PrintPackage Manual

Daylight Version 4.9
Release Date 08/01/11

Copyright notice

This document, the programs tablet, treetops, prado, xvthor, and xvmerlin are copyrighted © 1991-2011 by Daylight Chemical Information Systems, Inc. Daylight explicitly grants permission to reproduce this document under the condition that it is reproduced in its entirety, including this notice. All other rights are reserved.

Table of Contents


1. Intended audience and scope of this Guide
2. Introduction to the Daylight Printing Package
3. Treetops
4. Prado
5. Tablet
6. Printing from Thor and Merlin
Appendix 1: Printing PostScript Files
Appendix 2: The FDT File Format
Appendix 3: The TAB File Format
Appendix 4: Daylight PRINT Options

1. Intended audience and scope of this document.

This document should be read by everyone who intends to use the Daylight printing programs, collectively known as the Daylight "PrintPackage".

This Guide provides sufficient information for a novice Daylight user to successfully use the PrintPackage for a wide range of printing tasks. Additional relevant documentation can be found in the Daylight Theory Manual and Daylight Reference Manual (man pages) pertaining to the file formats used with the PrintPackage, such as TDT files, FDT files, and TAB files. The PrintPackage programs make use of the PostScript Level 2 printing language, by Adobe.

Also note that online help is available with each PrintPackage program by invoking the command-line option "-help".

2. Introduction to the Daylight PrintPackage

The Daylight PrintPackage is a set of programs which can convert data files written by Daylight programs such as THOR and Merlin to PostScript files. These files can include both text and structures extracted from a database, formatted in a variety of ways. It should also be noted that the PrintPackage programs are stand-alone programs and can process files not produced by Daylight software, for example, a tab-delimited spreadsheet dump.

The PrintPackage is responsible for producing PostScript files for printing or inclusion in another document. It is the responsibility of the local system manager to be able to print a PostScript file. However, some general guidelines are provided in Appendix 1 "Printing PostScript Files".

The PrintPackage currently is comprised of three programs: Treetops (for Thor data TREE TO PostScript), Prado (PRint A Depict Object), and Tablet. Treetops converts a 'Formatted Data Tree' file (FDT file) containing data for one or more substances to PostScript. FDT files are typically created by the Thor manager program Thorlookup (part of the ThorManager package). Prado writes a PostScript file of depictions for a list of input SMILES, in SMILES-file or TDT-file format. Tablet writes a table-style PostScript output file from an input TAB-file, which is typically written by Merlin for the current hitlist.

3. Treetops

Treetops is used for printing Thor data trees (TDTs). A good place to start learning Treetops usage is the online help text. We can produce this by entering "treetops -help" on the command line: 

% treetops -help
  treetops 4.71 Daylight CIS Inc. -- SYNTAX SUMMARY

  Convert tab-delimited datatree 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

       or:  treetops -help               (show this summary)
       or:  treetops -notes              (show release notes)
       or:  treetops -options            (show option summary)
       or:  treetops -settings           (show current settings)

By entering "treetops -options" we can display a list of available options: 

% treetops -options
  treetops 4.71 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           <size of font used for data, points>
   -PRINT_FOOTER             NONE|STANDARD
   -PRINT_LABELFONT          "Helvetica-BoldOblique"
   -PRINT_LABELSIZE          <size of font used for labels, points>
   -PRINT_LANGUAGE           PS|EPS
   -PRINT_LINEWIDTH          [THIN|NORMAL|WIDE|EXTRAWIDE]
   -PRINT_MARGINS            [BLEED|MINIMAL|NARROW|NORMAL|WIDE|HUGE]
   -PRINT_ORIENT             [TALL|WIDE]
   -PRINT_PAGELIMIT          <max number of pages to print>
   -PRINT_PAPER              [USLETTER|USLEGAL|USTABLOID|A3|A4|A5|B5|
                              COMPUTER|FANFOLD]
   -PRINT_PICTSIZE           <height of picture(s), points>
   -PRINT_SMARTS             NONE or SMARTS to highlight
   -PRINT_STEREO_ANG         <angular stereo separation, degrees>
   -PRINT_STEREO_SEP         <stereo image pair separation, points>
   -PRINT_TITLE              NONE or "any string"
   -PRINT_TITLEFONT          "Helvetica-Bold"
   -PRINT_TITLESIZE          <size of font used for title, points>

