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Analyzed 12 months ago. based on code collected 12 months ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Jan 18, 2023 — Jan 18, 2024 Showing page 285 of 297 Search / Filter on:
Issue #50 is completed.	Ahmet Bakan	More...				over 13 years ago
Issue #52: PCA buildCovariance method supports Trajectory instances. Frame _getCoordinates function is implemented to reduce memory operations.	Ahmet Bakan	More...				over 13 years ago
atomic _getData methods are revised. ensemble _getCoordinates/Coordsets functions are implemented. dynamics buildCovariance method is changed acoordingly.	Ahmet Bakan	More...				over 13 years ago
Small performance imporvement in superposeTraj.	Ahmet Bakan	More...				over 13 years ago
Issue #53 is completed. _get method return a view of the actual data array when possible. AtomSubset do not return views because arbitrary indexing of arrays make a deep copy of the array.	Ahmet Bakan	More...				over 13 years ago
A bug in select module raising exceptions when regular expressions are passed with name selections is fixed.	Ahmet Bakan	More...				over 13 years ago
getFrame is implemented for Trajectory class. Documentation maintained.	Ahmet Bakan	More...				over 13 years ago
Trajectory getCoordsets function is implemented.	Ahmet Bakan	More...				over 13 years ago
Most Trajectory methods are working fine. Implementation of Frame getRMSD and superpose methods are completed and methods are optimized. Superposition and RMSD calculation reproduces VMD results.	Ahmet Bakan	More...				over 13 years ago
ensemble getMSF function is optimized for memory usage and speed.	Ahmet Bakan	More...				over 13 years ago
Documentation updated/maintained.	Ahmet Bakan	More...				over 13 years ago
PCA.buildCovariance and performSVD accept Numpy arrays. buildCovariance method is optimized for speed in evaluation of PDB ensembles.	Ahmet Bakan	More...				over 13 years ago
ensemble superpose and rmsd calculation methods are optimized for speed/memory usage.	Ahmet Bakan	More...				over 13 years ago
calcRMSD and superpose functions are optimized for memory usage and speed.	Ahmet Bakan	More...				over 13 years ago
calcRMSD function is optimized and type/value checks are improved.	Ahmet Bakan	More...				over 13 years ago
parseDCD function is updated to work with new DCDFile class.	Ahmet Bakan	More...				over 13 years ago
Trajectory and TrajectoryFile classes are implemented. Coordinate parsing is optimized.	Ahmet Bakan	More...				over 13 years ago
Doc corrections and update in dynamics module.	Ahmet Bakan	More...				over 13 years ago
calcProjections calculates RMSD by default.	Ahmet Bakan	More...				over 13 years ago
Trajectory skip and goto methods are implemented. A bugfix in PDBEnsemble iterCoordsets method.	Ahmet Bakan	More...				over 13 years ago
calcProjection rmsd calculation is changed to use a more efficient way.	Ahmet Bakan	More...				over 13 years ago
A working implementation of Trajectory, Frame, and DCDTrajectory classes are complete.	Ahmet Bakan	More...				over 13 years ago
Documentation is maintained: (i) print statements are converted to functions, i.e. print() for compatibility with Py3K (ii) skipped doctests are incorporated, (iii) numeric results in doctests are rounded to 2-4 significant digits.	Ahmet Bakan	More...				over 13 years ago
PDBEnsemble function is specialized for analyzing PDB ensembles. Ensemble function is not suitable for this purpose anymore. This should increase efficiency and reduce confusions. In PDBEnsemble doc user is warned about how missing coordinates are threated.	Ahmet Bakan	More...				over 13 years ago
Minor fix in coordinate data type assignments and fetchPDB function.	Ahmet Bakan	More...				over 13 years ago
Bugfix in AtomPointer.copy function.	Ahmet Bakan	More...				over 13 years ago
calcProjection, showProjection, and showCrossProjection functions can optionally calculate/display RMSD.	Ahmet Bakan	More...				over 13 years ago
calc/showProjection function accept a Conformation as the first argument.	Ahmet Bakan	More...				over 13 years ago
Bugfix in +/- button.	Ahmet Bakan	More...				over 13 years ago
Doc update. Google Plus One is incorporated into documentation.	Ahmet Bakan	More...				over 13 years ago

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