This man(1) page gives information relevant to invoking the xvthor program. Once xvthor is running, use the "Help" button to view the Daylight Help Widget's "thor" topic. It gives detailed information about the xvthor program.
The Thor facility is organized in two parts: a "server" program providing a thor service (thorserver) and a "client" program providing a user interface (e.g. xvthor). The server has access to databases, and provides all searching and database-access capabilities. The Thor server(s) are normally started when the machine is booted and left running in the background. Assuming that a Thor server is running and available, its presence should be completely transparent to the user.
The following things are required before running xvthor:
a. you are working with an X-Windows displayThe shell script "xvthor4d" is a convenience program for users of SGI's X Windows system using the 4dwm display. It invokes xvthor(1) with several important options that are useful or required on SGI systems. See xvthor4d(1).
b. your machine must be licensed for the xvthor program
c. thorserver must be running on a machine accessible to you
d. thorserver must have the desired database loaded for searching
e. if the thor server is secured by a password, you must know it
f. if the desired database has a read password, you must know it
g. your local file system permissions allow you to run xvthor
h. the environment variable DY_ROOT points the Daylight directory (e.g. /usr/local/daylight/v442)
i. you have read permission for files in $DY_ROOT/etc and $DY_ROOT/help
-DATABASE_OPEN_FRAME_X X
-DATABASE_OPEN_FRAME_Y Y
Initial location for xvthor's "Open Database" panel. Default: X=20, Y=20.-FULLSCREENDEBUG TRUE|FALSE
There is a bug caused by an interaction between XView and SGI's X-Window system using the 4dwm window manager -- pressing an XView button causes the window manager to "lock up" permanently. This options, which was originally meant to be used by developers during program debugging, prevents this "lock up". Default: automatically set for different machines (see dy_sysprofile.opt).-LICENSEDATA file
The Daylight license file. Default: $DY_ROOT/etc/dy_license.dat.-THOR_DEFAULT_SERVER
Default name of server to display in "Open Database" Panel. Defaults is "" (use server on client's machine).-DEPICT_SUPPRESS_LABELS TRUE|FALSE
Suppress atom labelling for chains. Default TRUE.-THOR_DEPICT_FRAME_HEIGHT
Initial Depict-Widget geometry, and Depict-Widget popup-window geometry. Note that these override the Depict Widget's own options, i.e. DEPICT_FRAME_HEIGHT, etc.-THOR_GRINS_HEIGHT
Initial GRINS-Widget geometry. Note that these override the GRINS Widget's own options, i.e. GRINS_FRAME_HEIGHT, etc.-THOR_IPC_SERVICE service
Names the default TCP/IP service or "port" of the Thor server. Default: thor.-THOR_MAINFRAME_X X
Initial location of xvthor's main window. Default: X=20, Y=20.-THOR_MENU_DATATYPES
Datatypes allowed in datatypes menu. Default: "" (all datatypes).-THOR_PAINTCANVAS_HEIGHT width
Initial size (pixels) of the depiction canvas on xvthor's main window. Default: width=250, height=220.-THOR_PAINTCANVAS_MARGIN
Margin (pixels) between the depiction canvas and the left edge of xvthor's main window. Default: 10 (pixels).-THOR_SHOW_CONFORMATION TRUE|FALSE
Initial value for the "Show Conformation" button. If TRUE, the Trackball (3D) widget is automatically shown when a conformation is available. Default: FALSE (don't show).-THOR_SHOW_DEPICTION TRUE|FALSE
Initial value for the "Show Depiction" button. If TRUE, the Depict Widget is automatically shown when a SMILES is available. Default: TRUE (show depiction).-THOR_SHOW_FULLTDT TRUE|FALSE
Initial value for the "Show Datatree" button. If TRUE, the TDT Widget is automatically shown when a TDT is retrieved from a database. Default: FALSE (summarize only).-THOR_TITLE_DATATYPE tag
Datatype to use to label the Depiction canvas on xvthor's main window. Default "PCN" ("local name").-THOR_TRIM_DBNAMES TRUE|FALSE
FALSE means show the full name of the Thor server (e.g. "host:thor:user"). TRUE means trim server:service from db names if they match defaults (e.g. "host"). Default: TRUE.TDT-WIDGET OPTIONS:
The following options control the initial settings for the Thor Datatree (TDT) Widget.