  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"

By entering "treetops -settings" we can display the default values of all options: 

  % treetops -settings
  treetops 4.72 (c) Daylight CIS Inc. -- CURRENT OPTION SETTINGS

  DEPICT_SUPPRESS_LABELS .. TRUE
  PRINT_BINDER ...... NONE
  PRINT_BOLDWIDTH ... NORMAL
  PRINT_COLORMODE ... BOW
  PRINT_DATAFONT .... Helvetica
  PRINT_DATASIZE .... 10.00
  PRINT_DEPICT ...... SMILES|Isomer|Isomeric SMILES
  PRINT_FOOTER ...... STANDARD
  PRINT_LABELFONT ... Helvetica-BoldOblique
  PRINT_LABELSIZE ... 10.00
  PRINT_LANGUAGE .... PS
  PRINT_LINEWIDTH ... THIN
  PRINT_MARGINS ..... NORMAL
  PRINT_ORIENT ...... TALL
  PRINT_PAGELIMIT ... 100
  PRINT_PAPER ....... USLETTER
  PRINT_PICTSIZE .... 72.00
  PRINT_SCHEMA ...... NONE
  PRINT_SMARTS ...... NONE
  PRINT_STEREO ...... 3D-coords|3D coords
  PRINT_STEREO_ANG .. 5.00
  PRINT_STEREO_SEP .. 196.00
  PRINT_TEXT ........ NONE
  PRINT_TITLE ....... NONE
  PRINT_TITLEFONT ... Helvetica-Bold
  PRINT_TITLESIZE ... 14.00

The Treetops options are described more fully below.

PAGE FORMATTING OPTIONS:

DEPICT_SUPPRESS_LABELS
Suppress atom labelling for chains, one of [ TRUE | FALSE ].
PRINT_BINDER
If the pages printed are to be bound, appropriate spacing can be specified. Select one of: [ NONE | LEFT | TOP | LEFTRIGHT | TOPBOTTOM ].
PRINT_BOLDWIDTH
Specify the width of the lines used for highlighted parts of depictions, one of [ THIN | NORMAL | WIDE | EXRTAWIDE ].
PRINT_COLORMODE
Specify black-on-white, white-on-black, color-on-white, or color-on-black, one of [ BOW | WOB | COW | COB ].
PRINT_DATAFONT
Font for character data.
PRINT_DATASIZE
Size of font used for character data, in points.
PRINT_FOOTER
Print footer information and page number; one of [STANDARD|NONE].
PRINT_LABELFONT
Font for datatypes, footers, etc.
PRINT_LABELSIZE
Size of font used for labels.
PRINT_LANGUAGE
Format of output file, one of [PS|EPS]. PS (PostScript) is used to print directly, EPS (Encapsulated PostScript) is often used to include graphics within another document.
PRINT_LINEWIDTH
Specify the width of the lines used for depictions, one of [ THIN | NORMAL | WIDE | EXRTAWIDE ].
PRINT_MARGINS
One of: [ BLEED | MINIMAL | NARROW | NORMAL | WIDE | HUGE ].
PRINT_ORIENT
One of [ TALL | WIDE ].
PRINT_PAGELIMIT
Maximum number of pages to print.
PRINT_PAPER
Paper size; choose one of [ USLETTER | USLEGAL | USTABLOID | A3 | A4 | A5 | B5 | COMPUTER | FANFOLD].
PRINT_PICTSIZE
Size for structural depictions in points.
PRINT_SMARTS
Specifying a SMARTS with this option will highlight the atoms of the hit SMARTS in the input structures if there is a hit.
PRINT_STEREO_ANG
Stereo viewing angle for stereo depiction of conformations, in degrees.
PRINT_STEREO_SEP
Stereo image pair separation distance, in points.
PRINT_TITLE
Title for output document; appears at the top of each page.
PRINT_TITLEFONT
Font for title.
PRINT_TITLESIZE
Size of font used in title, in points.
DATA FORMATTING OPTIONS:
PRINT_DEPICT
Specify which datatypes are to be depicted; choose one of: NONE, ALL, or "tag|tag|...|tag". Note that these tags refer to the verbose name (_V datatype) of the datafield.
PRINT_SCHEMA
Useful for the Graph datatype, as in "-PRINT_SCHEMA Graph".
PRINT_STEREO
Use with 3-D data for stereo pairs.
PRINT_TEXT
Specify which datatypes are to be shown textually; choose one of NONE, ALL, or "tag|tag|...|tag". Note that data such as SMILES can be both depicted and printed as text.

