Compound Class Reference

The base class for atoms, molecules, and chemical groups. More...

#include <Compound.h>

Inheritance diagram for Compound:

Classes
class	SingleAtom
	Base class for single-atom Compound building blocks. More...
Public Types
enum	MatchStratagem { Match_Exact, Match_Idealized, Match_TopologyOnly }
Public Member Functions
Compound &	setTopLevelTransform (const Transform &transform)
	Set the orientation and location of this Compound.
const Transform &	getTopLevelTransform () const
Molecular topology methods

	Compound ()
	default Compound constructor.
	Compound (const Name &name)
	Construct a Compound with a type name.
int	getNumAtoms () const
size_t	getNumBondCenters () const
size_t	getNumBondCenters (Compound::AtomIndex atomIndex) const
size_t	getNumBonds () const
bool	hasAtom (const AtomPathName &name) const
bool	hasBondCenter (const BondCenterPathName &bondCenter) const
Compound::AtomIndex	getBondAtomIndex (Compound::BondIndex bondIndex, int which) const
Compound &	setBaseAtom (const Compound::AtomName &name, const Element &element, const Transform &location=Vec3(0))
	Add the first atom unconnected to anything else (yet).
Compound &	setBaseAtom (const Compound::AtomName &name, const Biotype &biotype, const Transform &location=Vec3(0))
	Add the first atom unconnected to anything else (yet).
Compound &	setBaseAtom (const Compound::SingleAtom &c, const Transform &=Transform())
	Add a first subcompound containing exactly one atom, so the Compound::AtomName can be reused for the Compound::Name.
Compound &	setBaseCompound (const Compound::Name &n, const Compound &c, const Transform &location=Transform())
	Add a first subcompound without attaching it to anything.
Compound &	bondAtom (const Compound::SingleAtom &c, const BondCenterPathName &parentBondName, mdunits::Length distance, Angle dihedral=0, BondMobility::Mobility=BondMobility::Default)
	Add a subcompound containing exactly one atom, so the Compound::AtomName can be reused for the Compound::Name.
Compound &	bondAtom (const Compound::SingleAtom &c, const BondCenterPathName &parentBondName)
	Bond atom using default bond length and dihedral angle.
Compound &	bondCompound (const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName, mdunits::Length distance, Angle dihedral=180 *Deg2Rad, BondMobility::Mobility mobility=BondMobility::Default)
	Add a subcompound attached by its inboard bond to an existing bond center.
Compound &	bondCompound (const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName)
	Add a subcompound attached by its inboard bond to an existing bond center.
Compound &	bondCompound (const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName, BondMobility::Mobility mobility)
	Add a subcompound attached by its inboard bond to an existing bond center.
Compound &	setInboardBondCenter (const Compound::BondCenterName &centerName)
	setInboardBondCenter assigns special status to a bond center.
Compound &	convertInboardBondCenterToOutboard ()
	Make so that this compound can no longer be a child to the geometry of another compound Raises an error if the inboard bond center is already bonded.
Compound &	addFirstBondCenter (const Compound::BondCenterName &centerName, const Compound::AtomPathName &atomName)
	Assign the very first bond center on a particular atom.
Compound &	addSecondBondCenter (const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1)
	Place a second bond center on an atom, placed a particular angle away from the first bond center.
Compound &	addPlanarBondCenter (const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2)
	Places a third or later bond center on an atom, in the same plane as the first two bond centers.
Compound &	addRightHandedBondCenter (const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2)
	Place a third or later bond center on an atom, defined by two angular displacements from the first and second bond centers, respectively.
Compound &	addLeftHandedBondCenter (const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2)
	Place a third or later bond center on an atom, defined by two angular displacements from the first and second bond centers, respectively.
Compound &	addRingClosingBond (const Compound::BondCenterPathName &centerName1, const Compound::BondCenterPathName &centerName2, mdunits::Length bondLength, Angle dihedral=180 *Deg2Rad, BondMobility::Mobility mobility=BondMobility::Default)
	Adds a covalent bond that is not part of the main tree-topology of bonds in a Compound.
Compound &	addRingClosingBond (const Compound::BondCenterPathName &centerName1, const Compound::BondCenterPathName &centerName2)
	Adds a covalent bond that is not part of the main tree-topology of bonds in a molecule.
const Compound &	getSubcompound (const Compound::Name &subcompoundName) const
Compound &	updSubcompound (const Compound::Name &subcompoundName)
Compound nomenclature methods

Compound &	setCompoundName (const Name &)
	Name a type of Compound.
const Name &	getCompoundName () const
Compound &	addCompoundSynonym (const Name &)
	Add an additional name for this class of compound.
const AtomPathName	getAtomName (Compound::AtomIndex) const
	Returns the most recently assigned name, if any, given to an atom in this compound.
const Element &	getAtomElement (Compound::AtomIndex) const
const Element &	getAtomElement (const Compound::AtomName &) const
	Name a type of Compound.
Compound &	nameAtom (const Compound::AtomName &newName, const AtomPathName &oldName)
Compound &	nameAtom (const Compound::AtomName &newName, const AtomPathName &oldName, BiotypeIndex biotype)
Compound &	defineDihedralAngle (const Compound::DihedralName &angleName, const Compound::AtomPathName &atom1, const Compound::AtomPathName &atom2, const Compound::AtomPathName &atom3, const Compound::AtomPathName &atom4, Angle offset=0 *Deg2Rad)
	Define a named dihedral angle using four atoms.
Compound &	defineDihedralAngle (const Compound::DihedralName &angleName, const Compound::BondCenterPathName &bond1, const Compound::BondCenterPathName &bond2, Angle offset=0 *Deg2Rad)
	Define a named dihedral in terms of two bond centers.
Compound &	setPdbResidueNumber (int resNum)
	Set value to populate "residue number" field for PDB file output.
int	getPdbResidueNumber () const
Compound &	setPdbResidueName (const String &resName)
	Set string to populate "residue type" field for PDB file output.
const String &	getPdbResidueName () const
Compound &	setPdbChainId (char chainId)
	Set character to populate "chain id" field for PDB file output.
char	getPdbChainId () const
Compound &	nameBondCenter (const Compound::BondCenterName &newName, const BondCenterPathName &oldName)
	Define a local name for a particular BondCenter in this Compound.
Compound &	inheritAtomNames (const Compound::Name &)
	Convenience method to locally import all of the atom names that a particular subcompound uses.
Compound &	inheritCompoundSynonyms (const Compound &otherCompound)
	Name a type of Compound.
Compound &	inheritBondCenterNames (const Compound::Name &)
	Convenience method to locally import all of the BondCenter names that a particular subcompound uses.
Compound::AtomIndex	getAtomIndex (const Compound::AtomPathName &) const
Compound simulation methods

void	setMultibodySystem (MultibodySystem &system)
	Add this Compound, including all of its subcompounds, to a CompoundSystem, for simulation etc.
Compound &	setBondMobility (BondMobility::Mobility mobility, const AtomPathName &atom1, const AtomPathName &atom2)
	Override the default rotatability of a bond.
Compound &	setBondMobility (BondMobility::Mobility mobility, Compound::BondIndex bondIndex)
	Override the default rotatability of a bond.
Compound &	setCompoundBondMobility (BondMobility::Mobility mobility)
	Set BondMobility for every bond in the Compound.
MobilizedBodyIndex	getAtomMobilizedBodyIndex (Compound::AtomIndex) const
	get the simbody MobilizedBody to which a particular atom is attached
Vec3	getAtomLocationInMobilizedBodyFrame (Compound::AtomIndex) const
	get the location of an Atom in the frame of the simbody MobilizedBody to which the Atom is attached
Compound &	setBiotypeIndex (const Compound::AtomPathName &atomName, BiotypeIndex biotype)
	define the Biotype for an Atom in this Compound
Compound &	setAtomBiotype (const Compound::AtomPathName &atomName, const String &biotypeResidueName, const String &biotypeAtomName, SimTK::Ordinality::Residue ordinality=SimTK::Ordinality::Any)
	Add this Compound, including all of its subcompounds, to a CompoundSystem, for simulation etc.
BiotypeIndex	getAtomBiotypeIndex (Compound::AtomIndex) const
DuMM::AtomIndex	getDuMMAtomIndex (Compound::AtomIndex) const
	get DuMMForceFieldSubsystem atom index corresponding to an atom in this Compound
Protected Member Functions
void	setDuMMAtomIndex (Compound::AtomIndex, DuMM::AtomIndex)
	Stores relationship between a Compound Atom and an Atom defined in a DuMMForcefieldSubsystem.
	Compound (CompoundRep *ip)
Friends
class	CompoundSystem
Molecular geometry methods

