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__init__(self,
elements,
name='',
alphabet=None,
origin=None,
entry_id='',
chain='',
unknown_res_type='X',
gap_chars=('~'))
Make a sequence object from a list of strings, using a mapping of
strings to element types. |
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__add__(self,
other)
TODO: Do this properly |
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_makeSeqElements(self,
elements)
Return a list of elements converted to proper sequence items |
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Sequence
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getSubsequence(self,
start,
end)
Return a sequence containing a subset of the elements in this one |
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setName(self,
name)
Set the name on the instance and emit a notification |
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bool
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hasVisibleResidues(self)
Returns True if any residues in the sequence are set to be visible,
False otherwise. |
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get(self,
index,
annotation=None)
Returns the item at the specified index. |
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index(self,
res)
Returns the index of the specified residue; raises ValueError if not
present |
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list
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getGaps(self)
Returns:
The indices of gaps in the sequence, if any |
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list of (object, int)
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getGapsByKeyFunc(self,
key_func)
Given a key function to reidentify residues, build a list of tuples
with gap information. |
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list of int
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getGapIndicesByKeyFunc(self,
gap_info,
key_func)
Converts a gap_info list and key func into a list of gap indices |
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_addGaps(self,
gaps)
Add gaps to the sequence from a list of gap indices |
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int
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getNumResidues(self)
Return the number of residues in the sequence, that is, the length of
the sequence without gaps |
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addGaps(self,
gaps)
Add gaps to the sequence at the specified indices |
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setGaps(self,
gaps)
Sets gaps on the sequence from a list of gap indices, relative to the
ungapped sequence |
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| _validateGapRemoval(self,
gaps) |
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removeGaps(self,
gaps)
Removes the specified gaps from the sequence |
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_removeAllGaps(self)
Remove gaps from the sequence |
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removeAllGaps(self)
Remove gaps from the sequence |
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insert(self,
index,
elements)
Insert a list of elements or sequence element into this sequence |
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mutate(self,
start,
end,
elements)
Mutate sequence elements starting at the given index to the provided
elements |
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remove(self,
start,
end=None)
Removes elements from the sequence from the index start and returns
the removed elements as a new sequence |
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append(self,
element)
Appends an element to the sequence |
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extend(self,
elements)
Extends the sequence with elements from a list |
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removeFromSequence(self,
filter_func,
start=0,
end=None)
Remove any residues matching the specified filter_func from the
sequence |
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sanitize(self,
start=0,
end=None)
Remove gaps and unknown sequence elements from sequence |
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float
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_getScore(self,
scoring_function,
reference,
consider_gaps=True)
Return a float scoring between the sequence and a reference sequence,
assuming that they're already aligned, calculated using provided
scoring_function method of Residue class. |
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float
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getIdentity(self,
reference,
consider_gaps=True)
Return a float scoring the identity between the sequence and a
reference sequence, assuming that they're already aligned |
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float
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getSimilarity(self,
reference,
consider_gaps=True)
Return a float score of the similarity count between the sequence and
a reference sequence, assuming that they're already aligned |
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float
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getHomology(self,
reference,
consider_gaps=True)
Return a float scoring the homology between the sequence and a
reference sequence, assuming that they're already aligned |
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float
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getSimilarityScore(self,
reference)
Return the total score of similarity between the sequence and a
reference sequence, assuming that they're already aligned. |
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int or None
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getNextResidueIndex(self,
index)
Return the index of the next residue in the sequence (ignoring gaps)
or None if there is none |
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schrodinginer.application.msv.domain.residue.Residue
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getNextResidue(self,
index)
Return the next residue in the sequence (ignoring gaps) or None if
there is none |
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int or None
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getPreviousResidueIndex(self,
index)
Return the index of the previous residue in the sequence (ignoring
gaps) or None if there is none |
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schrodinginer.application.msv.domain.residue.Residue
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getPreviousResidue(self,
index)
Return the next residue in the sequence (ignoring gaps) or None if
there is none |
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iter
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iterNeighbors(self)
Return an iterable of three element tuples consisting of (prev_res,
curr_res, next_res), ignoring gaps. |
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_updateSSAPositions(self,
_1,
_2)
Updates the stored indices of start and end positions of secondary
structure assignment blocks in the sequence. |
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int or None
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getSSAPosType(self,
index)
Return whether the residue at the specified index is at the start,
middle or end of a secondary structure block. |
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bool
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hasEntryID(self)
Return whether or not this sequence has an associated Entry ID in the
Project Table. |
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Inherited from Qt.QtCore.QObject:
connect,
emit
Inherited from PyQt4.QtCore.QObject:
__getattr__,
blockSignals,
childEvent,
children,
connectNotify,
customEvent,
deleteLater,
destroyed,
disconnect,
disconnectNotify,
dumpObjectInfo,
dumpObjectTree,
dynamicPropertyNames,
event,
eventFilter,
findChild,
findChildren,
inherits,
installEventFilter,
isWidgetType,
killTimer,
metaObject,
moveToThread,
objectName,
parent,
property,
pyqtConfigure,
receivers,
removeEventFilter,
sender,
senderSignalIndex,
setObjectName,
setParent,
setProperty,
signalsBlocked,
startTimer,
thread,
timerEvent,
tr,
trUtf8
Inherited from sip.simplewrapper:
__new__
Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__reduce__,
__reduce_ex__,
__setattr__,
__sizeof__,
__subclasshook__
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