-DATATREE_IREFS_EDITFILE file
File to show for Indirect-reference editing. Default: $DY_THORDB/irefs.tdt.-EXCLUDE_DATATYPES "tag,[tag...]"
Initial datatypes to be excluded from display. Tags can be separated by spaces, commas, "|", or tab. Default is "NONE".-INCLUDE_DATATYPES
Initial datatypes to include in display. Tags can be separated by spaces, commas, "|", or tab. Default is "ALL" (include all datatypes).-TDT_FRAME_HEIGHT height
Initial geometry for the TDT Widget.-TDT_GRAPHICS_PREFS "SMI ISM D3D D2D SMI2D"
A string containing one of more of SMI, ISM, D3D, D2D, or SMI2D, indicating the initial preference of whether to show structures and conformations graphically or textually. If the keyword is missing, they are shown textually. The SMI2D option specifies that 2D coordinates, if present, should be used for showing structures. This option is meaningful when specified with the SMI or ISM options. Default is "SMI ISM D3D" (show SMILES and Isomeric SMILES, and D3D graphically, show 2D textually, don't use 2D coordinates for showing structures).-TDT_GRAPHICS_SIZE pixels
Initial height (in pixels) of TDT-widget drawings (depictions and conformations). Default 100.-TDT_MAX_MPIXELS
Maximum number of pixels (in Mega-pixels) allowed to be set for the TDT_MPIXELS option. Default 8 (8 mega-pixels).-TDT_MPIXELS
Initial number of pixels (in Mega-Pixels) for the TDT widget's scrolling region. Default is 2 mega-pixels.-TDT_TEXT_PREFS
TDT Widget text preferences are character flags setting boolean properties. If prefaced by "NO" they're off; else if present, they're on. The recognized strings are: FIRSTONLY SHOWEMPTY EXPANDINDIR NTUPLESUM TRUNCATE. Default: "NOFIRSTONLY NOSHOWEMPTY EXPANDINDIR NTUPLESUM NOTRUNCATE".PRINTING OPTIONS:
The following options are used by the "Print" button on the TDT Widget.
-PRINT_COLORMODE BOW|WOB|COW|COB
Printing color mode [Black|White|Color] On [Black|White]. Default BOW (Black-On-White).-PRINT_DELETE_CMD command.
Command used to delete print file. Should contain a "%s", which is replaced by the filename. Default: /bin/rm -f "%s" &-PRINT_DIRECTORY
Directory to hold temporary print files. Default /tmp.-PRINT_EXECUTE_FG_CMD
Command used to execute print program "%s" in foreground (synchronously). Should contain "%s", which is replaced by the filename. Default: /bin/sh -f "%s"-PRINT_PS_COLOR_CMD
Command used to print color PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h %s &-PRINT_PS_COLOR_ZAP_CMD
Command used to print then delete color PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h -r -PPhaser %s &-PRINT_PS_MONO_CMD
Command used to print monochrome PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h %s &-PRINT_PS_MONO_ZAP_CMD
Command used to print then delete monochrome PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h -r %s &-PRINT_PS_VIEW_ZAP_CMD
Command used to preview PostScript file. Should contain "%s", which is replaced by the filename. Default: pageview -dpi 72 %s &
Daylight Theory Manual
Once xvthor is running, the "Help" button invokes the help widget with a detailed xvthor help page. Or, see the file $DY_ROOT/help/thor.hw.
Daylight Chemical Information Systems, Inc.