dt = forms.DecimalField(label=u"DT", help_text=u"Krok czasowy. Wartość kroku równa jedności to 48.9 fs", max_digits=5, decimal_places=2, min_value=0.01, initial=0.1, required=False)
damax = forms.DecimalField(label=u"DAMAX", help_text=u"Maksymalna dopuszczalna zmiana przyspieszenia podczas jednego kroku czasowego", max_digits=5, decimal_places=2, min_value=0.01, initial=1.0, required=False)
force_field = forms.ChoiceField(choices=FORCE_FIELD_CHOICES, label=u"Pole siłowe", required=False, initial='GAB')
- nrep = forms.IntegerField(label=u"NREP", help_text=u"Liczba replik", min_value=2, initial=16, required=False)
- nstex = forms.IntegerField(label=u"NSTEX", help_text=u"Liczba kroków po których następuje wymiana replik", min_value=2, initial=1000, required=False)
+
pdb_file = forms.CharField(label=u"Plik PDB", max_length=500, required=False)
- retmin = forms.IntegerField(label=u"RETMIN", help_text=u"Dolny zakres temparatur dla wymiany replik", min_value=2, initial=250, required=False)
- retmax = forms.IntegerField(label=u"RETMAX", help_text=u"Górny zakres temperatur dla wymiany replik", min_value=2, initial=450, required=False)
- sequence = forms.CharField(label=u"Sekwencja", widget=forms.Textarea(attrs={'rows': 2, 'cols': 40}), required=False)
+ #retmin = forms.IntegerField(label=u"RETMIN", help_text=u"Dolny zakres temparatur dla wymiany replik", min_value=2, initial=250, required=False)
+ #retmax = forms.IntegerField(label=u"RETMAX", help_text=u"Górny zakres temperatur dla wymiany replik", min_value=2, initial=450, required=False)
+ sequence = forms.CharField(label=u"Sekwencja", help_text=u"Sekwencja aminokwasów w zapisie jednoliterowym", widget=forms.Textarea(attrs={'rows': 2, 'cols': 40}), required=False)
application = forms.ChoiceField(choices=APPLICATION_CHOICES, label=u"Aplikacja", required=False, initial='unres-gab') # TODO choices
<!-- Nav tabs -->
<ul class="nav nav-tabs" style="margin-bottom: 20px">
- <li role="presentation" class="active"><a href="#basic" data-toggle="tab">MREMD</a></li>
+ <li role="presentation" class="active"><a href="#basic" data-toggle="tab">MD</a></li>
<li role="presentation"><a href="#resources" data-toggle="tab">Zasoby</a></li>
<li role="presentation"><a href="#files" data-toggle="tab">Pliki</a></li>
<li role="presentation"><a href="#environment" data-toggle="tab">Środowisko</a></li>
{% bootstrap_field form.ntwx layout="horizontal" form_group_class="form-group collapse" %}
{% bootstrap_field form.dt layout="horizontal" form_group_class="form-group collapse" %}
{% bootstrap_field form.damax layout="horizontal" form_group_class="form-group collapse" %}
- {% bootstrap_field form.nrep layout="horizontal" %}
- {% bootstrap_field form.nstex layout="horizontal" form_group_class="form-group collapse" %}
+
{% bootstrap_field form.pdb_file layout="horizontal" %}
{% bootstrap_field form.sequence layout="horizontal" %}
- {% bootstrap_field form.retmin layout="horizontal" form_group_class="form-group collapse" %}
- {% bootstrap_field form.retmax layout="horizontal" form_group_class="form-group collapse" %}
+
{% bootstrap_field form.master_file layout="horizontal" %}
<!-- {% bootstrap_field form.application layout="horizontal" %}
{% bootstrap_field form.executable layout="horizontal" form_group_class="form-group collapse" %}
{% bootstrap_field form.script layout="horizontal" form_group_class="form-group collapse" %}
- {% bootstrap_field form.arguments layout="horizontal" %}
+ {% bootstrap_field form.arguments layout="horizontal" %} -->
{% bootstrap_field form.note layout="horizontal" %}
- {% bootstrap_field form.grant layout="horizontal" form_group_class="form-group collapse" %} -->
+ {% bootstrap_field form.grant layout="horizontal" form_group_class="form-group collapse" %}
</fieldset>
<fieldset id="resources" class="tab-pane" role="tabpanel">
from qcg.utils import paginator_context, to_job_desc, to_form_data
from qcg.service import update_user_data, update_job, cancel, clean
+
+from django.utils import encoding
+import string
+import random
+import os
# for Debugging
from pprint import pprint
return {'job': job, 'task': task, 'form': form, 'env_formset': env_formset, 'template_form': template_form}
-def generate_mremd_inputfile(params, mremd_input):
- mremd_input = list()
- opis=params['note']
- mremd_input.append(opis[:73])
- mremd_input.append('SEED=-3059743 PDBREF MD EXTCONF RESCALE_MODE=2')
-
-
-
+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 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 mremd_input
+ return md_input
+
+
+def id_generator(size=6, chars=string.ascii_uppercase + string.digits):
+ return ''.join(random.choice(chars) for _ in range(size))
@login_required
def job_submit(request, template_id=None):
params['env_variables'] = [(env['name'], env['value'])
for env in env_formset.cleaned_data if env and not env['DELETE']]
- # tu wygenerować plik inputowy i go uploadować?
- mremd_input=list()
- print generate_mremd_inputfile(params,mremd_input)
-
+ # Generowanie pliku inputowego
+ #md_input=list()
+ md_input=generate_md_inputfile(params)
+ filename='input.'+id_generator(6)+'.tmp'
+ f = open(filename, 'w')
+ # for Debugging
+ for idx in md_input:
+ print idx
+ f.write("%s\n" % idx)
+ f.close()
+ os.remove(filename)
+
+ # Upload
params['persistent'] = True
# Debugging parametrów