Uses of Class
ffx.potential.bonded.MSGroup

Packages that use MSGroup

Package	Description
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.

Uses of MSGroup in ffx.potential

Subclasses of MSGroup in ffx.potential

Modifier and Type	Class	Description
class	MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Uses of MSGroup in ffx.potential.bonded

Subclasses of MSGroup in ffx.potential.bonded

Modifier and Type	Class	Description
class	Molecule	The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.
class	MultiResidue	The MultiResidue class allows switching between residues for uses such as sequence optimization.
class	Polymer	The Polymer class encapsulates a peptide or nucleotide chain.
class	Residue	The Residue class represents individual amino acids or nucleic acid bases.

Methods in ffx.potential.bonded with parameters of type MSGroup

Modifier and Type	Method	Description
static Atom	BondedUtils.buildH(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildH(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom bondedTo, int key, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHydrogenAtom(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, AtomType atomType, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
Joint	MSGroup.createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
Joint	MSGroup.createJoint(MSGroup group1, MSGroup group2, ForceField forceField)	Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
Joint	MultiResidue.createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
Joint	MultiResidue.createJoint(MSGroup group1, MSGroup group2, ForceField forceField)	Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.

Constructors in ffx.potential.bonded with parameters of type MSGroup

Modifier	Constructor	Description
	Joint(MSGroup group1, MSGroup group2, MSNode bondNode, MSNode angleNode, MSNode stretchBendNode, MSNode ureyBradleyNode, MSNode outOfPlaneNode, MSNode torsionNode, MSNode improperTorsionNode, MSNode stretchTorsionNode, MSNode angleTorsionNode, MSNode piOrbitalTorsionNode, MSNode torsionTorsionNode)	Constructs a Joint between Group 1 and Group 2.

Uses of MSGroup in ffx.ui

Subclasses of MSGroup in ffx.ui

Modifier and Type	Class	Description
class	FFXSystem	The FFXSystem class contains extensions to the generic MolecularAssembly class.