Copyright: Copyright ®1993 Hilton Evans


Contents

Copyright

Introduction

Editing

Keyboard

Managing Files

Main Menu

Register/Order

Support

Tutorial

Using the Mouse

NMR Demo Database


Copyright Notice

ChemPen+.

© 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
Registered ChemPen+ users receive the latest version of ChemPen+ and a printed manual.

Compuserve Members can register/order  via the Shareware registration service on Compuserve. GO SWREG and enter Registration ID:   11961.

Or use the following order form.

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 and intuitive. 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 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, such as t-butyl, are collections of atoms and bonds. 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.

Simple text is added to ChemPen+ drawings 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


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 grey 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 branch | CH3 and click near atoms 2 and 12.
2. From the main menu select branch | OH an click near atom 6.
3. Click Reset to stop branching.

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 button on the  Group Editor until
    numbers turn off.
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 menu item 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 menu item.
3. Right button click near right drawing to select it.

4. Type right arrow a couple of times to move the new structure right.

Result

Next Step

Previous Step


Drawing Step 9
Drawing - Step 9

Create a carbonyl and a double bond
1. Point the mouse pointer near the right structure's OH and type 2 to create a carbonyl.

2. Repeat step one to create the second double bond.
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 | choice from the Symbol Menu where choice
     is a  one  of the single 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. A blue square appears and the editor activates.

3. In the editor type the word 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

The keyboard can be used to navigate ChemPen+. The following key commands move the drawing without affecting the scroller.

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

Arrow keys move the drawing up, down, left and right by the amounts set by Jump under the Defaults menu.

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

The closest atom to the mouse pointer can be changed to one of several commonly used atoms by the following keystroke commands .

H - hydrogen, C - carbon, N - nitrogen, O - oxygen, B - boron, F - fluorine,

X - chlorine, Y - bromine, I - iodine , Q - silicon, P - phosphorous, S - sulfur,

Se - selenium

The closest bond to the mouse pointer can be modified by one of the following single key commands

1 	single bond

2 	double bond

3 	triple bond

4	resonance double bond

5	dots or hydrogen bond

A	toggles a bond between aromatic and non aromatic*

K	cuts or deletes a bond

L	links the two closest atoms with a new bond

+ , =  increments the charge of the closest atom by 1

-(minus) decreases the charge of the closest atom by 1.

* Aromaticity of a bond is only relevant to ChemPen+'s
 internal property prediction algorithm.

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.

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.

The Atom editor works with an  Atom Editor Menu

Also see Editing ,Menu Commands


Atom Editor Menus

Text Window edit symbol text in text window.

+1, -1 Increments or decrements the atom's charge by one.

+H , -H adds or subtracts a neutral hydrogen atom

+H(+) , -H(+) adds or subtracts a proton.

Left/Right toggles atom's symbol or text between left and right justified

Font launches the font dialog allowing you to change the font of the atom's symbol.

XHn toggles between explicit text, explicit hydrogens and no text. This is primarily useful for carbons.

Reflect reverses order of text characters.

Clone generates a clone of the selected atom.

Delete deletes selected atom and deletes any attached bonds.

Undo reverses editing.

Periodic Table -  clicking an elemental symbol changes selected atom to the clicked atom.


Atom Menu
Atoms Menu

Click this menu to add an atom, to form a bond between two existing atoms or to protonate and existing drawing with explicit hydrogens.

Also see: Menu Commands


Branch Menu
Branch

The group menu is used to branch a single bond, a hydrogen,  a halogen atom, or one of several common functional groups from an existing atom.


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

To enter text, select label from the Symbol menu and click the spot where you want to add text. To edit and existing click near the label with the right button.

Text is entered and edited with the Text Editor. The text editor is just the atom editor with some features disabled and no periodic table. Clicking an atom activates the other features.One line of text can be entered using the text editor.

Also see Editing


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.


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.


Editing Bonds

The bond editor tool is used change the character and appearance do bonds. 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.

The bond editor also has its own set of Bond Editor Menus

Also see Editing , Menu Commands


Bond Editor Slider

The bond editor slider pivots, rotates or zooms the selected bond depending on the setting of the radio buttons. Select Pivot to pivot the bond around one of its atom. Click near the pivot atom to select it.  Rotate rotates bond within the plane and around the bond's center. Zoom increases or decreases the length of the bond around its center.

Bond Editor Menus


Bond Editor Menu Commands

Aromatic - toggles bond between aromatic and non aromatic. *

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 dotted 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 thickness.

