GOODIES - NEW FEATURES FOR CHEMSKETCH

The “GOODIES” definition:

Additional buttons that extend the functionality of ChemSketch.

They are, actually, implemented as ACD/ChemBasic programs associated with 22 new

ChemSketch buttons. ACD/ChemBasic is a special programming language that enables you to
customize ACD software, and we think this is a great way to show off how useful it is—and at the
same time make your ChemSketch freeware even more versatile!

Note that you do not need to know anything about ACD/ChemBasic (although, if you wish, you
can learn it using the Goodies' code as example).
Just follow the installation instructions below and enjoy the new ChemSketch functionality!

Note also that you can remove these new buttons from your ChemSketch toolbar at any time.

Have fun!

The ACD/ChemBasic Development Team

1. REQUIREMENTS

Windows 95, Windows 98, Windows NT or Windows 2000

ChemBasic 5.0
ChemSketch 5.0 freeware or commercial ware

2. THE GOODIES PACKAGE

The Goodies package includes the following files and directories:

*.bas ChemBasic program files.

*.bmp Button pictures: Bitmap Files (with the same names as the
corresponding *.bas files).
*.sk2, *.sdf Auxiliary files that are used by some ChemBasic programs as templates
or samples.
template.htm Sample auxiliary file used by “Create HTML” Goody as a template web
page.
MOL Directory with auxiliary files used by “Nucleic Acid Builder” Goody as
templates.
readme.doc File with instructions on the installation of buttons into the ChemSketch
interface and other information.
filltmp.doc More instructions on the SK2 to HTML converter.
cbinstal.exe Installer program.
cbinstal.inf Installer auxiliary file containing a list of the *.bas and *.bmp files of the
new Goodies to be installed.
LPRINTER directories of big programs with corresponding names.
PEPBUILD
SUGARSK

3. GROUP INSTALLATION
Note that GOODIES package is included into a ChemBasic installation package. You will be
suggested to install goodies under ChemBasic installation process.

If you download Goodies package separately:

· Double click on the goodies2.exe once the download is complete.

· Specify the folder to which you want to extract the GOODIES package files in the
WinZip Self-Extractor dialog and click on the 'Unzip' button.

Note: it is recommended that you extract the Goodies package into a separate
folder, for example in the GOODIES sub-directory of your
ChemSketch+ChemBasic folder.

To install all the Goodies buttons at the same time into the ChemSketch interface:

1. Confirm that ACD/ChemSketch (or any other ACD software) is not running.
2. Double click on cbinstal.exe to run it. You should see a message box that 22
programs have been installed. Click OK to close it.
3. Run ACD/ChemSketch. The new buttons should appear on the new ChemBasic
Toolbar, displayed horizontally above the general toolbar the top of the workspace.

Notes:

· In this way you cannot install goodies for the ChemSketch of version 4.5 or earlier, though
you can use the goodies you used in the earlier versions for ChemSketch 5.0. To use them,
you should install each button separately as described below.

4. SINGLE BUTTON INSTALLATION

1. Start up ChemSketch.
2. Choose the ChemBasic Organizer command from the Options menu.
3. In the dialog box that appears click New and in the ChemBasic Program dialog box:
a) type goody name
b) specify the ChemBasic (*.bas) file
c) choose the toolbar for the goody location
d) associate the corresponding Button Bitmap File
e) click OK
The new button will appear.

5. REMOVING A GOODIES FROM THE CHEMSKETCH INTERFACE

1. Choose the ChemBasic Organizer... command from the Options menu.

2. Select the goody in the list.
3. Either click Delete (the goody will be removed from the list and from the toolbar) or clear the
mark in the check box near the goody (it will remove the button from the ChemSketch interface
only).
4. Click OK.
Note: You can only remove the Goodies buttons that you have previously installed.

6. VERY IMPORTANT NOTE - IRREVERSIBILITY

Clicking any Goodies button runs the corresponding ChemBasic program. Running a
ChemBasic program disables the UNDO option in ChemSketch, i.e. the GOODIES action
is not reversible! Be sure that your have created a back-up copy of your ChemSketch
document if it is necessary.

7. THE GOODIES

Document management and connection

InsPage.bas Insert Page

this Chemsketch button allows you to add a blank page BEFORE the current
page. Note that the usual way - through a Pages/New menu - adds a page to the
end of document. If you install this new button to the ChemSketch interface then
you will able to insert a blank page at any place of your document!

* Go to the page before which you want to insert a blank page and click Insert
Page button.

ClnPage.bas Clone Page

this button clones the current page (together with its contents) a given number of
times - it is very useful for filling in the document with page templates, tables,
titles, etc. ! New pages will be added at the end of a document.

