19 #ifndef OST_CHAIN_IMPL_HH
20 #define OST_CHAIN_IMPL_HH
22 #include <boost/enable_shared_from_this.hpp>
39 namespace ost {
namespace mol {
namespace impl {
43 public boost::enable_shared_from_this<ChainImpl>
146 return residue_list_;
162 const String& atom_name)
const;
201 int GetIndexForResNumInSequence(
const ResNum& number)
const;
207 std::list<Shift> shifts_;
ImageStateConstModOPAlgorithm< ShiftFnc > Shift
void Apply(EntityVisitor &v)
int GetBondCount() const
Get number of bonds of this chain.
EntityImplPtr GetEntity() const
ResidueImplPtr InsertResidueAfter(int index, const ResNum &n, const ResidueKey &k)
bool IsPolymer() const
whether the chain is a polymer
void SetInSequence(int index)
checks if the residue with that index breaks the in_sequence property and updates it accordingly ...
oligosaccharide (branched carbohydrate)
int GetAtomCount() const
Get number of atoms of this chain.
void SetType(const ChainType type)
Assign a type to a chain.
void DeleteResidue(const ResNum &number)
std::vector< ResidueImplPtr > ResidueImplList
geom::Vec3 GetCenterOfMass() const
ResidueImplPtr AppendResidue(const ResidueImplPtr &res, bool deep)
append new residue with exactly the same parameters as res, but no atoms and bonds ...
void AssignSecondaryStructure(SecStructure ss, const ResNum &start, const ResNum &end)
int GetResidueCount() const
Get number of residues of this chain.
geom::AlignedCuboid GetBounds() const
returns the axis-aligned bounding box of the entity
boost::shared_ptr< ResidueImpl > ResidueImplPtr
int GetIndexForResNum(const ResNum &number) const
void SetName(const String &new_name)
Secondary structure types as defined by DSSP. For convenience, the enum values match the characters u...
pointer_it< T > end(const std::vector< T > &values)
std::vector< ResNum > ResNumList
ResidueImplPtr InsertResidueBefore(int index, const ResNum &n, const ResidueKey &k)
ResidueImplPtr GetNext(const ResidueImplPtr &r) const
previous residue, not necessarily in sequence
int GetIndex(const ResidueImplPtr &res) const
void UpdateTransformedPos()
String GetDescription() const
Get information about a chain.
boost::shared_ptr< AtomImpl > AtomImplPtr
bool IsPolypeptide() const
whether the chain is a polypeptide
boost::shared_ptr< EntityImpl > EntityImplPtr
ResidueImplPtr FindResidue(const ResNum &number) const
Get residue by number. Returns a invalid pointer if the chain does not have any residue with this num...
Three dimensional vector class, using Real precision.
void SetDescription(const String desc)
Assign a description to a chain.
ResidueImplPtr GetPrev(const ResidueImplPtr &r) const
bool IsOligosaccharide() const
whether the chain is a polysaccharide
const ResidueImplList & GetResidueList() const
ResidueImplList & GetResidueList()
ChainImpl(const EntityImplPtr &e, const String &name)
AtomImplPtr FindAtom(const ResNum &number, const String &atom_name) const
bool IsPolysaccharide() const
whether the chain is a polysaccharide
base class for the implementation
bool IsPolynucleotide() const
whether the chain is a polynucleotide
bool InSequence() const
whether the residue numbers are in ascending order
polydeoxyribonucleotide/ -ribonucleotide hybrid
void RenumberAllResidues(int start, bool keep_spacing)
boost::weak_ptr< EntityImpl > EntityImplW
geom::Vec3 GetCenterOfAtoms() const
ChainType GetType() const
Get the type of a chain.