Copyright: Copyright ®1993 Hilton Evans


Contents
Table of Contents

Copyright Notice

Introduction

Editing

Keyboard

Managing Files

Main Menu

Ordering

Support

Tutorial

Using the Mouse


Copyright Notice

ChemPen+.

© Copyright 1994,1996 Hilton Evans. All rights reserved.

The distribution and sale of ChemPen+ are for the use of the original purchaser only. Registered users  of  ChemPen+ may execute programs on one machine at a time. duplication or copying for reasons other than backup purposes, ChemPen+ is in violation of United States Copyright Laws.


How to Register

ChemPen+ Order/Registration form

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 3.5" disks only.

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Introduction 1
 Introduction

ChemPen+ is designed to let chemists, chemistry students or chemical workers illustrate chemistry documentation. With ChemPen+ you easily create diagrams like Figure 1.

Figure 1

ChemPen+ was designed to be simple, intuitive and versatile. Drawings are created using  menus, mouse clicks and drags. Special editing tools further simplify drawing.  ChemPen+ is chemical aware. That is, the program  tries to keep your structures chemically accurate.

ChemPen+ drawings can be copied and pasted into popular Windows word processors and graphics applications. However ChemPen+ is not just a drawing program.  ChemPen+ is extensible. Special libraries are under development that will allow ChemPen+ to do special chemical calculations. For example a special C-13 NMR library is available to users now.

Next


Figure 1


Introduction 3
Introduction - 2

It helps to know a little about  ChemPen+' internal workings. ChemPen+ uses atom, bond, structure, symbol and label objects to create drawings. Atoms and bonds, the most basic elements, are used to create the other objects. ChemPen+ combines these objects to create a drawing.

Groups are collections of atoms and bonds such as t-butyl. Rings are a special class of  groups. When groups are created they are added to a group list. This makes selecting them for editing easier. A structure created by cloning an selected group of atoms and bonds is added to the drawing as a new group.

ChemPen+ drawings can be annotated with special atoms called Labels. Labels are added and edited with the Text Editor

Arrows and arcs are examples of Symbols. Symbols are added from the Symbol Menu. Symbols are edited with a special Symbol Editor. As ChemPen+ is improved, more symbols will be added.

Next


A copy or duplicate


Introduction 4
Introduction - 3

Drawing with ChemPen+ is done with  menus and  editors.  Editors activate only if their targets are present. The area where the drawing is displayed is referred to as the Pad. Vertical and horizontal scrollers let the user shift the drawing up, down, left and right. Up, down, left and right movement can also be done with the arrow keys.

To illustrate the drawing process Figure 1 is drawn. In each step the bold colored words state the  result of  each step. The actions to perform each step follow. Menu commands or button commands are  in bold letters.

Equivalent keyboard commands, if available, are revealed when you click on these letters. Target atoms, bonds, groups and symbols for each action are highlighted in red.

Undo and Redo restore a drawing to the its state prior to a drawing operation. Each of the editors has an Undo button to undo the last editing operation.

Click Tutorial for to learn how to draw with ChemPen+


Drawing Step 1
  Drawing with ChemPen+  - Step 1

This tutorial will get you started using ChemPen+ by illustrating the drawing process with an example. Most of the drawing is done with menus and where equivalent keyboard commands are available they are revealed if you click on the sequences of menu commands.

In some steps the target of an action is highlighted in red. This is the target, and the illustrated structure is the result of the action.

Add a cyclohexane ring
From the main menu select Ring,  Add,  6  then click near the left side of the Pad.

Result

Next Step


Drawing Step 2
Drawing-Step 2
Fuse a second cylclohexane to the right side bond of the first.
From the main menu select Ring, Fuse, 6 and click near to the right of the highlighted target bond.

Result

Next Step

Previous Step


Drawing Step 3
Drawing - Step 3
Repeat the previous step  fusing a third cyclohexane to the highlighted bond.

Click above and right of the highlighted target bond to fuse another ring.

Result

Next Step

Previous Step


Drawing - Step 4
Fuse a cyclopentyl ring to rightmost bond in the previous structure
Select Ring | Fuse | 5 and click near the target bond.

Result

Next Step

Previous Step


Drawing Step 5
Drawing - Step 5
Number the Structure-This optional step is just to make the next step easier to explain
1. Start above left of the structure and drag the mouse until the blue rectangle surrounds the
    structure. The group is highlighted  and the Group Editor activates.
2. Click the  On button in the Numbers box.

Result

Next Step

Previous Step


Drawing Step 6
Drawing - Step 6
Branch methyls from the previous structure and turn off numbering
1. From the main menu select Bond | CH3and near atoms 3, 5, and 12
2. Click Reset to stop branching.

