X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=files%2Fpbs8_new.csh;h=176cb104912285fb25d257bed83af28f35ef0001;hb=refs%2Fheads%2Fmaster;hp=1713c99f6549bccfb9bc54dad650eaf847dda780;hpb=a3b7f27a81cf442cdeeaff5b9c9b52298c282f5a;p=django_unres.git

diff --git a/files/pbs8_new.csh b/files/pbs8_new.csh
index 1713c99..176cb10 100755
--- a/files/pbs8_new.csh
+++ b/files/pbs8_new.csh
@@ -67,39 +67,66 @@ setenv CLUSTER_WHAM_BIN /users2/czarek/UNRES/git3_tmp/build/bin/cluster_wham-mul
 
 $MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
 
+if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
+#no allatom conversion/refinementkx for proteins with D-aminoacids
+ ln -s file_wham_T*K_ave.pdb ave
+ sed -n '/ENERGY/,/ENDMDL/p' ave >tmp.pdb
+ setenv numstruc `grep ENERGY tmp.pdb|wc -l`
+ setenv allline `cat tmp.pdb|wc -l`
+ setenv onestruc `echo $allline "/" $numstruc| bc -l|sed 's/\.0*//'`
+ foreach i (`seq 2 2 $numstruc`)
+   setenv headval `echo $i "*" $onestruc|bc -l`
+   setenv halfi `echo $i/2|bc`
+   head -n $headval tmp.pdb | tail -n $onestruc >MODEL${halfi}.pdb
+ end
+ rm ave tmp.pdb
+else
+# proteins with L-aminoacids only
 ln -s file_wham_T*K_ave.pdb ave
+setenv numstruc `awk '/ENERGY/{i++}END{print i/2}' ave`
 ../files/cluster2allatom.sh ave
 rm ave
 
 #amber min refinement
-foreach i (`seq 1 5`)
+foreach i (`seq 1 $numstruc`)
 ../files/refine.sh MODEL$i.pdb $ssbond
 end
+endif
 
 /users2/local/pymol_1.6/pymol -c ../files/model.pml
 
 if ( `grep -c pdbref file.inp` ) then
  awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
+ if ( -f "plik1ter.pdb" ) then
+  grep -v TER plik1ter.pdb | awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' > tmp.pdb
+  /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh plik.pdb |grep ATOM > plik1chain.pdb
+  /users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh plik2.pdb |grep ATOM >> plik1chain.pdb  
+  foreach i (`seq 1 $numstruc`)
+    sed /TER/q MODEL$i.pdb_ > tmp1.pdb
+    /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh tmp1.pdb |grep ATOM > MODEL${i}chain.pdb    
+    sed '0,/TER/d' MODEL$i.pdb_ > tmp2.pdb
+    /users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh tmp2.pdb |grep ATOM >> MODEL${i}chain.pdb    
+    rm tmp1.pdb tmp2.pdb MODEL$i.pdb_
+    ../files/DockQ.py MODEL${i}chain.pdb plik1chain.pdb > dockq_$i.out
+  end
+
+ endif
  /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
  rm tmp.pdb
 
- /users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
- /users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
- /users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
- /users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
- /users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
+ foreach i (`seq 1 $numstruc`)
+ /users2/local/bin/tmscore MODEL${i}.pdb plik1.pdb > tmscore${i}.out
+ end
  if (-e saxs.data) then
   awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
  endif
- rm plik1.pdb
+# rm plik1.pdb
 endif
 
 if (-e saxs.data) then
-awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
-awk -f ../files/saxs_dist.awk MODEL2.pdb > MODEL2_saxs.data
-awk -f ../files/saxs_dist.awk MODEL3.pdb > MODEL3_saxs.data
-awk -f ../files/saxs_dist.awk MODEL4.pdb > MODEL4_saxs.data
-awk -f ../files/saxs_dist.awk MODEL5.pdb > MODEL5_saxs.data
+foreach i (`seq 1 $numstruc`)
+awk -f ../files/saxs_dist.awk MODEL${i}.pdb > MODEL${i}_saxs.data
+end
 ../files/plot_saxs.py
 endif