From e749773a3661d801f766209e819904210a876531 Mon Sep 17 00:00:00 2001
From: JoanaMPereira <pereira.joanam@gmail.com>
Date: Tue, 26 Mar 2024 09:34:07 +0100
Subject: [PATCH] it now saves the data on the go so that it does not analyse
what was previously analysed
---
barrOs_library.py | 295 ++++++++++++++++++++++++----------------------
1 file changed, 153 insertions(+), 142 deletions(-)
diff --git a/barrOs_library.py b/barrOs_library.py
index b92733e..0f27ce2 100644
--- a/barrOs_library.py
+++ b/barrOs_library.py
@@ -10,6 +10,7 @@ import threading
import itertools
import os
import sys
+import json
import warnings
warnings.filterwarnings("ignore")
@@ -2310,26 +2311,32 @@ def run_barros(arguments, offset = 1, step = 2, local_angle_threshold = 25, max_
outmultimeric = "multimeric_barrel_sequences_matched_pdbs_job{}.fasta".format(job_number)
outmt = open(outmultimeric, 'w')
- data = {'PDBs': [],
- 'TMsegm': [],
- 'BB_diameter': [],
- 'BB_diameter_mad': [],
- 'Shear': [],
- 'Membrane_thickness': [],
- # 'a': [],
- # 'a_mad': [],
- # 'b': [],
- # 'b_mad': [],
- # 'h': [],
- # 'CAi-CAi+1': [],
- # 'CAi-CAi+1_mad': [],
- 'CAi-CAi+1-CAi+2': [],
- 'CAi-CAi+1-CAi+2_mad': [],
- 'CAi+2-CAi-CAi+1': [],
- 'CAi+2-CAi-CAi+1_mad': [],
- 'N_residues': [],
- 'N_chains': [],
- 'Multimeric': []}
+ outdata = "barrels_matched_pdbs_data_job{}.fasta".format(job_number)
+
+ if os.path.ifile(outdata):
+ data = json.load(open(outdata, 'r'))
+
+ else:
+ data = {'PDBs': [],
+ 'TMsegm': [],
+ 'BB_diameter': [],
+ 'BB_diameter_mad': [],
+ 'Shear': [],
+ 'Membrane_thickness': [],
+ # 'a': [],
+ # 'a_mad': [],
+ # 'b': [],
+ # 'b_mad': [],
+ # 'h': [],
+ # 'CAi-CAi+1': [],
+ # 'CAi-CAi+1_mad': [],
+ 'CAi-CAi+1-CAi+2': [],
+ 'CAi-CAi+1-CAi+2_mad': [],
+ 'CAi+2-CAi-CAi+1': [],
+ 'CAi+2-CAi-CAi+1_mad': [],
+ 'N_residues': [],
+ 'N_chains': [],
+ 'Multimeric': []}
for i, pdbID in enumerate(in_queue):
deleted_it = False
@@ -2400,140 +2407,144 @@ def run_barros(arguments, offset = 1, step = 2, local_angle_threshold = 25, max_
for pdbID, chainID, pdb_file, protein_type, membrane_thickness in target_chains:
- try:
- pdb_sequence, barrel_topology, chains, num_bb_regions, pdb_file = process_barrel(pdb_file, ID = pdbID, chainID = chainID, offset = offset, step = step, local_angle_threshold = local_angle_threshold, distance_threshold = distance_threshold, multimer_only=multimer_only)
- except:
- num_bb_regions = 0
+ if '{}_{}'.format(pdbID, chainID) not in data['PDBs']:
+
+ try:
+ pdb_sequence, barrel_topology, chains, num_bb_regions, pdb_file = process_barrel(pdb_file, ID = pdbID, chainID = chainID, offset = offset, step = step, local_angle_threshold = local_angle_threshold, distance_threshold = distance_threshold, multimer_only=multimer_only)
+ except:
+ num_bb_regions = 0
- # check if it has a barrel. If so, continue
- if num_bb_regions > 0 and len(pdb_sequence) < 10000:
- # get the sequence of the barrel region only
- barrel_seq, barrel_struct = remove_long_loops_from_barrel(pdb_sequence, pdb_file, barrel_topology, max_loop_size = 10)
+ # check if it has a barrel. If so, continue
