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](https://github.com/lightdock/lightdock/blob/master/lightdock/prep/starting_points.py#L209).
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](https://github.com/lightdock/lightdock/pull/36/commits/c8eeb16ba37c5f61957554e7dd9e51e20a806338) (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).