Name

Unix Synopsis

Description

This man(1) page gives information relevant to invoking 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 display
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

Options

-DATABASE_OPEN_FRAME_X X
-DATABASE_OPEN_FRAME_Y Y

Initial location for xvthor's "Open Database" panel. Default: X=20, Y=20.

Do not show implicit chiral hydrogens when not necessary for illustration of stereochemistry. Default FALSE.

Scalar value for shortening the length of bonds to hydrogen. The allowed range is 0.67 (67%) to 1.00 (100%). Default 1.00.

Use pre-v4.83 bond style renditions. Default FALSE.

Suppress atom labelling for chains. Default TRUE.

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).

Default name of server to display in "Open Database" Panel. Defaults is "" (use server on client's machine).

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.

Initial GRINS-Widget geometry. Note that these override the GRINS Widget's own options, i.e. GRINS_FRAME_HEIGHT, etc.

Names the default TCP/IP service or "port" of the Thor server. Default: thor.

Initial location of xvthor's main window. Default: X=20, Y=20.

Datatypes allowed in datatypes menu. Default: "" (all datatypes).

Initial size (pixels) of the depiction canvas on xvthor's main window. Default: width=250, height=220.

Margin (pixels) between the depiction canvas and the left edge of xvthor's main window. Default: 10 (pixels).

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).

Initial value for the "Show Depiction" button. If TRUE, the Depict Widget is automatically shown when a SMILES is available. Default: TRUE (show depiction).

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).

Datatype to use to label the Depiction canvas on xvthor's main window. Default "PCN" ("local name").

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.

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.

Initial datatypes to be excluded from display. Tags can be separated by spaces, commas, "|", or tab. Default is "NONE".

Initial datatypes to include in display. Tags can be separated by spaces, commas, "|", or tab. Default is "ALL" (include all datatypes).

Initial geometry for the TDT Widget.

A string containing one of more of SMI, ISM, SMI2D, D3D, or D2D, indicating the initial preference of whether to show structures (SMI=SMILES, ISM=Isomeric SMILES) and conformations (D3D=3D coordinates, D2D=2D coordinates) graphically or textually. The SMI2D option specifies that 2D coordinates, if present, should be used for showing SMILES. The SMILES affected by this option depends on TDT content. Isomeric SMILES is affected if 2D coordinates are present within its TDT subtree, otherwise the root SMILES is affected. Default: "SMI ISM D3D" (show SMILES, Isomeric SMILES, and 3D coordinates graphically, show 2D coordinates textually, and don't use 2D coordinates for SMILES).

Initial height (in pixels) of TDT-widget drawings (depictions and conformations). Default 100.

Maximum number of pixels (in Mega-pixels) allowed to be set for the TDT_MPIXELS option. Default 8 (8 mega-pixels).

Initial number of pixels (in Mega-Pixels) for the TDT widget's scrolling region. Default is 2 mega-pixels.

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".

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).

Command used to delete print file. Should contain a "%s", which is replaced by the filename. Default: /bin/rm -f "%s" &

Directory to hold temporary print files. Default /tmp.

Command used to execute print program "%s" in foreground (synchronously). Should contain "%s", which is replaced by the filename. Default: /bin/sh -f "%s"

Command used to print color PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h %s &

Command used to print then delete color PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h -r -PPhaser %s &

Command used to print monochrome PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h %s &

Command used to print then delete monochrome PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h -r %s &

Command used to preview PostScript file. Should contain "%s", which is replaced by the filename. Default: pageview -dpi 72 %s &

Return Value

Files

Daylight License

Related Topics

Daylight Theory Manual

Bugs