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Pre-release

@brianjimenez brianjimenez released this Jan 20, 2020 · 4 commits to master since this release

This version includes a new algorithm for generating the starting poses of glowworms when restraints are provided. It fixes some orientation degenerated cases (36f7417).

A bug when there is the string lightdock_ or swarm_ in the path has been fixed for lgd_filter_restraints.py (a3121cc).

Python 3 language level has been added to the Cython files, and env python3 is the default for all lgd_* supporting scripts (9c7149c, 197319c and 544c8b6).

Many new tests have been included to increase coverage (work in progress).

Assets 2
Pre-release
Pre-release

@brianjimenez brianjimenez released this Jan 4, 2020 · 16 commits to master since this release

This release fixes:

  • Buggy support for multiscoring (#2)
  • Clustering when DNA molecules are involved (455fe82)
Assets 2
Pre-release
Pre-release

@brianjimenez brianjimenez released this Sep 28, 2019 · 20 commits to master since this release

This release prepares the machinery for distributing LightDock using pip for the first time. Major changes include:

  • Code has been migrated to Python >3.5 series. This repository will container only Python3 source code. For older versions of the code (Python 2.7) repository is https://github.com/brianjimenez/lightdock.
  • setup.py compatible, including tests (still with nose, but planning to update in the future). For testing run python3 setup.py test.
  • Travis CI has been integrated.
  • All scripts have been reorganized to the bin folder. lightdock and lightdock_setup have been renamed to lightdock3.py and lightdock3_setup.py respectively to avoid problems with older versions of the software.
  • Refactoring to Python3 was not able to keep the same initial coordinates during lightdock3_setup.py due to a seed not being set for the random number generator in the old 2.7 implementation. init folders are still compatible, however, new setups will generate different initial coordinates for the glowworms in the system.
  • Membrane protocol and the use of MPI are still experimental. If you plan to make use of them, please contact us before to avoid problems.
  • License has changed to GPLv3.
Assets 2
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