Hbonds between probes

This version includes a minor revision of the HBonds objective. It now includes the "only_probes" parameter, by default set to False.
This parameter, when set to True, restrains the evaluation of the hydrogen bonds to those formed between the probe molecules.

New features and fixes

• Fix installation issues appeared from actualization on dependencies
• "Contacts" objective: contacts and clashes between all the atoms included in the search radius from the CB of all surrounding rotamers of the probe are taken into account in the clash/contact calculations.
  "only_internal" parameter is added. It can be used to take into account only intramolecular interactions of the probe.
• "Hbonds" objective: new "only_intermolecular" parameter allows to define if only intermolecular hydrogen bonds should be detected. If set to False, also intramolecular hydrogen bonds in "probes" would be considered.
• "Vina" objective: AutoDock scripts prepare_ligand4.py and prepare_receptor4.py are used to prepare the corresponding .pdqt files that will be used as input for AutoDock Vina scorer. If we use these scripts with default repair/cleanup options, problems appear with the actualization of coordinates in "_update_pdbqt_coordinates" method, because the order/number of is not necessarily the same after the repairs/cleanups. So:
  • No repairs nor cleanups will be performed on ligand/receptor molecules, so the user has to take into account that provided .mol2 or .pdb files have correct atom types and correct structure (including Hydrogen atoms that will be taken into account in the docking evaluation). Otherwise, AutoDock errors/warnings could appear (e.g. ValueError: Could not find atomic number for Lp Lp)
  • Gasteiger charges will be added during the preparation of the .pdbqt files.
  • All torsions of the ligand will be marked as inactive for AutoDock, because torsion changes are part of GaudiMM genes.
• New "smina" objective: New objective Smina is added. Based on a fork of Vina, it allows to customize the scoring function through: Smina custom scoring methods, user scoring function files or user atom type parameter files.
• "Search" gene: target parameter now can be either:
  • The anchor atom of the molecule we want to move, with syntax <molecule_name>/. For example, if we want to move Ligand using atom with serial number = 1 as pivot, we would specify Ligand/1. It's parsed to the actual chimera.Atom later on.
  • A name of gaudi.genes.molecule instance. In this case, the anchor atom for the movement of the molecule will be set to its nearest atom to the geometric center of the molecule.
• "Torsion" gene: Now the user can establish the concrete bonds that should be able to rotate. It can be done with the parameter rotatable_bonds, which expects a list of [SerialNumberAtom1, SerialNumberAtom2, SerialNumberAnchor].
• Genetic algorithm: After a new generation is carried out, similar individuals (taking into account similarity criteria established by the user) are discarded. Being two individuals similar, the one with worse score will be discarded.

Pre-alpha public release

Ready for community testing and suggestions!