NanoShaper + VMD workaround

NanoShaper_Docker_VMD.sh

 #!/bin/bash
-
-#Current Directory: complete path of the directory where input files are
-DIR="$( pwd )"
-
-CONF_PATH=${1?Error: Surface Configuration not given}
-
-echo "Surface Configuration: $1"
-
-docker run -it --mount type=bind,source=${DIR},target=/App gitlab.iit.it:4567/sdecherchi/nanoshaper $1
\ No newline at end of file
+echo "NanoShaper from Docker using VMD"
+
+export CONF=$1
+AAA=$(grep Root_FileName $1)
+echo $AAA
+set -- $AAA
+DIR=$(dirname "$3")
+echo $DIR
+docker run -it --mount type=bind,source=$DIR,target=$DIR gitlab.iit.it:4567/sdecherchi/nanoshaper $CONF

README.md

@@ -69,13 +69,8 @@ NanoShaper is GPL licensed software please read the attached license.txt file.
 	  	```
 		Note that you need to install docker on your system. 
 
-		Alternatevely, rename NanoShaper_Docker_VMD.sh into NanoShaper and just type
-		```console
-	  	cd <Path of the directory where input files are>
-	  	NanoShaper <Surface Configuration file>
-	   	```
-	    after properly adding the NanoShaper executable path to your $PATH variable
-		That might be useful when using nanoshaper docker image together with VMD.
-
+		In order to use nanoshaper docker image inside the molecolar visualization software VMD:
+		rename NanoShaper_Docker_VMD.sh into NanoShaper and add its path to your $PATH variable
+