3.1 Treetops Examples

Let's assume for these examples that an FDT file has been produced for the compound codeine by using the program Thorlookup and extracting data from an available database. Here is the FDT file (with tab's shown as "=>"): 

	SMILES=>COc1ccc2CC3C4C=CC(O)C5Oc1c2C54CCN3C
	=>Remark=>This data excerpted from Spresi93 and Pomona93c.
	=>SPRESI Registry Number=>126226-200
	=>SPRESI Registry Number=>126226-209
	=>=>Isomer=>COc1ccc2C[C@H]3[C@@H]4C=CC(O)C5Oc1c2[C@]54CCN3C
	=>SPRESI Registry Number=>126226-401
	=>=>Isomer=>COc1ccc2C[C@@H]3[C@H]4C=C[C@H](O)[C@@H]5Oc1c2C54CCN3C
	=>SPRESI Registry Number=>126226-602
	=>=>Isomer=>COc1ccc2C[C@@H]3[C@@H]4C=C[C@@H](O)[C@@H]5Oc1c2C54CCN3C
	=>SPRESI Registry Number=>126226-707
	=>=>Isomer=>COc1ccc2CC3C4C=C[C@@H](O)[C@H]5Oc1c2[C@]54CCN3C
	=>SPRESI Registry Number=>126226-803
	=>=>Isomer=>COc1ccc2C[C@@H]3[C@@H]4C=C[C@H](O)[C@@H]5Oc1c2C54CCN3C
	=>SPRESI Registry Number=>126226-811
	=>=>Isomer=>COc1ccc2C[C@@H]3[C@@H]4C=CC(O)C5Oc1c2[C@]54CCN3C
	=>POMONA Name=>PREINE
	=>=>Conformation=>-204.02=>Name=>PREINE=>3D-coords=>5.12,0.49,0.33,etc.,
	etc.,-3.77,-2.52,0.58=>Source=>
	=>=>Orientation=>CONCORD293=>TR matrix=>0.45545,-0.47645,0.65594,
		2.98298,-0.14266,-2.67709

If we use Treetops in its default mode to print this file, we will obtain:


4. Prado

Prado is used for printing depictions of structures. The online help text is obtained with "prado -help": 

% prado -help

  prado 4.71, Daylight CIS Inc. -- SYNTAX SUMMARY

  Print depictions from SMILES

    Usage:  prado [options] < in.[smi|tdt] > out.ps
       or:  prado [options]   in.[smi|tdt] > out.ps
       or:  prado [options]   in.[smi|tdt]   out.ps

       or:  prado -help               (show this summary)
       or:  prado -notes              (show release notes)
       or:  prado -options            (show option summary)
       or:  prado -settings           (show current settings)

The options are listed by entering "prado -options": 

% prado -options
  prado 4.71 Daylight CIS Inc. -- OPTION SUMMARY

  Print depictions from SMILES

    Usage:  prado [options] < in.[smi|tdt] > out.ps
       or:  prado [options]   in.[smi|tdt] > out.ps
       or:  prado [options]   in.[smi|tdt]   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_COLUMNS            <number of columns in depiction grid>
   -PRINT_FOOTER             [NONE|STANDARD]
   -PRINT_HINTS              [NONE|FROMTO]
   -PRINT_LABELSIZE          <footer font size in points>
   -PRINT_LANGUAGE           PS|EPS
   -PRINT_LINEWIDTH          [THIN|NORMAL|WIDE|EXTRAWIDE]
   -PRINT_MARGINS            [BLEED|MINIMAL|NARROW|NORMAL|WIDE|HUGE]
   -PRINT_NAMETAG            <.tdt tag to appear as name>
   -PRINT_ORIENT             [TALL|WIDE]
   -PRINT_PAGELIMIT          100
   -PRINT_PAPER              [USLETTER|USLEGAL|USTABLOID|A3|A4|A5|B5|
                              COMPUTER|FANFOLD]
   -PRINT_ROWS               <number of rows in depiction grid>
   -PRINT_SHADOW             [TRUE|FALSE]
   -PRINT_SMARTS             NONE or SMARTS to highlight
   -PRINT_TITLE              NONE or "any string"
   -PRINT_TITLESIZE          <title font size in points>

The Prado options are described more fully below.

