Rafal's code for NMR restraints

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

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index e2f0829..c6ab414 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -155,6 +155,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
              
+#---v
+          if instance.use_nmr:
+            control_line = control_line+' constr_dist=12 '
+#---^
           if instance.unres_ff =='NEWCT-9P':
             control_line = control_line+'tormode=2 cart'
             
@@ -190,6 +194,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
              
           if instance.unres_ff =='NEWCT-9P':
             control_line = control_line+'tormode=2 cart'
+#---v
+         if instance.use_nmr:
+           control_line = control_line+' constr_dist=12 '
+#---^
           
           cntrl_saxs=''
           if instance.saxs_data != '':
@@ -307,6 +315,22 @@ CUTOFF=7.00000 WCORR4=0.00000"""
             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
            else:
             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                  f.write(linmr)
+              fnmr.close()
+#---^
 
 
        if instance.type == 'remd' and instance.md_start != 'pdbstart':
@@ -324,6 +348,22 @@ CUTOFF=7.00000 WCORR4=0.00000"""
             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
            else:
             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+#---^
 
 
        if instance.saxs_data != '':
@@ -446,6 +486,10 @@ rm tmp_plik2.pdb act.rebuilt.pdb\n""")
               isampl=1
           else:
               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
+#---v
+          if instance.use_nmr:
+               f.write('{:79}'.format('with_dist_constr constr_dist=12')+'&\n')
+#---^
           f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
           if instance.md_pdbref:
             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
@@ -468,6 +512,23 @@ rm tmp_plik2.pdb act.rebuilt.pdb\n""")
 
           f.write(write_ssbond(instance.ssbond))
 
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+#---^
+
           if instance.type == 'dock':
             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
             f.write('READ2SIGMA \n')
@@ -528,6 +589,10 @@ rm tmp_plik2.pdb act.rebuilt.pdb\n""")
              +' nclust='+str(instance.remd_cluster_n))+'&\n')
           if instance.md_2d != '':
                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+#---v
+         if instance.use_nmr:
+            f.write('{:79}'.format('constr_dist=12 ')+'&\n')
+#---^
           if instance.type == 'dock':
                f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
           if instance.unres_ff =='NEWCT-9P':
@@ -538,6 +603,24 @@ rm tmp_plik2.pdb act.rebuilt.pdb\n""")
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
           f.write(write_ssbond(instance.ssbond))
+
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+#---^
+
           if instance.type == 'dock':
             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
             f.write('READ2SIGMA \n')
@@ -619,4 +702,4 @@ def delete_on_task_del(sender, instance, **kwargs):
            logger.warning("QDEL \"%s\" " % output)
          shutil.rmtree(instance.jobdirname)
          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)         
-         
\ No newline at end of file
+