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