Thorfilters Exercise #2 -- With Hints

Thorfilters Exercise #2 -- with HINTS!

TASK:

Retrieve 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.

PROCEDURE:

Verify that the thor server is running

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

Find all available databases which the thorserver has access to.

sun1% thorls sun0 acd021 acd021demo maybridge001 maybridge00demo maybridge97demo medchem00demo medchem02 medchem02demo medchem98demo mix97demo nci00 nci00demo nci96demo spresi95 spresi95demo spresi95preps spresi98rxn spresirxn98demo wdi00demo wdi00demo2d wdi023 wdi023demo wdi984demo

Lookup the datatypes for clogp and cmr in the medchem02_datatypes database

First, find the available options for thorlookup and thorlist

sun1% thorlookup

thorlookup 4.82, 2003 (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)

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)
 -BEFORE YYYY[MM[DD[HH[MM[.SS]]]]] output before timestamp  (default infinity)
 -SINCE YYYY[MM[DD[HH[MM[.SS]]]]]  output since timestamp   (default 0)
 -CACHE_LEVEL [WRITETHRU|READWRITE|WRITETHRU_ALL|READWRITE_ALL]

Then,

sun1%thorlist -SECURE_PASSWORDS FALSE \ medchem02_datatypes%@sun0:thor:thor%cognition > medchem02_datatypes.tdt

Then view the file medchem02_datatypes.tdt and find the datatypes that are for clogp and cmr

sun1% more medchem02_datatypes.tdt

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

sun1% vi dopamine.smi sun1% dtpad dopamine.smi put into file: NCCc1ccc(O)c(O)c1 dopamine sun1% thorlookup -SECURE_PASSWORDS FALSE -OUTPUT_FORMAT FDT \ medchem02%@sun0:thor:thor%cognition < dopamine.smi > dopamine.fdt

Create postscript file using treetops and view with postscript viewer

First, lookup options for treetops:

sun1% treetops -options

  treetops 4.82 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:
     -DEPICT_SUPPRESS_LABELS [TRUE|FALSE]
     -PRINT_BINDER      [NONE|LEFT|TOP|LEFTRIGHT|TOPBOTTOM]
     -PRINT_BOLDWIDTH   [THIN|NORMAL|WIDE|EXTRAWIDE]
     -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_LINEWIDTH   [THIN|NORMAL|WIDE|EXTRAWIDE]
     -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"

Then,

sun1% treetops file.fdt | pageview