molenc.sh can take a third optional argument

the encoding dictionary file from a previously encoded dataset

bin/molenc.sh

@@ -1,15 +1,19 @@
 #!/bin/bash
 
-# set -x # DEBUG
+#set -x # DEBUG
 
 # check input_fn and output_fn are passed
-if [ "$#" -ne 2 ]; then
-    echo "usage: molenc.sh input.smi output.txt"
+if [ "$#" -ne 2 ] && [ "$#" -ne 3 ]; then
+    echo "usage: molenc.sh input.smi output.txt [encoding.dix]"
     exit 1
 fi
 
 input=$1
 output=$2
+dico=""
+if [ "$#" -eq 3 ]; then
+    dico=$3
+fi
 
 std_log=$input'.std_log'
 tmp=`mktemp`
@@ -27,7 +31,11 @@ echo typing atoms...
 molenc_type_atoms.py $tmp_smi > $tmp_types
 echo encoding molecules...
 molenc_e -i $tmp_types -r 0:1 -o $tmp_enc
-molenc_d -i $tmp_enc -o $output
+if [ "$dico" != "" ]; then
+    molenc_d -i $tmp_enc -o $output -d $dico
+else
+    molenc_d -i $tmp_enc -o $output
+fi
 
 # cleanup
 rm -f $std_log $tmp $tmp_smi $tmp_types $tmp_enc