enum	PlanarBondMatchingPolicy { KeepPlanarBonds, DistortPlanarBonds }
	Compute atom location in local Compound frame. More...
Vec3	calcDefaultAtomLocationInGroundFrame (const AtomPathName &atomName) const
	Compute atom location in local Compound frame.
Vec3	calcDefaultAtomLocationInCompoundFrame (const AtomPathName &atomName) const
	Compute atom location in local Compound frame.
Compound &	setDefaultInboardBondLength (mdunits::Length)
	Sets default (initial) bond length of current or future Bond using this Compound's inboard BondCenter.
Compound &	setDefaultInboardDihedralAngle (Angle)
	Stores a default (initial) dihedral angle in the inboard BondCenter of this Compound.
Compound &	setDefaultBondAngle (Angle angle, const AtomPathName &atom1, const AtomPathName &atom2, const AtomPathName &atom3)
	Sets a default(initial) bond angle defined by three atoms.
Compound &	setDefaultBondLength (mdunits::Length length, const AtomPathName &atom1, const AtomPathName &atom2)
	Sets a default (inital) bond length defined by two atoms.
Compound &	setDefaultDihedralAngle (const DihedralName &dihedralName, Angle angleInRadians)
	Sets a default (initial) dihedral angle of a previously named dihedral.
Compound &	setDefaultDihedralAngle (Angle angle, Compound::AtomIndex atom1, Compound::AtomIndex atom2, Compound::AtomIndex atom3, Compound::AtomIndex atom4)
	Compute atom location in local Compound frame.
Compound &	setDefaultDihedralAngle (Angle angle, const Compound::AtomName &atom1, const Compound::AtomName &atom2, const Compound::AtomName &atom3, const Compound::AtomName &atom4)
	Compute atom location in local Compound frame.
Angle	calcDefaultDihedralAngle (const DihedralName &dihedralName) const
	Computes default (initial) dihedral angle of a previously named dihedral.
Compound &	setDihedralAngle (State &state, const DihedralName &dihedralName, Angle)
	Sets dynamic dihedral angle of a previously named dihedral.
Angle	calcDihedralAngle (const State &state, const DihedralName &dihedralName) const
	Computes dynamic dihedral angle of a previously named dihedral.
Transform	calcDefaultAtomFrameInCompoundFrame (Compound::AtomIndex) const
Vec3	calcAtomLocationInGroundFrame (const State &state, Compound::AtomIndex atomId) const
Vec3	calcAtomLocationInCompoundFrame (const State &state, Compound::AtomIndex atomId) const
	Compute atom location in local Compound frame.
Vec3	calcAtomVelocityInGroundFrame (const State &state, Compound::AtomIndex atomId) const
Vec3	calcAtomAccelerationInGroundFrame (const State &state, Compound::AtomIndex atomId) const
Transform	getSubcompoundFrameInParentFrame (const Compound::Name &subcompoundName) const
virtual AtomTargetLocations	createAtomTargets (const class PdbStructure &targetStructure) const
	Create a mapping between this Compound and atom locations in a PdbStructure.
virtual AtomTargetLocations	createAtomTargets (const class PdbChain &targetChain) const
	Compute atom location in local Compound frame.
virtual AtomTargetLocations	createAtomTargets (const class PdbResidue &targetResidue) const
	Compute atom location in local Compound frame.
Compound &	matchDefaultAtomChirality (const AtomTargetLocations &atomTargets, Angle planarityTolerance=90.0 *Deg2Rad, bool flipAll=true)
	Adjust stereochemistry about chiral atoms to match that seen in a set of atomic locations.
Compound &	matchDefaultBondLengths (const AtomTargetLocations &atomTargets)
	Compute atom location in local Compound frame.
Compound &	matchDefaultBondAngles (const AtomTargetLocations &atomTargets)
	Compute atom location in local Compound frame.
Compound &	matchDefaultDihedralAngles (const AtomTargetLocations &atomTargets, PlanarBondMatchingPolicy policy=KeepPlanarBonds)
	Compute atom location in local Compound frame.
Compound &	matchDefaultTopLevelTransform (const AtomTargetLocations &atomTargets)
	Compute atom location in local Compound frame.
TransformAndResidual	getTransformAndResidual (const Compound::AtomTargetLocations &atomTargets) const
	Compute atom location in local Compound frame.
Compound &	matchDefaultConfiguration (const AtomTargetLocations &atomTargets, MatchStratagem matchStratagem=Match_Exact)
	Adjust internal coordinates to match a collection of atom targets.
Compound &	fitDefaultConfiguration (const AtomTargetLocations &atomTargets, SimTK::Real targetRms)
	Optimize adjustable degrees of freedom to best match atom targets.
const Compound &	populateDefaultPdbChain (class PdbChain &, int &defaultNextResidueNumber, const Transform &transform=Transform()) const
	Write current default(initial) Compound configuration into a PdbChain object.
const Compound &	populatePdbChain (const State &state, class PdbChain &, int &defaultNextResidueNumber, const Transform &transform=Transform()) const
	Write dynamic Compound configuration into a PdbChain object.
std::ostream &	writeDefaultPdb (std::ostream &os, const Transform &transform=Transform()) const
	Write the default (initial) configuration in Protein Data Bank (PDB) format.
void	writeDefaultPdb (const char *outFileName, const Transform &transform) const
	/brief This polymorphism takes a char* file name rather than ostream, to save the user a couple of lines of code.
std::ostream &	writeDefaultPdb (std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const
	Write the default (initial) configuration in Protein Data Bank (PDB) format.
std::ostream &	writePdb (const State &state, std::ostream &os, const Transform &transform=Transform()) const
	Write the dynamic Compound configuration in Protein Data Bank (PDB) format.
std::ostream &	writePdb (const State &state, std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const
	Write the dynamic Compound configuration in Protein Data Bank (PDB) format.
Data types that identify subcomponents of molecular compounds

typedef String	Name
	Type for name of a particular subcompound within a Compound.
typedef String	AtomName
	Type for name of a particular atom within a Compound.
typedef String	BondCenterName
	Type for name of a particular bond center within a Compound or atom.
typedef String	DihedralName
	Type for name of a particular named dihedral angle within a Compound.
typedef String	BondCenterPathName
	Type for name of a particular bond center within a Compound, possibly including subcompound indirection.
typedef String	AtomPathName
	Type for name of a particular atom within a Compound, possibly including subcompound path.
typedef std::map< AtomIndex, Vec3 >	AtomTargetLocations
	Type for set of target atom locations to be used for structure matching.
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (Compound, AtomIndex)
	Compound::Index type is an integer index into subcompounds of a Compound.
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (Compound, LocalAtomIndex)
	Compound::LocalAtomIndex type is an integer index into atoms directly attached to a Compound, that is to say that the atom does not belong to any subcompounds of the Compound.
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (Compound, BondCenterIndex)
	Compound::BondCenterIndex type is an integer index into BondCenters of a Compound.
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (Compound, BondIndex)
	Compound::BondIndex type is an integer index into Bonds of a Compound.

Detailed Description

The base class for atoms, molecules, and chemical groups.

The Compound class is the base for all molecular entities in the SimTK Molmodel API.

Member Typedef Documentation

typedef String AtomName

Type for name of a particular atom within a Compound.

