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OpenStructure
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OpenStructure
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#include <chain_handle.hh>
Inherits ChainBase.
Additional Inherited Members | |
 Protected Member Functions inherited from ChainBase | |
| GenericPropContainerImpl * | GpImpl () |
| const GenericPropContainerImpl * | GpImpl () const |
| void | CheckValidity () const |
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.
| ChainHandle | ( | ) |
| ChainHandle | ( | const impl::ChainImplPtr & | impl | ) |
| void Apply | ( | EntityVisitor & | visitor | ) |
Apply visitor.
| 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.
| 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.
| 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.
| EntityView Select | ( | const Query & | q, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on a query object
| EntityView Select | ( | const String & | query_string, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on query String.
| void SetInSequence | ( | const int | index | ) |
checks whether res breaks the in sequence property and updates it accordingly
1.8.1.1