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# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
TODO:
- See items in EditCommand_StructureList
"""
from utilities.Comparison import same_vals
from command_support.EditCommand_StructureList import EditCommand_StructureList
_superclass = EditCommand_StructureList
class DnaSegmentList(EditCommand_StructureList):
"""
DnaSegmentList class provides an object that acts as a self.struct object
for MultipleDnaSegmentResize_EditCommand. It maintains an internal list
of structures (self._structList) which it loops through while resizing
multiple segments at once.
"""
def getBasesPerTurn(self):
"""
Returns the bases per turn for the currentStucture
of self's editcommand.
"""
assert self.editCommand.currentStruct
return self.editCommand.currentStruct.getBasesPerTurn()
def getDuplexRise(self):
"""
Returns the duplex rise for the currentStucture
of self's editcommand.
"""
if self.editCommand.currentStruct:
return self.editCommand.currentStruct.getDuplexRise()
if not self._structList:
return 3.18
firstSegment = self._structList[0]
return firstSegment.getDuplexRise()
def getNumberOfBasePairs(self):
"""
Returns the number of bae pairs (basepairs) per turn for the
currentStucture of self's editcommand.
"""
if self.editCommand.currentStruct:
return self.editCommand.currentStruct.getNumberOfBasePairs()
if not self._structList:
return 0
firstSegment = self._structList[0]
return firstSegment.getNumberOfBasePairs()
def getAxisEndAtomAtPosition(self, position):
"""
Returns the axis end atom of the 'currentStruct' of self's editCommand,
at the given position.
Example:
If there are 4 Dnasegments being resized at the same time, the two
resize handles will be at the average end positions. When you resize
these segments using , for example , the right handle, it loops through
the individual segments to resize those. While doing these, it needs to
know the resize end axis atom. How to get that information? In
self.updateAverageEndPoints() (which is called earlier), we create
two lists for each end. Example: all end1 points are in
self.endPoint_1_list (including their average end point which is
self.end1) . So in this routine, we determine which of the list to
use based on <position> (which is either of the average end points
i.e. self.end1 or self.end2) and then check which of the endPoints
of the editCommand's currentStruct lies in this list.
@TODO: This method will be SLOW if there are large number of structures
being edited at once (i.e. large self._structList) . Needs revision.
Needs revision.
We can't use a dictionary because dict.key cant be a Vector object
(example dict[key] != ([1.0, 2.0, 3.0])) see the disabled code that
tried to use has_key of dict. Need to come up with a better search
algorithm.
"""
new_position = None
for end in (self.end1, self.end2):
if same_vals(position, end):
if same_vals(end, self.end1):
lst = self.endPoints_1
else:
lst = self.endPoints_2
for e in self.editCommand.currentStruct.getAxisEndPoints():
for pos in lst:
if same_vals(pos, e):
new_position = e
break
if new_position is not None:
break
##if e in lst:
##new_position = e
##break
##if self.endPointsDict.has_key(position):
##for end in self.editCommand.currentStruct.getAxisEndPoints():
##if end in self.endPointsDict[position]:
##new_position = end
##break
if new_position is not None:
return self.editCommand.currentStruct.getAxisEndAtomAtPosition(
new_position)
return None
def is_PAM3_DnaSegment(self):
"""
Returns True if all segments in self._structList are PAM3 dna segments
@see: DnaSegment.is_PAM3_DnaSegment()
"""
if not self._structList:
return False
for segment in self._structList:
if not segment.is_PAM3_DnaSegment():
return False
return True
def getOtherAxisEndAtom(self, atom_at_one_end):
"""
Returns the axis atom at the other end of the DnaSegment
The DnaSegment object being 'currentStruct' of self's editCommand.
"""
return self.editCommand.currentStruct.getOtherAxisEndAtom(
atom_at_one_end)
def getAxisEndAtoms(self):
"""
Returns the axis end atoms of the DnaSegment. The DnaSegment object
being 'currentStruct' of self's editCommand.
"""
if self.editCommand.currentStruct:
return self.editCommand.currentStruct.getAxisEndAtoms()
if not self._structList:
return None, None
#If there is no 'currentStruct' of self's editcommand, just return
#the axis end atoms of the first segment in the list as a fall back.
#(Caller should be careful in specifying currentStruct attr )
firstSegment = self._structList[0]
return firstSegment.getAxisEndAtoms()
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