Jack Delany
The current release is 4.81. Is is a major release and includes a full distribution of the software and documentation. The following document gives an overview of the platforms supported and features included in the 4.81 release.
Platforms:
Compatibility:
None of the language specifications have changed between 4.7x and 4.81. 4.7x Thor databases are fully compatible with 4.81. No thor upgrade procedure is needed. A Daycart 4.7x -> 4.81 upgrade is required since package specifications and formats of "backing" index objects have changed. It is not necessary to modify data in base tables in Daycart as part of the upgrade.
Features:
$ thorping -PROCESS_ID TRUE thorping: Connection to localhost:thor succeeded Process id of server: 9839
The following one-liner puts the process id for the server into a shell variable:
$ tpid=`thorping -process_id true | grep Process | cut -c23-` $ echo $tpid 9839
Contrast this with the old contrib code (from KILL_DCIS_SERVERS) which attempts to get the process ID from the logfile or the output of "ps":
DY_THOR_LOG_FILE=${DY_THOR_LOG_FILE:-/tmp/thorserver.log}
if [ ! -f "$DY_THOR_LOG_FILE" ]; then
echo "DY_THOR_LOG_FILE not defined..."
PS=`ps -el | grep thors`
if [ "$PS" ]; then
i=`echo $PS | sed -e "s/^ *//" -e "s/ */ /g" | cut -f4 -d' '`
echo "Thorserver pid appears to be >>> $i <<< from ps:"
echo $PS
echo "You may wish to kill this process manually."
else
echo "Can't find Thorserver pid."
fi
else
tpid=`grep pid $DY_THOR_LOG_FILE | sed -e "s/^.*pid = //" -e "s/ //g"`
case "$tpid" in
[0-9][0-9]*) echo "Thorserver pid = $tpid" ;;
?) tpid="";
echo "Can't determine Thorserver pid." ;;
esac
fi
The toolkit uses valences in three ways when interpreting SMILES: filling hydrogens for the organic subset (B,C,N,O,P,S,H,F,Cl,I), determining bonding of aromatic atoms, and generating warnings.
| Database | Total in 4.71 | Go away | Unchanged | New in 4.81 | Total in 4.81 |
|---|---|---|---|---|---|
| ACD | 611 | 586 | 25 | 35 | 60 |
| Medchem | 166 | 113 | 53 | 119 | 172 |
| Spresi | 6779 | 5993 | 786 | 6059 | 6845 |
| WDI | 99 | 88 | 11 | 17 | 28 |
xsmiles can be generated for any valid molecule or reaction (anything for which a cansmiles can be generated). xsmiles have NO aromaticity. They are written with kekule bonding everywhere. Optionally, one can include explicit hydrogen counts everywhere.