Uses of Class
ffx.potential.bonded.Bond
Package
Description
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
The Parsers package handles reading/writing files to/from the internal data structure.
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Uses of Bond in ffx.potential
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Uses of Bond in ffx.potential.bonded
Modifier and TypeFieldDescriptionprotected Bond[]
BondedTerm.bonds
Bonds that are used to form this term.Modifier and TypeMethodDescriptionstatic Bond
Build a bond between two atoms.getBondBondedTerm.getBond
(int index) Get the constituent Bond specified by index.MSGroup.getBond
(int index) Returns the Bond at the supplied index.Returns the Bond with the given id.MultiResidue.getBond
(int index) Returns the Bond at the supplied index.Returns the Bond with the given id.PiOrbitalTorsion.getMiddleBond()
Get the middle bond that the Pi-Orbital Torsion is formed around.Modifier and TypeMethodDescriptionPolymerUtils.assignAtomTypes
(MolecularAssembly molecularAssembly, PDBFilter.PDBFileStandard fileStandard) Assign force field atoms types to common chemistries using "biotype" records.MSNode.getBondList()
Returns a List of all Bonds below the present MSNode.Atom.getBonds()
Gets the list of the Bonds this Atom helps to formPolymerUtils.locateDisulfideBonds
(List<String> ssbonds, MolecularAssembly molecularAssembly, Map<String, String> pdbToNewResMap) Locate disulfide bonds based on SSBOND records.Modifier and TypeMethodDescriptionMSGroup.createJoint
(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField) Create a joint between two chemical groups.MultiResidue.createJoint
(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField) Create a joint between two chemical groups.static PiOrbitalTorsion
PiOrbitalTorsion.piOrbitalTorsionFactory
(Bond bond, ForceField forceField) Attempt to create a new PiOrbitalTorsion based on the supplied bond and forceField.void
Specify that this Atom is part of a Bondvoid
Add constituent Bonds to the Term.static TorsionTorsion
TorsionTorsion.torsionTorsionFactory
(Bond firstBond, Angle angle, Bond lastBond, ForceField forceField) torsionTorsionFactory.Modifier and TypeMethodDescriptionstatic void
AminoAcidUtils.assignAminoAcidAtomTypes
(Residue residue, Residue previousResidue, Residue nextResidue, ForceField forceField, List<Bond> bondList) assignAminoAcidAtomTypes.static Residue
buildAIB.static Residue
AminoAcidUtils.buildAlanine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildAlanine.static Residue
AminoAcidUtils.buildArginine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildArginine.static Residue
AminoAcidUtils.buildAsparagine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildAsparagine.static Residue
AminoAcidUtils.buildAspartate
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildAspartate.static Bond
Build a bond between two atoms.static Residue
AminoAcidUtils.buildCysteine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildCysteine.static Residue
AminoAcidUtils.buildCystine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildCystine.static Residue
AminoAcidUtils.buildDeprotonatedCysteine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildDeprotonatedCysteine.static Residue
AminoAcidUtils.buildDeprotonatedLysine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildDeprotonatedLysine.static Residue
AminoAcidUtils.buildDeprotonatedTyrosine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildDeprotonatedTyrosine.static void
PolymerUtils.buildDisulfideBonds
(List<Bond> ssBondList, MolecularAssembly molecularAssembly, List<Bond> bondList) Assign parameters to disulfide bonds.static Residue
AminoAcidUtils.buildGlutamate
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildGlutamate.static Residue
AminoAcidUtils.buildGlutamine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildGlutamine.static Residue
AminoAcidUtils.buildGlycine
(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds) buildGlycine.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, 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 Residue
AminoAcidUtils.buildHistidine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildHistidine.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.static Residue
AminoAcidUtils.buildIsoleucine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildIsoleucine.static Residue
AminoAcidUtils.buildLeucine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildLeucine.static Residue
AminoAcidUtils.buildLysine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildLysine.static Residue
AminoAcidUtils.buildMethionine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond) buildMethionine.static Residue
AminoAcidUtils.buildNeutralAsparticAcid
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildNeutralAsparticAcid.static Residue
AminoAcidUtils.buildNeutralGlutamicAcid
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildNeutralGlutamicAcid.static Residue
AminoAcidUtils.buildNeutralHistidineD
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildNeutralHistidineD.static Residue
AminoAcidUtils.buildNeutralHistidineE
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildNeutralHistidineE.static Residue
AminoAcidUtils.buildOrnithine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildOrnithine.static Residue
buildPCA.static Residue
AminoAcidUtils.buildPhenylalanine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildPhenylalanine.static Residue
AminoAcidUtils.buildProline
(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds) buildProline.static Residue
AminoAcidUtils.buildSerine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildSerine.static Residue
AminoAcidUtils.buildThreonine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildThreonine.static Residue
AminoAcidUtils.buildTryptophan
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond) buildTryptophan.static Residue
AminoAcidUtils.buildTwoProtonAsparticAcid
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildTwoProtonAsparticAcid.static Residue
AminoAcidUtils.buildTwoProtonGlutamicAcid
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildTwoProtonGlutamicAcid.static Residue
AminoAcidUtils.buildTyrosine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildTyrosine.static Residue
AminoAcidUtils.buildValine
(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds) buildValine.ModifierConstructorDescriptionAngle constructorAngleTorsion
(Bond b1, Bond b2, Bond b3) Create a AngleTorsion from 3 connected bonds (no error checking)PiOrbitalTorsion
(Bond middleBond) Pi-Orbital Torsion constructor.protected
Create a Torsion from 3 connected bonds (no error checking)TorsionTorsion
(Bond firstBond, Angle angle, Bond lastBond, boolean reversed) Torsion-Torsion constructor. -
Uses of Bond in ffx.potential.constraint
Modifier and TypeMethodDescriptionstatic CcmaConstraint
CcmaConstraint.ccmaFactory
(List<Bond> constrainedBonds, List<Angle> constrainedAngles, Atom[] allAtoms, double[] masses, double nonzeroCutoff) Constructs a set of bond length Constraints to be satisfied using the Constaint Constraint Matrix Approximation, a parallelizable stable numeric method. -
Uses of Bond in ffx.potential.parsers