Compound::AtomName is not intrinsic to the atom itself, but rather the relationship between an atom and a particular Compound. A particular atom may have different names in a compound and its subcompounds. For example, a particular atom might have the name "methyl H1" in a Compound, and have the name "H1" within a subcompound of that Compound. Unlike AtomPathNames, AtomNames must not be qualified by subcompound indirection. e.g. "H1" is a valid AtomName and a valid AtomPathName, while "methyl/H1" (because of the "/" character) is not a valid AtomName, but is a valid AtomPathName.

typedef String AtomPathName

Type for name of a particular atom within a Compound, possibly including subcompound path.

Compound::AtomPathName is not intrinsic to the atom itself, but rather the relationship between an atom and a particular Compound. A particular atom may have different names in a compound and its subcompounds. For example, a particular atom might have the name "methyl H1" in a Compound, and have the name "H1" within a subcompound of that Compound. AtomPathNames may be qualified by subcompound indirection, in contrast to AtomNames. e.g. "H1" is a valid AtomName and a valid AtomPathName, while "methyl/H1" (because of the "/" character) is not a valid AtomName, but is a valid AtomPathName.

typedef std::map<AtomIndex, Vec3> AtomTargetLocations

Type for set of target atom locations to be used for structure matching.

typedef String BondCenterName

Type for name of a particular bond center within a Compound or atom.

Compound::BondCenterName is not intrinsic to the bond center itself, but rather the relationship between a bond center and a particular atom or Compound. BondCenterNames are local to a particular compound. In contrast, BondCenterPathNames may be qualified by subcompound indirection. e.g. "bond1" is a valid BondCenterName and a valid BondCenterPathName, while "methyl gamma/bond1" is not a valid BondCenterName, but is a valid BondCenterPathName.

typedef String BondCenterPathName

Type for name of a particular bond center within a Compound, possibly including subcompound indirection.

Compound::BondCenterPathName is not intrinsic to the bond center itself, but rather the relationship between a bond center and a particular Compound. BondCenterPathNames may be qualified by subcompound indirection, in contrast to BondCenterNames. e.g. "bond1" is a valid BondCenterName and a valid BondCenterPathName, while "methyl gamma/bond1" is not a valid BondCenterName, but is a valid BondCenterPathName.

typedef String DihedralName

Type for name of a particular named dihedral angle within a Compound.

Compound::DihedralName is not intrinsic to the dihedral angle itself, but rather the relationship between a dihedral angle and a particular Compound.

typedef String Name

Type for name of a particular subcompound within a Compound.

Compound::Name is used as an index to subcompounds of a parent compound, e.g. "methyl group gamma"

Member Enumeration Documentation

enum MatchStratagem

Enumerator:

Match_Exact
Match_Idealized
Match_TopologyOnly

enum PlanarBondMatchingPolicy

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Enumerator:

KeepPlanarBonds
DistortPlanarBonds

Constructor & Destructor Documentation

Compound ( )

default Compound constructor.

Create an empty compound object representing a simulatable molecular structure.

Compound ( const Name & name ) [explicit]

Construct a Compound with a type name.

Create an empty compound object representing a simulatable molecular structure. The name is intended to represent the class of molecule being represented. e.g. "ethane", not "ethane number 3"

Parameters:

name

name of the compound type, not the compound instance

Compound ( CompoundRep * ip ) [explicit, protected]

Member Function Documentation

Compound& addCompoundSynonym ( const Name & )

Add an additional name for this class of compound.

Adding synonyms can be useful for automatically resolving biotypes, if the compound name in the force field parameter file differs from that used to define the compound. See also setCompoundName()

Returns:: a reference to this compound object

Referenced by Adenylate::Adenylate(), Aspartate::Aspartate(), Cysteine::Cysteine(), Cytidylate::Cytidylate(), Glutamate::Glutamate(), Guanylate::Guanylate(), Histidine::Histidine(), NMethylAmideResidue::NMethylAmideResidue(), TwoNMethylGuanineBaseGroup::TwoNMethylGuanineBaseGroup(), TwoNMethylGuanylate::TwoNMethylGuanylate(), and Uridylate::Uridylate().

Compound& addFirstBondCenter	(	const Compound::BondCenterName &	centerName,
		const Compound::AtomPathName &	atomName
	)

Assign the very first bond center on a particular atom.

Returns:: a reference to this Compound object; a reference to this compound object

Parameters:

	centerName	name for the new BondCenter, must be unique within the Compound
	atomName	name of the Atom to attach the bond center to

Referenced by BivalentAtom::BivalentAtom(), QuadrivalentAtom::QuadrivalentAtom(), TrivalentAtom::TrivalentAtom(), and UnivalentAtom::UnivalentAtom().

Compound& addLeftHandedBondCenter	(	const Compound::BondCenterName &	centerName,
		const Compound::AtomName &	atomName,
		Angle	bondAngle1,
		Angle	bondAngle2
	)

Place a third or later bond center on an atom, defined by two angular displacements from the first and second bond centers, respectively.

Placed the new bond center such that the directions of the first, second, and new bond centers form a left-handed geometry.

Returns:: a reference to this compound object

Parameters:

	centerName	name for the new BondCenter, must be unique within the Compound
	atomName	name of the Atom to attach the bond center to
	bondAngle1	default bond bend angle relating the first bond center to the new bond center
	bondAngle2	default bond bend angle relating the second bond center to the new bond center

Referenced by QuadrivalentAtom::QuadrivalentAtom().

Compound& addPlanarBondCenter	(	const Compound::BondCenterName &	centerName,
		const Compound::AtomName &	atomName,
		Angle	bondAngle1,
		Angle	bondAngle2
	)

Places a third or later bond center on an atom, in the same plane as the first two bond centers.

The angle represents the angular distance from the first bond center on the atom. The second angle is used to determine whether the new bond center is on the same side of the plane as the second bond center.

Returns:: a reference to this compound object

Parameters:

	centerName	name for the new BondCenter, must be unique within the Compound
	atomName	name of the Atom to attach the bond center to
	bondAngle1	default bond bend angle relating the first bond center to the new bond center
	bondAngle2	APPROXIMATE default bond bend angle relating the second bond center to the new bond center

Referenced by TrivalentAtom::TrivalentAtom().

Compound& addRightHandedBondCenter	(	const Compound::BondCenterName &	centerName,
		const Compound::AtomName &	atomName,
		Angle	bondAngle1,
		Angle	bondAngle2
	)

Place a third or later bond center on an atom, defined by two angular displacements from the first and second bond centers, respectively.

Placed the new bond center such that the directions of the first, second, and new bond centers form a right-handed geometry.

Returns:: a reference to this compound object

Parameters:

	centerName	name for the new BondCenter, must be unique within the Compound
	atomName	name of the Atom to attach the bond center to
	bondAngle1	default bond bend angle relating the first bond center to the new bond center
	bondAngle2	default bond bend angle relating the second bond center to the new bond center

Referenced by QuadrivalentAtom::QuadrivalentAtom().

Compound& addRingClosingBond	(	const Compound::BondCenterPathName &	centerName1,
		const Compound::BondCenterPathName &	centerName2
	)

Adds a covalent bond that is not part of the main tree-topology of bonds in a molecule.

Such bonds are necessary when there are ring structures. These bonds will not correspond to MobilizedBodies when the molecule is realized as a simbody multibody model, and thus the bond lengths, bond angles, and dihedral angles for a ring closing bond might not be enforced in the simulation.

Returns:: a reference to this compound object

Parameters:

	centerName1	name of the first existing bond center in the new bond
	centerName2	name of the other existing bond center in the new bond

Compound& addRingClosingBond	(	const Compound::BondCenterPathName &	centerName1,
		const Compound::BondCenterPathName &	centerName2,
		mdunits::Length	bondLength,
		Angle	dihedral = `180 *Deg2Rad`,
		BondMobility::Mobility	mobility = `BondMobility::Default`
	)

Adds a covalent bond that is not part of the main tree-topology of bonds in a Compound.

