Lightdock

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](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](https://travis-ci.com/lightdock/lightdock).
- 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**.