Result

Next Step

Previous Step


Drawing Step 7a
Drawing - Step 7a
Convert diagonal branch to OH
1. Click the right button near the #5 CH3. The Atom Editor is activated.
2. From the Atom Editor Menu select Atom | Non-Metals | O. The CH3 changes to O.

2  On the periodic table click O. The CH3 changes to OH

3. Select the structure. Click the  Numbers Off button.

Result

Next Step

Previous Step


Drawing Step 7b
Drawing - Step 7b.

1. Select the Reverse button to change OH to HO.
2. Click the Atom Editor OK button.
3. Select the entire group and click the Numbers Off button on the  Group Editor
4. Click the Group Editor OK button

Result

Next Step

Previous Step


Drawing Step 8a
Drawing - Step 8a

Modify the Methyl bonds
1. Hold Shift and click the right mouse button near the right hand methyl.
The Bond Editor activates
2. Click the In | Out button until an out bond is formed.
3. Click near the right methyl bond and change it to a hatched bond with the In | Out button.
4. Click the OK button.

Result

Next Step

Previous Step


Drawing Step 8b
Drawing - Step 8b

Clone the Group

1. Select the entire group thus activating the  Group Editor
2. Click the Clone button.
3. Click the OK button.

Result

Next Step

Previous Step


Drawing Step 9
Drawing - Step 9

Create a carbonyl and a double bond
1. Hold shift and click near the right structure's OH. The Bond Editor activates.
2. Click the double button to create a carbonyl.
3. Click the highlighted bond in the right structure and click the double button.
4. Click the OK button.

Result

Next Step

Previous Step


Drawing Step 10
Drawing - Step 10
Add and modify an arrow
1. Select Symbol | Arrows | choicefrom the Symbol Menu where choice
     is a      one   of the arrows pictured in the sub menu.

2. Click between the two structures to place the arrow.
3. Click near the head or tail of the arrow. The symbol editor is activated.
4. Click +50% to increase the size by 50%.
5. Click the Style button until the arrow changes to the appearance below.
6. Click the OK button.

Result

Next Step

Previous Step


Drawing Step 11
Drawing  - Step 11

Add a label

1. Select Label from the main menu.

2. Click just above the arrow. The word label appears and the label editor activates.

3. Select the word label and type oxidation

4. Hit Enter or the OK button.

Result - The drawing is done!

Previous Step


Symbol Menu

Arrows, arcs and triangles are added from the symbol menu. As ChemPen+ develops and based on customer demand other symbols will be added.


Menu Commands Overview
 Menu Commands

All drawing is done from the Main Menu shown below.

File	Link
Alkane	Reset
Atoms	Ring
Branch	Symbol
Benzene	Symbol|Text
Font	Undo/Redo


Using the Keyboard;
Using the Keyboard

Besides entering and  editing text the keyboard can be used to navigate ChemPen+. All keyboard commands move the drawing while not the scrollers remain unchanged. The keystrokes that apply to ChemPen+ are defined below.

Tab - moves the drawing right 1/8th the Pad width.

Arrow keys- the up and down arrow keys move the drawing up or down by 1/8th the Pad height. The left and right arrow keys move the drawing left or right by 1/8th the Pad width.

Page Up, Page Down - the page up and down move the drawing up and down respectively by one page height

Also see: Entering and Editing Text


Editing Overview
Overview of Editing

ChemPen+ editing is done with the editing tools listed below. Each editing tool is activated either by selecting a target atom, bond, group, symbol or label. Selecting the object activates its applicable editor. Each ChemPen+ editor is listed below.

Atom Editor

Bond Editor

Group or Ring

Symbol

Text Editor

Also see Introduction


Editing Atoms

Use the Atom Editor's buttons, menus and text editor to change the currently selected atom.

To Activate the Atom Editor:
1. Right mouse button click near the target atom or
2. Select Edit|Atom and click near the target atom.

Also see Editing ,Menu Commands


The selected atom can be changed by clicking thean atom on the periodic table. By default carbons are shown as points. Explicit hydrogens are shown on other non-metals by default.


Edit the atom's symbol string using the text box


Launches the font dialog box letting you change the atom's font


Increments or decrements charge of atom. If atom is a non metal hydrogens are added.


Changes atom symbol style. Toggles between   explicit H's, hidden Hs and hidden.


Reflects and reverses the order of the string characters in the text box.


Shifts text left or right


Duplicates the atom


Deletes the atom and cuts attached bonds.


