number of clusters <> 5 scripts

diff --git a/files/pbs8.csh b/files/pbs8.csh
index 02bd93b..fb03463 100755 (executable)
--- a/files/pbs8.csh
+++ b/files/pbs8.csh
@@ -74,7 +74,7 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
  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)
+ 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
@@ -83,11 +83,12 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
 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
@@ -100,7 +101,7 @@ if ( `grep -c pdbref file.inp` ) 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`)
+  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
@@ -112,12 +113,9 @@ if ( `grep -c pdbref file.inp` ) then
  /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
@@ -125,11 +123,9 @@ if ( `grep -c pdbref file.inp` ) then
 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
 

diff --git a/files/pbs8_new.csh b/files/pbs8_new.csh
index 0c87f80..176cb10 100755 (executable)
--- a/files/pbs8_new.csh
+++ b/files/pbs8_new.csh
@@ -74,7 +74,7 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
  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)
+ 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
@@ -83,11 +83,12 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
 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
@@ -100,7 +101,7 @@ if ( `grep -c pdbref file.inp` ) 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`)
+  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
@@ -113,11 +114,9 @@ if ( `grep -c pdbref file.inp` ) then
  /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
@@ -125,11 +124,9 @@ if ( `grep -c pdbref file.inp` ) then
 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
 

diff --git a/files/pbs8_newct-9p.csh b/files/pbs8_newct-9p.csh
index 10d70d5..c1b1494 100755 (executable)
--- a/files/pbs8_newct-9p.csh
+++ b/files/pbs8_newct-9p.csh
@@ -74,7 +74,7 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
  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)
+ 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
@@ -83,11 +83,12 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
 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
@@ -100,7 +101,7 @@ if ( `grep -c pdbref file.inp` ) 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`)
+  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
@@ -112,11 +113,9 @@ if ( `grep -c pdbref file.inp` ) then
  /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
@@ -124,11 +123,9 @@ if ( `grep -c pdbref file.inp` ) then
 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