X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=qcg%2Fviews.py;h=073c08b4d2515ce958da8b952c8a63c949fe9671;hb=9f0267486fef6a929c431db5cb76a36e2f93ed54;hp=a45969479824212cb6f027c66c532085c85d0145;hpb=5e1c3d729bd5bb38ce285159d8df8ca696670094;p=qcg-portal.git

diff --git a/qcg/views.py b/qcg/views.py
index a459694..073c08b 100644
--- 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
 
 
@@ -194,44 +194,7 @@ 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 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):
@@ -262,6 +225,7 @@ def job_submit(request, template_id=None):
             md_input=generate_md_inputfile(params)
             url=os.path.splitext(params['pdb_file'])[0]+'_MD_genarated.inp'
             params['master_file']=url
+            params['stage_in'].append(params['pdb_file'])
             # Upload
             ftp = FTPOperation(request.session['proxy'])
             ftp.put(url)
@@ -270,13 +234,12 @@ def job_submit(request, template_id=None):
             ftp.stream.put(None)
             ftp.wait()
             
-
             params['persistent'] = True
             # Debugging parametrów
-            #pprint(params)
-
+            # pprint(params)
             job_desc = to_job_desc(params, request.session['proxy'])
 
+
             if save_template:
                 template = template_form.save(commit=False)
 
@@ -287,6 +250,7 @@ def job_submit(request, template_id=None):
                 return redirect(template)
 
             # wyłączenie wysyłania zadania - zakomentować poniżej
+            
             job = job_desc.submit()
 
             messages.success(request,