+ if num_bb_regions > 0 and len(pdb_sequence) < 10000:
+ # get the sequence of the barrel region only
+ barrel_seq, barrel_struct = remove_long_loops_from_barrel(pdb_sequence, pdb_file, barrel_topology, max_loop_size = 10)
- print('\n\t>{}TM_BARREL_{}_{}_{}'.format(num_bb_regions, protein_type, pdbID, chainID))
- print('\t',pdb_sequence)
- print('\t',barrel_topology,'\n')
+ print('\n\t>{}TM_BARREL_{}_{}_{}'.format(num_bb_regions, protein_type, pdbID, chainID))
+ print('\t',pdb_sequence)
+ print('\t',barrel_topology,'\n')
- outpt.write('>{}TM_BARREL_{}_{}_{}\n'.format(num_bb_regions, protein_type, pdbID, chainID))
- outpt.write('{}\n'.format(pdb_sequence))
- outpt.write('{}\n'.format(barrel_topology))
+ outpt.write('>{}TM_BARREL_{}_{}_{}\n'.format(num_bb_regions, protein_type, pdbID, chainID))
+ outpt.write('{}\n'.format(pdb_sequence))
+ outpt.write('{}\n'.format(barrel_topology))
- # if it is a membrane protein, check whether the barrel is inserted into the membrane. Otherwise consider it does not
- if protein_type == 'membrane':
- barrel_crosses_membrane, barrel_struct = find_if_barrel_crosses_membrane(pdb_sequence, pdb_file, barrel_topology, membrane_thickness, max_loop_size = max_loop_size)
- else:
- barrel_crosses_membrane = False
- print(" ... ... Barrel in {} crosses membrane: {}".format(pdbID, barrel_crosses_membrane))
-
- if protein_type != 'membrane' or (protein_type == 'membrane' and barrel_crosses_membrane):
- # if the barrel does not cross the membrane, move and rotate it so that it is in a reference position (centered in (0,0,0) with the axis of the pore in z)
- #if not barrel_crosses_membrane:
- print(" ... ... Trying to move the barrel to the reference position (centered in (0,0,0) with the axis of the pore in z)")
- pdb_file, curr_angle = move_barrel_to_reference_position(pdb_file, barrel_topology, center = [0,0,0])
-
- # calculate the diameter of the barrel ONLY (no loops at all)
- print(" ... ... Computing barrel diameter (excluding all loops)")
- barrel_seq, barrel_struct = remove_long_loops_from_barrel(pdb_sequence, pdb_file, barrel_topology, max_loop_size = 0)
- diameter, mad_diameter = get_barrel_diameter(barrel_struct, chainID, min_residue_numb = int(num_bb_regions/5.0), step_z = 1, membrane_thickness = membrane_thickness)
-
- if diameter is not None:
- print(" ... ... ... Barrel diameter: {} (+/- {}) Ang".format(round(diameter,2), round(mad_diameter,2)))
-
- # calculate the shear number
- print(" ... ... Computing the shear number")
- try:
- shear = shear_number(barrel_struct, show_path = False)
- if shear is not None:
- print(' ... ... ... Shear: {}'.format(shear))
- else:
- print(' ... ... ... Error: Not possible to compute the shear number')
- except:
- shear = None
- print(' ... ... ... Error: Not possible to compute the shear number')
-
- # calculate a (the distance between two adjacent CA assuming they are in the same line defined by the strand)
- # print(' ... ... Computing a and b')
- # a, mad_a = calculate_a(barrel_struct)
- # print(' ... ... ... a: {} (+/- {}) Ang'.format(round(a, 2), round(mad_a, 2)))
-
