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 ResidueImplList & | GetResidueList () const |
bool | InSequence () const |
ResidueImplList & | GetResidueList () |
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
Member Function Documentation
Append residue at end of chain.
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.
append new residue with exactly the same parameters as res, but no atoms and bonds
void DeleteAllResidues |
( |
|
) |
|
void DeleteResidue |
( |
const ResNum & |
number |
) |
|
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.
returns the axis-aligned bounding box of the entity
String GetDescription |
( |
|
) |
const [inline] |
Get information about a chain.
- Returns:
- description
Definition at line 103 of file chain_impl.hh.
int GetIndexForResNum |
( |
const ResNum & |
number |
) |
const |
previous residue, not necessarily in sequence
int GetResidueCount |
( |
|
) |
const |
Get number of residues of this chain.
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
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 SetDescription |
( |
const String |
desc |
) |
[inline] |
Assign a description to a chain.
- Parameters:
-
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: