ProtoSyn 1.1 Candidate

[JosePereiraUA]

Pull request for ProtoSyn candidate 1.1.

Changelog since ProtoSyn 1.0:

• IO:
  • Better .PDB loading regex;
  • Added support for loading multiple poses from trajectory;
  • Added read/write support for .XYZ and .PQR file formats;
  • Added the download method (directly retrieves poses from the Protein Data Bank);
• Methods:
  • Better travel_graph! methods;
  • Added assign_default_atom_names! based on given LGrammar;
  • Added Pose diagnostics;
  • Added support for links with external packages (for example, generating Gromacs MD files);
  • Added tautomers support in LGrammar instances (Peptides module);
  • Added support for NCAAs (non-canonical aminoacids) (Peptides module);
  • Added support for PTMs (post-translational modifications) (Peptides module);
  • Added support for secondary structure variation generation from Ramachandran maps (Peptides module);
  • Added multiple methods to generate carbon models (complete with multi-layer support, functionalization and porosity generation) (Materials module);
• Selections:
  • ChargeSelection
  • BondedToSelection
  • BondCountSelection
  • AromaticSelection
  • TerminalSelection overhaul;
  • ProteinSelection (Peptides module);
  • ChiSelection (Peptides module);
  • Phi/Psi/OmegaSelection (Peptides module);
• Calculators:
  • Caterpillar solvation overhaul;
  • Added HydrogenBonds EFC (EnergyFunctionComponent);
  • Added SASA EFC;
  • Added Radius of Gyration EFC;
  • Added Coulomb EFC (and electrostatics methods, such as assign_default_charges!)
  • Added Generalized Born (GB) EFC;
  • Added PyRosetta's REF-15 as an EFC;
  • Added aminoacid frequency and secondary structure propensity EFCs (Peptides module);
  • Added SeqDes model as an EFC (Peptides module);
• Other:
  • Added detailed callbacks to the Common module;
  • Multiple QoL updates to show available EFCs;
• Examples:
  • Added Example 14 - NCAAs
  • Added Example 15 - PTMs
• Various bug fixes
• Documentation update
• Unit testing update

---

Known problems:

• Doctests on docstrings are turned off for now. Multiple points of conflict were identified where new Base.show! methods for ProtoSyn types change the output in the jldoctests. These need to be updated but this can be done later.

[JosePereiraUA]

Known bug: In Travis CI, the install stage can't identify the installed torch and torchani Python packages.