Lightdock Versions Save

Minor changes:

• Added developer documentation: 56c63a3bad9ed5371deefdc6e127df747385573b
• Bug fixes: 94bec457d5ab946c46597ed2cfae645cff2be1e8, 9ae5f057ed6664f8c28e6cdac3284fca7e143a6b, 71cfd19e15ea02c007184b4b449d573f5f074766

New on this release:

• A new script for generating a coarse-grained artificial membrane: https://github.com/lightdock/lightdock/issues/5
• Blocking residues as restraints: e13d3211ab4110e52c708288b726ec4611f02d5e
• A new nucleic scoring function DDNA: 60331163bd040f5e6d043e5e34eedbc26c4b424d

Moved from beta

New beta pre-release:

• Drops support for Python 3.5 as the latest version from BioPython (LightDock might not use BioPython in the future and recover 3.5 support).
• Fixes a bug when ANM was not enabled in lgd_top.py support script.
• New support scripts 2e0a361097c3681635b57c6e5175c008df991a39:
  • bin/lgd_rank_swarm.py -> Generates a ranking only for a given swarm.
  • bin/lgd_flatten.py -> transforms 3D to 1D ANM matrix (this is used for the Rust implementation of LightDock which does not support NumPy 3D matrices, https://github.com/lightdock/lightdock-rust).
  • bin/lgd_copy_structures.py -> easy copy generated structures in each swarm to a unique analysis folder.
• Added more tests to command line validators.

• More tests related to membrane beads management.
• Improved error messages and warnings for several scoring functions.
• Updated Readme and docs.

This version includes a new algorithm for generating the starting poses of glowworms when restraints are provided. It fixes some orientation degenerated cases (36f7417664ac5d1e4aa769ff45eff57ee90818f5).

A bug when there is the string lightdock_ or swarm_ in the path has been fixed for lgd_filter_restraints.py (a3121cc634a922c8e7550562b3817beb180e580e).

Python 3 language level has been added to the Cython files, and env python3 is the default for all lgd_* supporting scripts (9c7149c1972b704bd4a11da101eada1602a942d9, 197319cad637f6404726e59b5ad1ff875e37971d and 544c8b61794f04c771b96fa15101856e5fa270e2).

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

This release fixes:

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

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.