OpenStructure
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#include <sequence_impl.hh>
Inherits GenericPropContainerImpl.
Public Member Functions | |
int | GetResidueIndex (int pos) const |
int | GetPos (int residue_index) const |
int | GetFirstNonGap () const |
int | GetLastNonGap () const |
const String & | GetName () const |
void | SetName (const String &name) |
void | Cut (int start, int n) |
void | ShiftRegion (int start, int end, int amount) |
const String & | GetString () const |
void | SetString (const String &seq) |
void | Normalise () |
void | Replace (const String &str, int start, int end) |
String | GetGaplessString () const |
int | GetOffset () const |
int | GetIndex (const String &substr) const |
void | SetOffset (int offset) |
int | GetLength () const |
SequenceImpl (const String &seq_name, const String &sequence_string, const String &role) | |
char | GetOneLetterCode (int position) const |
void | SetOneLetterCode (int position, char new_char) |
mol::ResidueView | GetResidue (int position) const |
mol::EntityView | GetAttachedView () const |
void | AttachView (const mol::EntityView &view) |
SequenceImplPtr | Copy () const |
void | AttachView (const mol::EntityView &view, const String &chain_name) |
bool | HasAttachedView () const |
void | Append (char olc) |
char & | operator[] (size_t index) |
char | operator[] (size_t index) const |
const String & | GetRole () const |
void | SetRole (const String &role) |
Public Member Functions inherited from GenericPropContainerImpl | |
GenericPropContainerImpl () | |
~GenericPropContainerImpl () | |
GenericPropContainerImpl (const GenericPropContainerImpl &rhs) | |
GenericPropContainerImpl & | operator= (const GenericPropContainerImpl &r) |
GenericPropValue & | GenericProp (const String &key) |
const GenericPropValue & | GenericProp (const String &key) const |
bool | HasProp (const String &key) const |
void | ClearProps () |
void | RemoveProp (const String &key) |
void | Assign (const GenericPropContainerImpl &impl) |
PropertyMap | GetPropMap () const |
std::vector< String > | GetPropList () const |
Static Public Member Functions | |
static SequenceImplPtr | FromString (const String &seq_name, const String &sequence_string, const String &role="UNKNOWN") |
Definition at line 49 of file sequence_impl.hh.
SequenceImpl | ( | const String & | seq_name, |
const String & | sequence_string, | ||
const String & | role | ||
) |
Construct new sequence object from sequence_string.
If you want to check whether the sequence String does only contain valid characters use CreateSequence
instead.
void Append | ( | char | olc | ) |
void AttachView | ( | const mol::EntityView & | view | ) |
attach entity view to sequence
IntegrityError | when the view contains more than one chain |
void AttachView | ( | const mol::EntityView & | view, |
const String & | chain_name | ||
) |
attach entity view to sequence
The sequence is mapped onto the chain with given name
SequenceImplPtr Copy | ( | ) | const |
create copy sequence
The newly created sequence has the same attached view.
void Cut | ( | int | start, |
int | n | ||
) |
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static |
Construct new sequence object from sequence_string.
mol::EntityView GetAttachedView | ( | ) | const |
get attached view. may be an invalid entity view
int GetFirstNonGap | ( | ) | const |
Get position of first non-gap character in sequence.
String GetGaplessString | ( | ) | const |
Get sequence as String ignoring gaps.
int GetIndex | ( | const String & | substr | ) | const |
int GetLastNonGap | ( | ) | const |
Get position of last non-gap character in sequence.
int GetLength | ( | ) | const |
Get lenght of sequence, including gaps.
const String& GetName | ( | ) | const |
int GetOffset | ( | ) | const |
Get sequence offset from N-terminus.
char GetOneLetterCode | ( | int | position | ) | const |
get one letter code of residue at position
int GetPos | ( | int | residue_index | ) | const |
Get zero-based index for given residue number.
out_of_range,if | number is not included in sequence. |
mol::ResidueView GetResidue | ( | int | position | ) | const |
get residue at position
will return the residue view at the given sequence position or an invalid residue view when no view is attached, the index is out of bounds or the position contains a gap.
int GetResidueIndex | ( | int | pos | ) | const |
Get residue index corresponding to given sequence position.
pos | zero-based index |
out_of_range | if pos is not in [0, length-1]. |
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inline |
Definition at line 156 of file sequence_impl.hh.
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inline |
Definition at line 78 of file sequence_impl.hh.
bool HasAttachedView | ( | ) | const |
whether the sequence has an attached view
void Normalise | ( | ) |
Remove everything 'unusual' from sequence.
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inline |
Definition at line 148 of file sequence_impl.hh.
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inline |
Definition at line 152 of file sequence_impl.hh.
void Replace | ( | const String & | str, |
int | start, | ||
int | end | ||
) |
replace substring starting from start to end
void SetName | ( | const String & | name | ) |
void SetOffset | ( | int | offset | ) |
Set sequence offset.
By default the sequence offset is zero, i.e. the beginning of the sequence lies exactly at the N-terminus. Setting the sequence offset to a positive number will shift the sequence towards the C-terminus.
void SetOneLetterCode | ( | int | position, |
char | new_char | ||
) |
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inline |
Definition at line 161 of file sequence_impl.hh.
void SetString | ( | const String & | seq | ) |
Set sequence String.
void ShiftRegion | ( | int | start, |
int | end, | ||
int | amount | ||
) |