Helpfile for Structurer v0.6b 17th Feb 1999 Copyright Daniel Barron


RISC OS 3.10, 3.11, 3.5, 3.6, 3.7 and above only.

It may, and should work, on all versions of RISC OS and ARM processors.

A Traffik Software release.  Programmer: Daniel Barron.



Legal
~~~~~

This program is Freeware.  The author retains copyright.  No one can alter
this program and re-distribute without the authors permission.  This
program can be distributed freely so long as the distributor does not claim
to be the author or to hold the copyright and it is distributed without
modification.  The author cannot accept any liability for any loss or damage
arising from the use of this application.  Structurer is supplied in good
faith.



Structurer Overview
~~~~~~~~~~~~~~~~~~~

This program converts drawn organic molecules into the IUPAC name.  The
interface is very crude and was knocked together in only a couple of hours.
The main interest is the modular IUPAC engine I have spent 500 hours
producing and designing.  The point of this program is to show off my
engine - not to provide a desktop application.

Even though this is just the skeleton engine with a simple interface
bolted on, it is a fully working and useable program.

By skeleton I mean the bare bones of a modular system which includes all
the main parts to make it work, along with a number of naming modules
to demonstrate it working.

There are no known Acorn packages which do this.  The only other package
I know which does this is on the PC called Autonom.  Autonom is written
by a team of programmers and has been developed over a number of years
and so is more comprehensive than my beta skeleton package.

This is a damn clever program.  I am writing a java version which will
be the flagship version.  Being in java it'll work on my website and
standalone on any platform.



Structurer Instructions
~~~~~~~~~~~~~~~~~~~~~~~

Double click on its icon in the directory viewer to load and then press
1, 2, 3 or 4 to select your monitor type.

Now you are at the drawing molecule stage.  Follow the instructions below
to draw your molecules:


How to add an atom

*       First select the atom type to add by pressing the appropriate 
        key, E.g. 'C' for carbon, then
*       Press the select (left) button on the mouse with the pointer in the 
        correct position on the screen.

Note that the interface will not allow you to place atoms too close 
together.


How to remove an atom

*       Move the pointer of the mouse over the atom you wish to 
        remove, then
*       Press the adjust (right) button.

Note that the interface will only allow a small amount of error in the 
positioning if the mouse pointer over an atom.  And that all 
bonds connected to the atom to be removed will automatically also
be removed for you.


How to bond two atoms together

*       First select the bond order of the bond by pressing '1', '2', or '3', 
        then
*       Move the pointer of the mouse over the first atom you wish to 
        join and click select, then
*       Move the pointer of the mouse over the second atom you wish 
        to join the first atom to and click select.

Note that you can abort a bond addition by pressing 'A' after first selecting 
the first atom.  You do not need to bond atoms as soon as you have 
drawn them and can leave adding bonds until the end.  You can draw 
a bond over the top of another bond to replace it with one of a 
different bond order.
How to remove a bond

*       First select bond removal by pressing '0', then
*       Move the pointer of the mouse over the first atom the bond is 
        joined to and click select, then
*       Move the pointer of the mouse over the second atom that the 
        bond is joined to and click select.

Note that you can abort a bond addition or removal by pressing 'A' 
after first selecting the first atom.


How to submit the structure to the IUPAC parser

*       Make sure that all atoms are joined and that there are no 
        valency violations, then
*       Press the menu (middle) button, then
*       When you have finished noting the name and wish to draw 
        another or amend the original, press the Space Bar.


The summary list of keys

        0       -       Remove bond
        1       -       Add a single bond
        2       -       Add a double bond
        3       -       Add a triple bond
        A       -       Abort bond action
        C       -       Add a carbon atom
        O       -       Add a oxygen atom
        N       -       Add a nitrogen atom
        F       -       Add a fluorine atom
        I       -       Add an iodine atom
        B       -       Add a bromine atom
        P       -       Add a phosphorus atom
        S       -       Add a sulfur atom
        L       -       Add a chlorine atom
        E       -       Add a silicon atom
        SPACE   -       Clear screen after name displayed
        MENU    -       Submit structure
        SELECT  -       Do action
        ADJUST  -       Remove bond action

I do appologe for the spelling of sulphur as sulfur, but due to the mad
americanisation of the entire world, the IUPAC spelling is the latter.



More Advanced Instructions
~~~~~~~~~~~~~~~~~~~~~~~~~~

