From: Dawid Jagieła <lightnir@gmail.com>
Date: Mon, 7 Sep 2015 21:14:27 +0000 (+0200)
Subject: generowanie lokalnie pliku inputowego
X-Git-Tag: v1.1~42
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=f1feda98350bcbcd03ba5f79a41b33acd8161ade;p=qcg-portal.git

generowanie lokalnie pliku inputowego
---

diff --git a/qcg/forms.py b/qcg/forms.py
index 3427317..18d5f8b 100644
--- a/qcg/forms.py
+++ b/qcg/forms.py
@@ -121,12 +121,11 @@ class JobDescriptionForm(forms.Form):
     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
diff --git a/qcg/templates/qcg/job_submit_form.html b/qcg/templates/qcg/job_submit_form.html
index f44c109..7e3007d 100644
--- a/qcg/templates/qcg/job_submit_form.html
+++ b/qcg/templates/qcg/job_submit_form.html
@@ -2,7 +2,7 @@
 
 <!-- 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>
@@ -18,21 +18,19 @@
         {% 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">
diff --git a/qcg/views.py b/qcg/views.py
index 5e8f0a0..3f37df1 100644
--- a/qcg/views.py
+++ b/qcg/views.py
@@ -26,6 +26,11 @@ from qcg.models import JobTemplate
 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
 
@@ -187,16 +192,48 @@ def process_details(request, job, task=None):
 
     return {'job': job, 'task': task, 'form': form, 'env_formset': env_formset, 'template_form': template_form}
 
-def generate_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):
@@ -219,10 +256,19 @@ 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