PAGE FORMATTING OPTIONS:

DEPICT_SUPPRESS_LABELS
Suppress atom labelling for chains, one of [ TRUE | FALSE ].
PRINT_BINDER
If the pages printed are to be bound, appropriate spacing can be specified. Select one of: [ NONE | LEFT | TOP | LEFTRIGHT | TOP | BOTTOM ].
PRINT_BOLDWIDTH
Specify the width of the lines used for highlighted parts of depictions, one of [ THIN | NORMAL | WIDE | EXRTAWIDE ].
PRINT_COLORMODE
Specify black-on-white, white-on-black, color-on-white, or color-on-black, one of [ BOW | WOB | COW | COB ].
PRINT_COLUMNS
Number of columns in depiction grid.
PRINT_FOOTER
Print footer information and page number; one of [ STANDARD | NONE ].
PRINT_LABELSIZE
Size of font used for labels.
PRINT_LANGUAGE
Format of output file, one of [ PS | EPS ]. PS (PostScript) is used to print directly, EPS (Encapsulated PostScript) is often used to include graphics within another document.
PRINT_LINEWIDTH
Specify the width of the lines used for depictions, one of [ THIN | NORMAL | WIDE | EXRTAWIDE ].
PRINT_MARGINS
One of: [BLEED|MINIMAL|NARROW|NORMAL|WIDE|HUGE].
PRINT_NAMETAG
Specify which datatype from the TDT file should be used to title each depiction (use brief tag).
PRINT_ORIENT
One of [ TALL| WIDE ].
PRINT_PAGELIMIT
Maximum number of pages to print.
PRINT_PAPER
Paper size; choose one of [ USLETTER | USLEGAL | USTABLOID | A3 | A4 | A5 | B5 | COMPUTER | FANFOLD].
PRINT_ROWS
Number of rows in depiction grid.
PRINT_SHADOW
Shadow-style boxes desired? Choose TRUE or FALSE.
PRINT_SMARTS
Specifying a SMARTS with this option will highlight atoms of the hit SMARTS in the input structures if there is a hit.
PRINT_TITLE
Title for output document; appears at the top of each page.
PRINT_TITLEFONT
Font for title.
PRINT_TITLESIZE
Size of font used in title, in points.

4.1 Prado Examples

Here's a sample SMILES file which we will use as input for Prado: 

	NCCc1ccc(O)c(O)c1 DOPAMINE
	CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12 CAFFEINE
	CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1 LSD
	N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76 STRYCHNINE
	OCC1OC(O)C(O)C(O)C1O GLUCOSE
	Nc1cc(nc(N)n1=O)N2CCCCC2 MINOXIDIL
	C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5 MORPHINE
	N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3 MERCUROUS CARBAZONE COMPLEX
	NC(Cc1c[nH]c2ccccc12)C(O)=O TRYPTOPHAN
	COC(=O)COc1ccccc1 PHENOXYACETICACID,METHYLESTER
	[Cl-].[Cl-].NC(=O)c2cc[n+](COC[n+]1ccccc1C=NO)cc2 HI-6 
	CCCN(CCC)C1Cc2c[nH]c3ccc(OC)c(C1)c23 BAYR1531
	CN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13 DIAZEPAM
	CC12CCC3C(CCC4=CC(=O)CCC34C)C2CCC1O TESTOSTERONE
	CC4=O[Rh]1([CH2]=C12=[CH2][Rh]23(O=C(=[CH]=C(=O3)C)C)C#O)(O=C(=[CH]4)C)C#O AACRHC

Here's what we get when we print with Prado in its default mode:


