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Fixes on the scoring API contributed by @alchemistcai

This post release fixes several problems with tests and Pathlib after upgrading ProDy to version 2.4.0 (thanks @danielkovtun).

Issue #44 is also addressed (thanks @alchemistcai).

Travis CI has been abandoned in favor of GitHub Actions. At the moment, only testing in Python 3.8 is enabled (3.9 and 3.10 will come once the testing code is migrated to use nose alternatives).

Post release to account for the fix of issue #38

This new release includes several new features on the setup step of the simulation:

New option fixed distance (fd)

At the setup step, it is possible now to place swarms over receptor surface using fd (fixed distance) parameters. Distance is specified in Å.

New option swarms per restraint (spr)

Prior to version 0.9.3, default number of calculated swarms when filtering for restraints on the receptor partner was 10. This number has been increased to 20 by default. For a custom option, please use spr flag on lightdock3_setup.py.

Swarm position

Calculation of swarms over the receptor surface has been improved, fixing scenarios where swarm was too close to surface (protein-peptide). This makes definition of swarms different to previous releases.

New numeration for swarms

File describing swarm centers (init/swarm_centers.pdb) in PDB format now includes swarm numeration for a rapid identification by sequence number.

Dense sampling

If a denser sampling is required, -ds flag might be activated during setup (lightdock3_setup.py). This option disables the final clustering of swarms, providing a much denser number of swarms (see figure below, swarms depicted in red, receptor in white, a restraint in blue).

Swarms and restraints

Receptor restraints (both active and passive) filter out swarms which are not close enough to those defined restraints. restraint-swarm center distance-only criteria is sensitive to swarms which do not have a direct vision line to a given restraint. In order to account for this limitation, a new filter has been implemented using a calculated convex hull using surface atoms.

Support for HETATM restraints

Ligands and other entities defined as HETATM might be now defined as restraints.

Experimental DUMMY beads

There is a new type of bead supported, DUMMY, which can be used as a space filling bead. A script to create DUMMY beads from HETATM ligands is here (experimental, expected to change in the future). DUMMY beads are not supported in the Python version of LightDock, only in Rust (and very limited, expected to change in the future).

Fixes for #25 and #29

This new release includes:

• Fixes reference counting errors as described in https://github.com/lightdock/lightdock/issues/19
• Updated to use ProDy version 2.0.1 ) (https://github.com/lightdock/lightdock/issues/20)
• More permissive when calculating ANM for nucleic with ProDy: https://github.com/lightdock/lightdock/pull/23/commits/b6c30a099de5d47e8ddeea30c4a73b541f83df39 & https://github.com/lightdock/lightdock/pull/23/commits/958392e45160bedd997243d60ad8c5fff085f3d9
• When using residue restraints, new flag flip for automatically calculating on 50% of pre-oriented poses a 180 degrees flip: https://github.com/lightdock/lightdock/pull/23/commits/a8374db310cf44fb7a0e5d4344822b6c380b145e

This new release includes:

• Minor fix not affecting any previous simulation: 394557a
• Support for ANM in receptor if membrane beads are specified: b30bb55 (issue #15)
• New flag --now to remove crystal waters from input structures: 03ab11e
• NumPy is not required anymore before installing the lightdock Pip package: 4724cb2 (issue #14)
• Support for residue insertion codes in restraints: 03ab11e & 86290a8 (useful in antibody-antigen)
• Use of black and flake8 tools for code linting and formatting.
• Several new tests

Major improvements:

• Support for installation on Google Colab
• Number of swarms automatically calculated

• Fixes support for MPI: issue #9
• Fixes problem with scipy dependency to continue supporting Python 3.6+
• Minor: 50a28d35075855d1d938cc8f9e3b40d4922c4b0d c64e12b9fe66f1f9778a4cd1fe76ba701e4e8c3d 3d191b31c754a61f3ce582064b825d7e957440ea

This release includes all the previous changes from https://github.com/lightdock/lightdock/releases/tag/0.8.1b1 and:

• Removes BioPython from dependencies (rotamer code which have been removed and bin/lgd_cluster_bsas.py)
• More tests to improve coverage
• Fix for issue #8
• A patch to avoid infinite loop in setup (0186e41d5caff1a91c3e4ce0e275ff6e18fb079b). There is a timeout of 10 minutes now, but code for generating starting swarm centers over the surface will change in the future to deal with corner and degenerate cases.

Important: Please note RMSD calculation in lgd_cluster_bsas.py is using ProDy so slight differences in cluster.repr cluster file might appear.