Such bonds are necessary when there are ring structures. These bonds will not correspond to MobilizedBodies when the molecule is realized as a simbody multibody model, and thus the bond lengths, bond angles, dihedral angles, and mobility for a ring closing bond might not be enforced in the simulation.

Returns:: a reference to this compound object

Parameters:

	centerName1	name of the first existing bond center in the new bond
	centerName2	name of the other existing bond center in the new bond
	bondLength	default bond length in nanometers of the new bond (might have no effect)
	dihedral	default dihedral angle about new bond, with respect to the first other bond center on each atom
	mobility	type of motion permitted in the bond connecting parent to new subcompound

Referenced by AdenineBase::AdenineBase(), CytosineBase::CytosineBase(), GuanineBase::GuanineBase(), Histidine::Histidine(), P12::P12(), Phenylalanine::Phenylalanine(), Proline::Proline(), PurineBaseCore::PurineBaseCore(), Tryptophan::Tryptophan(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), Tyrosine::Tyrosine(), and UracilBase::UracilBase().

Compound& addSecondBondCenter	(	const Compound::BondCenterName &	centerName,
		const Compound::AtomName &	atomName,
		Angle	bondAngle1
	)

Place a second bond center on an atom, placed a particular angle away from the first bond center.

Returns:: a reference to this compound object

Parameters:

	centerName	name for the new BondCenter, must be unique within the Compound
	atomName	name of the Atom to attach the bond center to
	bondAngle1	default bond bend angle relating the first two bond centers of the atom

Referenced by BivalentAtom::BivalentAtom(), QuadrivalentAtom::QuadrivalentAtom(), and TrivalentAtom::TrivalentAtom().

Compound& bondAtom	(	const Compound::SingleAtom &	c,
		const BondCenterPathName &	parentBondName
	)

Bond atom using default bond length and dihedral angle.

Bond length and dihedral angle must have already been predefined in the parent *or* the child BondCenter, but not both

Returns:: a reference to this compound object

Parameters:

	c	the new subcompound to attach to this compound (a copy of the subcompound will be attached)
	parentBondName	name of the bond center on the parent Compound to which the new subcompound will be attached

Compound& bondAtom	(	const Compound::SingleAtom &	c,
		const BondCenterPathName &	parentBondName,
		mdunits::Length	distance,
		Angle	dihedral = `0`,
		BondMobility::Mobility	= `BondMobility::Default`
	)

Add a subcompound containing exactly one atom, so the Compound::AtomName can be reused for the Compound::Name.

This atom is connected to existing material.

Returns:: a reference to this compound object

Parameters:

	c	the new subcompound to attach to this compound (a copy of the subcompound will be attached)
	parentBondName	name of the bond center on the parent Compound to which the new subcompound will be attached
	distance	default bond length in nanometers of new bond connecting new subcompound to parent Compound
	dihedral	default dihedral angle about new bond, with respect to the first bond center on each atom

Referenced by AcetylResidue::AcetylResidue(), AdenineBase::AdenineBase(), Alanine::Alanine(), AlcoholOHGroup::AlcoholOHGroup(), Arginine::Arginine(), AromaticSixMemberedCHGroup::AromaticSixMemberedCHGroup(), Asparagine::Asparagine(), BetaBranchedAminoAcidResidue::BetaBranchedAminoAcidResidue(), CarboxylateGroup::CarboxylateGroup(), Cysteine::Cysteine(), CytosineBase::CytosineBase(), Glutamate::Glutamate(), Glutamine::Glutamine(), Glycine::Glycine(), GuanineBase::GuanineBase(), Histidine::Histidine(), HNAminoAcidResidue::HNAminoAcidResidue(), Leucine::Leucine(), Lysine::Lysine(), Methane::Methane(), Methionine::Methionine(), MethyleneGroup::MethyleneGroup(), MethylGroup::MethylGroup(), NMethylAmideResidue::NMethylAmideResidue(), P12::P12(), Phenylalanine::Phenylalanine(), PrimaryAmineGroup::PrimaryAmineGroup(), Proline::Proline(), PurineBaseCore::PurineBaseCore(), Tryptophan::Tryptophan(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), Tyrosine::Tyrosine(), UracilBase::UracilBase(), Valine::Valine(), and Water::Water().

Compound& bondCompound	(	const Compound::Name &	n,
		const Compound &	c,
		const BondCenterPathName &	parentBondName,
		BondMobility::Mobility	mobility
	)

Add a subcompound attached by its inboard bond to an existing bond center.

Shorter version uses default bond length and dihedral angle, which must have been predefined in the parent *or* the child BondCenter, but not both.

Returns:: a reference to this compound object

Parameters:

	n	name for the new subcompound from the viewpoint of the parent Compound
	c	the new subcompound to attach to this compound (a copy of the subcompound will be attached)
	parentBondName	name of the bond center on the parent Compound to which the new subcompound will be attached
	mobility	type of motion permitted in the bond connecting parent to new subcompound

Compound& bondCompound	(	const Compound::Name &	n,
		const Compound &	c,
		const BondCenterPathName &	parentBondName
	)

Add a subcompound attached by its inboard bond to an existing bond center.

Shorter version uses default bond length and dihedral angle, which must have been predefined in the parent *or* the child BondCenter, but not both.

Returns:: a reference to this compound object

Parameters:

	n	name for the new subcompound from the viewpoint of the parent Compound
	c	the new subcompound to attach to this compound (a copy of the subcompound will be attached)
	parentBondName	name of the bond center on the parent Compound to which the new subcompound will be attached

Compound& bondCompound	(	const Compound::Name &	n,
		const Compound &	c,
		const BondCenterPathName &	parentBondName,
		mdunits::Length	distance,
		Angle	dihedral = `180 *Deg2Rad`,
		BondMobility::Mobility	mobility = `BondMobility::Default`
	)

Add a subcompound attached by its inboard bond to an existing bond center.

Returns:: a reference to this compound object

Parameters:

	n	name for the new subcompound from the viewpoint of the parent Compound
	c	the new subcompound to attach to this compound (a copy of the subcompound will be attached)
	parentBondName	name of the bond center on the parent Compound to which the new subcompound will be attached
	distance	default bond length in nanometers of new bond connecting new subcompound to parent Compound
	dihedral	default dihedral angle about new bond, with respect to the first other bond center on each atom
	mobility	allowed motion in new bond

Referenced by Adenylate::Adenylate(), Aspartate::Aspartate(), BetaUnbranchedAminoAcidResidue::BetaUnbranchedAminoAcidResidue(), Cytidylate::Cytidylate(), Ethane::Ethane(), Glutamate::Glutamate(), Guanylate::Guanylate(), Isoleucine::Isoleucine(), Lysine::Lysine(), P12::P12(), RNA::RNA(), Serine::Serine(), Threonine::Threonine(), TwoNMethylGuanylate::TwoNMethylGuanylate(), Tyrosine::Tyrosine(), Uridylate::Uridylate(), and Valine::Valine().

Vec3 calcAtomAccelerationInGroundFrame	(	const State &	state,
		Compound::AtomIndex	atomId
	)			const

Returns:: vector acceleration in nanometers per picosecond squared

Parameters:

	state	simbody State representing current configuration
	atomId	integer index of Atom with respect to this Compound

Vec3 calcAtomLocationInCompoundFrame	(	const State &	state,
		Compound::AtomIndex	atomId
	)			const

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Parameters:

	state	simbody State representing current configuration
	atomId	integer index of Atom with respect to this Compound

Vec3 calcAtomLocationInGroundFrame	(	const State &	state,
		Compound::AtomIndex	atomId
	)			const

Returns:: location in orthogonal nanometers

Parameters:

	state	simbody State representing current configuration
	atomId	integer index of Atom with respect to this Compound

Vec3 calcAtomVelocityInGroundFrame	(	const State &	state,
		Compound::AtomIndex	atomId
	)			const

Returns:: vector velocity in nanometers per picosecond

Parameters:

	state	simbody State representing current configuration
	atomId	integer index of Atom with respect to this Compound

Transform calcDefaultAtomFrameInCompoundFrame ( Compound::AtomIndex ) const

Returns:: location and orientation of Atom with respect to this Compound

Vec3 calcDefaultAtomLocationInCompoundFrame ( const AtomPathName & atomName ) const

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Parameters:

atomName

name of the atom from viewpoint of Compound

Vec3 calcDefaultAtomLocationInGroundFrame ( const AtomPathName & atomName ) const

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Parameters:

atomName

name of the atom from viewpoint of Compound

Referenced by LigandDroplet::LigandDroplet(), and WaterDroplet::WaterDroplet().

