problems with json ssbond

[django_unres.git] / django_simple / todo / views.py

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 4f09e49..4ffb0e7 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -6,6 +6,7 @@ from .models import Task
 import datetime
 import os
 import subprocess
+import json
 
 res_codes = [
                 # 20 canonical amino acids
@@ -34,18 +35,45 @@ def seq_add_x(sequence):
 def from_pdb(file):
     sequence = []
     ssbond = []
+    ssbond_ch = []
+    ires = []
+    chain_start = {}
+    chain_end = {}
+    unres_shift = {}
+    chain=[]
+    ichain=0
+    newchain = True
+    
     for line in file:
+            if line[0:6] == 'COMPND' and line[11:17] == 'CHAIN:':
+              tmp=line[18:]
+              chain_=tmp.split(', ')
+              chain_[-1]=chain_[-1][0]
+              chain.extend(chain_)
+    
             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
               aa = three_to_one.get(line[17:20])
-              sequence.append(aa)
+              i = int(line[22:26])
+              if newchain or i!=ires[-1]:
+                sequence.append(aa)
+                ires.append(i)
+                if newchain:
+                 chain_start[chain[ichain]]=i
+                 newchain = False
             if line[0:3] == 'TER':
               sequence.append('XX')
+              chain_end[chain[ichain]]=i
+              ichain=ichain+1
+              newchain = True
             if line[0:6] == 'SSBOND':
               b=[]
               b.append(int(line[17:21]))
               b.append(int(line[31:35]))
               ssbond.append(b)
-                                                                                    
+              c = []
+              c.append((line[15:16]))
+              c.append((line[29:30]))
+              ssbond_ch.append(c)                                                                      
             if line[0:3] == 'END':
               break
     while sequence[-1] == 'XX':
@@ -56,7 +84,15 @@ def from_pdb(file):
     if sequence[-1] != 'G':
             sequence.append('X')
     seq=''.join(sequence)
-    return seq,ssbond
+#    if ires[0] != 1:
+#            ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond]
+    i=0
+    for c in chain:
+      unres_shift[c]=i+chain_start[c]
+      i=i-(chain_end[c]-chain_start[c])-3
+    ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)]     
+
+    return seq,json.dumps(ssbond)
 
 
 @login_required
@@ -125,6 +161,7 @@ def add_min_a(request,task_id):
              task.min_pdbout=form.cleaned_data["min_pdbout"]
              task.myfile1=form.cleaned_data["file1"]
              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
+             task.unres_ff=form.cleaned_data["unres_ff"]
 
              seq,task.ssbond=from_pdb(task.myfile1)
              task.md_seq=""
@@ -222,7 +259,7 @@ def add_md_a(request,task_id):
              task.md_tau=form.cleaned_data["md_tau"]
              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
-
+             task.unres_ff=form.cleaned_data["unres_ff"]
              
              task.ready=True
              basename = str(task.owner)
@@ -249,6 +286,7 @@ def add_remd(request,task_id):
              task.md_start=form.cleaned_data["md_start"]
              task.myfile1=form.cleaned_data["file1"]
              task.md_pdbref=form.cleaned_data["md_pdbref"]
+             task.md_ntwx=task.remd_nstex 
 
              task.md_seq=""
              if task.md_start == "pdbstart" or task.md_pdbref:
@@ -312,10 +350,13 @@ def add_remd_a(request,task_id):
              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
              task.remd_nrep=form.cleaned_data["remd_nrep"]
              task.remd_nstex=form.cleaned_data["remd_nstex"]
+             task.md_ntwx=form.cleaned_data["md_ntwx"]             
+             task.md_ntwe=form.cleaned_data["md_ntwe"]
 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 
              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
+             task.unres_ff=form.cleaned_data["unres_ff"]
              
              basename = str(task.owner)
              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
@@ -423,6 +464,30 @@ def refresh_done(request):
                  elif i==5:
                      task.remd_model5=' '.join(line.split()[-6:])
 
+          for i in range(1,6):
+            with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
+               text=''
+               for line in f:
+                 if 'RMSD of  the common residues=' in line:
+                   text=' RMSD='+line.split()[5]
+                 if 'TM-score    =' in line:
+                   text=text+' TMscore='+line.split()[2]
+                 if 'GDT-TS-score=' in line:
+                   text=text+' GDT_TS='+line.split()[1]
+                    
+               if i==1:
+                     task.remd_model1=task.remd_model1+text
+               elif i==2:
+                     task.remd_model2=task.remd_model2+text
+               elif i==3:
+                     task.remd_model3=task.remd_model3+text
+               elif i==4:
+                     task.remd_model4=task.remd_model4+text
+               elif i==5:
+                     task.remd_model5=task.remd_model5+text
+
+
+
          if task.type=='remd':  
           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
 
@@ -434,15 +499,15 @@ def refresh_done(request):
                   if i>6:
                        break
                   if i==1:
-                     task.remd_model1=task.remd_model1+'Cluster1 probability= '+line1.split()[2]
+                     task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2]
                   elif i==2:
-                     task.remd_model2=task.remd_model2+'Cluster2 probability= '+line1.split()[2]
+                     task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2]
                   elif i==3:
-                     task.remd_model3=task.remd_model3+'Cluster3 probability= '+line1.split()[2]
+                     task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2]
                   elif i==4:
-                     task.remd_model4=task.remd_model4+'Cluster4 probability= '+line1.split()[2]
+                     task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2]
                   elif i==5:
-                     task.remd_model5=task.remd_model5+'Cluster5 probability= '+line1.split()[2]
+                     task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]