Writing PB in file¶
Table of Contents
The API allows to write all the files the command line tools can. This
includes the outputs of PBassign. The functions to handle several file
formats are available in the pbxplore.io module.
In [1]:
from pprint import pprint
import urllib.request
import os
# print date & versions
import datetime
print("Date & time:",datetime.datetime.now())
import sys
print("Python version:", sys.version)
Date & time: 2017-10-17 22:24:53.854345
Python version: 3.5.2 (default, Nov 17 2016, 17:05:23)
[GCC 5.4.0 20160609]
In [2]:
import pbxplore as pbx
print("PBxplore version:", pbx.__version__)
PBxplore version: 1.3.8
Fasta files¶
The most common way to save PB sequences is to write them in a fasta file.
PBxplore allows two ways to write fasta files. The sequences can be
written either all at once or one at a time. To write a batch of
sequences at once, we need a list of sequences and a list of the
corresponding sequence names. The writing function here is
pbxplore.io.write_fasta().
In [3]:
names = []
pb_sequences = []
pdb_name, _ = urllib.request.urlretrieve('https://files.rcsb.org/view/2LFU.pdb', '2LFU.pdb')
for chain_name, chain in pbx.chains_from_files([pdb_name]):
dihedrals = chain.get_phi_psi_angles()
pb_seq = pbx.assign(dihedrals)
names.append(chain_name)
pb_sequences.append(pb_seq)
pprint(names)
pprint(pb_sequences)
with open('output.fasta', 'w') as outfile:
pbx.io.write_fasta(outfile, pb_sequences, names)
['2LFU.pdb | model 1 | chain A',
'2LFU.pdb | model 2 | chain A',
'2LFU.pdb | model 3 | chain A',
'2LFU.pdb | model 4 | chain A',
'2LFU.pdb | model 5 | chain A',
'2LFU.pdb | model 6 | chain A',
'2LFU.pdb | model 7 | chain A',
'2LFU.pdb | model 8 | chain A',
'2LFU.pdb | model 9 | chain A',
'2LFU.pdb | model 10 | chain A']
['ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ',
'ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ',
'ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ',
'ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ',
'ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadddddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddfklmaccddddddfbgghiafehiadddddddfklpacfZZ',
'ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadddddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddfklmaccddddehiaehbgcdehiadddddddfehjlpcZZ',
'ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapadddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddfklpaccdddddfklmaacdfehpadddddehjblckknZZ',
'ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblbacddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddefklpaccdddddfklmbfbehehiaddddddffkgoiehZZ',
'ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdcdddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddfklmpccddddehiacbcbdfehpadddddehjklmklmZZ',
'ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapaccdddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddfklpaccddddddfbcfbacfehpadddddddekpghiaZZ']
Read 10 chain(s) in 2LFU.pdb
In [4]:
!cat output.fasta
!rm output.fasta
>2LFU.pdb | model 1 | chain A
ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcd
dddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddf
klmaccddddddfbgniaghiapaddddddfklnoambZZ
>2LFU.pdb | model 2 | chain A
ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghia
dddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddf
klpaccdddddfklmlmgcdehiaddddddfklmmgopZZ
>2LFU.pdb | model 3 | chain A
ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpa
cddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddef
klpaccddddddfkgojbdfehpaddddddfkbccfbgZZ
>2LFU.pdb | model 4 | chain A
ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddd
dddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddf
klmpccdddddddehiabghehiaddddddfklpccfkZZ
>2LFU.pdb | model 5 | chain A
ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadd
dddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddf
klmaccddddddfbgghiafehiadddddddfklpacfZZ
>2LFU.pdb | model 6 | chain A
ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadd
dddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddf
klmaccddddehiaehbgcdehiadddddddfehjlpcZZ
>2LFU.pdb | model 7 | chain A
ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapa
dddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddf
klpaccdddddfklmaacdfehpadddddehjblckknZZ
>2LFU.pdb | model 8 | chain A
ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblba
cddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddef
klpaccdddddfklmbfbehehiaddddddffkgoiehZZ
>2LFU.pdb | model 9 | chain A
ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdc
dddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddf
klmpccddddehiacbcbdfehpadddddehjklmklmZZ
>2LFU.pdb | model 10 | chain A
ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapacc
dddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddf
klpaccddddddfbcfbacfehpadddddddekpghiaZZ
Sequences can be written once at a time using the
pbxplore.io.write_fasta_entry() function.
