ResidueHandle Class Reference

Residue handle. More...

#include <residue_handle.hh>

Inherits ost::mol::ResidueBase.

Public Member Functions
	ResidueHandle ()
	ResidueHandle (const impl::ResidueImplPtr &impl)
EntityHandle	GetEntity () const
AtomHandle	GetCentralAtom () const
geom::Vec3	GetCentralNormal () const
double	GetMass () const
geom::Vec3	GetCenterOfMass () const
geom::Vec3	GetCenterOfAtoms () const
geom::Vec3	GetGeometricCenter () const
geom::Vec3	GetGeometricStart () const
geom::Vec3	GetGeometricEnd () const
ChainHandle	GetChain () const
ResidueHandle	GetPrev () const
ResidueHandle	GetNext () const
AtomHandle	FindAtom (const String &aname) const
void	Apply (EntityVisitor &visitor)
AtomHandleList	GetAtomList () const
int	GetAtomCount () const
int	GetBondCount () const
TorsionHandle	FindTorsion (const String &torsion_name) const
TorsionHandleList	GetTorsionList () const
int	GetIndex () const
AtomHandleIter	AtomsBegin () const
ResidueHandle	GetHandle () const
unsigned long	GetHashCode () const
AtomHandleIter	AtomsEnd () const
EntityView	Select (const Query &q, QueryFlags flags=0) const
EntityView	Select (const String &query_string, QueryFlags flags=0) const
bool	operator== (const ResidueHandle &ref) const
bool	operator!= (const ResidueHandle &ref) const
Alternative atom positions
Alternative atom positions have traditionally been used to indicate that the position of an atom is not limited to one point, but that the atom may occur at more than one position. The following functions let you work with alternative atom locations on the level of residues.
bool	HasAltAtomGroup (const String &group) const
const String &	GetCurrentAltGroupName () const
std::vector< String >	GetAltAtomGroupNames () const
bool	HasAltAtoms () const
geom::Vec3	GetAltAtomPos (const AtomHandle &atom, const String &group) const
bool	SwitchAtomPos (const String &group)

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Detailed Description

Residue handle.

In a polymer a residue is a single unit such as a nucleotide or an amino acid. In case of ligands, a residue ofter represents a completye molecule, such as a HEM group.

Every residue belongs to a chain and has a defined position (GetIndex) in that chain. In a peptide chain, the previous (towards N-terminus) and next (towards C-terminus) can be obtained with GetPrev() and GetNext() respectively.

A residue consist of one or more atoms. The list of atoms can be retrieved with GetAtomList(), wheras FindAtom() will locate a particular atom in the residue.

To add atoms to the residue, you have to request an editor and call EditorBase::InsertAtom() or EditorBase::InsertAltAtom()

 XCSEditor edi=residue.GetEntity().RequestXCSEditor();
 edi.InsertAtom(residue, "CA", geom.Vec3(1.0, 0.0, 0.0));

Definition at line 54 of file residue_handle.hh.

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Constructor & Destructor Documentation

ResidueHandle

(

)

ResidueHandle

(

const impl::ResidueImplPtr &

impl

)

[inline]

Definition at line 58 of file residue_handle.hh.

---

Member Function Documentation

void Apply

(

EntityVisitor &

visitor

)

Apply entity visitor.

Parameters:

visitor

is the entity visitor to apply

See also:

EntityVisitor

AtomHandleIter AtomsBegin

(

)

const

Get iterator pointing to the beginning of the atoms.

Atom iterators are not fail-safe, meaning that when new atoms are inserted the iterators become invalid and the behaviour is undefined. To iterate over the residue while inserting/deleting atoms use GetAtomList().

See also:

AtomsEnd(), GetAtomList()

AtomHandleIter AtomsEnd

(

)

const

Get iterator pointing to the beginning of the atoms.

See also:

AtomsBegin(), GetAtomList()

AtomHandle FindAtom

(

const String &

aname

)

const

Find atom by name.

Parameters:

aname

is the atom name

TorsionHandle FindTorsion

(

const String &

torsion_name

)

const

Find torsion by name.

