update 14082023

draskot · Aug 14, 2023 · bc42de5 · bc42de5
1 parent a5092b6
commit bc42de5
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Showing 3 changed files with 2 additions and 5 deletions.
diff --git a/download_Drugbank_fasta_structures b/download_Drugbank_fasta_structures
@@ -12,7 +12,8 @@ do
     if  [ $type == P ] && [ ! -e $vini_dir/ligands/fasta_files/${drug}.fasta ]
     then
         echo -n "."
-        grep "$drug" drugbank?vocabulary.csv > tmp
+        #grep "$drug" drugbank?vocabulary.csv > tmp
+        grep "$drug" drugbank_vocabulary.csv > tmp
         if  [  -s tmp ]
         then
             inline=`head -1 tmp | awk -F','   '{print $1}'`

diff --git a/drugbank?vocabulary.csv → drugbank_vocabulary.csv b/drugbank?vocabulary.csv → drugbank_vocabulary.csv
diff --git a/malavini b/malavini
@@ -150,10 +150,6 @@ do
                                  python clean_pdb_keep_ligand.py complex_${comp_index}.pdb -ignorechain
                                  mv complex_${comp_index}.pdb_00.pdb complex_${comp_index}.pdb
                                  conda deactivate
-                                 #cp $vini_dir/1AKI.pdb ./complex_${comp_index}.pdb #next 4L for debug
-                                 #python ${ROSETTA_TOOLS}/clean_pdb.py complex_${comp_index}.pdb A   #clean receptor
-                                 #mv complex_${comp_index}_A.pdb complex_${comp_index}.pdb
-                                 #rm *fasta
                              else
                                  obabel $comp_source/complex_${comp_index}.pdbqt -O complex_${comp_index}.pdb
                              fi