-1]
+ structure = PDBParser().get_structure(pdb_code, pdb)
+ model = structure[0]
+
+ # Check if multiple models available
+ if len(list(structure.get_models())) != 0:
+ try:
+ if not os.path.exists('{}.txt'.format(MODEL_FILENAME)):
+ with open('{}.txt'.format(MODEL_FILENAME), 'w') as outfile:
+ outfile.write(pdb_code)
+ else:
+ with open('{}.txt'.format(MODEL_FILENAME), 'a') as outfile:
+ outfile.write(str(pdb_code) + '\n')
+ except IOError as e:
+ LOG.error('{}'.format(e))
+ sys.exit(1)
+
+ # Check if 3D structure contains alternative atomic locations
+ if get_altloc(model) != 0:
+ try:
+ if not os.path.exists('{}.txt'.format(ALTLOC_FILENAME)):
+ with open('{}.txt'.format(ALTLOC_FILENAME), 'w') as outfile:
+ outfile.write(str(pdb_code) + '\n')
+ else:
+ with open('{}.txt'.format(ALTLOC_FILENAME), 'a') as outfile:
+ outfile.write(str(pdb_code) + '\n')
+ except IOError as e:
+ LOG.error('{}'.format(e))
+ sys.exit(1)
+ else:
+
+ # Get the first copy of each chain
+ target_partner_chain = select_first_chain(get_protein_assembly(structure))
+ print(target_partner_chain)
+
+ # Check if 3D structure contains more than two molecule IDs
+ if len(target_partner_chain) > 2:
+ try:
+ if not os.path.exists('{}.txt'.format(NODIMER_FILENAME)):
+ with open('{}.txt'.format(NODIMER_FILENAME), 'w') as outfile:
+ outfile.write(pdb_code)
+ else:
+ with open('{}.txt'.format(NODIMER_FILENAME), 'a') as outfile:
+ outfile.write(str(pdb_code) + '\n')
+ except IOError as e:
+ LOG.error('{}'.format(e))
+ sys.exit(1)
+
+
+ # Remove heteroatom (protein/protein complex, no ligand)
+ for chain in target_partner_chain:
+ residue_to_remove = remove_hetatm(model, chain)
+ for residue in residue_to_remove:
+ model[chain].detach_child(residue[1])
+
+
+ # Get all chain-chain combinations
+ subset = permutation(target_partner_chain)
+
+
+ # Calculate chain-chain distance (interaction patch)
+ for chain_pair in subset:
+ target = chain_pair[0]
+ partner = chain_pair[1]
+
+ if len(model[target].get_list()) > 3 and len(model[partner].get_list()) > 3:
+
+ get_interface_residues(target, partner, model, 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),
+ preserve_atom_numbering = True)
+
+
+
+ end = time.time()
+ print('TIME: {}'.format(end - start))
class ChainSelection(Select):
- def __init__(self, chain):
- self.chain = chain
+ def __init__(self, chain):
+ self.chain = chain
- def accept_chain(self, chain):
- if chain.get_id() == self.chain:
- return 1
- else:
- return 0
+ def accept_chain(self, chain):
+ if chain.get_id() == self.chain:
+ return 1
+ else:
+ return 0
def get_altloc(model):
- altloc = 0
- for chain in model.child_list:
- for residue in chain.get_list():
- if residue.is_disordered():
- altloc = altloc + 1
- break
- return altloc
+ altloc = 0
+ for chain in model.child_list:
+ for residue in chain.get_list():
+ if residue.is_disordered():
+ altloc = altloc + 1
+ break
+ return altloc
def get_protein_assembly(structure):
- assembly = {}
- for molecule in structure.header['compound'].keys():
- assembly[molecule] = []
- for chain in structure.header['compound'][molecule]['chain'].split(','):
- assembly[molecule].append(chain.strip().upper())
- return assembly
- # {'1': ['A', 'C', 'E'], '2': ['B', 'D']}
+ assembly = {}
+ for molecule in structure.header['compound'].keys():
+ assembly[molecule] = []
+ for chain in structure.header['compound'][molecule]['chain'].split(','):
+ assembly[molecule].append(chain.strip().upper())
+ return assembly
+ # {'1': ['A', 'C', 'E'], '2': ['B', 'D']}
def select_first_chain(assembly):
- chain_id = []
- for molecule in assembly.keys():
- chain_id.append(assembly[molecule][0])
- return chain_id
- # ['A', 'B']
+ chain_id = []
+ for molecule in assembly.keys():
+ chain_id.append(assembly[molecule][0])