Note:

For the PHI, ISP and PSI torsions of the backbone use the designated GetPhiTorsion and GetPsiTorsion methods, respectively.

Parameters:

torsion_name

is the name of the torsion you are looking for. Torsions are named with uppercase letters.

Returns:

The torsion, or an invalid torsion handle if the residues does not have a torsion with the given name.

See also:

ResidueBase::GetPhiTorsion, ResidueBase::GetPsiTorsion

std::vector<String> GetAltAtomGroupNames

(

)

const

Get names of alternative atom groups.

geom::Vec3 GetAltAtomPos	(	const AtomHandle &	atom,
		const String &	group
	)			const

Get alternative atom position for given atom.

If the atom is not in group, an IntegrityError is thrown.

int GetAtomCount

(

)

const

Get number of atoms of this residue.

AtomHandleList GetAtomList

(

)

const

Get number of atoms of this residue.

See also:

ResidueHandle::GetAtomCount

int GetBondCount

(

)

const

Get number of bonds of this residue. This method might NOT work as expected (see warning below).

Warning:

For a bond between two different residues, it is not clearly defined to which residue it belongs. Therefore, this method works only correctly if the residue has NO bonds to any other residues!

geom::Vec3 GetCenterOfAtoms

(

)

const

Get entity's center of atoms (not mass weighted).

Returns the center of all the atoms in an entity. This is similar to GetCenterOfMass(), but the atoms are not mass weighted

geom::Vec3 GetCenterOfMass

(

)

const

Get entity's center of mass (mass weighted).

AtomHandle GetCentralAtom

(

)

const

returns main atom, ie CA for amino acids

geom::Vec3 GetCentralNormal

(

)

const

Returns:

return specific normal of residue, usually CA-CB dir for AA

ChainHandle GetChain

(

)

const

The chain this residue is attached to.

const String& GetCurrentAltGroupName

(

)

const

Name of active alternative atom group.

Returns:

The alternative atom group name or an empty String, if the atom does not have any alternative atoms.

EntityHandle GetEntity

(

)

const

geom::Vec3 GetGeometricCenter

(

)

const

Get entity's geometric center.

Returns the geometric center of the entity's bounding box by calculating (GetGeometricStart()+GetGeometricEnd())/2

geom::Vec3 GetGeometricEnd

(

)

const

Get entity's maximum cartesian coordinates.

geom::Vec3 GetGeometricStart

(

)

const

Get entity's minimum cartesian coordinates.

ResidueHandle GetHandle

(

)

const

get this handle

This method exists as a convenience duck-typing in Python.

unsigned long GetHashCode

(

)

const

int GetIndex

(

)

const

Get position of residue in chain.

double GetMass

(

)

const

Get entity's mass.

ResidueHandle GetNext

(

)

const

Get next residue in chain.

Returns:

Invalid handle, when there is no next residue.

ResidueHandle GetPrev

(

)

const

Get previous residue in chain.

Returns:

Invalid handle, when there is no previous residue.

TorsionHandleList GetTorsionList

(

)

const

Get list of all torsion angles of this residue.

bool HasAltAtomGroup

(

const String &

group

)

const

Test if residue has group of alternative atoms with a certain name.

bool HasAltAtoms

(

)

const

Test if the residue has any alternative atom positions.

bool operator!=

(

const ResidueHandle &

ref

)

const

bool operator==

(

const ResidueHandle &

ref

)

const

EntityView Select	(	const String &	query_string,
		QueryFlags	flags = 0
	)			const

return view based on query String.

See also:

Query

EntityView Select	(	const Query &	q,
		QueryFlags	flags = 0
	)			const

return view based on a query object

See also:

Query

bool SwitchAtomPos

(

const String &

group

)

switch atoms that have alternative positions to the position in the group. Atoms that do not have an alternative position are left untouched.

Parameters:

group

is the group name to switch to.

Returns:

True, if such a group exists, false if not.

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The documentation for this class was generated from the following file:

• stage/include/ost/mol/residue_handle.hh