Angle calcDefaultDihedralAngle ( const DihedralName & dihedralName ) const

Computes default (initial) dihedral angle of a previously named dihedral.

Returns:: dihedral angle in radians with respect to first other bond centers of bonded atoms

Parameters:

dihedralName

name of predefined dihedral angle with respect to this Compound

Referenced by Ethane::calcDefaultTorsionAngle().

Angle calcDihedralAngle	(	const State &	state,
		const DihedralName &	dihedralName
	)			const

Computes dynamic dihedral angle of a previously named dihedral.

Returns:: dihedral angle in radians with respect to first other bond centers of bonded atoms

Parameters:

	state	simbody State object representing the current configuration
	dihedralName	name of predefined dihedral angle with respect to this Compound

Compound& convertInboardBondCenterToOutboard ( )

Make so that this compound can no longer be a child to the geometry of another compound Raises an error if the inboard bond center is already bonded.

Returns:: a reference to this compound object

Referenced by AcetylResidue::AcetylResidue(), Ethane::Ethane(), Methane::Methane(), and RNA::RNA().

virtual AtomTargetLocations createAtomTargets ( const class PdbResidue & targetResidue ) const [virtual]

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

virtual AtomTargetLocations createAtomTargets ( const class PdbChain & targetChain ) const [virtual]

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Reimplemented in Biopolymer.

virtual AtomTargetLocations createAtomTargets ( const class PdbStructure & targetStructure ) const [virtual]

Create a mapping between this Compound and atom locations in a PdbStructure.

For use in the process of importing a configuration from a PDB file

Reimplemented in Biopolymer.

Referenced by P12::P12().

Compound& defineDihedralAngle	(	const Compound::DihedralName &	angleName,
		const Compound::BondCenterPathName &	bond1,
		const Compound::BondCenterPathName &	bond2,
		Angle	offset = `0 *Deg2Rad`
	)

Define a named dihedral in terms of two bond centers.

Useful in cases where not all four atoms have been placed yet. The bond centers must be from two atoms that are bonded (atoms 2 and 3 of 4) But are NOT the bond centers that connect the two middle atoms.

The offset parameter is used in cases where the dihedral angle definition differs from the IUPAC definition of dihedral angles using four atoms. For example the definition of protein phi and psi angles is 180 degrees offset from the standard four-atom dihedral angle definition.

Returns:: a reference to this compound object

Parameters:

	angleName	unique name for new dihedral angle definition
	bond1	first bond center, connecting atom 2 to atom 1
	bond2	second bond center, connecting atom 3 to atom 4
	offset	nomenclature offset

Compound& defineDihedralAngle	(	const Compound::DihedralName &	angleName,
		const Compound::AtomPathName &	atom1,
		const Compound::AtomPathName &	atom2,
		const Compound::AtomPathName &	atom3,
		const Compound::AtomPathName &	atom4,
		Angle	offset = `0 *Deg2Rad`
	)

Define a named dihedral angle using four atoms.

The offset parameter is used in cases where the dihedral angle definition differs from the IUPAC definition of dihedral angles using four atoms. For example the definition of protein phi and psi angles is 180 degrees offset from the standard four-atom dihedral angle definition.

Returns:: a reference to this compound object

Parameters:

	angleName	unique name for new dihedral angle definition
	atom1	first atom name
	atom2	second atom name
	atom3	third atom name
	atom4	fourth atom name
	offset	nomenclature offset

Referenced by Adenylate::Adenylate(), Arginine::Arginine(), Asparagine::Asparagine(), Aspartate::Aspartate(), BetaBranchedAminoAcidResidue::BetaBranchedAminoAcidResidue(), BetaUnbranchedAminoAcidResidue::BetaUnbranchedAminoAcidResidue(), Cysteine::Cysteine(), Cytidylate::Cytidylate(), Ethane::Ethane(), Glutamate::Glutamate(), Glutamine::Glutamine(), Guanylate::Guanylate(), Histidine::Histidine(), Isoleucine::Isoleucine(), Leucine::Leucine(), Lysine::Lysine(), Methionine::Methionine(), NMethylAmideResidue::NMethylAmideResidue(), P12::P12(), Phenylalanine::Phenylalanine(), Proline::Proline(), RNA::RNA(), Serine::Serine(), Tryptophan::Tryptophan(), TwoNMethylGuanylate::TwoNMethylGuanylate(), Tyrosine::Tyrosine(), Uridylate::Uridylate(), and Valine::Valine().

Compound& fitDefaultConfiguration	(	const AtomTargetLocations &	atomTargets,
		SimTK::Real	targetRms
	)

Optimize adjustable degrees of freedom to best match atom targets.

BiotypeIndex getAtomBiotypeIndex ( Compound::AtomIndex ) const

Returns:: the biotype assigned to an Atom in this Compound

const Element& getAtomElement ( const Compound::AtomName & ) const

Name a type of Compound.

Sets the name for this class of compound, e.g. "ethane", not "ethane number 3". The compound name can be important for automatic resolution of atom types for during force field resolution.

Returns:: a reference to this compound object

const Element& getAtomElement ( Compound::AtomIndex ) const

Returns:: chemical element of atom

Compound::AtomIndex getAtomIndex ( const Compound::AtomPathName & ) const

Returns:: integer index of named atom, with repect to this Compound

Vec3 getAtomLocationInMobilizedBodyFrame ( Compound::AtomIndex ) const

get the location of an Atom in the frame of the simbody MobilizedBody to which the Atom is attached

Requires that this Compound has already been modeled in a CompoundSystem

Returns:: location in orthogonal nanometers with respect to the rigid body to which the atom is attached

Referenced by RNA::calcRNABaseNormal().

MobilizedBodyIndex getAtomMobilizedBodyIndex ( Compound::AtomIndex ) const

get the simbody MobilizedBody to which a particular atom is attached

Requires that this Compound has already been modeled in a CompoundSystem

Returns:: the integer index of the MobilizedBody in the CompoundSystem

Referenced by RNA::calcRNABaseNormal().

const AtomPathName getAtomName ( Compound::AtomIndex ) const

Returns the most recently assigned name, if any, given to an atom in this compound.

Referenced by LigandDroplet::LigandDroplet(), and WaterDroplet::WaterDroplet().

Compound::AtomIndex getBondAtomIndex	(	Compound::BondIndex	bondIndex,
		int	which
	)			const

Returns:: true if Compound contains a subcompound by that name (relative to this Compound); integer index of one of the two atoms involved in a particular covalent bond

Parameters:

	bondIndex	integer index of a bond in this Compound
	which	zero(0) for parent-side (rootward) atom of bond, one(1) for child-side (leafward) atom

const Name& getCompoundName ( ) const

Returns:: name of Compound type

Referenced by RibonucleosideResidue::withPhosphodiester().

DuMM::AtomIndex getDuMMAtomIndex ( Compound::AtomIndex ) const

get DuMMForceFieldSubsystem atom index corresponding to an atom in this Compound

Requires that this Compound has already been modeled in a CompoundSystem

Returns:: an AtomIndex in the DuMMForceFieldSubystem

int getNumAtoms ( ) const

Returns:: the number of atoms in the Compound, including those within subcompounds.