Undoes atom editing


Atom Editor Menus
 Adding an Atom

Click on the atom you want to add then click on the pad to add the atom


Atom Menu

Activates periodic table

To add an atom click its symbol on the periodic table then click the location on the pad where the atom is to be added.

Also see: Menu Commands


Branch Menu
Branch

The group menu is used to branch groups from an existing group or to link two atoms.


Alkane Menu

Alkanes are added to the drawing or branched from existing atoms by selecting them from the alkane menu. The number is the length of the linear chain. T-butyl can be added. T-butyl, i-propyl and vinyl can be branched.


Benzene Menu

Benzene can be added to the pad, branched to an existing atom or fused to an existing bond by selecting the appropriate item on the benzene menu.


Ring Menu

Rings are added to the pad,  branched from existing atoms or fused to existing bonds by selecting the appropriate item on the ring menu.


Entering and Editing Labels

Text labels are entered and edited with the text editor. The text editor is just the atom editor with some features disabled. Clicking an atom when the text editor is active activates its other features.  To enter a label click Label in the main menu and click the location on the Pad where to place the text. Text is entered in the text window.  A blinking caret appears where the text will be entered and typed text appears as red on the Pad.


Reset

Turns off drawing command repetition. If a drawing command is invoked, repeated clicking on the Pad will repeat the operation until Reset is pressed. Reset is grayed when inactive. Selection of another menu command replaces the currently active drawing command.


Undo
Undo and Reset

Undo reverses the most recent drawing command.  Undo does not correct the very first drawing action as this can be undone by using File | New. Undo can be undone with the Redo command.


Label Font

Opens a font choosing dialog allowing the user to change the label's font.


Label Text

Toggles the labels font between regular, italic, bold, and bold italic.


Text Box

Use the text box to enter or edit a label's text.


Label Undo

Restores selected label to pre edited condition.


Delete

Deletes the Label.


Clone

Creates a duplicate of the label and puts it in the Pad's upper left corner.


OK

Press OK when done


Atom Text Editor
Entering and Editing Formulas

The text editor is used to enter or modify an atom's text. Text entered in this window is formatted into molecular formula format. Pluses(+) and minuses(-) are treated as charges and are made superscripts. Numbers are converted to subscripts. In future versions of ChemPen+ will implement more sophisticated treatments of the text.


Atom Editor -  Font Button

Use the  Font button to open the font selection dialog and to change the font of the selected atom or label fonts.


Atom Editor - Reverse Text

Use the Reflect button to reverse the order of the characters in a symbol or molecular formula.


 Atom Left/Right Button

Use the  Left/Right to shift the atom's text left or right. The button's title changes according to the condition of the specific atom selected


Atom Style Button

Use the Style button to change the style of an atom. The button's title toggles between the various styles, e.g.  C, or CH3, available to a given atom. The numbers and types of styles will change as ChemPen+ evolves.


Atom Delete Button

Use the Delete button to delete an atom and its attached bonds.


Atom Undo Button

Use the Undo button to undo any change.


Atom Editor - OK

Use the OK button to close the editor and accept the editing changes.


Atom Editor -Text Box

Enter formulas or enter text for atoms or labels into the Atom Editor Text box. Text is entered by normal typing. For atoms the  current implementation of ChemPen+ treats characters as follows. Numbers become subscripts. Pluses(+) and minuses(-) become superscripts. Letters are unaffected.

For Labels all characters are treated the same.


Atom Editor Help Button

Displays the Help topic for this button.


Atom Editor Clone Button'

Duplicates the currently selected atom or label and puts the copy in the upper left corner of the

Pad.


Editing Bonds

The bond editor tool is used change the character and appearance do bonds. To activate the bond editor do one of the following.
To Activate the Bond Editor
Select a bond with Ctrl | R Mouse Button or
Click bond | Editor and click near the bond to be edited or
Click Edit | bond and click near the bond to be edited.

Also see Editing , Menu Commands


The bond editor slider pivots, rotates or zooms the selected bond depending on the setting of the radiobuttons.


single - changes a bond to a single bond

double- changes bond to a double bond.

triple - changes bond to a triple bond.

resonance - changes bond to double bond with one dotted line

dots - changes bond to a dottet line such as in a hydrogen bond.

Out - toggles the bond between out, in and in the plane.

<|> - shifts a multiple bond left or right.

Flip - exchanges the head of an out pointing bond.

Line - changes the line thickeness.

Delete - deletes the bond and saturates its atoms.


Editing Groups
Editing Groups and Rings

Use the Group Editor tool to edit rings and other structures. To activate the Group Editor select a  group by click Ctrl | right mouse button near the target ring or group. Alternatively, select a group of atoms by dragging the mouse until the atoms are surrounded by the blue rectangle.  Click each part of the Group Editor to learn its function.

