thorfilters_hints.html

Daylight Summer School 2001, June 5-7, Santa Fe, NM

Daylight Worksheet - Using Thorfilters and Sthorman -- with HINTS!

Thorfilters provide a command line interface to the thor and merlin servers. Shell scripts of thorfilter commands are highly useful for database administration (this will be covered in day 2). These exercises will introduce you to thorfilter commands and interfacing with Daylight databases without an XView interface.

Task: Lookup the clogp and cmr value for dopamine(NCCc1ccc(O)c(O)c1) and create a postscript file which displays the output with structural depictions and TDT data.

Verify that the thor server is running

thorping servername

sun1% thorping sun0 
thorping: Connection to sun0:thor succeeded

Find all available databases which the thorserver has access to.

thorls sun0

sun1% thorls sun0
  LOPAC
  SMARTS
  acd992
  asinex98
  ccr97
  ccr972demo
  chemsynth97demo
  csc-plate
  ic97demo
  maybridge001
  maybridge99
  maybridge991
  maybridge99demo
  medchem00
  medchem99demo
  mix97demo
  nci95
  nci96
  spresi95demo
  spresirxn98demo
  tocris2000
  wdi001
  wdi991demo

Find the available options for thorlookup and thorlist

thorlookup

sun1% thorlookup

thorlookup 4.62, 1993 (c) Daylight CIS, Inc.

Usage:  thorlookup database [options] [[infile] outfile]

Database syntax:  base[%basepw][@host[:service[:user]]][%hostpw]
Infile  formats:  .smi .tdt       (default is .smi)
Outfile formats:  .smi .tdt .fdt  (default is .tdt)

Options:
  -EXCLUDE_DATATYPES ..... NONE or [tag tag .. tag]
  -EXPAND_INDIRECT_DATA .. [TRUE|FALSE]  (default: TRUE)
  -RAW_DATA .............. [TRUE|FALSE]  (default: FALSE)
  -INCLUDE_DATATYPES ..... ALL  or [tag tag .. tag]
  -INPUT_FORMAT .......... [SMI|TDT]     (default: per infile/SMI)
  -OUTPUT_FORMAT ......... [SMI|TDT|FDT] (default: per outfile/TDT)
  -REJECT_LOG ............ NONE or file  (default: NONE)
  -RETRIEVE_ALL .......... [TRUE|FALSE]  (default: FALSE)
  -SECURE_PASSWORDS ...... [TRUE|FALSE]  (default: TRUE)
  -THOR_IPC_SERVICE ...... thor service  (default: "thor")

Notes:
  If infile/outfile not specified, stdin/stdout are used.
  INCLUDE_DATATYPES is processed before EXCLUDE_DATATYPES.
  Formatted data tree (.fdt) files are suitable for treetops input.
  Tags may be delimited by space, bar (|), or comma (,).

   ERROR: program requires 1-3 parameters (thorlookup)

thorlist

sun1% thorlist
ERROR: missing database name
 
Usage: thorlist [options] database [outfile]

Database syntax:  base[%basepw][@host[:service[:user]]][%hostpw]

Options:
 -KEEP_INDIRECT_DATA TRUE|FALSE .. don't expand indir-refs  (default TRUE)
 -TDT_OUTPUT_FORMAT LIST|DUMP ... 1-line or multi-line TDT (default LIST)
 -MAJOR_REPORT N ................. # TDTs for major reports (default 500)
 -MINOR_REPORT N ................. # TDTs for minor reports (default 10)
 -DO_RECORDS N ................... output N TDTs then stop  (default ALL)
 -SKIP_RECORDS N ................. skip N TDTs of output    (default 0)
 -DEAL n/N ....................... only process nth of each N TDTs
 -THOR_IPC_SERVICE service ....... tcp/ip service name      (default `thor')
 -SECURE_PASSWORDS TRUE|FALSE .... interactive passwords    (default TRUE)
 -CACHE_LEVEL [WRITETHRU|READWRITE|WRITETHRU_ALL|READWRITE_ALL]

Lookup the datatypes for clogp and cmr in the medchem00_datatypes database

thorlist -SECURE_PASSWORDS FALSE \ medchem00_datatypes%@sun0:thor:thor%cognition \ > medchem00_datatypes.tdt

sun1% more medchem00_datatypes.tdt
...
$D
_V<"CMR;Error level;Version">
_B<"CMR;CMR/err;CMR/ver">
_N<"NUMERIC;INDIRECT $I;">
_P<"*;*;">
_S
_D<"Estimate of the polarizability by CMR algorithm;Error level, 0=OK;Version of CLOGP which computed estimate">
_M
_O
TS<199805201341.58>
|
...
$D
_V<"CLOGP;Error level;Version">
_B<"CLOGP;CLOGP/err;CLOGP/ver">
_N<"NUMERIC;INDIRECT $I;">
_P<"*;*;">
_S<"Estimate of the LogP(o/w) coefficient by CLOGP3 algorithm;Error Level;Version">
_D<"Estimate of the LogP(o/w) coefficient by CLOGP3 algorithm;Error level ">
_M
_O
TS<199805201341.58>
|

