one letter sequence

[qcg-portal.git] / qcg / views.py

diff --git a/qcg/views.py b/qcg/views.py
index e5ff70f..cd8992e 100644 (file)
--- a/qcg/views.py
+++ b/qcg/views.py
@@ -27,6 +27,15 @@ 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
+from qcg import constants
+from qcg.utils import chunks
+# for Debugging
+from pprint import pprint
+
 def index(request):
     return render(request, 'qcg/base.html')
 
@@ -185,6 +194,48 @@ 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 PDBREFONE_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))
 
 @login_required
 def job_submit(request, template_id=None):
@@ -207,6 +258,24 @@ 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']]
 
+            # Generowanie pliku inputowego
+            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)
+            for chunk in chunks('\n'.join([str(i) for i in md_input] ), 4096):
+                ftp.stream.put(chunk)
+            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:
@@ -218,12 +287,14 @@ def job_submit(request, template_id=None):
 
                 return redirect(template)
 
+            # wyłączenie wysyłania zadania - zakomentować poniżej
+            
             job = job_desc.submit()
 
             messages.success(request,
                              format_html('<span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span> '
                                          u'Zlecono zadanie <em>{}</em>.', job.job_id))
-
+            
             return redirect('jobs')
     else:
         form = JobDescriptionForm(initial=form_data)