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The Molecular Biology Toolkit – Geometry Generation Capabilities Apostol Gramada John Moreland PI: Phil Bourne Supported by: SPAM project: NIH NIGMS 1P01GM63208-01A1 Outline An application developer perspective General Description of the package-Class Hierarchy
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PI: Phil Bourne
Create a Geometry Class and set parameters
Generate the Java3D object that can be directly attached to the graphical scene.
need to add/remove/edit fragments rather than chains
smooth transition requires setting boundary tangents, normals in advance
specific rendering properties
coil = new CoilGeometry( )
coil.setCoordinates( double coords )
coil.setColorMap( float colorMap )
coil.setPreviousCaCoord( double coord)
branchGroup = coil.generateJ3dGeometry( )Creating Geometry
a single line of code
automatic rendering quality-performance control
SsGeometry.drawSs(group, structureMap, structureStyles, hash)
PsGeometry.drawBonds(group, bonds, structureStyles, quality, mode, hash)
PsGeometry.drawAtoms( group, atoms, structureStyles, quality, hash )Creating Geometry cont’d
100-200 vertices (even for moderate quality) – memory intensive
Shading – hardware intensive
Typically many atoms to render
John wrote a customized sphere class so that geometry is shared for the same type of atoms
Appearance attributes also shared within a given type classSpheres
A larger number of parameters -> more difficult to control the shape of the interpolated curve
May not work with a piecewise interpolation approach
Priestle smoothing (CA coordinates, normals)
Independent interpolation for normal/binormal
Orthogonality is not always strictly enforcedSolution
Covalent bond detection for ball-and-stick rendering
hydrogen bonding for secondary structure assignment (in the Kabsch-Sander algorithm)
Some types of surface representation require calculation of the same order of magnitude, i.e. n2
Very time consuming for big structures.
Implemented an Octree-based algorithm for the determination of the closest neighbors within a given sphere in 3D.
Complexity reduced to
Overhead associated with building the tree is of the same order of magnitude
Typical observed speed-up 10-20 timesPerformance challenges