Also see Editing ,Menu Commands


Group Editor Slider
X, Y, Z, Pivot, Zoom

Use the slider to Rotate. Pivot or Zoom the structure. X, Y and Z radio buttons select the rotation axis. Pivoting occurs around the Z axis.


 Numbering
Determines basis of numbering. When Drawing is checked numbering starts at one plus the highest number of an already numbered atom. When Drawing is unchecked numbering starts at 1.


Bonds button
The bonds button shifts all of the multiple bonds in a group

left or right toggling between styles below.


Group Line Thickness
Line button

The line button toggles between line thicknesses of 0, 1 and 2. Thickness 0 and 1 are the same until pasted into another application as a picture where a thickness of 1 changes with zoom while a thickness of 0 remains constant.


±50% Zoom
Enlarges or shrinks the group by a one time 50%.


Group Font
Font button

Font launches the font dialog which allows the user to change the font of the selected group.


Group Fuse
Combines selected atoms and bonds into a new group that can be selected with the control right mouse button.


Numbering Atoms
Numbers button

Use the Numbers button to number the selected atoms. If the Group box is checked numbering starts from 1 with respect to the group. If Drawing is

A selected group of atoms can be numbered by selecting Numbers. If  the Group box is checked and Drawing unchecked the numbering starts at 1. If Drawing and Group are checked, numbering runs from the highest number of any previously numbered group in the drawing plus 1. Any other combination of checks results in no numbering.


Reflect/Reflect Group
Reflect/Flip buttons

Reflect replaces the structure with its mirror image. Flip replaces its image with its upside down image.


Group Editor Buttons

Clone creates a saturated duplicate of the selected group.

Fuse 	combines the selected atoms and bonds into a  new group

Reflect  reflects structure through its vertical axis.

Flip 	flips structure about its horizontal axis.

+50%, -50%	zooms structure by amounts indicate

+90o, -90o	rotates structure by 1/4th turn.

+45o, -45o	rotates structure by 1/8th turn.

Delete, Undo	delete structure or undo all editing.


Delete and Undo
Delete deletes a group and all bonds connecting it to non selected atoms. Undo undoes all editing since group editor was started.
Note: The group editor will not delete labels or symbols.


Numbers turns group numbering on or off


Clone
Creates a duplicate of the selected group. If the selector cuts into bonds they are cut and replaced by implicit hydrogens.
Note: This group editor button  does not clone labels or 	symbols.


Numbering Check Box - determines if group numbering is relative to the selected group or the entire drawing.


Rotate 90o or 45o

Rotates tilts, turns or rotates the group by 90 degrees or 45 degrees depending on which slider function is selected. Has no effect when pivot or zoom is selected.


OK saves the edited structure and closes the group editor.


Editing Symbols

Use the symbol editing tool to edit symbols such as arrows and arcs. To activate the Symbol Editor click the Right Mouse Button with the cursor near the target symbol. Alternatively from the main menu click Symbol | Editor and click near the target symbol. Click each part of the illustration in this figure to learn its function.

Also see Editing


Symbol Editor Buttons

Reflect and Flip are inactive
90o,-90o,

+45o,-45o 	rotate the symbol by the amount shown.

+50%, -50%	zooms the symbol by the amount shown

line  	changes the line thickness

Style's	affect depends on the symbol

Clone	creates a duplicate of the selected symbol

Delete	deletes the selected symbol


Symbol Editor Radio Buttons

The radio buttons determine the function of the slider namely Zoom or Rotate


Symbol Editor Slider

The slider rotates or zooms the symbols depending on the setting of the radio buttons.


Managing Files

Opening, saving and exchanging ChemPen+ drawings is done, from the File Menu. Click on a menu item to learn its function

Also see Menu Commands


File New erases the current drawing, if any and starts a new drawing. If there is a drawing on the Pad you are prompted to confirm the operation. The new drawing is given the file name untitled.chp.


File Open
File Open executes the file open dialog below.The Preview window lets you see a scaled down view of the selected file. The information button will display any information entered by the creator. Click each part of the figure to learn its function. If you click the OK button the previewed drawing replaces the current drawing on the pad, if any. If the Pad contains a drawing you are prompted to erase it and load a file.


File Save

File Save excutes the file save dialog if the name of the file drawing is untitled. Ok saves the drawing to disk. If the filename already exists you are prompted to confirm the saving. File Save is inactive in the demo. version of ChemPen+.


