new TorsionScan: Brute force approach to spinning torsions. Spins rotatable bonds by user specified value (in degrees). Option to specify an RMSD where structures are saved out only if they deviate by the user specified amount (helps identify unique conformations). Method crosses sulfur bonds, so not intended for proteins.
SuperposeCrystals: Update z prime specification.
SaveAsP1: Include replicates expansion for PDB files.
DualTopology: Update implementation of alchemical atom selection.
Atom: Add methods to check for atoms connected by rings (1_4-1_8). Only checks through seven member rings (i.e., 1-8 bonded).
CIFFilter: Now is able to parse CIF files that do not have crystallographic information.
ForceFieldFilter: Added FINER logging that is helpful for debugging.
PDBFilter: Add functionality for replicates expansion.
XYZFilter: Add method comment to replicates expansion.
ROY files: Update to include AMOEBA forcefield constants.
PotentialUtils: Added method for PDB files to be saved as replicates.
ProgressiveAlignmentOfCrystals: Edits to logging.
LambdaGradientTest: Update values to correspond to corrected ROY files.
new TorsionScan: Brute force approach to spinning torsions. Spins rotatable bonds by user specified value (in degrees). Option to specify an RMSD where structures are saved out only if they deviate by the user specified amount (helps identify unique conformations). Method crosses sulfur bonds, so not intended for proteins.
SuperposeCrystals: Update z prime specification.
SaveAsP1: Include replicates expansion for PDB files.
DualTopology: Update implementation of alchemical atom selection.
Atom: Add methods to check for atoms connected by rings (1_4-1_8). Only checks through seven member rings (i.e., 1-8 bonded).
CIFFilter: Now is able to parse CIF files that do not have crystallographic information.
ForceFieldFilter: Added FINER logging that is helpful for debugging.
PDBFilter: Add functionality for replicates expansion.
XYZFilter: Add method comment to replicates expansion.
ROY files: Update to include AMOEBA forcefield constants.
PotentialUtils: Added method for PDB files to be saved as replicates.
ProgressiveAlignmentOfCrystals: Edits to logging.
LambdaGradientTest: Update values to correspond to corrected ROY files.