Referenced by LigandDroplet::LigandDroplet(), and WaterDroplet::WaterDroplet().

size_t getNumBondCenters ( Compound::AtomIndex atomIndex ) const

Returns:: total number of BondCenters in a particular atom of a Compound

size_t getNumBondCenters ( ) const

Returns:: total number of BondCenters in a Compound, including its subcompounds

size_t getNumBonds ( ) const

Returns:: total number of Bonds in a Compound, including its subcompounds

Referenced by P12::P12().

char getPdbChainId ( ) const

Returns:: character that would populate "chain id" field for PDB file output for this Compound

Referenced by RibonucleosideResidue::withPhosphodiester().

const String& getPdbResidueName ( ) const

Returns:: string that would be used to populate "residue type" field for this Compound in a PDB file

Referenced by RNA::RNA(), and RibonucleosideResidue::withPhosphodiester().

int getPdbResidueNumber ( ) const

Returns:: integer that would appear in "residue number" field for this Compound in a PDB file

Referenced by RibonucleosideResidue::withPhosphodiester().

const Compound& getSubcompound ( const Compound::Name & subcompoundName ) const

Returns:: read-only reference to a subcompound of this Compound; mutable reference to a subcompound of this Compound; read-only reference to a subcompound of this Compound

Parameters:

subcompoundName

name of subcompound

Transform getSubcompoundFrameInParentFrame ( const Compound::Name & subcompoundName ) const

Returns:: default (initial) location and orientation of a subcompound with respect to this Compound

Parameters:

subcompoundName

name of subcompound with respect to this Compound

const Transform& getTopLevelTransform ( ) const

Returns:: the orientation and location of this Compound

Referenced by CompoundSystem::adoptCompound().

TransformAndResidual getTransformAndResidual ( const Compound::AtomTargetLocations & atomTargets ) const

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

bool hasAtom ( const AtomPathName & name ) const

Returns:: total number of subcompounds in a compoud, including sub-subcompounds etc.; true if Compound contains an atom by that name (relative to this Compound)

Parameters:

name

name of the atom relative to this compound.

Referenced by RNA::RNA().

bool hasBondCenter ( const BondCenterPathName & bondCenter ) const

Returns:: true if Compound contains a BondCenter (half-bond) by that name (relative to this Compound)

Parameters:

bondCenter

name of the BondCenter relative to this compound.

Compound& inheritAtomNames ( const Compound::Name & )

Convenience method to locally import all of the atom names that a particular subcompound uses.

Returns:: a reference to this compound object

Referenced by Adenylate::Adenylate(), Cytidylate::Cytidylate(), Guanylate::Guanylate(), Methane::Methane(), RNA::RNA(), TwoNMethylGuanylate::TwoNMethylGuanylate(), and Uridylate::Uridylate().

Compound& inheritBondCenterNames ( const Compound::Name & )

Convenience method to locally import all of the BondCenter names that a particular subcompound uses.

Returns:: a reference to this compound object

Compound& inheritCompoundSynonyms ( const Compound & otherCompound )

Name a type of Compound.

Sets the name for this class of compound, e.g. "ethane", not "ethane number 3". The compound name can be important for automatic resolution of atom types for during force field resolution.

Returns:: a reference to this compound object

Compound& matchDefaultAtomChirality	(	const AtomTargetLocations &	atomTargets,
		Angle	planarityTolerance = `90.0 *Deg2Rad`,
		bool	flipAll = `true`
	)

Adjust stereochemistry about chiral atoms to match that seen in a set of atomic locations.

Choose a small value of planarityTolerance parameter to break the planarity of out-of-plane atoms from the target set

Returns:: a reference to this compound

Parameters:

	atomTargets	another set of atom locations to match chirality of
	planarityTolerance	break planarity of BondCenters more than this angle out of plane (radians)
	flipAll	whether to invert each mismatched BondCenter, or all at once

Referenced by P12::P12().

Compound& matchDefaultBondAngles ( const AtomTargetLocations & atomTargets )

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Referenced by P12::P12().

Compound& matchDefaultBondLengths ( const AtomTargetLocations & atomTargets )

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Referenced by P12::P12().

Compound& matchDefaultConfiguration	(	const AtomTargetLocations &	atomTargets,
		MatchStratagem	matchStratagem = `Match_Exact`
	)			`[inline]`

Adjust internal coordinates to match a collection of atom targets.

References Compound::DistortPlanarBonds, Compound::KeepPlanarBonds, Compound::Match_Exact, Compound::Match_Idealized, and Compound::Match_TopologyOnly.

Compound& matchDefaultDihedralAngles	(	const AtomTargetLocations &	atomTargets,
		PlanarBondMatchingPolicy	policy = `KeepPlanarBonds`
	)

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Parameters:

	atomTargets	set of atom locations to match dihedrals of
	policy	whether to keep ideal torsions on bonds between planar atoms

Referenced by P12::P12().

Compound& matchDefaultTopLevelTransform ( const AtomTargetLocations & atomTargets )

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Referenced by P12::P12().

Compound& nameAtom	(	const Compound::AtomName &	newName,
		const AtomPathName &	oldName,
		BiotypeIndex	biotype
	)

Returns:: a reference to this compound object

Parameters:

	newName	new name for this atom; name is local to this Compound
	oldName	previous name; can be a subcompound-qualified Atom name
	biotype	new Biotype for the atom, with respect to this Compound

Compound& nameAtom	(	const Compound::AtomName &	newName,
		const AtomPathName &	oldName
	)

Returns:: reference to this compound object

Parameters:

	newName	new name for this atom; name is local to this Compound
	oldName	previous name; can be a subcompound-qualified Atom name

Referenced by AcetylResidue::AcetylResidue(), Aspartate::Aspartate(), BetaUnbranchedAminoAcidResidue::BetaUnbranchedAminoAcidResidue(), Ethane::Ethane(), Glutamate::Glutamate(), Glycine::Glycine(), HNAminoAcidResidue::HNAminoAcidResidue(), Isoleucine::Isoleucine(), Lysine::Lysine(), P12::P12(), Serine::Serine(), Threonine::Threonine(), Tyrosine::Tyrosine(), and Valine::Valine().

Compound& nameBondCenter	(	const Compound::BondCenterName &	newName,
		const BondCenterPathName &	oldName
	)

Define a local name for a particular BondCenter in this Compound.

Returns:: a reference to this compound object

Parameters:

	newName	new local name for bond center
	oldName	previous name, can be a subcompound-qualified name

Referenced by AcetylResidue::AcetylResidue(), AlcoholOHGroup::AlcoholOHGroup(), BetaBranchedAminoAcidResidue::BetaBranchedAminoAcidResidue(), BetaUnbranchedAminoAcidResidue::BetaUnbranchedAminoAcidResidue(), CarboxylateGroup::CarboxylateGroup(), MethyleneGroup::MethyleneGroup(), MethylGroup::MethylGroup(), NMethylAmideResidue::NMethylAmideResidue(), and PurineBaseCore::PurineBaseCore().

const Compound& populateDefaultPdbChain	(	class PdbChain &	,
		int &	defaultNextResidueNumber,
		const Transform &	transform = `Transform()`
	)			const

Write current default(initial) Compound configuration into a PdbChain object.

const Compound& populatePdbChain	(	const State &	state,
		class PdbChain &	,
		int &	defaultNextResidueNumber,
		const Transform &	transform = `Transform()`
	)			const

Write dynamic Compound configuration into a PdbChain object.

Compound& setAtomBiotype	(	const Compound::AtomPathName &	atomName,
		const String &	biotypeResidueName,
		const String &	biotypeAtomName,
		SimTK::Ordinality::Residue	ordinality = `SimTK::Ordinality::Any`
	)			`[inline]`

Add this Compound, including all of its subcompounds, to a CompoundSystem, for simulation etc.

This Compound will become a top-level object with the CompoundSystem.

References Biotype::defineBiotype(), Biotype::exists(), Biotype::get(), Biotype::getElement(), Biotype::getIndex(), and Biotype::getValence().

Referenced by AcetylResidue::AcetylResidue(), Alanine::Alanine(), NMethylAmideResidue::NMethylAmideResidue(), and P12::P12().