File SaveAs

File SaveAs prompts you for a file name, even if the  drawing has been given a filename, and saves the drawing to disk. If the filename already exists, you are prompted to confirm the save. SaveAs is deactivated in the demo. version of ChemPen+


File Information

File Information executes the file information dialog

Use the dialog to the name of the drawing, the name of the creator and to add eight lines of comments. The information is saved with the drawing


File Copy

Copy puts a bit map or  metafile image of the drawing on the Clipboard that can be pasted into another application. Metafiles, which often appear on the clipboard as pictures, in general give better quality printed and displayed images than bit maps. Bit maps are included for applications that don't accept Metafiles.


Bit Maps

Bit maps are raster representations of pictures. ChemPen+ copies its drawings to the clipboard in metafile or bit map format. Because of their larger file size and poorer scaling characteristics, betimes should only be used when the pasted to application requires them.


Metafiles

Metafiles are special sets of instructions that represent a drawing a set of commands. ChemPen+ copies drawings to the clipboard in metafile or bit map format. Because of their relative device independence and generally smaller size Metafiles are the preferred ChemPen+ drawing format to copy to the clipboard.


File Import

File Import opens the file open dialog and lets you load a drawing without erasing the present drawing. The new drawing is inserted to the right of the current drawing.


File Configure

Use Configure to  set line, the  default line width; path; font; and bond the default bond length. The size of the jump that occurs when a drawing or structure is moved with the arrow keys can also be changed from this menu. For programs with NMR libraries NMR nuclei can be selected from here. The information is saved in file named !ChemPen.cfg. If !ChemPen.cfg is found in the same directory as ChemPen.exe, the drawing is initialized with the !ChemPen.cfg data. If !ChemPen.cfg is not in ChemPen+'s directory then it's created upon starting ChemPen+.


File Exit

Shuts down the application. If a drawing exists you are prompted to save it.


Loading and Importing Drawings

Use the File Open/Import dialog to load existing drawings


Label

Adds a label to the drawing and activates the label editor.


Symbol

Symbols such as, [image], are added to a drawing using the symbol menu. Examples of symbols are arcs, arrows  and the triangle. Symbols can be edited with the Symbol Editor.  As ChemPen+ is developed other symbols will be added.


Atom

Adds an atom to the drawing. Also launches the Atom Editor


Bond
branch

Branches a single bond or links to atoms. If Branch or CH3 is selected, clicking near an atom forms branches until Reset is selected or a different menu item is selected. If Link is chosen clicking twice near two different atoms will form a single bond. Repeated selection of pairs of atoms bonds them until Reset is selected.

Note: no link occurs if either atom's valence is exceeded.

Also see: Editing Bonds


Ring

Adds, branches, links or fuses a ring to an existing structure. If Add is chosen a ring is drawn centered at the point on the drawing where the mouse is clicked. If Branch is selected, clicking near an atom branches from that atom. Branching occurs if the valence of the target atom is not exceeded. If Fuse is selected, clicking near a bond fuses the ring to that bond. The ring will not be fused if  the valence of the atoms will be exceeded. If Join is selected, clicking near an atom joins an apex of the selected ring to the target atom. The ring is joined if the valence is not exceeded.


Font

Launches the font dialog that allows the user to change the current drawing font. The font is in effect until the application is closed.


Font Dialog


Link

To form a new bond between two existing atoms select link then click near each of the two atoms. Use RESET to stop linking.


Special Menu

The special menu provides access to libraries and options that extend ChemPen+' functionality. All versions of ChemPen+ come with a molecular weight calculator under the special menu. When an extension is added its selection appears in the special menu.


Using the Mouse

ChemPen+ uses the mouse in several ways to simplify work. Combining the shift and control keys with the right mouse button have special functions in ChemPen+.

Clicking the right mouse button - selects the nearest atom or symbol and activates  the Atom Editor or the Symbol Editor

Holding Shift and clicking the right mouse button - selects the nearest bond and activates the bond editor

Holding Ctrl while clicking the right mouse button - selects the nearest ring or group and activates the Group Editor.

Dragging the mouse from above and  left of any group of atoms to below and right of the atoms and combines them into a group activating the Group Editor. The selected group is highlighted.

Also see Editing


Customer Support

Customer Support for ChemPen+ is available to registered users via America On-line, via Internet mail or by US Mail. If you have a question, want to report a bug or have a problem with ChemPen+write to the following. For registered copies be sure to include your registration number in any correspondence.

America Online:	HFEvans

Compuserve:	102303.2120

Internet Mail: 	HFEvans@AOL.com

102303.2120@Compuserve.com

U.S. Mail: 	Hilton Evans

232 Canton Street#312

Randolph, MA 02368