Find the datatypes in the above tdt file that are for clogp and cmr

Use thorlookup to output a FDT file with clogp, cmr for Dopamine

 sun1% vi dopamine.smi 
        OR 
 sgi2% jot dopamine.smi  (on SGI systems)
 sun1% dtpad dopamine.smi (on SUN systems)
 put into file:
         NCCc1ccc(O)c(O)c1 dopamine
 sun1% thorlookup -SECURE_PASSWORDS FALSE -OUTPUT_FORMAT FDT  \
         medchem00%@sun0:thor:thor%cognition < dopamine.smi > dopamine.fdt

Lookup options for treetops

treetops -options

sun1% treetops -options

  treetops 4.62 Daylight CIS Inc. -- OPTION SUMMARY

  Convert tab-delimited file to PostScript file with depictions

    Usage:  treetops [options] < in.fdt > out.ps
       or:  treetops [options] in.fdt > out.ps
       or:  treetops [options] in.fdt out.ps

  Page formatting options:
     -PRINT_BINDER      [NONE|LEFT|TOP|LEFTRIGHT|TOPBOTTOM]
     -PRINT_COLORMODE   [BOW|WOB|COW|COB]
     -PRINT_DATAFONT    "Helvetica"
     -PRINT_DATASIZE    
     -PRINT_FOOTER      NONE|STANDARD
     -PRINT_LABELFONT   "Helvetica-BoldOblique"
     -PRINT_LABELSIZE   
     -PRINT_LANGUAGE    PS|EPS
     -PRINT_MARGINS     [BLEED|MINIMAL|NARROW|NORMAL|WIDE|HUGE]
     -PRINT_ORIENT      [TALL|WIDE]
     -PRINT_PAGELIMIT   
     -PRINT_PAPER       [USLETTER|USLEGAL|USTABLOID|A3|A4|A5|B5|
                         COMPUTER|FANFOLD]
     -PRINT_PICTSIZE    
     -PRINT_SMARTS      NONE or SMARTS to highlight
     -PRINT_STEREO_ANG  
     -PRINT_STEREO_SEP  
     -PRINT_TITLE       NONE or "any string"
     -PRINT_TITLEFONT   "Helvetica-Bold"
     -PRINT_TITLESIZE   

  Data formatting options:
     -PRINT_DEPICT      NONE or "tag,tag,...,tag"
     -PRINT_SCHEMA      NONE or "tag,tag,...,tag"
     -PRINT_STEREO      NONE or "tag,tag,...,tag"
     -PRINT_TEXT        NONE or "tag,tag,...,tag"

Create postscript file using treetops and view with postscript viewer
sun1% treetops file.fdt | pageview (on SUN systems) (The lab SGI's do not have a postscript viewer, so send results to the printer) sgi2% treetops file.fdt | mugprint (on SGI systems)

Give database access to a new user with sthorman

sun1% sthorman Version: sthorman 4.62 .................................................... . STHORMAN -- Serial THOR Manager Program. . . . . Enter "?" for help at any prompt. . . The menu selection "." goes to top-level menu. . .................................................... STHORMAN needs to be connected to a server. Enter machine the server is running on: ("sun1") Enter port (service) of server: ("thor") Enter username: ("norah") thor Enter server username's password: Connected to new server. Current service: sun1:thor SERVER MENU (TOP LEVEL MENU): 1) Connect to a new server 2) List server's version 3) List current users 4) Change server security... 5) Databases... 6) Send message to users... 7) Evict user... 0) Quit Enter menu selection (or '?'): 4 SERVER SECURITY MENU: 1) List users 2) List hosts 3) Add/Change user 4) Add host 5) Remove user 6) Remove host 7) Set exclusion mode 0) Go back to server menu Enter menu selection (or '?'): 3 Current service: sun1:thor Enter user name: newuser This user does NOT exist, make new user? ("yes") yes Enter password for newuser: Enter authorization password: New user has been added for newuser to server list. SERVER SECURITY MENU: 1) List users 2) List hosts 3) Add/Change user 4) Add host 5) Remove user 6) Remove host 7) Set exclusion mode 0) Go back to server menu Enter menu selection (or '?'): 0 SERVER MENU (TOP LEVEL MENU): 1) Connect to a new server 2) List server's version 3) List current users 4) Change server security... 5) Databases... 6) Send message to users... 7) Evict user... 0) Quit Enter menu selection (or '?'): 0 Are you sure you want to quit? ("yes") yes sthorman is finished.

Daylight Chemical Information Systems Inc.
support@daylight.com