Public Member Functions
ChainHandle Class Reference

#include <chain_handle.hh>

Inherits ChainBase.

Public Member Functions

 ChainHandle ()
 ChainHandle (const impl::ChainImplPtr &impl)
EntityHandle GetEntity () const
void Apply (EntityVisitor &visitor)
ResidueHandle GetPrev (const ResidueHandle &rh)
ResidueHandle GetNext (const ResidueHandle &rh)
int GetAtomCount () const
int GetBondCount () const
int GetResidueCount () const
AtomHandleList GetAtomList () const
ResidueHandleList GetResidueList () const
ResidueHandleIter ResiduesBegin () const
ResidueHandleIter ResiduesEnd () const
AtomHandleIter AtomsBegin () const
AtomHandleIter AtomsEnd () const
Real GetMass () const
geom::Vec3 GetCenterOfMass () const
geom::Vec3 GetCenterOfAtoms () const
geom::AlignedCuboid GetBounds () const
void AssignSecondaryStructure (SecStructure ss, const ResNum &start, const ResNum &end)
EntityView Select (const Query &q, QueryFlags flags=0) const
EntityView Select (const String &query_string, QueryFlags flags=0) const
ChainHandle GetHandle () const
bool InSequence () const
bool operator== (const ChainHandle &ref) const
bool operator!= (const ChainHandle &ref) const
Single item addressing
ResidueHandle FindResidue (const ResNum &num) const
AtomHandle FindAtom (const ResNum &num, const String &atom_name) const
ResidueHandle GetResidueByIndex (int index) const
- Public Member Functions inherited from ChainBase
 ChainBase ()
 ChainBase (const impl::ChainImplPtr &impl)
String GetName () const
const impl::ChainImplPtrImpl () const
impl::ChainImplPtrImpl ()
 operator bool () const
bool IsValid () const
- Public Member Functions inherited from GenericPropContainer< ChainBase >
void ClearProps ()
void SetStringProp (const String &key, const String &value)
void SetFloatProp (const String &key, Real value)
void SetIntProp (const String &key, int value)
void SetBoolProp (const String &key, bool value)
void RemoveProp (const String &key)
- Public Member Functions inherited from ConstGenericPropContainer< ChainBase >
bool HasProp (const String &key) const
String GetPropAsString (const String &key) const
String GetStringProp (const String &key) const
String GetStringProp (const String &key, const String &def) const
Real GetFloatProp (const String &key) const
Real GetFloatProp (const String &key, Real def) const
int GetIntProp (const String &key) const
int GetIntProp (const String &key, int def) const
bool GetBoolProp (const String &key) const
bool GetBoolProp (const String &key, bool def) const
std::map< String,
GetPropMap () const
std::vector< StringGetPropList () const

Additional Inherited Members

- Protected Member Functions inherited from ChainBase
GenericPropContainerImplGpImpl ()
const GenericPropContainerImplGpImpl () const
void CheckValidity () const

Detailed Description

linear chain of residues

In peptide chain, the residues are ordered from N- to C-terminus. To obtain the n-th residue in the chain, use GetResidueByIndex. Alternatively, the residues may be adressed by their residue number with FindResidue. Residue numbers are unique within a chain. It is however not guaranteed that the residue numbers are in ascending order.

New residues are inserted via one of the editors obtained from EntityHandle::EditXCS() or EntityHandle::EditICS(). To append a residue to the C-terminal end, use EditorBase::AppendResidue, to insert after or before a specific residue, EditorBase::InsertResidueAfter and ditorBase::InsertResidueABefore will do the job, respectively.

Definition at line 53 of file chain_handle.hh.

Constructor & Destructor Documentation

ChainHandle ( const impl::ChainImplPtr impl)

Member Function Documentation

void Apply ( EntityVisitor visitor)

Apply visitor.

visitoris the visitor to apply
void AssignSecondaryStructure ( SecStructure  ss,
const ResNum start,
const ResNum end 

assign secondary structure to the inclusive residue range start, end

AtomHandleIter AtomsBegin ( ) const
AtomHandleIter AtomsEnd ( ) const
AtomHandle FindAtom ( const ResNum num,
const String atom_name 
) const
ResidueHandle FindResidue ( const ResNum num) const

Find residue by number. If the chain does not contain a residue with the given number, an invalid ResidueHandle will be returned.

See also:
ResidueBase::IsValid, FindAtom, EntityHandle::FindResidue
int GetAtomCount ( ) const

Get number of atoms of this chain.

AtomHandleList GetAtomList ( ) const

Retrieve atoms of this chain as a list.

The atoms are ordered by atom number in ascending order. If you only want to determine the number of atoms, use the dedicated ChainHandle::GetAtomCount

int GetBondCount ( ) const

Get number of all inclusive bonds of this chain.

For a bond between two different chains, it is not clearly defined to which chain it belongs. Therefore, this method will only return the number of bonds where both bonded atoms are within the same chain (all inclusive bonds).
geom::AlignedCuboid GetBounds ( ) const
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)

EntityHandle GetEntity ( ) const

Get parent entity.

ChainHandle GetHandle ( ) const

get this handle

Useful for duck-typing in Python and in templates

Real GetMass ( ) const

Get entity's mass.

ResidueHandle GetNext ( const ResidueHandle rh)
ResidueHandle GetPrev ( const ResidueHandle rh)

Get residue before the given residue.

A previous residue is returned regardless whether the residues are connected by a bond.

ResidueHandle GetResidueByIndex ( int  index) const

Get residue by index.

Indices are start at zero

int GetResidueCount ( ) const

Get number of residues of this chain.

See also:
ResidueHandleList GetResidueList ( ) const

Get residues of this chain as a list.

The residues are ordered by residue number in ascending order. If you only want to determine the number of residues, use the dedicated ChainHandle::GetResidueCount

bool InSequence ( ) const

whether the residues form an ordered sequence with respect to their reside numbers.

bool operator!= ( const ChainHandle ref) const
bool operator== ( const ChainHandle ref) const
ResidueHandleIter ResiduesBegin ( ) const

Get iterator pointing to begin of residues.

 \note   Iterators are not fail-safe, meaning that the behaviour is
         undefined when using a ResidueHandleIter and residues are inserted
         or removed from the chain

ResidueHandleIter res_it=chain.ResiduesBegin(), res_end=chain.ResiduesEnd(); for (; res_it!=res_end; ++res_it) { ResidueHandle res=*res_it; // do something with residue }

ResidueHandleIter ResiduesEnd ( ) const

Get iterator pointing to the end of the residues.

See also:
EntityView Select ( const Query q,
QueryFlags  flags = 0 
) const

return view based on a query object

See also:
EntityView Select ( const String query_string,
QueryFlags  flags = 0 
) const

return view based on query String.

See also:

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