Compound& setBaseAtom	(	const Compound::SingleAtom &	c,
		const Transform &	= `Transform()`
	)

Add a first subcompound containing exactly one atom, so the Compound::AtomName can be reused for the Compound::Name.

This atom is not connected to anything else (yet).

Returns:: a reference to this compound object

Parameters:

c

single-atom Compound to add as first subcompound of this Compound

Compound& setBaseAtom	(	const Compound::AtomName &	name,
		const Biotype &	biotype,
		const Transform &	location = `Vec3(0)`
	)

Add the first atom unconnected to anything else (yet).

Returns:: a reference to this compound object

Parameters:

	name	name of the new atom being created
	biotype	Biotype of the new atom being created
	location	default location of the new atom being created in orthogonal nanometers. Defaults to (0,0,0)

Compound& setBaseAtom	(	const Compound::AtomName &	name,
		const Element &	element,
		const Transform &	location = `Vec3(0)`
	)

Add the first atom unconnected to anything else (yet).

Returns:: a reference to this compound object

Parameters:

	name	name of the new atom being created
	element	chemical element of the new atom being created
	location	default location of the new atom being created in orthogonal nanometers. Defaults to (0,0,0)

Referenced by AlcoholOHGroup::AlcoholOHGroup(), Argon::Argon(), AromaticSixMemberedCHGroup::AromaticSixMemberedCHGroup(), CalciumIon::CalciumIon(), CarboxylateGroup::CarboxylateGroup(), CesiumIon::CesiumIon(), ChlorideIon::ChlorideIon(), CytosineBase::CytosineBase(), LithiumIon::LithiumIon(), MagnesiumIon::MagnesiumIon(), MethyleneGroup::MethyleneGroup(), MethylGroup::MethylGroup(), NMethylAmideResidue::NMethylAmideResidue(), PotassiumIon::PotassiumIon(), PrimaryAmineGroup::PrimaryAmineGroup(), PurineBaseCore::PurineBaseCore(), RubidiumIon::RubidiumIon(), SingleAtom::SingleAtom(), SodiumIon::SodiumIon(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), UracilBase::UracilBase(), Water::Water(), and ZincIon::ZincIon().

Compound& setBaseCompound	(	const Compound::Name &	n,
		const Compound &	c,
		const Transform &	location = `Transform()`
	)

Add a first subcompound without attaching it to anything.

Returns:: a reference to this compound object

Parameters:

	n	name for new subcompound, from viewpoint of parent
	c	new subcompound to be copied and attached to parent Compound
	location	default location of the new atom being created in orthogonal nanometers. Defaults to (0,0,0)

Referenced by AcetylResidue::AcetylResidue(), Ethane::Ethane(), Methane::Methane(), and P12::P12().

Compound& setBiotypeIndex	(	const Compound::AtomPathName &	atomName,
		BiotypeIndex	biotype
	)

define the Biotype for an Atom in this Compound

Returns:: a reference to this compound object

Parameters:

	atomName	name of the atom in the context of this Compound
	biotype	integer index of an existing Biotype known to the Biotype class

Referenced by Methane::Methane(), RNA::RNA(), Serine::Serine(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), TwoNMethylGuanylate::TwoNMethylGuanylate(), and Water::Water().

Compound& setBondMobility	(	BondMobility::Mobility	mobility,
		Compound::BondIndex	bondIndex
	)

Override the default rotatability of a bond.

Returns:: a reference to this compound object

Parameters:

	mobility	the new allowed motion of the bond
	bondIndex	the integer index of the Bond in the context of this Compound

Compound& setBondMobility	(	BondMobility::Mobility	mobility,
		const AtomPathName &	atom1,
		const AtomPathName &	atom2
	)

Override the default rotatability of a bond.

Returns:: a reference to this compound object

Parameters:

	mobility	the new allowed motion of the bond
	atom1	the name of the first atom defining the Bond
	atom2	the name of the second atom defining the Bond

Referenced by Arginine::Arginine(), Asparagine::Asparagine(), Glutamine::Glutamine(), Histidine::Histidine(), P12::P12(), Phenylalanine::Phenylalanine(), Proline::Proline(), RNA::setRNABondMobility(), Tryptophan::Tryptophan(), and Tyrosine::Tyrosine().

Compound& setCompoundBondMobility ( BondMobility::Mobility mobility )

Set BondMobility for every bond in the Compound.

Returns:: A reference to this Compound

Compound& setCompoundName ( const Name & )

Name a type of Compound.

Sets the name for this class of compound, e.g. "ethane", not "ethane number 3". The compound name can be important for automatic resolution of atom types for during force field resolution.

Returns:: a reference to this compound object

Referenced by AlcoholOHGroup::AlcoholOHGroup(), AliphaticCarbon::AliphaticCarbon(), AliphaticHydrogen::AliphaticHydrogen(), Argon::Argon(), AromaticSixMemberedCHGroup::AromaticSixMemberedCHGroup(), BivalentAtom::BivalentAtom(), CalciumIon::CalciumIon(), CesiumIon::CesiumIon(), ChlorideIon::ChlorideIon(), Ethane::Ethane(), LithiumIon::LithiumIon(), MagnesiumIon::MagnesiumIon(), Methane::Methane(), MethyleneGroup::MethyleneGroup(), MethylGroup::MethylGroup(), PotassiumIon::PotassiumIon(), QuadrivalentAtom::QuadrivalentAtom(), RubidiumIon::RubidiumIon(), SingleAtom::SingleAtom(), SodiumIon::SodiumIon(), TrivalentAtom::TrivalentAtom(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), UnivalentAtom::UnivalentAtom(), and ZincIon::ZincIon().

Compound& setDefaultBondAngle	(	Angle	angle,
		const AtomPathName &	atom1,
		const AtomPathName &	atom2,
		const AtomPathName &	atom3
	)

Sets a default(initial) bond angle defined by three atoms.

Warning:: setDefaultBondAngle only works if one of the two bond centers is bond center 1 or 2

Todo:

remove this restriction

Returns:: a reference to this compound object

Parameters:

	angle	new default bond angle in radians
	atom1	name of first atom defining bond angle
	atom2	name of middle atom defining bond angle
	atom3	name of third atom defining bond angle

Referenced by Cysteine::Cysteine(), Proline::Proline(), and Water::Water().

Compound& setDefaultBondLength	(	mdunits::Length	length,
		const AtomPathName &	atom1,
		const AtomPathName &	atom2
	)

Sets a default (inital) bond length defined by two atoms.

Returns:: a reference to this compound object

Parameters:

	length	default bond length in nanometers
	atom1	name of first atom in bond
	atom2	name of second atom in bond

Compound& setDefaultDihedralAngle	(	Angle	angle,
		const Compound::AtomName &	atom1,
		const Compound::AtomName &	atom2,
		const Compound::AtomName &	atom3,
		const Compound::AtomName &	atom4
	)

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Compound& setDefaultDihedralAngle	(	Angle	angle,
		Compound::AtomIndex	atom1,
		Compound::AtomIndex	atom2,
		Compound::AtomIndex	atom3,
		Compound::AtomIndex	atom4
	)

Compute atom location in local Compound frame.

Returns:: default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Compound& setDefaultDihedralAngle	(	const DihedralName &	dihedralName,
		Angle	angleInRadians
	)

Sets a default (initial) dihedral angle of a previously named dihedral.

Returns:: a reference to this compound object

Parameters:

	dihedralName	name of predefined dihedral angle with respect to this Compound
	angleInRadians	new dihedral angle in radians

Referenced by Adenylate::Adenylate(), Asparagine::Asparagine(), Aspartate::Aspartate(), BetaBranchedAminoAcidResidue::BetaBranchedAminoAcidResidue(), BetaUnbranchedAminoAcidResidue::BetaUnbranchedAminoAcidResidue(), Cytidylate::Cytidylate(), Glutamate::Glutamate(), Glutamine::Glutamine(), Guanylate::Guanylate(), Histidine::Histidine(), Isoleucine::Isoleucine(), Leucine::Leucine(), P12::P12(), Phenylalanine::Phenylalanine(), RNA::RNA(), Proline::setDefaultDownPucker(), Ethane::setDefaultTorsionAngle(), Proline::setDefaultUpPucker(), Tryptophan::Tryptophan(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), TwoNMethylGuanylate::TwoNMethylGuanylate(), Tyrosine::Tyrosine(), Uridylate::Uridylate(), and Valine::Valine().

