This is the class used to perform the structural alignment. This class
will check at initialization time if Prime is installed by trying to
import schrodinger.applications.ska and will fail if it's not installed
as nothing more can be done.
There are a number of properties that can be set for instances of this
class which are used to control how the alignment is done:
gap_penalty - default = 2.0 deletion_penalty = default = 1.0
use_scanning_alignment - default = False window_length - default = 5
minimum_similarity - default = 1.0 minimum_length - default = 2
use_automatic_settings - default = False use_standard_residues - default
= False reorder_by_connectivity - default = False
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__init__(self)
Construct an instance of a StructAlign object. |
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| _setGapPenalty(self,
penalty) |
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| _setDeletionPenalty(self,
penalty) |
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| _getDeletionPenalty(self) |
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| _setUseScanningAlignment(self,
scanning_alignment) |
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| _getUseScanningAlignment(self) |
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| _setWindowLength(self,
length) |
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| _setMinimumSimilarity(self,
min_sim) |
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| _getMinimumSimilarity(self) |
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| _setMinimumLength(self,
min_length) |
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align(self,
ref_st,
sts)
Perform a structural alignment on the Structure objects in the list
'sts' relative to the reference structure 'ref_st' Each structure in
the list is aligned relative to the reference structure. |
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alignStructure(self,
ref_st,
mob_st)
Perform a structural alignment on the mob_st structure relative to
the ref_st structure. |
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Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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