Transcript - ChemAxon

JChem Base and Cartridge
latest
Presenting: Szabolcs Csepregi
UGM, June, 2007
Contents
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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:
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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 subexpressions from CT columns
New in JChem Base & Cartridge
Fingerprint statistics on table
easier 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
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)
Representation: Pseudo atoms (See More dialog in Marvin or
the Beilstein generics dialog in ISIS/Draw)
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:
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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