Delete - deletes the bond and saturates its atoms.

* This is only relevent for ChemPen+'s internal property prediction routines.


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 gray rectangle. The group editor has a set of  Group Editor Menus

Also see Editing ,Menu Commands


Group Editor Menu Commands

Bonds The bonds button shifts all of the multiple bonds in a group left or right toggling between styles to the left.

Clone creates a duplicate of the selected group. Cut bonds are replaced by implicit hydrogens.

Flip flips structure about its horizontal axis.

Fuse combines the selected atoms and bonds into a  new group

Numbers toggles numbering of selected group on and off. If the drawing box is checked numbering starts at the highest number of the entire drawing.

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

Reflect  reflects structure through its vertical 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.


Group Slider Functions

The function of the slider is determined by the selected radio button.  Tilt, and Turn rotate the selected group around in plane the vertical and horizontal axes

Rotate rotates the group within the plane.

Pivot rotates  group around a pivot atom. Click near pivot atom to select it.

Zoom continuously enlarges or shrinks the selected group.


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. Click each part of the illustration in this figure to learn its function. Click Symbol Editor Menu to learn about its function.

Also see Editing


Symbol Editor Menus

Reflect and Flip reverse some symbos up/down or left right.

90o,-90o ,+45o,-45o rotate some symbols by the angle shown.

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

line  	changes the line thickness

Style	affect depends on the symbol

Clone	creates a duplicate of the selected symbol

Delete	deletes the selected symbol

Undo	reverses current editing.


Symbol Editor Radio Buttons

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

Use Defaults to  set line, the  default line width; path;  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+. with a set of default values


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


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

Found under the Atoms menu, Link is used to  form a new bond between two existing atoms select link then click near each of the two atoms. Use RESET to stop linking. You can also link to close neighbor atoms by typing L with the mouse pointer between them.


Calculate Menu
File | Calculate Menu

The File | Calculate menu  provides access to optional libraries and options that extend ChemPen+' functionality. All versions of ChemPen+ come with a molecular weight calculator under the calculate menu. A  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


NMR Prediction
NMR Prediction Demonstration Database
Included with ChemPen+ is a proprietary property prediction module that is implemented for predicting NMR shifts. ChemPen+ generates numerical codes analogous to those developed by Dr. Wolfgang Bremser at BASF. Unlike HOSE codes, which are strings composed of bond and symbol codes, each ChemPen+ code consists of a set of seven numbers. The first six numbers  encode connectivity, saturation, hybridization, charge, and element types in the first six hierarchical rings radiating from the target atom. The seventh layer encodes the rings, ranging from 3 to 7 atoms, containing the target atom.

Activating the NMRTool generates a set of numerical codes for the current structure. The predictor first trys to find exact matches. Short of exact matches, the predictor searches for matches of the first six, then five, then four numbers on down to the first and most significant code. As a last resort, the predictor will vary the number of hydrogens of the first neighbor atoms to find a match. Continue


 NMR Prediction Continued
The demonstration database consists shifts compiled from a small random sample of assigned NMR spectra. The included database is very limited. Optional databases will be made available in the near future. Like HOSE codes ChemPen code prediction assumes two atoms with the similar or identical codes have the same electronic environment. Use the NMR Tool to predict NMR shifts or to update the NMR shift database.

Draw the target structure for NMR prediction without symbols or group abbreviations such as COOH. Groups must be explicitly drawn. Select File | Calculate | NMR Shifts to activate NMR Tool.To change nucleon, select File | Calculate| XX  where XX is the desired nucleon.


Enter Shift(s) -  Enter one or more shifts separated by spaces.
Delete -  deletes shift if its score is 100%.
Del All -  deletes displayed shifts with scores of 100%
OK - Updates and saves database; closes NMRTool
Cancel - deletes newly added peaks. Closes NMR Tool.
Score - the percent match between the codes of the estimated atom and the closest matching codes in the   NMR database.
Nucleon - NMR nucleus selected from the File | Defaults menu.


Customer Support

Customer Support for ChemPen+ is available to registered users  via Internet mail, Compuserve 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.

Compuserve:	102303.2120

Internet Mail: 	HFEvans@ICI.com

102303.2120@Compuserve.com

U.S. Mail: 	Hilton Evans

232 Canton Street #312

Randolph, MA 02368

For Latest Information and to Download Demo Version of ChemPen+

WWW:	http://www.ici.net/cust_pages/hfevans/chempen.htm