Compound& setDefaultInboardBondLength ( mdunits::Length )

Sets default (initial) bond length of current or future Bond using this Compound's inboard BondCenter.

Default inboard bond length and dihedral should only be set when the future bonding partners of this compound are restricted to a particular atom type

Returns:: a reference to this compound object

Referenced by AlcoholOHGroup::AlcoholOHGroup(), AliphaticCarbon::AliphaticCarbon(), AliphaticHydrogen::AliphaticHydrogen(), AromaticSixMemberedCHGroup::AromaticSixMemberedCHGroup(), CarboxylateGroup::CarboxylateGroup(), MethyleneGroup::MethyleneGroup(), MethylGroup::MethylGroup(), NMethylAmideResidue::NMethylAmideResidue(), and PrimaryAmineGroup::PrimaryAmineGroup().

Compound& setDefaultInboardDihedralAngle ( Angle )

Stores a default (initial) dihedral angle in the inboard BondCenter of this Compound.

If exactly one of the two BondCenters that are joined to form a Bond has default geometry set, then the bondCompound() lacking explicit geometry arguments may be used to create the Bond.

Returns:: a reference to this compound object

Compound& setDihedralAngle	(	State &	state,
		const DihedralName &	dihedralName,
		Angle
	)

Sets dynamic dihedral angle of a previously named dihedral.

The dihedral angle must be an adjustable parameter of the dynamic model.

Returns:: a reference to this compound object

Parameters:

	state	simbody State object representing the current configuration
	dihedralName	name of predefined dihedral angle with respect to this Compound

void setDuMMAtomIndex	(	Compound::AtomIndex	,
		DuMM::AtomIndex
	)			`[protected]`

Stores relationship between a Compound Atom and an Atom defined in a DuMMForcefieldSubsystem.

Compound& setInboardBondCenter ( const Compound::BondCenterName & centerName )

setInboardBondCenter assigns special status to a bond center.

There can be at most one inboard bond center in a Compound. Only an inboard bond center can be used to bond to a parent compound

Returns:: a reference to this compound object

Parameters:

centerName

name of existing BondCenter to use as inboard BondCenter

Referenced by BivalentAtom::BivalentAtom(), QuadrivalentAtom::QuadrivalentAtom(), TrivalentAtom::TrivalentAtom(), and UnivalentAtom::UnivalentAtom().

void setMultibodySystem ( MultibodySystem & system )

Add this Compound, including all of its subcompounds, to a CompoundSystem, for simulation etc.

This Compound will become a top-level object with the CompoundSystem.

Referenced by CompoundSystem::adoptCompound().

Compound& setPdbChainId ( char chainId )

Set character to populate "chain id" field for PDB file output.

Returns:: a reference to this compound object

Parameters:

chainId

Protein Data Bank "chain Id" for this Compound

Referenced by LigandDroplet::LigandDroplet(), P12::P12(), and WaterDroplet::WaterDroplet().

Compound& setPdbResidueName ( const String & resName )

Set string to populate "residue type" field for PDB file output.

Returns:: a reference to this compound object

Referenced by Argon::Argon(), CalciumIon::CalciumIon(), CesiumIon::CesiumIon(), ChlorideIon::ChlorideIon(), Ethane::Ethane(), LigandDroplet::LigandDroplet(), LithiumIon::LithiumIon(), MagnesiumIon::MagnesiumIon(), P12::P12(), PotassiumIon::PotassiumIon(), RubidiumIon::RubidiumIon(), SodiumIon::SodiumIon(), TwoNMethylGuanidineGroup::TwoNMethylGuanidineGroup(), WaterDroplet::WaterDroplet(), and ZincIon::ZincIon().

Compound& setPdbResidueNumber ( int resNum )

Set value to populate "residue number" field for PDB file output.

Returns:: a reference to this compound object

Referenced by Protein::initialize(), LigandDroplet::LigandDroplet(), P12::P12(), RNA::RNA(), and WaterDroplet::WaterDroplet().

Compound& setTopLevelTransform ( const Transform & transform )

Set the orientation and location of this Compound.

Referenced by CompoundSystem::adoptCompound().

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	Compound	,
		BondIndex
	)

Compound::BondIndex type is an integer index into Bonds of a Compound.

It is NOT instrinsic to the Bond, but represents the relationship between a Bond and precisely one of its parent compounds.

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	Compound	,
		BondCenterIndex
	)

Compound::BondCenterIndex type is an integer index into BondCenters of a Compound.

It is NOT instrinsic to the BondCenter, but represents the relationship between a BondCenter and precisely one of its parent compounds.

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	Compound	,
		LocalAtomIndex
	)

Compound::LocalAtomIndex type is an integer index into atoms directly attached to a Compound, that is to say that the atom does not belong to any subcompounds of the Compound.

This index type should ordinarily not be used by clients of the Molmodel API

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	Compound	,
		AtomIndex
	)

Compound::Index type is an integer index into subcompounds of a Compound.

It is NOT instrinsic to the subcompound, but represents the relationship between a subcompound and precisely one of its parent compounds. Compound::AtomIndex type is an integer index into atoms of a Compound. It is NOT instrinsic to the atom, but represents the relationship between an atom and precisely one of its parent compounds.

Compound& updSubcompound ( const Compound::Name & subcompoundName )

Returns:: mutable reference to a subcompound of this Compound

Parameters:

subcompoundName

name of subcompound

std::ostream& writeDefaultPdb	(	std::ostream &	os,
		int &	nextAtomSerialNumber,
		const Transform &	transform = `Transform()`
	)			const

Write the default (initial) configuration in Protein Data Bank (PDB) format.

integer nextAtomSerialNumber reference is incremented within writeDefaultPdb method, so that subsequent calls to this method using the same integer variable will continue numbering atoms where the previous call left off.

Parameters:

	os	output stream to write PDB coordinates to
	nextAtomSerialNumber	mutable integer reference containing the next desired atom serial number
	transform	optional change to location and orientation of molecule

void writeDefaultPdb	(	const char *	outFileName,
		const Transform &	transform
	)			const

/brief This polymorphism takes a char* file name rather than ostream, to save the user a couple of lines of code.

std::ostream& writeDefaultPdb	(	std::ostream &	os,
		const Transform &	transform = `Transform()`
	)			const

Write the default (initial) configuration in Protein Data Bank (PDB) format.

Starting with the first atom's serial number as one(1).

Parameters:

	os	output stream to write PDB coordinates to
	transform	optional change to location and orientation of molecule

std::ostream& writePdb	(	const State &	state,
		std::ostream &	os,
		int &	nextAtomSerialNumber,
		const Transform &	transform = `Transform()`
	)			const

Write the dynamic Compound configuration in Protein Data Bank (PDB) format.

integer nextAtomSerialNumber reference is incremented within writePdb method, so that subsequent calls to this method using the same integer variable will continue numbering atoms where the previous call left off.

Parameters:

	state	simbody state representing the current configuration of the molecule
	os	output stream to write PDB coordinates to
	nextAtomSerialNumber	mutable integer reference containing the next desired atom serial number
	transform	optional change to location and orientation of molecule

std::ostream& writePdb	(	const State &	state,
		std::ostream &	os,
		const Transform &	transform = `Transform()`
	)			const

Write the dynamic Compound configuration in Protein Data Bank (PDB) format.

Starting with the first atom's serial number as one(1).

Parameters:

	state	simbody state representing the current configuration of the molecule
	os	output stream to write PDB coordinates to
	transform	optional change to location and orientation of molecule

Referenced by PeriodicPdbWriter::handleEvent().