When drawing a molecule you need to know what this version of my engine
is capable of:

What it CAN handle:

         rings
         chains
         some non-carbon chains & rings (nitrogen, silicon & phosphorus)
         ketones
         aldehydes
         cyanides
         carboxylic acids to a large extent
         nitrosos
         thiols
         amines
         imines
         halogens (Cl, Br, I & F)
         alcohols
         multiple hydrides
         complex hydride depth to at least 3 levels
         multiple bonds - i.e. double & triple
         multiple bonds to the parent hydride from a sub-hydride of order 2 & 3
         all IUPAC punctuation name standards associated with the above
         nitrogen, carbon, silicon, [hydrogen], oxygen, halogens, phosphorus,sulfur


What it CAN'T handle:

         esters, ethers, or similar (R-C-O-C-R')
         acid halides (but easy to add with hetero chain finder tool)
         hydroperoxides (but easy to add with hetero chain finder tool)
         peroxides
         salts of carboxylic acids (not too hard to add)
         thiolates
         fused rings
         more than a simple guess at the parent hydride
         functional groups not mentioned above
         non-systematic rings, e.g. benzene

Basically avoid -C-O-C- or, less importantly, more than 1 ring in a structure.

To see some examples of what the current engine can handle have a look inside
this applications directory and you will see 2 draw files.  Load them and be
amazed.



PointView Further Developments
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I hope to reduce the can't list and add much much more to the can list.

If any company would like to buy or licence the engine or even pay me to
work further on it then contact me as below.

If any chemistry student who can be bothered to write a wimp interface
for my engine then contact me.  This would not be very difficult to do
at all as the input required is only a connection table.  The output
can be in any form.

Suggestions are welcomed.  Replies to suggestions may come.



Structurer Registration
~~~~~~~~~~~~~~~~~~~~~~~

There is no registration necessary.  The program is freeware.  However, if
you still feel inclined to send me some sort of reward, monetary or otherwise,
do not hesitate one second!

To receive the latest version send a cheque or postal order for 5 pounds
sterling to Daniel Barron. Address:

         91 Newland Park
         Hull
         HU5 2DT
         England
         
Please allow 2 weeks for delivery.  I need to wait for cheque to clear.  I
also need to wait for the post to be redirected to my current address which
changes as I am at different places.  This cost includes postage + FREE disk
etc.

Cash IS accepted, but AT YOUR OWN RISK.

Or you can email me and I might even email you the latest copy free of charge!



Structurer Contacts
~~~~~~~~~~~~~~~~~~~

To contact me for whatever reason, even to report bugs use the above address
or email me:

daniel@beebug.co.uk

I have no access to the Internet apart from at work.


Another way to contact me is to check out my web pages:




Structurer Known Bugs
~~~~~~~~~~~~~~~~~~~~~

None, so go away.  I don't spend 500 hours over 1 year to get comments like "I
know its free, but could you just add something simple like stereo chemical nomenclature... oh and I found a bug... ".

Well, acutally I don't mind that much...


History
~~~~~~~

version                info

0.55  April 1996       The first fully working version that included all the
                       minimum requirements I needed.
0.60  Feb 1997         Finally got the parent cyclo-hydride locant minimising routine to work properly.
0.61  Feb 1997         Fixed a couple of minor bugs.


My Computer
~~~~~~~~~~~

I have a Risc PC 600 with:

48 Mb DRAM
2 Mb VRAM
StrongARM 202 Mhz
OS 3.7
586 133 PC card
420 Mb ADFS hard disk
1.27 Gb RapIDE hard disk & interface
9 Gb IDE
6-speed CD drive
2-speed CD drive
6.6 SCSI CD drive
2-speed CD writer
Colour vision digitiser
Risc TV
Cannon BJC-4000
Cumana SCSI II
Idek 8617 17 monitor
I-cubed net card
3 486DX processors as decoration to the unused 5 bay
1 Pentium 90 processor as decoration above the Acorn symbol

