ChainImpl Class Reference

#include <chain_impl.hh>

Inherits ost::GenericPropContainerImpl.

Data Structures

struct  Shift

Public Member Functions

 ChainImpl (const EntityImplPtr &e, const String &name)
void SetName (const String &new_name)
String GetName () const
void SetType (const ChainType type)
ChainType GetType () const
bool IsPolymer () const
bool IsPolysaccharide () const
bool IsPolypeptide () const
bool IsPolynucleotide () const
void SetDescription (const String desc)
String GetDescription () const
ResidueImplPtr AppendResidue (const ResidueImplPtr &res, bool deep)
ResidueImplPtr InsertResidueBefore (int index, const ResNum &n, const ResidueKey &k)
ResidueImplPtr InsertResidueAfter (int index, const ResNum &n, const ResidueKey &k)
ResidueImplPtr AppendResidue (const ResidueKey &k)
ResidueImplPtr AppendResidue (const ResidueKey &k, const ResNum &n)
ResidueImplPtr GetPrev (const ResidueImplPtr &r) const
ResidueImplPtr GetNext (const ResidueImplPtr &r) const
const ResidueImplListGetResidueList () const
bool InSequence () const
ResidueImplListGetResidueList ()
Real GetMass () const
geom::Vec3 GetCenterOfMass () const
geom::Vec3 GetCenterOfAtoms () const
geom::AlignedCuboid GetBounds () const
ResidueImplPtr FindResidue (const ResNum &number) const
AtomImplPtr FindAtom (const ResNum &number, const String &atom_name) const
int GetResidueCount () const
int GetAtomCount () const
int GetBondCount () const
void Apply (EntityVisitor &v)
EntityImplPtr GetEntity () const
void DeleteResidue (const ResNum &number)
void DeleteResidue (const ResidueImplPtr &residue)
void DeleteAllResidues ()
void ReorderResidues ()
void RenumberAllResidues (int start, bool keep_spacing)
void RenumberAllResidues (const ResNumList &new_numbers)
int GetIndex (const ResidueImplPtr &res) const
void AssignSecondaryStructure (SecStructure ss, const ResNum &start, const ResNum &end)
int GetIndexForResNum (const ResNum &number) const
void SetInSequence (int index)
void UpdateTransformedPos ()

Detailed Description

Definition at line 42 of file chain_impl.hh.


Constructor & Destructor Documentation

ChainImpl ( const EntityImplPtr e,
const String name 
)

Member Function Documentation

ResidueImplPtr AppendResidue ( const ResidueKey k,
const ResNum n 
)

Append residue at end of chain.

ResidueImplPtr AppendResidue ( const ResidueKey k  ) 

Append residue at end of chain.

Residue number will be automatically set to last+1. The first residue will have the number 1. insertion code from a previous residue are copied.

ResidueImplPtr AppendResidue ( const ResidueImplPtr res,
bool  deep 
)

append new residue with exactly the same parameters as res, but no atoms and bonds

void Apply ( EntityVisitor v  ) 
void AssignSecondaryStructure ( SecStructure  ss,
const ResNum start,
const ResNum end 
)
void DeleteAllResidues (  ) 
void DeleteResidue ( const ResidueImplPtr residue  ) 
void DeleteResidue ( const ResNum number  ) 
AtomImplPtr FindAtom ( const ResNum number,
const String atom_name 
) const
ResidueImplPtr FindResidue ( const ResNum number  )  const

Get residue by number. Returns a invalid pointer if the chain does not have any residue with this number.

int GetAtomCount (  )  const

Get number of atoms of this chain.

int GetBondCount (  )  const

Get number of bonds of this chain.

geom::AlignedCuboid GetBounds (  )  const

returns the axis-aligned bounding box of the entity

geom::Vec3 GetCenterOfAtoms (  )  const
geom::Vec3 GetCenterOfMass (  )  const
String GetDescription (  )  const [inline]

Get information about a chain.

Returns:
description

Definition at line 103 of file chain_impl.hh.

EntityImplPtr GetEntity (  )  const
int GetIndex ( const ResidueImplPtr res  )  const
int GetIndexForResNum ( const ResNum number  )  const
Real GetMass (  )  const
String GetName (  )  const
ResidueImplPtr GetNext ( const ResidueImplPtr r  )  const

previous residue, not necessarily in sequence

ResidueImplPtr GetPrev ( const ResidueImplPtr r  )  const
int GetResidueCount (  )  const

Get number of residues of this chain.

ResidueImplList& GetResidueList (  )  [inline]

Definition at line 138 of file chain_impl.hh.

const ResidueImplList& GetResidueList (  )  const
ChainType GetType (  )  const [inline]

Get the type of a chain.

Returns:
chain type of ChainType

Definition at line 62 of file chain_impl.hh.

bool InSequence (  )  const

whether the residue numbers are in ascending order

ResidueImplPtr InsertResidueAfter ( int  index,
const ResNum n,
const ResidueKey k 
)
ResidueImplPtr InsertResidueBefore ( int  index,
const ResNum n,
const ResidueKey k 
)
bool IsPolymer (  )  const [inline]

whether the chain is a polymer

Definition at line 68 of file chain_impl.hh.

bool IsPolynucleotide (  )  const [inline]

whether the chain is a polynucleotide

Definition at line 86 of file chain_impl.hh.

bool IsPolypeptide (  )  const [inline]

whether the chain is a polypeptide

Definition at line 80 of file chain_impl.hh.

bool IsPolysaccharide (  )  const [inline]

whether the chain is a polysaccharide

Definition at line 75 of file chain_impl.hh.

void RenumberAllResidues ( const ResNumList new_numbers  ) 
void RenumberAllResidues ( int  start,
bool  keep_spacing 
)
void ReorderResidues (  ) 
void SetDescription ( const String  desc  )  [inline]

Assign a description to a chain.

Parameters:
desc description

Definition at line 95 of file chain_impl.hh.

void SetInSequence ( int  index  ) 

checks if the residue with that index breaks the in_sequence property and updates it accordingly

void SetName ( const String new_name  ) 
void SetType ( const ChainType  type  )  [inline]

Assign a type to a chain.

Parameters:
type chain type of ChainType

Definition at line 54 of file chain_impl.hh.

void UpdateTransformedPos (  ) 

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