- # b, mad_b = calculate_b(barrel_struct)
- # print(' ... ... ... b: {} (+/- {}) Ang'.format(round(b, 2), round(mad_b, 2)))
-
- # calculate the median distance between two adjacent c-alphas
- # print(' ... ... Computing local CA geometric features (distance to next CA and and the bond angles to CAi-1 and CAi+2)')
- # c, mad_c = calculate_c(barrel_struct)
- # print(' ... ... ... CAi-CAi+1 distance: {} (+/- {}) Ang'.format(round(c, 2), round(mad_c, 2)))
- theta1, theta1_mad, kappa, kappa_mad = calculate_CA_pseudoangles(barrel_struct)
- print(' ... ... ... CAi-CAi+1-CAi+2 angle: {} (+/- {}) degrees'.format(round(theta1, 2), round(theta1_mad, 2)))
- print(' ... ... ... CAi+2-CAi-CAi+1 angle: {} (+/- {}) degrees'.format(round(kappa, 2), round(kappa_mad, 2)))
- # h = sqrt(c**2-a**2)
- # print(' ... ... ... h: {} Ang'.format(round(h, 2)))
-
- # save all results into the dictionary
- data['PDBs'].append('{}_{}'.format(pdbID, chainID))
- data['TMsegm'].append(num_bb_regions)
- data['BB_diameter'].append(diameter)
- data['BB_diameter_mad'].append(mad_diameter)
- data['Shear'].append(shear)
- data['Membrane_thickness'].append(membrane_thickness)
- # data['a'].append(a)
- # data['a_mad'].append(mad_a)
- # data['b'].append(b)
- # data['b_mad'].append(mad_b)
- # data['CAi-CAi+1'].append(c)
- # data['CAi-CAi+1_mad'].append(mad_c)
- data['CAi-CAi+1-CAi+2'].append(theta1)
- data['CAi-CAi+1-CAi+2_mad'].append(theta1_mad)
- data['CAi+2-CAi-CAi+1'].append(kappa)
- data['CAi+2-CAi-CAi+1_mad'].append(kappa_mad)
- # data['h'].append(h)
- data['N_residues'].append(len(pdb_sequence))
-
- # extract the sequence of the barrel domain only
- print(" ... Getting final barrel structure without N- and C-termini")
- print(' ... ... Masking out internal loops from the topology string')
- masked_topology = mask_loops(barrel_topology, chains)
- barrel_seq, barrel_struct = remove_long_loops_from_barrel(pdb_sequence, pdb_file, masked_topology, max_loop_size = 10, chains=chains)
- print(" ... ... Saved as: {}".format(barrel_struct))
-
- # check if the barrel is multimeric and save the sequences accordingly
- chains_in_barrel = get_chains_in_pdb(barrel_struct, source_pdb=False)[0]
- n_chains = len(chains_in_barrel)
- data['N_chains'].append(n_chains)
- data['Multimeric'].append(n_chains > 1)
-
- if n_chains > 1:
- chains_seqs = get_chains_sequence(pdb_sequence,chains)
- for chain in chains_in_barrel:
- outmt.write('>{}TM_BARREL_{}_{}_{}\n'.format(num_bb_regions, protein_type, pdbID, chain))
- outmt.write('{}\n'.format(chains_seqs[chain]))
-
+ # if it is a membrane protein, check whether the barrel is inserted into the membrane. Otherwise consider it does not
+ if protein_type == 'membrane':
+ barrel_crosses_membrane, barrel_struct = find_if_barrel_crosses_membrane(pdb_sequence, pdb_file, barrel_topology, membrane_thickness, max_loop_size = max_loop_size)
else:
- outbb.write('>{}TM_BARREL_{}_{}_{}\n'.format(num_bb_regions, protein_type, pdbID, chainID))
- outbb.write('{}\n'.format(barrel_seq))
- else:
- print('... ... There is a barrel in {}_{} but it does not cross the membrane\n'.format(pdbID, chainID))