If we specify a SMARTS to highlight, we also see the effect of increased line width. Here the SMARTS are highlighted with "EXTRAWIDE" lines:


5. Tablet

Tablet is used for printing tables representing Merlin hitlists. Here's the online help text, obtained by entering "tablet -help": 

% tablet -help
  tablet 4.71 Daylight CIS Inc. -- SYNTAX SUMMARY
  Convert tab-delimited file to PostScript file with depictions
    Usage:  tablet [options] in.tab > out.ps
          or:  tablet [options] in.tab out.ps
          or:  tablet -help             (show this summary)
          or:  tablet -notes            (show release notes)
          or:  tablet -options          (show option summary)
          or:  tablet -settings         (show current settings)

Here's the option list obtained by entering "tablet -options". 

% tablet -options
  tablet 4.71 Daylight CIS Inc. -- OPTION SUMMARY

  Convert tab-delimited file to PostScript file with depictions
    Usage:  tablet [options] < in.tab > out.ps
          or:  tablet [options] in.tab > out.ps
          or:  tablet [options] in.tab out.ps
  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           <size of font used for data, points>
   -PRINT_FOOTER             NONE|STANDARD
   -PRINT_LABELFONT          "Helvetica-BoldOblique"
   -PRINT_LABELSIZE          <size of font used for labels, points>
   -PRINT_LANGUAGE           PS|EPS
   -PRINT_LINEWIDTH          [THIN|NORMAL|WIDE|EXTRAWIDE]
   -PRINT_MARGINS            [BLEED|MINIMAL|NARROW|NORMAL|WIDE|HUGE]
   -PRINT_ORIENT             [TALL|WIDE]
   -PRINT_PAPER              [USLETTER|USLEGAL|USTABLOID|A3|A4|A5|B5|
                                  COMPUTER|FANFOLD]
   -PRINT_PAGELIMIT          <max number of pages to print>
   -PRINT_PICTSIZE           <height of pictures in points> 
   -PRINT_SMARTS             [NONE|SMARTS to highlight]
   -PRINT_SMILES             [TEXT|DEPICTION]
   -PRINT_TITLE              "any string" or NONE
   -PRINT_TITLEFONT          "Helvetica-Bold"
   -PRINT_TITLESIZE          <size of font used for title, points>

The tablet options are described more fully below.

OPTIONS:

DEPICT_SUPPRESS_LABELS [TRUE | FALSE]
Suppress atom labelling for chains, one of [ TRUE | FALSE ].
LICENSEDATA file
The Daylight license file. Default: /usr/local/daylight/dy_license.dat.
PRINT_BINDER [ NONE | LEFT | TOP | LEFTRIGHT | TOPBOTTOM ]
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_COLFORMS char[char...]
A string defining the format to be used for each column. Each character in this string corresponds to the format of one column. If there are more columns than characters in the string, the value of the last format character is used for all remaining columns. The default value is "G", which applies G to all columns. The format characters are:
     C .. center ... equal space on left and right
     D .. decimal .. line up (first) decimal points
     G .. general .. guess R if all digits, J if space, else L
     J .. justify .. line up left and right by expanding spaces
     L .. left ..... line up left extent, right is ragged
     R .. right .... line up right extent, left is ragged
     S .. SMILES ... treat as SMILES
PRINT_COLORMODE [ BOW | WOB | COW | COB ]
Printing color mode [Black | White | Color] On [Black | White]. Default BOW (Black-On-White).
PRINT_FOOTER [ STANDARD | NONE ]
Print footer information and page number. Default is STANDARD.
PRINT_LANGUAGE [ PS | EPS ]
Output language (PS = PostScript, EPS = Encapsulated PostScript)
PRINT_LINEWIDTH [ THIN | NORMAL | WIDE | EXTRAWIDE ]
Regular Graphic line width (shows background, borders, structures). 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_PAGELIMIT N
Limit number of pages of output to produce (0 means no limit). Default is 100.
PRINT_PICTSIZE size
Size of embedded pictures in printed output (see -PRINT_DEPICT, above). Default: 72 (points).
PRINT_SMILES [ TEXT | DEPICTION ]
Given the choice, should SMILES be printed as text or picture? Default: DEPICTION.
PRINT_SMARTS smarts
A SMARTS string, if given, causes that substructure to be highlighted in every structure drawn. Default is"NONE" (no highlighting).
PRINT_DATAFONT font
Font used to print data. Default: Helvetica.
PRINT_DATASIZE size
Size of font used to print data. Default: 10 (points).
PRINT_LABELFONT font
Font used to print labels. Default: Helvetica-BoldOblique.
PRINT_LABELSIZE size
Size of printed labels. Default: 10.
PRINT_TITLE title
Title for printed output. Default NONE (no title).
PRINT_TITLEFONT
Font used to print title. Default Helvetica-Bold.
PRINT_TITLESIZE
Font size used to print title. Default 14.
PRINT_TITLEPICT TRUE | FALSE
Print PRINT_TITLE as a depiction? Default FALSE.
PRINT_TPICTSIZE
The size of the depicted title. Only has effect if PRINT_TITLEPICT is TRUE. Default: 144 (points).

