Protein analysis engine - Develop engine core - Open Source & Linux Lab

Develop engine core

Time tracking

Estimated time	193.50 hours
Spent time	186.90 hours

about 20 months late (06/10/2010)

Molecular vector machine implementation and visualization

95%

51 closed (93%) 4 open (7%)

Related issues

Task #132: Setup iteration "Simple state machine"
Task #136: Make environment
Task #137: Read triplet sequence
Task #138: Read decoded proteins
Task #139: Simple state machine
Task #140: State editing interface
Task #141: Self-teaching algorithm review
Task #142: Self-teaching state machine
Task #143: Molecular vector machine
Task #144: State machine work visualization
Task #145: Molecular vector machine visualisation
Task #555: Migration to a new version of bioclipse
Task #556: Make a modeling module prototype
Task #557: Reading pdb format on C#
Task #558: Generate an ASPX page with results if modeling
Task #1374: Implement core package
Task #1516: Draw a dodecahedron
Task #1596: Modify standard JMol Bioclipse Editor
Task #1606: Show protein outline
Task #1786: Use CdkJmolAdapter in JmolEditor
Task #1810: Know about personal atom type
Task #1812: Know about bioclipse and cdk IMolecule
Task #1848: Log4j console
Task #1977: Rejar Jmol.jar
Task #1978: Change Jmol plugin dependencies
Task #1980: Commit Jmol.jar into github
Task #1995: Understand positioning principals
Task #1996: Calculate center of model position
Task #1997: Precise dodecahedron positioning
Task #1998: Mark dodecahedron verticies
Task #1999: Coordinates transformation
Task #2000: Extract molecular model from net.bioclipse.jmol plugin
Task #2023: get new Jmol.jar with egit
Task #2046: add info about CA atoms to molecule
Task #2057: investigate why dodecahedron disappears when duplicate view is hidden
Task #2100: correct position when switching "move dodecahedron" off/on
Task #2102: Refactor dodecahedron functions
Task #2103: zoom dodecadron for smart positioning
Task #2129: Show rotation axis
Task #2130: Rotation aroud the main axis
Task #2143: rotate dodecahedron to side chain
Task #2203: Draw hydrogen coherence
Task #2221: Process all aminoacids in protein functionality
Bug #1517: Null pointer exception after opening file
Bug #1607: Experimental full protein structure doesn't show
Bug #1665: Works only with project "Protein Engine"
Bug #1919: Molecule in experimental structure shows with holes
Bug #1979: duplicate view isn't restored
Bug #2099: dodecahedron isn't always positioned smartly
Bug #2101: translate zoom events to duplicate panel
Bug #2152: dodecahedron is distorted
Bug #2159: some atom types are broken
Feature #1608: Manual mode for dodecahedron
Feature #1954: Eliminate vecmath package in Jmol.jar
Feature #1955: Automatic dodecahedron positioning