#include <chain_handle.hh>
Inherits ChainBase.
Additional Inherited Members | |
 Protected Member Functions inherited from ChainBase | |
| GenericPropContainerImpl * | GpImpl () |
| const GenericPropContainerImpl * | GpImpl () 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 | ( | ) |
| ChainHandle | ( | const impl::ChainImplPtr & | impl | ) |
Member Function Documentation
| void Apply | ( | EntityVisitor & | visitor | ) |
Apply visitor.
- Parameters:
-
visitor is 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.
| 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.
- Warning:
- 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:
- EntityHandle::GetResidueCount()
| 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
@code
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:
- ResiduesBegin
| EntityView Select | ( | const Query & | q, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on a query object
- See also:
- Query
| EntityView Select | ( | const String & | query_string, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on query String.
- See also:
- Query
The documentation for this class was generated from the following file:
- stage/include/ost/mol/chain_handle.hh
