Release Date: 1 February 2008
Namexvmerlin - Merlin client program using XView windows interface
Unix Synopsisxvmerlin [options] [database@server ...]
DescriptionThe Merlin program is designed to allow an end-user to rapidly and flexibly explore data in Thor chemical information databases. Daylight Version 4 software includes the program `xvmerlin' which is an XView implementation of Merlin for systems using MIT X-Windows displays.
This man(1) page gives information relevant to invoking the xvmerlin program. Once xvmerlin is running, use the "Help" button to view the Daylight Help Widget's "merlin" topic. It gives detailed information about the xvmerlin program.
The Merlin facility is organized in two parts: a "server" program providing a merlin service (merlinserver) and a "client" program providing a user interface (e.g. xvmerlin). The server has access to databases, and provides all searching and database-access capabilities. The Merlin server(s) are normally started when the machine is booted and left running in the background. Assuming that a Merlin server is running and available, its presence should be completely transparent to the user.
The following things are required before running xvmerlin:
a. you are working with an X-Windows displayxvmerlin has the ability to save its current state (open databases, columns, and column locations). When you use the "Quit" item of the "File" menu, one of the choices is "Yes, save state then quit". The state is saved as an option file, by default the file $HOME/.dy_merlinprofile.opt (controlled by option MERLIN_PROFILE, described below). To restore the state, your Daylight-options file ($HOME/dy_profile.opt) should contain the following line:
#include $HOME/.dy_merlinprofile.optThe shell script "xvmerlin4d" is a convenience program for users of SGI's X Windows system using the 4dwm display. It invokes xvmerlin(1) with several important options that are useful or required on SGI systems. See xvmerlin4d(1).
ExamplesStart xvmerlin, naming two other hosts where Merlin servers are running:
xvmerlin -merlin_server_list \\xvmerlin can be invoked with one or more databases. The syntax for database names is described in database(5).
xvmerlin wdi95@hostSuppose you quit xvmerlin via the "Yes, save state then quit" button. You can edit $HOME/dy_profile.dat as described above, or you can use the saved state directly like this:
xvmerlin -MERLIN_PROFILE $HOME/dy_merlinprofile.optStart xvmerlin and open the world drug index (WDI) database:
xvmerlin wdi95Any option (see OPTIONS, below) can be specified in your personal options file, usually $HOME/dy_profile.opt, or on the command line, or can be set in your environment, prefixed with "DY_". For example, the following three are equivalent (these are csh(1) examples):
OptionsThe xvmerlin application has a large number of configurable features; there is a correspondingly large number of options.
GENERAL XVMERLIN OPTIONS:
Do not show implicit chiral hydrogens when not necessary for illustration of stereochemistry. Default FALSE.-DEPICT_HLEN_PCT [0.67 - 1.00]
Scalar value for shortening the length of bonds to hydrogen. The allowed range is 0.67 (67%) to 1.00 (100%). Default 1.00.-DEPICT_OLD_STYLE TRUE|FALSE
Use pre-v4.83 bond style renditions. Default FALSE.-DEPICT_SUPPRESS_LABELS TRUE|FALSE
Suppress atom labelling for chains. Default TRUE.-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 option, 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).-MERLIN_ADJUST_ACTION action
Initial values for the "adjust" (middle) and "select" (right) mouse buttons. Choices are:-MERLIN_ALTERNATE_THORBASE
Names alternate Thor database for xvmerlin's "Show alternate datatree" button. No default.-MERLIN_COLS_MAXINIT N
Maximum number of columns on startup. Default is 4.-MERLIN_DEPICT_MAXSMI N
Maximum length of SMILES to depict in scrolling region (0 = no limit). Any SMILES longer than this number is shown as text. Default 80.-MERLIN_DEPICT_2D_COORDS TRUE|FALSE
Preference of whether to show 2D coordinates graphically or textually. The SMILES used for the depiction depends on TDT content. Isomeric SMILES is used if 2D coordinates are within its TDT subtree, otherwise the root SMILES is used. Default: FALSE (don't depict 2D coordinates). Side Effect: If TRUE, the cell containing the SMILES will be shown with the 2D coordinates. In other words, the SMILES and 2D cells will appear identical.-MERLIN_DEPICT_2D_SMILES TRUE|FALSE
Preference of whether to show SMILES using 2D coordinates. The SMILES cell affected by this option depends on TDT content. Isomeric SMILES is affected if 2D coordinates are within its TDT subtree, otherwise the root SMILES is affected. Default: FALSE (don't show SMILES using 2D coordinates).-MERLIN_DISPLAY_SMILES DEPICTION|TEXT
Whether to display SMILES and Isomeric SMILES columns as pictures or text. Default is DEPICTION.-MERLIN_DTMENU_COLUMNS N
Number of columns in datatype menu (0 means "use XView default"). Default 0.-MERLIN_ENABLE_STORE TRUE|FALSE
Enable "Store", "Recall", and "Exchange" features in Merlin programs. Default TRUE.-MERLIN_ENABLE_THORLOOKUP TRUE|FALSE
Flag to enable xvmerlin to connect to Thor server & open database. Enables "Show Datatree" and "Tautomer Search" features. Default TRUE.-MERLIN_ENABLE_UNDO TRUE|FALSE
Enable "Undo" feature. Default TRUE.-MERLIN_INIT_COLS datatype_tag
Datatypes for creating initial columns. Default is two columns: "$SMI SIMILARITY".-MERLIN_IPC_SERVICE service
Names the default TCP/IP service or "port" of the Thor and Merlin servers. Default: "merlin" and "thor"-MERLIN_LINES_PER_ROW N
Display lines per logical row in xvmerlin. Default is 4.-MERLIN_MAINFRAME_INVERT TRUE|FALSE
Invert fore/background of primary frame in xvmerlin. Default TRUE.-MERLIN_SERVER_LIST "server [server...]"
