secondary structure restraints for md and remd

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index 16d942a..c0b1667 100644 (file)
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -7,6 +7,14 @@ from .models import FF_CHOICE
 import json
 import urllib
 
+def code_2d(line):
+   msg=''
+   set ='HEC-'
+   line2 = ''.join([c for c in line if c in set])
+   if line2 != line:
+    msg='use only H,E,C or - letters'
+   return(msg)
+
 def pdb_missing_res(file):
    msg=''
    newchain = True
@@ -230,6 +238,11 @@ class TaskForm_md_a(forms.Form):
                      'field is ignored when uploading starting/reference PDB file',
                      required=False,
                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+     md_2d = forms.CharField(label='Secondary structure restraints',
+                     help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
+                     required=False,
+                     widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+
      file1 = forms.FileField(label='Upload a PDB file',required=False,
                   help_text='starting structure for pdbstart/reference structure')
      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
@@ -272,6 +285,7 @@ class TaskForm_md_a(forms.Form):
              pdbid = cleaned_data.get("pdbid")
              md_seq = cleaned_data.get("md_seq")
              md_pdbref = cleaned_data.get("md_pdbref")
+             md_2d = cleaned_data.get("md_2d")
               
              if md_start == 'pdbstart' and not (file1 or pdbid):
                 msg = 'pdbstart with no PDB file or code'
@@ -301,7 +315,11 @@ class TaskForm_md_a(forms.Form):
                  msg=pdb_missing_res(file1)
                  if msg != '':
                    self.add_error('file1',msg)
-
+             
+             if md_2d:
+                 msg=code_2d(md_2d)
+                 if msg != '':
+                   self.add_error('md_2d',msg)
 
 class TaskForm_remd(forms.Form):
      name = forms.CharField(max_length=20)
@@ -374,6 +392,10 @@ class TaskForm_remd_a(forms.Form):
                       'field is ignored when uploading starting/reference PDB file',
                      required=False,
                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+     md_2d = forms.CharField(label='Secondary structure restraints',
+                     help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
+                     required=False,
+                     widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
      file1 = forms.FileField(label='Upload a PDB file',required=False,
                   help_text='starting structure for pdbstart/reference structure')
      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
@@ -432,6 +454,7 @@ class TaskForm_remd_a(forms.Form):
              pdbid = cleaned_data.get("pdbid")
              md_seq = cleaned_data.get("md_seq")
              md_pdbref = cleaned_data.get("md_pdbref")
+             md_2d = cleaned_data.get("md_2d")
               
              if md_start == 'pdbstart' and not (file1 or pdbid):
                 msg = 'pdbstart with no PDB file or code'
@@ -462,6 +485,11 @@ class TaskForm_remd_a(forms.Form):
                  if msg != '':
                    self.add_error('file1',msg)
 
+             if md_2d:
+                 msg=code_2d(md_2d)
+                 if msg != '':
+                   self.add_error('md_2d',msg)
+
 
 
 class TaskForm_list(forms.Form):

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 2badbc2..4d9270c 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -13,6 +13,36 @@ import textwrap
 logging.basicConfig()
 logger = logging.getLogger(__name__)
 
+def seq_2d_write(line):
+   line=line.replace(" ", "")
+   out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
+   for i in range(1,4):
+     out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+   for e in line[:-3]:
+     i+=1
+     if e=='-':
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+     elif e=='H':
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
+     elif e=='E':
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
+   return(out)
+
+def seq_2d_write_50(line):
+   line=line.replace(" ", "")
+   out='{:d}\n'.format(len(line))
+   for i in range(1,4):
+     out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
+   for e in line[:-3]:
+     i+=1
+     if e=='-':
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
+     elif e=='H':
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
+     elif e=='E':
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
+   return(out)
+
 def write_ssbond(ssbond):
    list=[]
    if ssbond!='':
@@ -211,8 +241,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
        if instance.type == 'min' or instance.md_start == 'pdbstart':
           f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
-          f.write('0\n')
-
+          if instance.md_seq_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(instance.md_seq_2d))
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -221,7 +253,12 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write(str(len(seq))+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
-          f.write('0\n0\n')
+          f.write('0\n')
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(instance.md_2d))
+
 
        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 
@@ -230,7 +267,12 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write(str(len(seq))+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
-          f.write('0\n0\n')
+          f.write('0\n')
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(instance.md_2d))
+
 
        if instance.saxs_data != '':
              lines=instance.saxs_data.split('\n')
@@ -322,19 +364,23 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_pdbref:
             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
-            f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
-                    ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
           else:    
             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
-            f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+          f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
+                 
           f.write('nres='+str(len(seq))+' one_letter\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
 
           f.write(write_ssbond(instance.ssbond))
 
