| Jul 1 2004 |
[ s_blastdbDir | s_editor | s_entryDelimiter | s_errorFormat | s_fieldDelimiter | s_helpEngine | s_icmhome | s_inxDir | s_icmPrompt | s_imageViewer | s_javaCodeBase | s_labelHeader | s_lib | s_logDir | s_out | s_pdbDir | s_projectDir | s_printCommand | s_prositeDat | s_psViewer | s_reslib | s_skipMessages | s_tempDir | s_translateString | s_userDir | s_usrlib | s_webEntrezLink | s_webViewer | s_xpdbDir ]
s_blastdbDir=Getenv("BLASTDB")
to your ~/.icm/user_startup.icm file.
The find database family of sequence/pattern search commands use the s_blastdbDir directory.
Attention!!! Always use the call to the program which starts the program in the foreground. For example: use "jot -f" rather than just "jot", since the default is running in the background. Examples: s_editor = "vi" # good old vi, does not require a separate window s_editor = "jot -f" # popular SGI editor s_editor = "xedit" # simple and exists for X on every platform s_editor = "notepad" # exists for PCs
Default: ("#____________________________ %i") Example: s_entryDelimiter="//\n" # EMBL-database delimiter
Examples:
s_errorFormat="" # do NOT print error messages
s_errorFormat=" Error> %s" # standard error messages
s_errorFormat=" Erreur> %s" # French version
# html-padding
s_errorFormat="<hr><h3>%s</h3><hr>"
s_errorFormat=" Fehler> der Betrieb ist verboten"
# replace all the messages by this text
Important. If a character is duplicated in s_fieldDelimiter (e.g. s_fieldDelimiter="::" ), then multiple occurrences of this character will be ignored. Otherwise, EMPTY fields will be created between each pair of identical delimiter characters. In write table s_fieldDelimiter is honored only if is a one-letter symbol, like "," or "\t". See also the opposite operation, merging members of string array into one string: Sum( S_, s_separator ) Examples: s_fieldDelimiter="\t" # "aaa\t\t bbb" splits into "aaa",""," bbb" s_fieldDelimiter="\t\t" # "aaa\t\t bbb" splits into "aaa"," bbb"Default ( " \t\t" i.e. two blanks, two tabs, meaning skip multiple blanks or tabs). Another reasonable possibility is " \t\t\n\n" which means skip blanks,tabs and carriage returns.
Examples: s_helpEngine="/usr/bin/netscape" s_helpEngine="mozilla" # make sure you can start it in the UNIX shell s_helpEngine="icm" # why would one need more?
The Linux icm-rpm package creates s_icmhome in /usr/icm directory.
See also: read index , write index table, write index .
Examples: s_icmPrompt="%## " # for askets s_icmPrompt="" # for super-askets s_icmPrompt="%T> " # for anxious paranoiac freaks s_icmPrompt="MY_ICM/%o/%e/%T/%#> " # for the verbose s_icmPrompt="Hi-hi|%e-^%o+%T> " # for the messy s_icmPrompt="Icm command number %#> " # for the retarded s_icmPrompt="Hey dude, type something" # for dudes s_icmPrompt="%o/%e> " # for humble and wise researches Default: "icm/%o> "
Default for SGIs ( "imgview").
Default: "/Java/"
s_labelHeader=" "Default ( "" - an empty string).
Default ( "icm").
The same logic applies to the _crashlog.icm file which is created when ICM crashes. Examples: s_logDir = "." # _seslog.icm stored in the current working directory s_logDir = "" # to the current working directory
Default ( "is where the string/text is stored" ).
The pdb directory also contains the derived_data subdirectory with useful files ( pdb sequences, index files etc. ) Example: s_pdbDir ="ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/pdb/" pdbDirStyle = "ab/pdb1abc.ent.Z" s_pdbDir = "/data/pdb/" read sarray s_pdbDir+"/derived_data/index/source.idx" source = Tolower(Trim(Field(source,1))) for i=1,Nof(source) read pdb source[i] # do some analysis delete a_*. endforDefault ( "/data/pdb/"). It is usually redefined in the _startup file.
Example: s_printCommand = "lp -c -d ColorPrn22" write image postscript print # save image and print
Default ( "prosite.dat" ). It is usually redefined to s_icmhome+"prosite.dat" in the _startup file.
unix $s_psViewer </tt><i>your PostScript file name</i> Default ( "/usr/opt/bin/gs -q" ).
Default ( "icm").
Example: a = 1 if = 2 # deliberately generate error Error> [2073] illegal IF: wrong condition in if=2 s_skipMessages = "[2073]" if = 2 # now no message is generated if Error(number)==2073 quit a = yes # generates another error Error> [696] wrong assignment or name conflict s_skipMessages = "[2073][696]" a = yes # hides the error message 234*2352352532 Warning> [147] number 2352352532 is too big for an integer (>2147483647) 0 s_skipMessages = "[2073][696][147]" # suppress the warning 234*2352352532 0 See also: errorAction , s_errorFormat . Default ( "[3000][3012]" just to show an example).
Default ( "/usr/tmp/").
Default ( ".:*0#" ).
The suggested _startup file sets this variable to a subdirectory .icm of the user $HOME directory ( $USERPROFILE for Windows), but you may set it anywhere you want. Default ( "$HOME/.icm/").
Default ( "usr").
See also: webEntrezOption, Default ( "http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&uid=%s&Dopt=%c").
Examples: s_webViewer="/usr/bin/netscape" s_webViewer="Mozilla"Default ( "netscape").
Here we compare the execution times for the pdb and xpdb files: eos:/home/ruben/icm> time ./icm -s -e 'read object "/data/xpdb/1ffk.ob"' 0.450u 0.090s 0:00.54 100.0% eos:/home/ruben/icm> time ./icm -s -e 'read pdb "/data/pdb/ff/pdb1ffk.ent.Z"' 38.800u 0.430s 0:42.11 93.1%
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