Activity for Martin Manak
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Martin Manak committed [c2ab77]
Added counting tetrahedra at edges
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Merge branch 'compression' of ssh://git.code.sf.net/p/awvoronoi/source into compression
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Javadoc
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BUGFIX: Vectors.normalize() - problems with zero-length and low-magnitude vectors
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DelaunayCellDiscovery: Vertices explicitly marked as redundant will be skipped
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BUGFIX: Integer4.toArray outputs four fields
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Added the support of integer and double pairs and triplets
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PDBX 4.1.2 supports pdbx-v42.xsd and pdbx-v50.xsd and requires Java 8
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schema-atoms 1.1.2 depends on jaxb-api (removed in newer JVMs)
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delaunay-cell-discovery 1.0.7 -> awvoronoi 1.0.6
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awvoronoi 1.0.6
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awvoronoi-run 1.0.6 -> awvoronoi 1.0.6, caver-delaunay-factory 1.0.8, schema-pdbx 4.1.2, schema-atoms 1.1.2
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caver-delaunay-factory 1.0.8 -> delaunay-cell-discovery 1.0.7
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Updated README.txt
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Input/Output can have different formating of the "frame" variable
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Added missing main() and removed superfluous help option
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awvoronoi - FileUtil.getJarName
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Array2D returns also its size in bytes
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An abstract basic class for writing command-line applications.
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Fixed wrong variable name
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Merge branch 'master' of ssh://git.code.sf.net/p/awvoronoi/source
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NetCDF input provides the number of frames
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Added PrimitiveType enum for easier work with primitive types
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Frames with missing input coordinates are detected and the computation can be stopped
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Removed getJarName from utilities, and made conversion to URI somehow more robust
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Replaced net.sf.awvoronoi.util.Function by java.util.function.Function. Added a better interface for computing cell orientation.
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Added parsing of index-intervals from a string, e.g., "0-20,30,35"
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Array2D instances can be allocated by a factory class.
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TriangulationData - corrected comments
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Triangulation cells can be explicitly oriented.
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Arrays can be read from or written to a TAR.XZ archive.
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SimpleTriangulationData - added a copy constructor
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Added the computation of exit-points
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IndexIntervals can stream their values.
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Replaced ViewArray2D by IndirectArray2D with more general functionality
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Created a stand-alone command line application for computing exit-points.
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Awvoronoi-run - added conversions, compression, TAR.XZ output, simplified and refactorized code
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Coments.
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Merge branch 'master' of ssh://git.code.sf.net/p/awvoronoi/source
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Merge branch 'master' into caver-analyst-R2
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awvoronoi - POM version 2.0.0-caver-analyst-R2-u02
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FEATURE: Probe-regions can be merged by considering a smaller probe
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BUGFIX: io-chem: Fixed a bug in structures starting with a ligand (array index out of bounds)
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Merge branch 'master' into caver-analyst-R2
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Merge branch 'master' into caver-analyst-R2
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BUGFIX: JGromacs divides all PDB coordinates by 10, so we have to multiply them to cancel this behavior
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Merge remote-tracking branch 'origin/master' into HEAD
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Changed the version number for CAVER Analyst R2 (update 01)
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BUGFIX: Probe accessibility computation - index was out of bounds when there was no infinite cell
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BUGFIX: Vectors.normalize() - problems with zero-length and low-magnitude vectors
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Handling of weighted points with duplicated positions and single-region VD.
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Java 7, 8: diamond-references and lambda-expressions. Added comments.
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DelaunayCellDiscovery: Vertices explicitly marked as redundant will be skipped
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DelaunayCellDiscovery version >= 1.0.6, diamond references, try-with-resource.
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Version changed to 2.0.0-caver-analyst-R2.
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Substantial changes in the API. New package "analysis" includes the computation of probe-regions (former cavities), their boundaries and probe-accessibility. Available via ProbeAccessibility class.
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Better controll over parallelism in ProbeAnalysis
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Stand-alone classes for the computation of regions, boundaries and accessibility are now package-protected in favor of the ProbeAnalysis class
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Hidden package-protected classes in the methods of the ProbeAnalysis class
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Added the code for computing the boundary of cavities (Connolly surface)
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A cavity can be obtained as a map of element types to the corresponding elements
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Added a shortcut for obtaining the geometries of face vertices
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BUGFIX: Bridges leading to nodes at infinity and their relation to singular edges
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Each pairs of vertices that constitutes a singular edge is represented as a pair of ints instead of one long
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AwVoronoi 2.0 beta.
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AwVoronoi-run 2.0.0-beta
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Added the computation of cavities and accessibility
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Simple interface (TriangulationData), extremal points on Voronoi edges (Nodes), new IO (binary files, ZIP), processing of more input frames in one run.
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BUGFIX: When the Delaunay cell discovery does not work (imprecise computation), BruteForce fallback will be used instead.
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Fixed a bug that prevented ParallelComponentDis...
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Release 1.0.4.
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Updated version numbers in POMs (snapshots; hal...
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Incremented version numbers in POMs: awvoronoi,...
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BUGFIX: NullPointerException when computing Vor...
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Updated versions: projects, maven compiler plug...
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Removed obsolete project extra-pdbxml
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BUGFIX: TopologyException for cells with very l...
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AngularComparer replaced by AngularComparator a...
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BUGFIX - Also handle degenerated quadratic equa...
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Fixed the usage of infinite cells (the geometry...
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Each cavity has now a list of cells instead of ...
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Tracing outer faces - recursion replaced by usi...
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The awvoronoi library was redesigned.
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Added level of detail and display lists for sph...
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Changed the awvoronoi dependency to the version...
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Cavity Search - updated awvoronoi dependency, C...
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Fixed a bug in the class CavityFinder throwing ...
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Fix - at least one cavity passes even on low pe...
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Dependencies updated, Quasi triangulation renam...
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Added the ability to read a quasi-triangulation...
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Ignored Visualisation/target/
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Merge
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Merged
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Merged
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Moved all files to a project directory.
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Merged
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