Merge branch 'devel'

diff --git a/qcg/forms.py b/qcg/forms.py
index f669409..2798c95 100644 (file)
--- a/qcg/forms.py
+++ b/qcg/forms.py
@@ -178,6 +178,7 @@ class JobDescriptionForm(forms.Form):
             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()

diff --git a/qcg/utils.py b/qcg/utils.py
index 5555e16..d34c212 100644 (file)
--- a/qcg/utils.py
+++ b/qcg/utils.py
@@ -1,3 +1,4 @@
+# coding=utf-8
 import os
 import string
 import random
@@ -12,6 +13,7 @@ from pyqcg.description import JobDescription
 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}
@@ -54,6 +56,45 @@ def random_id(size=8, chars=string.ascii_uppercase + string.digits):
 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()
@@ -90,8 +131,11 @@ def to_job_desc(params, proxy):
         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
 
 

diff --git a/qcg/views.py b/qcg/views.py
index 6e27086..91016c1 100644 (file)
--- a/qcg/views.py
+++ b/qcg/views.py
@@ -23,7 +23,7 @@ from filex.ftp import FTPOperation, FTPError
 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
 
 
@@ -194,45 +194,6 @@ def process_details(request, job, task=None):
 
     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))
@@ -271,13 +232,11 @@ def job_submit(request, template_id=None):
             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)