Package ffx.potential.bonded
@ParametersAreNonnullByDefault
package ffx.potential.bonded
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
- Since:
- 1.0
- Author:
- Michael J. Schnieders
-
ClassDescriptionUtilities for creating Amino Acid residues.The 20 standard amino acids.Constant
AIBConstantALASingle letter amino acid codes (need toConstantAminoAcidBackboneAtomsConstantARGConstantASDConstantASHConstantASNConstantASPConstantCYDConstantCYSConstantCYSConstantGLDConstantGLHConstantGlutamineAtomNamesConstantGLUConstantGLYConstantGlycineBackboneAtomsConstantHIDConstantHIEConstantHistidineAtomsConstantILEConstantLEUConstantLYDConstantLYSConstantMethionineAtomNamesConstantORNConstantPCAConstantPHEConstantPROConstantProlineBackboneAtomsThe location of a residue within a chain.ConstantSERThis interface is used by the "Build" routines.ConstantTHRConstantTRPConstantTYDConstantTYRConstantVALThe Angle class represents an angle formed between three linearly bonded atoms.The AngleTorsion class represents an angle torsion coupling between four bonded atoms.The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.Element symbols for the first 109 elements.The Bond class represents a covalent bond formed between two atoms.The BondedEnergy interface.The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).Utilities for placing atoms.This exception is thrown when an atom type could not be assigned.This exception is thrown when a heavy atom is not found.The ImproperTorsion class represents an Improper Torsion.The Joint class contains the geometry produced by the FGroup Joiner method.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.The MSGroup class has one sub-node containing atoms, and one that contains molecular mechanics/geometry terms.The MSNode class forms the basic unit that all data classes extend.The MSRoot class is the root of the Force Field X data structure.The MultiResidue class allows switching between residues for uses such as sequence optimization.Utilities for importing atoms from PDB files and checking their names.Common HETATOM labels for water and ions.Utilities for creating Nucleic Acid residues.The 4 RNA bases, 4 DNA bases, and mono- di- and triphosphate.Since enumeration values must start with a letter, an 'M' is added to modified bases whose IUPAC name starts with an integer.The OutOfPlaneBend class represents an Out-Of-Plane Bend.The Pi-Orbital Torsion class.The Polymer class encapsulates a peptide or nucleotide chain.Utilities for creating polymers.A relative solvation term for chemical perturbations.Citations: Wolfenden et al: Wolfenden, R., Andersson, L., Cullis, P.The RendererCache class defines constants related to rendering modes and caches primitives for the Renderer.The Residue class represents individual amino acids or nucleic acid bases.Residue type [NA, AA, UNK].The ResidueState class encodes the current chemical and coordinate state of a Residue, particularly a MultiResidue, for ease of reverting coordinates.RestraintDistance class.The ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.The ROLSP class is used for Proof-Of-Concept Parallel Recusive Over Length Scales (ROLS) Methods (currently only on shared memory systems).The Rotamer Class usually represents one immutable amino acid Rotamer.The Rotamer Library Class manages a library of side-chain Rotamers for amino acids, and a library of backbone Rotamers for nucleic acids.The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.The StretchTorsion class represents a coupling between a torsional angle and the three bonds contained in the torsion, as defined in the 2017 AMOEBA nucleic acid force field.SturmMethod class.The Torsion class represents a torsional angle formed between four bonded atoms.The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.The UreyBradley class.