New test file to exercise the SMILES canonicalizer.

test/cansmiles_shuffle.sh

@@ -0,0 +1,77 @@
+#!/bin/sh
+#======================================================================
+# FILE:		cansmiles_shuffle.sh
+# AUTHOR:	Craig A. James
+# DESCRIPTION:
+#	Tests SMILES canonicalization.  For each SMILES of input:
+#
+#	  * Writes the SMILES (repeats it) N times
+#
+#	  * Runs the N repeated SMILES through "babel ... -o smi -xC", (the
+#	    "anti-canonicalizer" option that generates randomly-ordered
+#	    SMILES) to generate N different but equivalent SMILES.
+#
+#	  * The N random SMILES are canonicalized using "babel ... -o can",
+#	    which in theory should result in N identical SMILES.
+#
+#	  * The N canonical smiles are run through "sort -u" (sort-unique),
+#	    which should produce a file with exactly one SMILES.
+#
+#	  * The final output file's lines are counted.  If there is more
+#	    than one line (more than one SMILES), it is reported as
+#	    an error.
+#
+#======================================================================	
+# Copyright (c) 2009, Craig A. James, eMolecules Inc.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation version 2 of the License.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#======================================================================
+
+niter=$1
+echo "$0: $niter shuffles per molecule";
+
+n=0
+errors=0
+tmpfile=/tmp/babel$$.smi
+canfile=/tmp/babel$$.can
+
+unset xpg_echo
+
+while read -r smiles ; do
+
+  # Generate N random SMILES for this molecule
+  n=`expr $n + 1`
+  (
+   i=0
+   while test $i -lt $niter ; do
+      /bin/echo $smiles
+      i=`expr $i + 1`
+   done
+  ) | babel -i smi -o smi -xC >$tmpfile 2>/dev/null 
+
+  # Canonicalize them: They should all come out the same
+  babel $tmpfile -o can 2>/dev/null | sort -u >$canfile
+
+  # We should only have one SMILES now.  Any more (or zero) is an error.
+  count=`wc --lines <$canfile`
+  if [ "$count" -ne "1" ] ; then
+    echo ""
+    echo "error: Record $n: Got $count SMILES for one molecule:"
+    cat $canfile
+    errors=`expr $errors + 1`
+  fi
+
+  echo -n "."
+done
+
+echo ""
+echo "$n SMILES tested, $errors errors."
+rm $tmpfile $canfile
+