- if delete:
- os.system("rm {}*".format(pdb_file[:-4]))
+ barrel_crosses_membrane = False
+ print(" ... ... Barrel in {} crosses membrane: {}".format(pdbID, barrel_crosses_membrane))
+
+ if protein_type != 'membrane' or (protein_type == 'membrane' and barrel_crosses_membrane):
+ # if the barrel does not cross the membrane, move and rotate it so that it is in a reference position (centered in (0,0,0) with the axis of the pore in z)
+ #if not barrel_crosses_membrane:
+ print(" ... ... Trying to move the barrel to the reference position (centered in (0,0,0) with the axis of the pore in z)")
+ pdb_file, curr_angle = move_barrel_to_reference_position(pdb_file, barrel_topology, center = [0,0,0])
+
+ # calculate the diameter of the barrel ONLY (no loops at all)
+ print(" ... ... Computing barrel diameter (excluding all loops)")
+ barrel_seq, barrel_struct = remove_long_loops_from_barrel(pdb_sequence, pdb_file, barrel_topology, max_loop_size = 0)
+ diameter, mad_diameter = get_barrel_diameter(barrel_struct, chainID, min_residue_numb = int(num_bb_regions/5.0), step_z = 1, membrane_thickness = membrane_thickness)
+
+ if diameter is not None:
+ print(" ... ... ... Barrel diameter: {} (+/- {}) Ang".format(round(diameter,2), round(mad_diameter,2)))
+
+ # calculate the shear number
+ print(" ... ... Computing the shear number")
+ try:
+ shear = shear_number(barrel_struct, show_path = False)
+ if shear is not None:
+ print(' ... ... ... Shear: {}'.format(shear))
+ else:
+ print(' ... ... ... Error: Not possible to compute the shear number')
+ except:
+ shear = None
+ print(' ... ... ... Error: Not possible to compute the shear number')
- if extract_hairpins and os.path.isfile(barrel_struct):
- save_hairpins(pdb_sequence, pdb_file, barrel_topology, chains=chains, outfolder='hairpins')
+ # calculate a (the distance between two adjacent CA assuming they are in the same line defined by the strand)
+ # print(' ... ... Computing a and b')
+ # a, mad_a = calculate_a(barrel_struct)
+ # print(' ... ... ... a: {} (+/- {}) Ang'.format(round(a, 2), round(mad_a, 2)))
+
+ # b, mad_b = calculate_b(barrel_struct)
+ # print(' ... ... ... b: {} (+/- {}) Ang'.format(round(b, 2), round(mad_b, 2)))
+
+ # calculate the median distance between two adjacent c-alphas
+ # print(' ... ... Computing local CA geometric features (distance to next CA and and the bond angles to CAi-1 and CAi+2)')
+ # c, mad_c = calculate_c(barrel_struct)
+ # print(' ... ... ... CAi-CAi+1 distance: {} (+/- {}) Ang'.format(round(c, 2), round(mad_c, 2)))
+ theta1, theta1_mad, kappa, kappa_mad = calculate_CA_pseudoangles(barrel_struct)
+ print(' ... ... ... CAi-CAi+1-CAi+2 angle: {} (+/- {}) degrees'.format(round(theta1, 2), round(theta1_mad, 2)))
+ print(' ... ... ... CAi+2-CAi-CAi+1 angle: {} (+/- {}) degrees'.format(round(kappa, 2), round(kappa_mad, 2)))
+ # h = sqrt(c**2-a**2)
+ # print(' ... ... ... h: {} Ang'.format(round(h, 2)))
+
+ # save all results into the dictionary
+ data['PDBs'].append('{}_{}'.format(pdbID, chainID))
+ data['TMsegm'].append(num_bb_regions)
+ data['BB_diameter'].append(diameter)