In [5]:
pdb_name, _ = urllib.request.urlretrieve('https://files.rcsb.org/view/2LFU.pdb', '2LFU.pdb')
with open('output.fasta', 'w') as outfile:
for chain_name, chain in pbx.chains_from_files([pdb_name]):
dihedrals = chain.get_phi_psi_angles()
pb_seq = pbx.assign(dihedrals)
pbx.io.write_fasta_entry(outfile, pb_seq, chain_name)
Read 10 chain(s) in 2LFU.pdb
In [6]:
!cat output.fasta
!rm output.fasta
>2LFU.pdb | model 1 | chain A
ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcd
dddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddf
klmaccddddddfbgniaghiapaddddddfklnoambZZ
>2LFU.pdb | model 2 | chain A
ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghia
dddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddf
klpaccdddddfklmlmgcdehiaddddddfklmmgopZZ
>2LFU.pdb | model 3 | chain A
ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpa
cddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddef
klpaccddddddfkgojbdfehpaddddddfkbccfbgZZ
>2LFU.pdb | model 4 | chain A
ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddd
dddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddf
klmpccdddddddehiabghehiaddddddfklpccfkZZ
>2LFU.pdb | model 5 | chain A
ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadd
dddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddf
klmaccddddddfbgghiafehiadddddddfklpacfZZ
>2LFU.pdb | model 6 | chain A
ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadd
dddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddf
klmaccddddehiaehbgcdehiadddddddfehjlpcZZ
>2LFU.pdb | model 7 | chain A
ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapa
dddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddf
klpaccdddddfklmaacdfehpadddddehjblckknZZ
>2LFU.pdb | model 8 | chain A
ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblba
cddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddef
klpaccdddddfklmbfbehehiaddddddffkgoiehZZ
>2LFU.pdb | model 9 | chain A
ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdc
dddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddf
klmpccddddehiacbcbdfehpadddddehjklmklmZZ
>2LFU.pdb | model 10 | chain A
ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapacc
dddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddf
klpaccddddddfbcfbacfehpadddddddekpghiaZZ
By default, the lines in fasta files are wrapped at 60 caracters as
defined in pbxplore.io.fasta.FASTA_WIDTH. Both
pbxplore.io.write_fasta() and pbxplore.io.write_fasta_entry()
have a width optionnal argument that allows to control the wrapping.
In [7]:
print(pb_sequences[0])
ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ
In [8]:
with open('output.fasta', 'w') as outfile:
for width in (60, 70, 80):
pbx.io.write_fasta_entry(outfile, pb_sequences[0],
'width={} blocks'.format(width),
width=width)
In [9]:
!cat output.fasta
!rm output.fasta
>width=60 blocks
ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcd
dddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddf
klmaccddddddfbgniaghiapaddddddfklnoambZZ
>width=70 blocks
ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddf
klopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniagh
iapaddddddfklnoambZZ
>width=80 blocks
ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopaddddd
fhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ
Dihedral angles¶
One needs the phi and psi dihedral angles to assign protein block sequences. Having these angles, it is sometime convenient to store them in a file. This can be done easily.
In [10]:
pdb_name, _ = urllib.request.urlretrieve('https://files.rcsb.org/view/2LFU.pdb', '2LFU.pdb')
with open('output.phipsi', 'w') as outfile:
for chain_name, chain in pbx.chains_from_files([pdb_name]):
dihedral = chain.get_phi_psi_angles()
for res in sorted(dihedral):
phi = "{:8.2f}".format(dihedral[res]["phi"]) if dihedral[res]["phi"] else " None"
psi = "{:8.2f}".format(dihedral[res]["psi"]) if dihedral[res]["psi"] else " None"
print("{} {:6d} {} {} ".format(chain_name, res, phi, psi), file=outfile)
Read 10 chain(s) in 2LFU.pdb
Note it’s better to write the dihedral for each PDB/frame due to the high memory cost to store all of them in a list.
The output is formated with one line per residue. The first columns repeat the name given for the chain, then is the residue id followed by the phi and the psi angle. If an angle is not defined, ‘None’ is written instead.
