dock DockQ

[django_unres.git] / files / pbs8_new.csh

diff --git a/files/pbs8_new.csh b/files/pbs8_new.csh
index 0382652..0c87f80 100755 (executable)
--- a/files/pbs8_new.csh
+++ b/files/pbs8_new.csh
@@ -12,7 +12,7 @@ setenv THETPARPDB $DD/thetaml_ext.5parm
 setenv ROTPARPDB $DD/scgauss_ext.parm
 setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
 setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
-setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv TORDPAR $DD/torsion_double_631Gdp_old_ext.parm
 setenv ELEPAR $DD/electr_631Gdp_ext.parm
 setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
 setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
@@ -67,22 +67,72 @@ 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 (2 4 6 8 10)
+   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
 ../files/cluster2allatom.sh ave
 rm ave
 
 #amber min refinement
 foreach i (`seq 1 5`)
-../files/refine.sh MODEL$i.pdb
+../files/refine.sh MODEL$i.pdb $ssbond
 end
+endif
 
 /users2/local/pymol_1.6/pymol -c ../files/model.pml
 
-/users2/local/bin/tmscore MODEL1.pdb plik.pdb > tmscore1.out
-/users2/local/bin/tmscore MODEL2.pdb plik.pdb > tmscore2.out
-/users2/local/bin/tmscore MODEL3.pdb plik.pdb > tmscore3.out
-/users2/local/bin/tmscore MODEL4.pdb plik.pdb > tmscore4.out
-/users2/local/bin/tmscore MODEL5.pdb plik.pdb > tmscore5.out
+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($0,23)}' > tmp.pdb
+  /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh plik.pdb |grep ATOM > plik1chain.pdb
+  /users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh plik2.pdb |grep ATOM >> plik1chain.pdb  
+  foreach i (`seq 1 5`)
+    sed /TER/q MODEL$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
+ if (-e saxs.data) then
+  awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
+ endif
+# 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
+../files/plot_saxs.py
+endif
+
 
 #END
 touch finished