* Make the page which you wish to clone active (open it).
* Click the Clone Page button.
* In the dialog box that appears specify the number of clones and click OK.

Note: A ChemSketch document can contain no more than 100 pages. You will be
prompted, if your document is full.

MvCpPage.bas Move/Copy Page

moves or, optionally, creates a copy of a current page. This new button allows
you to change the page order in your documents!

* Go to the page which you wish to move or copy.

* Click on the Move/Copy Page button.
* In the dialog box that appears type in number of the page after which you wish
to place the current page and click OK.
* Select Yes in the Message Box which appears if you want to copy the current
page. Select No if you want to just move it. Click Cancel to stop program
execution.

Rdrpg.bas Reorder Pages

This is advanced version of a Move/Copy Page Goody. It allows you to cut-and-

paste or copy-and-paste a sequence of pages to a new position within the same
document.
If you are preparing a long document and want to move, for example, pages 3-5
to start at page 10 instead, this is the Goody for you. You can cut and paste OR
copy and paste the pages being moved.

DelPage.bas Delete Pages

pressing this button deletes a RANGE OF PAGES. Note that the usual way -
through a Pages/Delete menu - removes only one page at a time.
 * Click on the Delete Pages button.
* in the dialog box which appears type the sequence of pages to delete.
* You will be prompted about disabling Undo after program execution. Choose
OK if you wish to delete the pages. Click Cancel to abort program execution.

Rnmpg.bas Rename Pages

This Goody permits you to change the name of the pages in your document.
The names of the pages are shown when you click on the “Page 1/1” button at
the bottom of your ChemSketch Window. This is extremely helpful for long
ChemSketch documents.

Annpg.bas Insert Page Numbers/Annotations

Allows to insert page numbers or complex annotations in your document.

* Open or create a document.

* Click on the Annotate Pages button
* Type in a page annotation template in dialog box that appears
* Click OK
Note that annotation will be inserted in a left-bottom corner of the page.

Annotation template keys:

$P - inserts page numbers
$N - inserts pages names (that can be inserted using Rename Pages goody or
using Pages/Rename command)
You can also include any fixed text into your annotation template.
For example:
Template “$P” will insert page numbers
Template “$N” will print page names in a left-bottom corner of each page
Template “Page $P” will insert “Page 1”, “Page 2”, etc. annotations
Template: “Page $P: $N” will insert “Page 1: Page Name”, etc. Annotations
Template that not contains any keys will insert fixed text for each page - you can,
for example, sign all pages with your name.

AnnotDoc.bas Annotate Document

assigns page names based on the content of the leftmost top textbox on each
page. This is very convenient for managing large documents and presentations!

* Open or create a document.

* Click on the Annotate Document button.
* After program execution click on the page counter from the bottom status line
to see page names.

Browser.bas Document Browser

this button optionally can

a) open file by file all ChemSketch's documents from the specified directory (and
mask) and show them to you;
b) search the contents of the documents from the specified directory (and mask)
according to a specified text string
This is a very useful tool for searching and previewing ChemSketch documents.

* Click on the Document Browser button.

To look through directory:
 * Select YES in the Message Box that appears.
* Type in the path and mask in the two dialog boxes which will be opened one
by one.
* The Document browser will open file by file and suggest you to select
options:
Select YES to leave the current file open and find the next file;
Select NO to close the current file and find next;
Select CANCEL to stop program execution (for example, if you have already
found needed document).
To search documents from any directory according to text string:
* Select NO in the Message Box that appears.
* Type in string, path and mask in three dialog boxes which will be opened
one after another.
* The Document browser will open documents which contain specified strings
one by one and inform you about each success with a Message Box:
Select YES if you wish to search the next file;
Select NO to stop program execution.
* Note that only 10 documents can be open in ChemSketch at a time. You will be
prompted if you try to open more documents.

Format Conversion

filltmp.bas Create HTML

This button is an SK2-to-HTML converter. It exports all the selected pages of a

current document into an HTML file, which you may then view with your favorite
web-browser. Note: Requires ChemSketch 4.01. More details may be found
in FillTmpHelp.doc.

Sk2VRML.bas Sketch-To-VRML Converter

this button exports all the molecules of a current page into a VRML 2.0 file,
which you may then view with Cosmo, GLView, or ANother VRML browser you
like.

* Draw structures which you wish to export on the active page.

* Click on the Sketch-To-VRML Converter button.
* Select OK in the Ready to export... message box which appears (or CANCEL
to abort program).
* Type in the WRL file name together with path and click OK. Note that if you
have typed in the filename only, the program will place the resulting WRL file in
the same directory with sk2vrml.bas.
* Specify a needed structure presentation by typing the corresponding letter in
the next dialog box and click OK.