In [11]:
!head output.phipsi
!tail output.phipsi
!rm output.phipsi
2LFU.pdb | model 1 | chain A 276 None 44.77
2LFU.pdb | model 1 | chain A 277 -81.67 15.27
2LFU.pdb | model 1 | chain A 278 -79.03 -21.52
2LFU.pdb | model 1 | chain A 279 -144.43 64.08
2LFU.pdb | model 1 | chain A 280 -84.23 144.90
2LFU.pdb | model 1 | chain A 281 70.83 -64.01
2LFU.pdb | model 1 | chain A 282 -107.77 93.35
2LFU.pdb | model 1 | chain A 283 -71.42 108.03
2LFU.pdb | model 1 | chain A 284 -72.99 99.31
2LFU.pdb | model 1 | chain A 285 -92.93 2.32
2LFU.pdb | model 10 | chain A 426 -88.16 127.99
2LFU.pdb | model 10 | chain A 427 -107.40 -161.76
2LFU.pdb | model 10 | chain A 428 -72.12 -14.94
2LFU.pdb | model 10 | chain A 429 66.62 -81.17
2LFU.pdb | model 10 | chain A 430 -141.67 111.76
2LFU.pdb | model 10 | chain A 431 -69.37 141.19
2LFU.pdb | model 10 | chain A 432 76.08 -75.91
2LFU.pdb | model 10 | chain A 433 -149.23 167.34
2LFU.pdb | model 10 | chain A 434 -63.43 -27.06
2LFU.pdb | model 10 | chain A 435 -166.70 None
Read fasta files¶
We want to read sequences that we wrote in files. PBxplore provides a
function to read fasta files: the pbxplore.io.read_fasta() function.
In [12]:
def pdb_to_fasta_pb(pdb_path, fasta_path):
"""
Write a fasta file with all the PB sequences from a PDB
"""
with open(fasta_path, 'w') as outfile:
for chain_name, chain in pbx.chains_from_files([pdb_path]):
dihedrals = chain.get_phi_psi_angles()
pb_seq = pbx.assign(dihedrals)
pbx.io.write_fasta_entry(outfile, pb_seq, chain_name)
# Write a fasta file
pdb_name, _ = urllib.request.urlretrieve('https://files.rcsb.org/view/2LFU.pdb', '2LFU.pdb')
pdb_to_fasta_pb(pdb_name, 'output.fasta')
# Read a list of headers and a list of sequences from a fasta file
names, sequences = pbx.io.read_fasta('output.fasta')
print('names:')
pprint(names)
print('sequences:')
pprint(sequences)
!rm output.fasta
read 10 sequences in output.fasta
names:
['2LFU.pdb | model 1 | chain A',
'2LFU.pdb | model 2 | chain A',
'2LFU.pdb | model 3 | chain A',
'2LFU.pdb | model 4 | chain A',
'2LFU.pdb | model 5 | chain A',
'2LFU.pdb | model 6 | chain A',
'2LFU.pdb | model 7 | chain A',
'2LFU.pdb | model 8 | chain A',
'2LFU.pdb | model 9 | chain A',
'2LFU.pdb | model 10 | chain A']
sequences:
['ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ',
'ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ',
'ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ',
'ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ',
'ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadddddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddfklmaccddddddfbgghiafehiadddddddfklpacfZZ',
'ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadddddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddfklmaccddddehiaehbgcdehiadddddddfehjlpcZZ',
'ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapadddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddfklpaccdddddfklmaacdfehpadddddehjblckknZZ',
'ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblbacddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddefklpaccdddddfklmbfbehehiaddddddffkgoiehZZ',
'ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdcdddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddfklmpccddddehiacbcbdfehpadddddehjklmklmZZ',
'ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapaccdddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddfklpaccddddddfbcfbacfehpadddddddekpghiaZZ']
Read 10 chain(s) in 2LFU.pdb
If the sequences we want to read are spread amongst several fasta files,
then we can use the pbxplore.io.read_several_fasta() function that
takes a list of fasta file path as argument instead of a single path.
In [13]:
# Write several fasta files
pdbname, _ = urllib.request.urlretrieve('https://files.rcsb.org/view/1BTA.pdb', '1BTA.pdb')
pdb_to_fasta_pb(pdbname, '1BTA.fasta')
pdbname, _ = urllib.request.urlretrieve('https://files.rcsb.org/view/2LFU.pdb', '2LFU.pdb')
pdb_to_fasta_pb(pdb_name, '2FLU.fasta')
# Read the fasta files
names, sequences = pbx.io.read_several_fasta(['1BTA.fasta', '2FLU.fasta'])
# Print the first entries
print('names:')
pprint(names[:5])
print('sequences:')
pprint(sequences[:5])
!rm 1BTA.fasta 2FLU.fasta
Read 1 chain(s) in 1BTA.pdb
read 1 sequences in 1BTA.fasta
read 10 sequences in 2FLU.fasta
names:
['1BTA.pdb | chain A',
'2LFU.pdb | model 1 | chain A',
'2LFU.pdb | model 2 | chain A',
'2LFU.pdb | model 3 | chain A',
'2LFU.pdb | model 4 | chain A']
sequences:
['ZZdddfklonbfklmmmmmmmmnopafklnoiaklmmmmmnoopacddddddehkllmmmmngoilmmmmmmmmmmmmnopacdcddZZ',
'ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ',
'ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ',
'ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ',
'ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ']
Read 10 chain(s) in 2LFU.pdb