+          if instance.md_2d != '':
+             f.write(seq_2d_write_50(instance.md_2d))
+
           if instance.saxs_data != '':
              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
              lines=instance.saxs_data.split('\n')
@@ -366,12 +412,16 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write('{:79}'.format('nres='+str(len(seq))
              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
              +' temper='+str(instance.remd_cluter_temp))+'&\n')
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
                   ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
           f.write(w+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
           f.write(write_ssbond(instance.ssbond))
+          if instance.md_2d != '':
+             f.write(seq_2d_write_50(instance.md_2d))
           if instance.saxs_data != '':
              lines=instance.saxs_data.split('\n')
              for line in lines:

diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py
index da15522..ee54314 100644 (file)
--- a/django_simple/todo/models.py
+++ b/django_simple/todo/models.py
@@ -65,6 +65,7 @@ class Task(models.Model):
     md_scal_fric = models.FloatField(default=0.02)
     md_mdpdb = models.BooleanField(default=False)
     md_seq = models.TextField(max_length=2000,default='')
+    md_2d = models.TextField(max_length=2000,default='')
     
 #remd
     remd_nrep = models.IntegerField(default=8)

diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index af51ef1..e2251f3 100644 (file)
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -77,6 +77,13 @@ Created {{ task.created_date  }}
                        </li>           
 
                        <li class="list-group-item task-item">
+                           <div class="col-md-4"> secondary structure
+                           restraints </div>
+                           <div class="col-md-8">{{ task.md_2d}}</div>
+                       </li>           
+
+
+                       <li class="list-group-item task-item">
                            <div class="col-md-6"> SSBOND </div>
                            <div class="col-md-6">{{ task.ssbond}}</div>
                        </li>           

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 6a244b0..0387f29 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -29,12 +29,45 @@ res_codes = [
 
 three_to_one = dict(res_codes)
 
+def seq_2d_from_pdb(seq_2d,seq):
+    if seq_2d =='':
+      return(seq_2d)
+    seq_2d=seq_2d.replace('C', '-')
+    seq_2d_tmp=''
+    ii=0
+    for i in range(0,len(seq)):
+      if seq[i]=='X':
+         seq_2d_tmp=seq_2d_tmp+'-'
+      else:
+         if len(seq_2d)>=ii:
+            seq_2d_tmp=seq_2d_tmp+seq_2d[ii]
+            ii+=1
+    tmp=''
+    for i in range(0,len(seq_2d_tmp),40):
+      tmp=tmp+seq_2d_tmp[i:i+40]+" "
+    return(tmp)
+
+def seq_2d_add_x(seq_2d,seq,seq_form):
+    if seq_2d =='':
+      return(seq_2d)
+    seq_2d=seq_2d[:len(seq_form)]
+    seq_2d=seq_2d.replace('C', '-')
+    if seq_form[0] !='X' and seq[0] == 'X':
+      seq_2d='-'+seq_2d
+    if seq_form[-1] !='X' and seq[-1] == 'X':
+      seq_2d=seq_2d+'-'
+    seq_2d=seq_2d[:len(seq)]
+    tmp=''
+    for i in range(0,len(seq_2d),40):
+      tmp=tmp+seq_2d[i:i+40]+" "
+    return(tmp)
+
 def seq_add_x(sequence):
-    if sequence[0] != 'G' and sequence[0] != 'g':
+    if sequence[0] != 'G' and sequence[0] != 'g' and sequence[0] != 'X':
         sequence='X'+sequence
-    if sequence[-1] != 'G' and sequence[-1] != 'g':
+    if sequence[-1] != 'G' and sequence[-1] != 'g' and sequence[-1] != 'X':
         sequence=sequence+'X'
-    set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnghlrwaveym'
+    set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnhlrwaveym'
     sequence = ''.join([c for c in sequence if c in set])
 
     return(sequence)    
@@ -311,8 +344,11 @@ def add_md_a(request,task_id):
              task.md_seq=""
              if task.md_start == "pdbstart" or task.md_pdbref:
                seq,task.ssbond=from_pdb(task.myfile1)
+               task.md_2d=seq_2d_from_pdb(form.cleaned_data["md_2d"],seq)
              else:
                seq=seq_add_x(form.cleaned_data["md_seq"])
+               task.md_2d=seq_2d_add_x(form.cleaned_data["md_2d"],seq,form.cleaned_data["md_seq"])               
+
              for i in range(0,len(seq),40):
                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 
@@ -488,8 +524,11 @@ def add_remd_a(request,task_id):
              task.md_seq=""
              if task.md_start == "pdbstart" or task.md_pdbref:
                seq,task.ssbond=from_pdb(task.myfile1)
+               task.md_2d=seq_2d_from_pdb(form.cleaned_data["md_2d"],seq)
              else:
                seq=seq_add_x(form.cleaned_data["md_seq"])
+               task.md_2d=seq_2d_add_x(form.cleaned_data["md_2d"],seq,form.cleaned_data["md_seq"])               
+
              for i in range(0,len(seq),40):
                 task.md_seq=task.md_seq+seq[i:i+40]+" "