Tab files are normally produced by Merlin via the 'Save hitlist as .TAB file...' command. Here's a sample (with tab's shown as "=>"): 

	SMILES=>CAS No=>Local name=>Activity=>CLOGP
	NCCc1ccc(O)c(O)c1=>51-61-6=>DOPAMINE=>ADRENERGIC=>-0.051
	Cn1cnc2n(C)c(=O)n(C)c(=O)c12=>58-08-2=>CAFFEINE=>STIMULANT=>0.056
	CCN(CC)C(=O)C1CN(C)C2Cc3c[nH]c4cccc(C2=C1)c34=>50-37-3=>
      "LYSERGICACID,DIETHYLAMIDE"=>HALLLUCINOGENIC (5-HT2-AGONIST)=>2.498
	O=C1CC2OCC=C3CN4CCC56C4CC3C2C6N1c7ccccc75=>57-24-9=>STRYCHNINE=>
      CNS STIMULANT (VET)=>-0.365
	OCC1OC(O)C(O)C(O)C1O=>50-99-7=>GLUCOSE=>""=>-3.529
	Nc1cc(nc(N)n1=O)N2CCCCC2=>38304-91-5=>MINOXIDIL=>ANTIHYPERTENSIVE=>1.068
	CN1CCC23C4Oc5c3c(CC1C2C=CC4O)ccc5O=>57-27-2=>MORPHINE=>
      ANALGESIC (NARCOTIC)=>0.182
	N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3=>""=>MERCUROUS CARBAZONE COMPLEX=>""=>""

Here's the Tablet output we obtain with the default options:


6. Printing from Thor and Merlin

Treetops style output can also be printed directly from the Thor application program, and Prado and Tablet style output can be printed directly from the Merlin program.

Thor uses Treetops to print a Thor Data Tree (TDT) from the TDT Widget. After displaying the TDT Widget with the 'Show Datatree' button, the 'Print', button becomes available. Pressing this button results in three things happening: (1) The TDT is sent to a Treetops for conversion to a PostScript file located in a directory specified by option PRINT_DIRECTORY, (2) A print command is performed as specified by the Daylight option: PRINT_PS_MONO_ZAP_CMD or PRINT_PS_COLOR_ZAP_CMD (where the choice is determined by option PRINT_COLOR_MODE), and (3) the temporary PostScript file is deleted.

Merlin uses Tablet and Prado in an analogous way. From the 'File' menu on the Merlin window, select either 'Print Hitlist...' for Tablet style output, or 'Print Depictions...' for Prado style output. One of the following two control panel will appear:


Merlin allows full control over the printed output via these panels, which are really just an interface for setting any of the Tablet and Prado options. Similarly to Thor, when a Merlin print button is pressed, a temporary TAB or SMILES file is produced for the current hitlist, this file is processed by Tablet or Prado, and the resulting temporary PostScript file is printed .

Although Thor offers less interactive control over the printed output, in fact all of the options available to Treetops can be set for Thor. However, they must be set before starting the Thor client program. Similarly, Prado and Tablet options can be set prior to starting Merlin. These options can be set on the Thor/Merlin command line, or in Daylight option-specification files, or via local environment variables. For more help on setting options, see the Daylight Administrator's Guide.

