Accessing JChem Base with a JavaScript Application for Search

and Registration

John McNeilNovember 1, 2012

john@mcneilco.comwww.mcneilco.com

“We make tools to help bench scientists be more productive, efficient, and creative.”

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Structure/Lot CRUD REST Services

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Analytical Files

JChemBase

Client Architecture

View Controller

Model

Simple MVC Salt Registration

Salt List

Salt 1

Salt 2

2

0New Salt registration

Register New Salt

*Salt abbrev:

*Salt mol weight 22.9898

*Salt name SodiumSalt structure:

Draw or paste structure in Marvin plugin

Na

SaveCancel

New Salt Controller

Nested MVC Client“The Onion”

Salt Form

Salt List

Salt 1

Salt 2

Salt 1: Equiv.:

2Salt 2: Equiv.:

Na

0

none

New Salt registration

Register New Salt

*Salt abbrev:

*Salt mol weight 22.9898

*Salt name SodiumSalt structure:

Draw or paste structure in Marvin plugin

Na

SaveCancel

Salt Form

Salt Equivilent

Salt 1

Salt Form Controller

Salt Equivalent ControllerSalt Select ControllerSalt Option ControllerNew Salt Controller

2

0

View Controller

Model

Compound Registration and Search Application

Compound Registration Overview

1) Enter Structure and search for matches

2) Enter salt and lot information

Search Panel

Behavior Driven Development

Design and Specification

Next StepCancel

Structure from last step

Use Parent structure SGD-12345

StructureMatch 1

Mol. Wt. 123

Mol formula:

Registration Step 2: Review Structure and Salt Form Matches

Is Virtual:

Back

Stereo Category: none Stereo Comment: none

Register new SGD

Requested Structure:

If Is Virtual Clicked, disable all but stereo information on next page

If Is Virtual Clicked, all use existing SGDw options are disabled and register new is selected

Show Salt Forms

Use SGD-12345-Na

Use SGD-12345-C14Na

Salt 1: Equiv.: 1Na

C14 num labeled 1Isotipe 1: CAS number:

Common name:

Salt 1: Equiv.: 1Na CAS number:

Common name:

Use Parent structure SGD-0001

If an existing isotope/salt form is selected, then a new lot is made with the next lot number for that salt form

Only show isotopes and salts actually added, even though model supports up to 3

#RegSearchResults_ParentView

#RegSearchResults_ParentListView

#RegSearchResults_SaltForm

#RegSearchResultsView

server

#RegSearchResults_SaltView

#RegSearchResults_SaltListView

Lot Form Sepc

Properties

SaveCancel

Lot Mol. Wt.: 123

Physical state:

Color: blue

Purity (%): 98

Purity measured by:

Supplier:

Supplier compound ID:

Lot comments:

Amount:

=

*Notebook-Page:

Drag Analytical Files here: 3 files loaded

solid mg

View/Edit Files

Retain: mg

HPLC

*Synthesis Date: 25-May-11

Back

Draw or PasteStructure of Parent with Isotopes

[This is pre-populated with parent on left as a shortcut for the user]

Salt 1: Equiv.: 2

Salt 2: Equiv.:

Salt 3: Equiv.:

Na

none

Add new salt

0

Isotope: C14

Add new isotope

num labeled.: 1

none

0CAS number:

Common name:

*Stereo Category: Scalemic

Standardized Struct from drawn stuct

Stereo Comment:

Parent Structure: Enter Isotope/salt structure

"new compound", or "new salt of SDD-nnnnn" or new lot of SGD-nnbnn-mm"

If an existing SGD is selected in the previous step, stereo fields are filled in but disabled

*Chemist: jmcneil

Validate that notebook format is 1234-043

%e.e.:

Pop-up is populated from LDAP, Defaults to logged in user.

Isotope: none num labeled.:

0

JM&C to propose options for physical state and purity measured by

Dropping files opens file manager where comments per file can be added

Clicking button opens Upload Analytic File panel

Also save the date this form completed

Always give 3 salt options, no more

isotope is "none" by default. N mods field is disabled and = 0 if Isotope is "none"

Stored as IsoSaltForm alias

If a new isotope/salt form is shown, then the lot counter for that SGD-salt starts at 1 for this lot

Salt is "none" by default. Equiv field is disabled and = 0 if Salt is "none"

If a user picks new structure on the previous page, and there were exact structure matches, than the stereo categories for those matches are disabled in this select listCategories are: Scalemic, Racemic, Achiral, or See Comments

Pop-up date pickerDefault to today

The number of equivalents does not change the salt form

If an salt form is selected in the previous step (as opposed to parent), the salt, isotope, CAS, and common name fields are filled in but disabled

server

server

server

Salt Registration Form

New Salt registration

Register New Salt

*Salt abbrev:

*Salt mol weight 22.9898

*Salt name SodiumSalt structure:

Draw or paste structure in Marvin plugin

Na

SaveCancel

Name and abbreviation are required and must be unique

Structure is optional, but if supplied must be unique

These are pop up panels that float above lot registration page

#NewSaltView

server

server

Demo Test and Development Process

Conclusions

• ChemAxon tools can be used in a variety of architectures

• Structure services can be used and re-used with multiple clients

• For interactive user interfaces, modern MVC architectures work well

• Behavior driven development is a robust practice that minimizes maintenance and enhancement costs

Thank You

Team

• Brian Bolt

• On Khongsaly

• Guy Oshiro

• Matthew Shaw

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