Release 2.5

This release incorporates years of significant updates. Some of which include:
-Incorporation in library of numerous cofactors
-N and C terminal residue support and automatic model assembly with them
-Great simplification of adding molecules to the library
-Projects directory with some relatively easy to run general programs, where basic usage is detailed in Readme
-Optional Polarizable electrostatic forcefeild using the maxwell-garnet formula to modify the local effective dielectric based on polarizability
-A backbone sequence alphabet and structural classifier implementation using a Residues-per-turn binning method
-A basic UI built in QT as a starting point for further development (not built by default, but functional in Linux)
-Very fast and accurate SVD Fortran structural alignment algorithm for aligning pdbs to each other or the z axis (protAlign) and for aligning library residues into input pdb position
-Finalization of Evolutionary algorithm for design of monomers, heteromers and cofactor binding proteins (protEvolver)
and many other minor and under the hood improvements

Release 2.1

This update generalizes the residue class to accept independent ligands, removes deprecated ligand code from a previous incomplete ligand implementation, and adds the ligands SF4 and OEC to the library for calculation and building. It also removes the remaining deprecated svmt library code.

Release 2.0

This is a major update to protCAD that upgrades the nonbonded terms of the force field to amber14. protCAD also now has full hydrogen support and is now explicit hydrogen by default. Additionally, polarizabilities now come from amber14 vdw atom types for the local dielectric calculations. The implicit solvent model added is now formally complete with the Gill hydrophobic solvation term as part of the implicit solvent model in addition to the local dielectric generalized born model.
protCAD also now by default only includes residues from a pdb that are included in it's library so that it can more easily be used for database analysis without curation of pdbs to prevent segfaults or errors. However all molecules and residues not defined in library are omitted from the pdb upon import into object, though if not defined in the library nothing could actually be done with it anyway.

For a list of all supported residues and their library index order see : https://github.com/protCAD/protcad/blob/master/data/aaBaseline.frc

Release 1.3

This update improves the accuracy of the Generalized Born solvation potential in protEnergy(), adds a final form of the Gill hydrophobic solvation or solvent entropy term and scales the 1-4 VDW energies down to 25% of it's true value for better alignment with the AMBER forcefield.

Release 1.2

This update removes many deprecated functions and source code that the removal of should not cause backward compatibility problems for programs created within the last 10 years, aside from modifying some input parameters. Please modify the include and object initialization parameters to match 'example.cc' for recommended defaults parameters and removal of antiquated function includes. This should be all that is necessary to resolve any backwards compatibility issues. This update also adds a new non-redundant implicit solvent energy function 'protEnergy()'. This function minimizes the number of calculations done on the same protein object over iteration and speeds up the process of energy calculation anywhere from 2 to 3000 times depending on the degree of changes made to the structure. This update also adds a new chlorophyll-proline residue to the library built by Debalina Datta (https://github.com/debalina1992).

Release 1.1

This update merges the two makefiles into one, removes the unnecessary lib directory and linking to it, adds a histidine-bound chlorophyll residue to the library, optimizes the local dielectric code for efficiency and adds a needed residue removal function.

protCAD release version 1.0

This version removes antiquated libraries, adds proper readme information and reorganizes the makefiles and directory structure for ease of use. It also includes local dielectric electrostatic screening for use in the protein object.