PDB Agent Project

since 2003-10-16

PDB agent is a software to easy the query of PDB database. It's a sub project of xINDUS, and sub sub project of INDUS(my part)

Under JDK1.4.1, JBuilder 8.0 and JBuilder 9.0. Tested both in WindowsXP and Redhat 9.0


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Steps	New Features	New JDK/Package used	New class/Package	Notes	Indus Lines*
1.0.2 (2003-11-02)	- batch query to remote pdb database ( return a list) - open pdb, and mmcif file , locally or remotely - do visualization - do parsing - ID List-source-information GUI	javax.swing.table. Java3D MBT	Deleted all webmol classes edu.isu.indus.util.FileFilterEx New edu.isu.indus     PDBAgent (privously PDBApp)     PDBAgentApplet (privously PDBViewerApplet) edu.isu.indus.db    INDUSConnection edu.isu.indus.db.pdb    PDB3DViewer    PDBConnection (modified)    PDBException    PDBParser    PDBSearchFields edu.isu.indus.gui    PDBActions (extract from PDBGUI)    PDBGUI  (modified) edu.isu.indus.gui.control    ProteinTable edu.isu.indus.gui.dlg    AboutBoxDialog    InspectorFrame edu.isu.indus.util    Utility edu.isu.indus.util.gui    GUIUtils    LabelledItemPanel    ProgressBarWin    StandardDialog		Class 20 Code 2684 Cmnt 841
1.0.1 (2003-10-20)	- Split panel for source view and XML view - PDBViewer -> PDB Connection to save UI  independent functions - PDBViewerUI -> GUI contruction - Menu Bar - Open Local File - Visualization based on webmol	java.awt. java.awt.image java.awt.geom	webmol.gui webmol.gui.dialog webmol.gui.win webmol.math webmol.pdb webmol.test webmol.util webmol.util.ps webmol.visualization edu.isu.indus.pdb.PDBConnection edu.isu.indus.util.FileFilterEx edu.isu.indus     PDBApp     PDBGUI (privously PDBViewer)		Class 7 Code 691 Cmnt 300
1.0.0 (2003-10-16)	Return plain text and xml PDB file of given PDB ID	JAXP java.util.zip java.net javax.swing	edu.isu.indus     PDBViewer     PDBViewerApplet edu.isu.indus.util.Debug edu.isu.indus.xml.XTree		Class 4 Code 557 Cmnt 106

* Lines: no blank lines ; only for edu.isu.indus package.

Todo List:

1. store query result in RDBMS
2. translate SQL to native query
3. enhanced ID List, more helpful information
4. data extract based on DB query
5. a prosite agent will motif cross-query

Todebug list

- out of memory when read large PDB file without warning message

 Reference : see Developing resources to INDUS project