+ return chain_id
+ # ['A', 'B']
def permutation(list_id):
- subset = []
- for permutation in itertools.permutations(list_id, 2):
- subset.append(permutation)
- print subset
- return subset
- # [(['A'], ['B']), (['B'], ['A'])]
+ subset = []
+ for permutation in itertools.permutations(list_id, 2):
+ subset.append(permutation)
+ print(subset)
+ return subset
+ # [(['A'], ['B']), (['B'], ['A'])]
def remove_hetatm(model, chain):
- residue_to_remove = []
- for residue in model[chain].get_residues():
- if residue.id[0] != ' ':
- residue_to_remove.append((model[chain].id, residue.id))
- return residue_to_remove
+ residue_to_remove = []
+ for residue in model[chain].get_residues():
+ if residue.id[0] != ' ':
+ residue_to_remove.append((model[chain].id, residue.id))
+ return residue_to_remove
def get_interface_residues(target, partner, model, distance):
- ires = []
- with open('{}_{}{}_{}.txt'.format(model.parent.id, \
- target, partner, distance), 'wb') as outfile:
+ ires = []
+ with open('{}_{}{}_{}.txt'.format(model.parent.id, target, partner, distance), 'wb') as outfile:
- for rest in model[target].get_residues():
- if ''.join(map(str,(rest.get_parent().get_id(), '.',
- rest.get_resname(), rest.get_id()[1]))):
- for atomt in rest.get_atoms():
-
- for atomp in model[partner].get_atoms():
- xt = atomt.get_coord()[0]
- xp = atomp.get_coord()[0]
- dist_x = calculate_euclidist_x(xt, xp)
+ for rest in model[target].get_residues():
+ if ''.join(map(str,(rest.get_parent().get_id(), '.',
+ rest.get_resname(), rest.get_id()[1]))):
+ for atomt in rest.get_atoms():
+
+ for atomp in model[partner].get_atoms():
+ xt = atomt.get_coord()[0]
+ xp = atomp.get_coord()[0]
+ dist_x = calculate_euclidist_x(xt, xp)
- if dist_x < float(distance):
- yt = atomt.get_coord()[1]
- yp = atomp.get_coord()[1]
- dist_xy = calculate_euclidist_xy(xt, yt, xp, yp)
+ if dist_x < float(distance):
+ yt = atomt.get_coord()[1]
+ yp = atomp.get_coord()[1]
+ dist_xy = calculate_euclidist_xy(xt, yt, xp, yp)
- if dist_xy < float(distance):
- zt = atomt.get_coord()[2]
- zp = atomp.get_coord()[2]
- dist_xyz = calculate_euclidist_xyz(xt, yt, zt, xp, yp, zp)
+ if dist_xy < float(distance):
+ zt = atomt.get_coord()[2]
+ zp = atomp.get_coord()[2]
+ dist_xyz = calculate_euclidist_xyz(xt, yt, zt, xp, yp, zp)
- if dist_xyz < float(distance):
- ires.append(''.join(map(str, \
- (rest.get_parent().get_id(), '.', \
- rest.get_resname(), rest.get_id()[1])))
+ if dist_xyz < float(distance):
+ ires.append(''.join(map(str,
+ (rest.get_parent().get_id(), '.',
+ rest.get_resname(), rest.get_id()[1]))))
- for element in ires:
- outfile.write(element + '\n')
+ for element in ires:
+ outfile.write(element + '\n')
def calculate_euclidist_x(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
+ """
+ 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 calculate_euclidist_xy(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
-
-
+ """
+ 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 calculate_euclidist_xyz(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
+ """
+ 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)
+ 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 =
- textwrap.dedent('''
- 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}''')
- options = parser.parse_args()
-
- if options.distance is None:
- options.distance = 6.0
-
- setlogger()
- main(options.file, options.distance)
+ parser = argparse.ArgumentParser(description =
+ textwrap.dedent('''
+ 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}'''))
+ options = parser.parse_args()
+
+ if options.distance is None:
+ options.distance = 6.0
+
+ setlogger()
+ main(options.file, options.distance)
--
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