Server(s) to search for open pools on startup (blank = local machine). See the man page server(5) for server syntax-MERLIN_TANIMOTO_VERYHIGH R
Minimum Tanimoto similarity level considered "very high". Default R = 0.90.-MERLIN_TANIMOTO_HIGH R
Minimum Tanimoto similarity level considered "high". Default R = 0.75.-MERLIN_TANIMOTO_MODERATE R
Minimum Tanimoto similarity level considered "moderate". Default R = 0.60.-MERLIN_TANIMOTO_ROUGH R
Minimum Tanimoto similarity level considered "rough". Default R = 0.50.-MERLIN_VERBOSE_MESSAGES TRUE|FALSE
If TRUE, show error, notes and warning messages as soon as they are available. If FALSE, the "Messages" button is un-greyed (made active) when messages are available, but the Message Widget doesn't pop-up until the "Messages" button is pushed. Default TRUE.-MERLIN_WHOABUDDY_SIZE N
Ask "OK?" if hitlist-save bigger than this. Default N = 10000.-MERLIN_ZOOMFRAME_FONT
Name of default font to use for xvmerlin's "zoom frame". (The "zoom frame" is the window created by "Show Text..." and "Show Depiction" menu items.) Default -b&h-lucidatypewriter-medium-r-normal-sans-14-*-*-*-m-*-*-1.-MERLIN_ZOOMFRAME_INVERT
Invert fore/background of the "zoom frame" in xvmerlin. (The "zoom frame" is the window created by "Show Text..." and "Show Depiction" menu items.) Default TRUE.-SHOW_FOOTER TRUE|FALSE
TRUE causes footers to be used on the windows. Suggested TRUE only for the olwm window manager (i.e. Sun computers). Use FALSE for the mwm window managers and its relatives (i.e. non-Sun computers). Default: automatically set for different machines (see dy_sysprofile.opt).-USE_TRANSIENT_WINDOWS TRUE|FALSE Force widgets to open/close with
main window. Default: automatically set for different machines (see dy_sysprofile.opt).GEOMETRY OPTIONS:
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.-MERLIN_GRINS_HEIGHT
Initial GRINS-Widget geometry. Note that these override the GRINS Widget's own options, i.e. GRINS_FRAME_HEIGHT, etc.-MERLIN_KEYPADFRAME_X
Initial location of the popup "keypad".-MERLIN_MAINFRAME_HEIGHT
Initial geometry of xvmerlin's main window.-MERLIN_SEARCHFRAME_X
Initial location of xvmerlin's search panel.-MERLIN_TRACKBALL_HEIGHT
Initial geometry of xvmerlin's trackball (3D) widget. Note that these override the Trackball Widget's own options, i.e. TRACKBALL_FRAME_HEIGHT, etc.-MERLIN_ZOOMFRAME_HEIGHT
Initial geometry of xvmerlin's "zoomframe".-WINDOW_FRAME_FOOTERSIZE
Size of frame headers and footers on X-Windows displays. Default 24.PRINTING OPTIONS:
Paper margin to get extra room for binding. Default NONE.-PRINT_BOLDWIDTH THIN|NORMAL|WIDE|EXTRAWIDE
Bold graphic line width (shows foreground, substructure). Default NORMAL.-PRINT_COLORMODE BOW|WOB|COW|COB
Printing color mode [Black|White|Color] On [Black|White]. Default BOW (Black-On-White).-PRINT_COLUMNS N
Number of columns in grid of depictions. Default 3.-PRINT_DATAFONT font
Font used to print data. Default Helvetica.-PRINT_DATASIZE N
Font size used to print data. Default 10 (points).-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_LABELFONT
Font used to print labels. Default Helvetica-BoldOblique.-PRINT_LABELSIZE
Font size used to print labels. Default 10 (points).-PRINT_LINEWIDTH THIN|NORMAL|WIDE|EXTRAWIDE
Normal graphic line width for depictions. Default THIN.-PRINT_MARGINS BLEED|MINIMAL|NARROW|NORMAL|WIDE|HUGE
Basic print margins. Default NORMAL.-PRINT_ORIENT TALL|WIDE
Paper orientation for printing. Default TALL.-PRINT_PAPER paper
Choices are: USLETTER, USLEGAL, USTABLOID, A3, A4, A5, B5, COMPUTER, FANFOLD. Default USLETTER.-PRINT_PICTSIZE size
Size of embedded pictures in printed output. Default 72 (points).-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_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 &-PRINT_ROWS N
Number of rows in grid of depictions. Default 5.-PRINT_SHADOW TRUE|FALSE
If TRUE, display drop shadows on white-background depictions. Default TRUE.-PRINT_SMILES TEXT|DEPICTION
Should SMILES be printed as text or picture? Default DEPICTION.-PRINT_TITLE title
Title for printed output. Default NONE (no title).-PRINT_TITLEFONT font
Font used to print title. Default Helvetica-Bold.-PRINT_TITLESIZE
Font size used to print title. Default 14.CONTEXT OPTIONS:
The context options are normally set when you use the "Quit" menu item, then select the "Yes, save state then quit" button. xvmerlin can save up to eight databases and their context, using the options specified below. Note that each group of 8 options is summarized by the [1-8] notation, i.e. MERLIN_PAGE1_POOL, MERLIN_PAGE2_POOL, ..., MERLIN_PAGE8_POOL are all represented as MERLIN_PAGE[1-8]_POOL.
Names an options file for xvmerlin to read that contains a saved state (the options listed below). Default: $HOME/.dy_merlinprofile.opt-MERLIN_RESTORE_CONTEXT
These two options provide security for a saved context. When the context is saved, the user is asked to provide a restoration password. All passwords that were required to create the original context (the servers' and databases' passwords) are encrypted using this context-restoration password. When the context is restored, the databases can be re-opened without the user having to re-enter each password. And because the passwords are encrypted, they are never stored as clear-text anywhere.-MERLIN_PAGE[1-8]_POOL
The names of the databases to be re-opened when the context is restored.-MERLIN_PAGE[1-8]_POOLPW
Passwords for the databases. Note that these are encrypted, and require the context-restoration password to be useful. See MERLIN_RESTORE_PASSWORD, above.-MERLIN_PAGE[1-8]_BASE
The Thor database corresponding to MERLIN_PAGE[1-8]_POOL, above.-MERLIN_PAGE[1-8]_BASEPW
The password for the Thor databases.-MERLIN_PAGE[1-8]_COLS
Columns to create for each of the Merlin databases. This includes the column's datatype, field number, function, and geometry.TDT-WIDGET OPTIONS:
The following options control the initial settings for the Thor Datatree (TDT) Widget.
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).-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_MONO_CMD
Command used to print monochrome PostScript file. Should contain "%s", which is replaced by the filename. Default: lpr -h %s &-PRINT_COLORMODE
These printing options are used by the TDT widget, as well as by other parts of xvmerlin(1). They are described under "PRINTING OPTIONS", above.-TDT_FRAME_HEIGHT height
Initial geometry for the TDT Widget.-TDT_GRAPHICS_PREFS "SMI ISM D3D"
A string containing one of more of SMI, ISM, or D3D, indicating the initial preference of whether to show structures and conformations graphically or textually. If the keyword is missing, they are shown textually. Default is "SMI ISM D3D" (show SMILES and Isomeric SMILES, and D3D graphically).-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".
Return Valuexvmerlin returns status 1 if there is a problem during initialization, and returns status 0 if it exits normally.
Daylight Licenseprograms: merlin
Related Topicsxvmerlin4d(1) xvthor(1) merlinserver(1) thorfilters(1) sthorman(1) licensing(5)
Daylight Theory Manual
BugsSee $DY_ROOT/readme-v4xx for the latest list of bugs.