Appendix 1: Printing PostScript Files

Printer Setup for Daylight Software 4.x

Daylight Software version 4.x provides the capability to print text and graphics for chemical structures and data directly from the applications, or via PostScript files. However, for Daylight's printing capabilities to work, the computer and printer must be correctly configured. In general, this will mean configuring the system to print a PostScript file with the command "lpr foo.ps".

The procedure for setting up a computer and printer to print a PostScript file will vary from machine to machine. The following summary is intended to help with getting started, not to be a complete set of instructions.

  • Printing a PS file requires a PS interpreter, either loaded as software on the computer, or, more typically, built into the printer, a PS printer such as the Apple LaserWriter.
  • The printer must be connected to the computer by either a serial, parallel, or network connection, depending on the capabilities of the machine and printing software. A "network" printer may be attached directly to a network, or may be attached via a printserver host.
  • SunOS machines need to have "NewsPrint" software loaded to print proficiently. SGI/IRIX machines do not need additional software, but to talk to lpr-spooling daemons on other machines with Berkeley-style UNIX, the "eoe2.sw.bsdlpr BSD Line Printer Spooling Utilities" software must have been loaded from the system disk. Otherwise, the ATT-style lp-spooling system can be used on SGI/IRIX machines.
  • UNIX machines require that each printer have an entry in /etc/printcap. Refer to your system documentation for the specific entries needed.
  • In many typical situations, one printer will serve several hosts and users. If this is an Apple LaserWriter, for example, this printer will be considered a "serial printer" by the host to which it is connected (the printserver), and a "network printer" by the other hosts. Each machine will have an entry in its /etc/printcap describing this printer. Alternately, it may be possible to use "rsh" to avoid the need to define a printer on a given machine. For example, the command: "cat foo.ps | rsh crawdad lpr - " may work to print from a host with no printer defined, via printserver "crawdad".

Appendix 2: The FDT File Format

The "FDT" file format (Formatted Data Tree) was introduced by Daylight to support the Daylight PrintPackage, although it may well find other uses.

Unlike the TDT format, which contains abbreviations and indirect references which rely on other files or databases for their meaning, the FDT format contains verbose datatype tags, and expanded indirect data. Therefore, the FDT format is self-contained.

Tabs are used as delimiters, both to separate data-tags and datafields, and to signify the tree-depth of a line in the FDT file. Each line in the FDT file represents one datatype, and if a datatype consists of multiple fields, the line goes <datatag><tab><value><tab><datatag2><value><tab><datatag3><value>, etc.

See the Treetops section of this manual for an example.

Appendix 3: The TAB File Format

The TAB format is now also defined as the input format for Tablet. The TAB format is written by Merlin in saving hitlists.

The TAB format represents an RxC grid of R rows and C columns, as is displayed on Merlin's main canvas. There are R+1 lines in the TAB file, with the first line containing the column titles. This format is equivalent to certain common spreadsheet file formats, which can enable data transfer.

See the Tablet section of this manual for an example.

 

Appendix 4: Daylight PRINT Options

In addition to the Daylight options listed herein for the Treetops, Prado, and Tablet programs, there are a few Daylight options used by other application programs to actually print an output PostScript file, and perform other related duties. These options are listed below:

PRINT_DIRECTORY
The directory for temporary print files.
PRINT_EXECUTE_FG_CMD
Command used to execute print program synchronously. This is used when the next action is dependent on this command.
PRINT_EXECUTE_BG_CMD
Command used to execute a command in the background. This is used when the next action is not dependent on this command, for example a delete command or send-to-printer command.
PRINT_DELETE_CMD
Command used to delete temporary print file, such as an FDT or TAB file.
PRINT_PS_MONO_CMD
Command used to print a PS file and not delete it.
PRINT_PS_MONO_ZAP_CMD
Command used to print a PS file and delete it (this is the default).
PRINT_PS_COLOR_CMD
Command used to print a color PS file and not delete it.
PRINT_PS_COLOR_ZAP_CMD
Command used to print a color PS file and delete it.
PRINT_PS_VIEW_CMD
Command used to view a PS file on the display (the system must have software to do this) and not delete it.
PRINT_PS_VIEW_ZAP_CMD Command used to view a PS file on the display (the system must have software to do this) and delete it.