def plot_prediction_templates(n_templates=3, n_templates_plot=None):
'''Plot the prediction together with the templates'''
# Parse arguments
n_templates = int(n_templates)
if n_templates_plot is None:
n_templates_plot = n_templates
else:
n_templates_plot = int(n_templates_plot)
# Delete previous objects
pymol.cmd.delete('all')
# Get the prediction
predfile = '../results/1yje_A-multiple_n_'+str(n_templates)+'.pdb'
predid = '1yje_A-multiple_n_'+str(n_templates)
pymol.cmd.load(predfile)
pymol.cmd.color('red', predid)
# Get the template codes
# 1:n_templates_plot+1 because we want to exclude the target (which appears first on the list otherwise).
templates = read_templates('../data/templates/most_relevant.dat')[1:n_templates_plot+1]
print templates
# Load structures
for template in templates:
id = template['id'].upper()
chain = template['chain']
pymol.cmd.load(pdb_folder+id+'.pdb')
pymol.cmd.align('('+id+' and chain '+chain+')', predid)
pymol.cmd.hide(representation='line', selection='all')
pymol.cmd.show(representation='cartoon', selection=predid)
for template in templates:
id = template['id'].upper()
chain = template['chain']
pymol.cmd.show(representation='cartoon',
selection='('+id+' and chain '+chain+')')
pymol.cmd.center()
pymol.cmd.bg_color('white')
def plot_prediction_templates(n_templates_plot=2):
'''Plot the prediction together with the templates'''
# Parse arguments
n_templates_plot= int(n_templates_plot)
# Delete previous objects
pymol.cmd.delete('all')
# Get the prediction
predfile = '../results/1yje_A-multiple_n_'+str(n_templates)+'.pdb'
predid = '1yje_A-multiple_n_'+str(n_templates)
pymol.cmd.load(predfile)
pymol.cmd.color('red', predid)
# Get the template codes
templates = read_templates('../data/templates/most_relevant.dat')[:n_templates_plot]
# Load structures
for template in templates:
id = template['id'].upper()
pymol.cmd.load(pdb_folder+id+'.pdb')
pymol.cmd.align(id, predid)
pymol.cmd.hide(representation='line', selection='all')
pymol.cmd.show(representation='cartoon', selection=predid)
for template in templates:
id = template['id'].upper()
chain = template['chain']
pymol.cmd.show(representation='cartoon',
selection='('+id+' and chain '+chain+')')
pymol.cmd.center()
pymol.cmd.bg_color('white')
# work in the tmp folder
if not os.path.isdir('data/tmp'):
os.mkdir('data/tmp')
os.chdir('data/tmp')
try:
#the environment object is needed to do pretty much everything
env = environ()
#.pdb files must be stored herein
env.io.atom_files_directory = ['../templates/pdb/']
# align the unknown sequence with all templates
seqname = (os.path.basename(seqfile).split('.')[0])
seqname = seqname[:-1]+seqname[-1].upper()
templates = read_templates('../templates/most_relevant.dat')[:n_templates]
n_templates = len(templates)
# check whether the alignment exists already
if not os.path.isfile(seqname+'-multiple_n_'+str(n_templates)+'.ali'):
aln = alignment(env)
for template in templates:
id = template['id']
chain = template['chain']
tplname = get_tplname(template)
mdl = model(env, file=id, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(mdl, align_codes=tplname, atom_files=id+'.pdb')
# add the unknown sequence to the alignment.
aln.append(file=seqfile, align_codes=seqname)
author: Fabio Zanini
date: 13/06/12
content: Download a PDB sequence from the database and save it into a file
with the same name in the data/pdb folder
'''
import urllib
# From http://boscoh.com/protein/fetching-pdb-files-remotely-in-pure-python-code
def fetch_pdb(id):
url = 'http://www.rcsb.org/pdb/files/%s.pdb' % id
return urllib.urlopen(url).read()
def get_save_pdb(id):
'''Get the PDB file and save it in the right folder'''
pdbstring = fetch_pdb(id)
with open('data/templates/pdb/'+id+'.pdb','w') as pdbfile:
pdbfile.write(pdbstring)
# Script
if __name__ == '__main__':
templatefilename = 'data/templates/most_relevant.dat'
from read_templates import read_templates
templates = read_templates(templatefilename)
for template in templates:
id = template['id']
print 'downloading', id, '...'
get_save_pdb()
print 'done'