SDF2Sk.bas SDF-To-Sketch Converter

this long-awaited button imports the data (molecules, texts, etc.) from a file in
MDL's SDF format into Sketch document. Each record in the SDF file becomes
a page. LIMITATION: no more than 100 records may be imported (ChemSketch
document may contain 100 pages maximum)

* Click on the SDF-To-Sketch Converter button.

* In the dialog box which appears type in the full path and name (or mask) of the
SDF file which you want to import and click OK.
 Note:
1. If you type in the filename without specifying the full path, the program will
search your SDF file in ChemBasic program directory. So, if you place the
needed SDF file in the same directory with sdf2sk.bas then it will be enough to
specify the file name without a path. If you place The SDF file in ChemBasic’s
program sub-directory then it will be enough to type in only the sub-directory
name.
2. “*” and “?” are acceptable in the file-mask.

* If the file contains more than one structure, the program will ask you how many
structures per page should be inserted. Specify the number and click OK.
* Then specify the field containing molecules and click OK.
Note:
A ChemSketch document can contain no more than 100 pages. If the SDF file
contains more than 100 records then you will be prompted about partial SDF
conversion (and the number of successfully imported records).

expsdf.bas Sketch-to-SDF Converter

This Goody will export the sketch of one or more molecules drawn in the
ChemSketch Window as an SDF file.
Hint: use Import SDF Goody to check.

Drawing management

TabWiz.bas Table Wizard

this button creates a table from the objects on the active page (i.e. aligns objects
according to a specified number of rows and columns and optionally add
markup) or an empty table.

To create a table from the objects on the page

* Click on the Table Wizard button.
* You will be informed about the number of objects on the page and some
suggestions by which to align them. Select YES.
* Specify the number of rows and columns in the dialog boxes that appear one
by one.
* Then select YES or NO if you want to mark-up the table using the Message Box
that appears.
To create an empty table
* Run the Table Wizard with blank page active
or
* Select NO in the Message Box which will suggest that you align objects.

Chemistry-related

ReplElem.bas Replace Element

this button replaces all atoms of one type with another. This is very useful for
drawing, for example, perfluorinated structures.
Note that program execution is possible only with a single structure on the page.
besides to be able to replace hydrogens, they should be drawn explicitly (use the
Explicit Hydrogens goodie if necessary).
 * Draw or leave only one structure on the page and click this button.
* In the dialog box which appears specify the element which you want to be
replaced and click OK.
* In the next dialog box specify an element that should replace the one specified
above and click OK.

Explhydr.bas Explicit Hydrogens

When a structure is drawn, ChemSketch automatically adds hydrogens to fill the

valence, but the bonds to the hydrogen are not explicitly shown.

* Draw structure(s) on the page and click this button. Note that program
processes all molecules on the page.

Note: you can use standard ChemSketch command - Tools/Remove Explicit

Hydrogens - to revert this goody action.

Desalt.bas Remove Spectator Ions (Desalt)

An SDF file that contains one or more salt structure entries can be changed to a
“one-molecule-per-entry” SDF file. Remove the smallest ion, either by MW or
by number of atoms. For example, sodium acetate will have the sodium atom
removed, and acetic acid will remain behind. (Note: the molecule left behind is
put into neutral form.) A special sample file, “salts.sdf” with 5 salts in it, has been
included for testing. Hint: use the “Import SDF” Goody to double-check
Newfile.sdf.

Lprinter.bas Label Printer

creates labels for chemicals and prints them on the Avery Standard (45 template
sheets included) or your own sheets.

* Draw the structures for which you want to create labels and click this button.
* You can create labels for structures from the *.sdf file if you run this program
with an empty active page.

For more information see lprinter.txt

SolCalc.bas Aqueous Solution Calculator

this button calculates the weight of compound required for preparing an aqueous
solution of the user-defined volume and molar concentration for the structure
drawn on the active page.
Note that program execution is possible only with a single structure on the page.

* Draw or leave one structure on the page and click this button.
* Specify the required molar concentration and solution volume in the dialog box
which appears.
* See the result in the Message Box which appears.

PepBuild.bas Peptide Builder

this button builds a 3D peptide structure from your amino acids sequence.
Open pepbuild.sk2 as a guide to using this button.
SugarSk.bas Carbohydrate Builder

this button makes the structure from carbohydrate abbreviation names and
performs a 3D optimization at your request.
For information about how to work with this program see sugarsk.txt

NuclBld.bas Nucleic Acid Builder

This button builds a 3D nucleic acid (DNA, RNA) structure (one or two chains)
from your input sequence.