+ data['BB_diameter_mad'].append(mad_diameter)
+ data['Shear'].append(shear)
+ data['Membrane_thickness'].append(membrane_thickness)
+ # data['a'].append(a)
+ # data['a_mad'].append(mad_a)
+ # data['b'].append(b)
+ # data['b_mad'].append(mad_b)
+ # data['CAi-CAi+1'].append(c)
+ # data['CAi-CAi+1_mad'].append(mad_c)
+ data['CAi-CAi+1-CAi+2'].append(theta1)
+ data['CAi-CAi+1-CAi+2_mad'].append(theta1_mad)
+ data['CAi+2-CAi-CAi+1'].append(kappa)
+ data['CAi+2-CAi-CAi+1_mad'].append(kappa_mad)
+ # data['h'].append(h)
+ data['N_residues'].append(len(pdb_sequence))
+
+ # extract the sequence of the barrel domain only
+ print(" ... Getting final barrel structure without N- and C-termini")
+ print(' ... ... Masking out internal loops from the topology string')
+ masked_topology = mask_loops(barrel_topology, chains)
+ barrel_seq, barrel_struct = remove_long_loops_from_barrel(pdb_sequence, pdb_file, masked_topology, max_loop_size = 10, chains=chains)
+ print(" ... ... Saved as: {}".format(barrel_struct))
+
+ # check if the barrel is multimeric and save the sequences accordingly
+ chains_in_barrel = get_chains_in_pdb(barrel_struct, source_pdb=False)[0]
+ n_chains = len(chains_in_barrel)
+ data['N_chains'].append(n_chains)
+ data['Multimeric'].append(n_chains > 1)
+
+ if n_chains > 1:
+ chains_seqs = get_chains_sequence(pdb_sequence,chains)
+ for chain in chains_in_barrel:
+ outmt.write('>{}TM_BARREL_{}_{}_{}\n'.format(num_bb_regions, protein_type, pdbID, chain))
+ outmt.write('{}\n'.format(chains_seqs[chain]))
+
+ else:
+ outbb.write('>{}TM_BARREL_{}_{}_{}\n'.format(num_bb_regions, protein_type, pdbID, chainID))
+ outbb.write('{}\n'.format(barrel_seq))
+ else:
+ print('... ... There is a barrel in {}_{} but it does not cross the membrane\n'.format(pdbID, chainID))
+ if delete:
+ os.system("rm {}*".format(pdb_file[:-4]))
+ if extract_hairpins and os.path.isfile(barrel_struct):
+ save_hairpins(pdb_sequence, pdb_file, barrel_topology, chains=chains, outfolder='hairpins')
+ # save intermediate collected data
+ json.dump(data, outdata, indent=4)
- else:
- print('... ... Not able to detect barrel topology for {}_{}\n'.format(pdbID, chainID))
- if delete:
- os.system("rm {}*".format(pdb_file[:-4]))
else:
- seqstruct, pdb_sequence, chains = get_secondary_structure(pdb_file)
-
- outbb.write('>NaN_TM_BARREL_{}_{}_{}\n'.format(protein_type, pdbID, chainID))
- outbb.write('{}\n'.format(pdb_sequence))
+ print('... ... Not able to detect barrel topology for {}_{}\n'.format(pdbID, chainID))
+ if delete:
+ os.system("rm {}*".format(pdb_file[:-4]))
+
+ else:
+ seqstruct, pdb_sequence, chains = get_secondary_structure(pdb_file)
+
+ outbb.write('>NaN_TM_BARREL_{}_{}_{}\n'.format(protein_type, pdbID, chainID))
+ outbb.write('{}\n'.format(pdb_sequence))
- if extract_hairpins:
- save_hairpins(pdb_sequence, pdb_file, seqstruct, marker='E', chains=chains, outfolder='hairpins')
+ if extract_hairpins:
+ save_hairpins(pdb_sequence, pdb_file, seqstruct, marker='E', chains=chains, outfolder='hairpins')
else:
--
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