self._init_user_choices('arguments', data, initial)
self._init_user_choices('native', data, initial)
self._init_user_choices('stage_in', data, initial)
+ self._init_user_choices('force_field', data, initial)
def clean(self):
data = super(JobDescriptionForm, self).clean()
+# coding=utf-8
import os
import string
import random
from filex.ftp import FTPOperation
from qcg import constants
+from django.utils import encoding
def get_attributes(obj, attrs):
return {name: getattr(obj, name) for name in attrs if getattr(obj, name) is not None}
def chunks(seq, size):
return (seq[pos:pos + size] for pos in xrange(0, len(seq), size))
+def generate_md_inputfile(params):
+ md_input = list()
+ # Opis pliku wyjsciowego
+ opis=params['note'][:80]
+ md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore'))
+ # Dane kontrolne obliczen
+ md_input.append('SEED=-3059743 PDBREF ONE_LETTER MD EXTCONF RESCALE_MODE=2')
+ ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe'])
+ ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf'
+ md_input.append('{:<79}&'.format(ctl_data))
+ md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512')
+ # Paramatry pól siłowych
+ if params['force_field'] == 'GAB':
+ # Wagi pola GAB
+ md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &')
+ md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &')
+ md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &')
+ md_input.append('WVDWPP=0.11371 WHPB=1.00000 &')
+ md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0')
+ else:
+ # Wagi pola E0LLY
+ md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &')
+ md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &')
+ md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &')
+ md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &')
+ md_input.append('CUTOFF=7.00000 WCORR4=0.00000')
+ # Plik PDB
+ md_input.append(params['pdb_file'].split('/')[-1])
+ # Sekwencja aminokwasów
+ md_input.append(len(params['sequence']))
+ seq_str=params['sequence']
+ while seq_str:
+ md_input.append(seq_str[:80])
+ seq_str=seq_str[80:]
+ md_input.append(' 0')
+ md_input.append(' 0')
+
+ return md_input
+
def to_job_desc(params, proxy):
QCG.start()
desc.set_reservation(params['reservation'])
if params['watch_output']:
desc.set_watch_output(params['watch_output'], params['watch_output_pattern'])
+
# TODO monitoring
+ print desc.sequence
+
return desc
from filex.views import make_url
from qcg.forms import FiltersForm, ColumnsForm, JobDescriptionForm, EnvFormSet, JobTemplateForm
from qcg.models import JobTemplate
-from qcg.utils import paginator_context, to_job_desc, to_form_data
+from qcg.utils import paginator_context, to_job_desc, to_form_data, generate_md_inputfile
from qcg.service import update_user_data, update_job, cancel, clean
return {'job': job, 'task': task, 'form': form, 'env_formset': env_formset, 'template_form': template_form}
-def generate_md_inputfile(params):
- md_input = list()
- # Opis pliku wyjsciowego
- opis=params['note'][:80]
- md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore'))
- # Dane kontrolne obliczeń
- md_input.append('SEED=-3059743 PDBREF ONE_LETTER MD EXTCONF RESCALE_MODE=2')
- ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe'])
- ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf'
- md_input.append('{:<79}&'.format(ctl_data))
- md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512')
- # Paramatry pól siłowych
- if params['force_field'] == 'GAB':
- # Wagi pola GAB
- md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &')
- md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &')
- md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &')
- md_input.append('WVDWPP=0.11371 WHPB=1.00000 &')
- md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0')
- else:
- # Wagi pola E0LLY
- md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &')
- md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &')
- md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &')
- md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &')
- md_input.append('CUTOFF=7.00000 WCORR4=0.00000')
- # Plik PDB
- md_input.append(params['pdb_file'].split('/')[-1])
- # Sekwencja aminokwasów
- md_input.append(len(params['sequence']))
- seq_str=params['sequence']
- while seq_str:
- md_input.append(seq_str[:80])
- seq_str=seq_str[80:]
- md_input.append(' 0')
- md_input.append(' 0')
-
- return md_input
-
def id_generator(size=6, chars=string.ascii_uppercase + string.digits):
return ''.join(random.choice(chars) for _ in range(size))
ftp.stream.put(None)
ftp.wait()
-
params['persistent'] = True
- # Debugging parametrów
- #pprint(params)
job_desc = to_job_desc(params, request.session['proxy'])
+
if save_template:
template = template_form.save(commit=False)