UGM, June, 2007 Presenting: Szabolcs Csepregi JChem Base and Cartridge latest.

UGM, June, 2007

Presenting: Szabolcs Csepregi

JChem Base and Cartridge latest

Contents

• New in JChem Base & Cartridge architecture

• Search feature improvements• Cartridge-specific news• Future plans & development discussions

Notations: – already released (available in latest version) – available to try out in alpha version

New in JChem Base & Cartridge

• Table types introduced:– Molecule– Reaction– Any structure– Markush– Query

• Reaction similarity for reaction tables

New in JChem Base & Cartridge

• Chemical Terms (calculated) columns– Example: asymmetricAtomCount()+3*ringCount()+0.5*logP()

– Can use all CXN calculations + mathematical & logical operators

– Automatically updated when structure inserted or updated

– Search with Chemical Terms filter uses stored sub-expressions from CT columns

New in JChem Base & Cartridge

Fingerprint statistics on tableeasier tuning for search speed(see speed tuning presentation last year)

New in JChem Base & Cartridge

• Installer• Sortable chemical formula

column (Proper sorting of numbers, not alphanumeric)

• JSP example enhancements– Display options (partial clean,

handling of alignment & hit coloring)

– More search options (ignore stereo, charge, isotope, vague bond options, etc.)

– Markush tables: enumeration controls• Progressive return of search hits (hits are

returned during search) – provides improved speed!

New in JChem Base & Cartridge

API (programming interface) improvements:

• Hit coloring and alignment• Unified search options of database and in-

memory search• Custom atom & bond comparators to modify

search behaviour (for advanced usage)Examples:– Define your own extra stereochemistry rules– Also consider atom maps, atom values, etc

New search features

• Component, mixture and formulation (ordered mixture) brackets

• Reacting center bond query feature (Search for changing, unmodified, etc. bonds during reaction search.)

New search features

New query atom types

Representation: Pseudo atoms (See More dialog in Marvin or the Beilstein generics dialog in ISIS/Draw)

Query atom type

Description

AH Any atom type, including H

QH Heteroatom or H

M Metal

MH Metal or H

X Halogen

XH Halogen or H

Gn Member of group (column) n in the periodic system (n = 1..18, G17 is the same as X)

Cartridge-specific news

• Optional CLOB storage of structure as structure column type ("US-ASCII" encoding only)

• jcf package (overloaded functional equivalents, replaces old jcf_... functions)

• Partitioned JChem index • Providing cost estimations to Oracle optimizer • JChem Server improvement: HTTP(Tomcat)

replaced by RMI to reduce communication overhead & simpler installation

• Speed enhancements– HTTP(Tomcat) -> RMI– Early return of first hits

Instant JChem released

• Easy-to-setup, easy-to-use GUI• Most of JChem Base functionality available• Access of remote JChem Base databases

for:– Administration– Data entry & import– Searching & browsing– Sharing data

See separate lecture later today

Future plans & discussions

Next major version (Q3 2007):• Coordination compounds insert and search

• Easier installation of Cartridge

• Database field access from Chemical Terms expressions

• Tautomer duplicate filtering option

Future plans & discussions

Later major version (during next year):• Pharmacophore query types (customizable

pharmacophore point types of Screen) • 3D searching (all conformers or multiple conformations)• “Parent search” (ignore stereo and search only largest

fragment)• Chemical formula search with formula query language• Web service interface for JChem Server • Computational cluster support• Start to extend Markush tool to patent area (longer term

– will be discussed in detail tomorrow)• Integration of Screen descriptors with Cartridge• ...?

Further info

• JChem Base resources http://www.chemaxon.com/product/jc_base.html

• JChem Cartridge resources http://www.chemaxon.com/product/jc_cart.html

• Instant JChem resources http://www.chemaxon.com/product/ijc.html

• Forum topics:– JChem Base, Cartridge & Searching:

Home -> Forums -> Support -> Structure search and chemical database

– Instant JChem: Home -> Forums -> Support -> Instant JChem