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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PeptideGroup.py - ...
@author: Bruce, Mark
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from foundation.Group import Group
from utilities.constants import gensym
from utilities.icon_utilities import imagename_to_pixmap
from utilities import debug_flags
from utilities.debug import print_compact_stack
class PeptideGroup(Group):
"""
Model object which packages together some Dna Segments, Dna Strands,
and other objects needed to represent all their PAM atoms and markers.
Specific kinds of Group member contents include:
- PeptideSegments (optionally inside Groups)
- Groups (someday might be called Blocks when they occur in this context;
note that class Block is deprecated and should not be used for these)
- DnaMarkers (a kind of Jig, always inside an owning PeptideSegment)
As other attributes:
- whatever other properties the user needs to assign, which are not
covered by the member nodes or superclass attributes. [nim?]
"""
# This should be a tuple of classifications that appear in
# files_mmp._GROUP_CLASSIFICATIONS, most general first.
# See comment in class Group for more info. [bruce 080115]
_mmp_group_classifications = ('PeptideGroup',)
# Open/closed state of the Dna Group in the Model Tree --
# default closed.
open = False
autodelete_when_empty = True
# (but only if current command permits that for this class --
# see comment near Group.autodelete_when_empty for more info,
# and implems of Command.keep_empty_group)
def node_icon(self, display_prefs):
"""
Model Tree node icon for the Peptide group node
@see: Group.all_content_is_hidden()
"""
open = display_prefs.get('open', False)
if open:
if self.all_content_is_hidden():
return imagename_to_pixmap("modeltree/PeptideGroup-expanded-hide.png")
else:
return imagename_to_pixmap("modeltree/PeptideGroup-expanded.png")
else:
if self.all_content_is_hidden():
return imagename_to_pixmap("modeltree/PeptideGroup-collapsed-hide.png")
else:
return imagename_to_pixmap("modeltree/PeptideGroup-collapsed.png")
# Note: some methods below this point are examples or experiments or stubs,
# and are likely to be revised significantly or replaced.
# [bruce 080115 comment]
# example method:
def getSegments(self):
"""
Return a list of all our PeptideSegment objects.
"""
return self.get_topmost_subnodes_of_class(self.assy.PeptideSegment)
def isEmpty(self):
"""
Returns True if there are no Peptide chunks as its members
(Returns True even when there are empty PeptideSegment objects inside)
@see: InsertPeptide_EditCommand._finalizeStructure where this test is used.
"""
#May be for the short term, we can use self.getAtomList()? But that
#doesn't ensure if the DnaGroup always has atom of type either
#'strand' or 'axis' .
if len(self.getSegments()) == 0:
return True
else:
return False
def addSegment(self, segment):
"""
Adds a new segment object for this dnaGroup.
@param segment: The PeptideSegment to be added to this PeptideGroup object
@type: B{PeptideSegment}
"""
self.addchild(segment)
def getProps(self):
"""
Method to support Dna duplex editing. see Group.__init__ for
a comment
THIS IS THE DEFAULT IMPLEMENTATION. TO BE MODIFIED
"""
#Should it supply the Dna Segment list (children) and then add
#individual segments when setProps is called??
# [probably not; see B&N email discussion from when this comment was added]
if self.editCommand:
props = ()
return props
def setProps(self, props):
"""
Method to support Dna duplex editing. see Group.__init__ for
a comment
THIS IS THE DEFAULT IMPLEMENTATION. TO BE MODIFIED
"""
#Should it accept the Dna Segment list and then add individual segments?
pass
def edit(self):
"""
@see: Group.edit()
"""
commandSequencer = self.assy.w.commandSequencer
commandSequencer.userEnterCommand('BUILD_Peptide', always_update = True)
currentCommand = commandSequencer.currentCommand
assert currentCommand.commandName == 'BUILD_Peptide'
currentCommand.editStructure(self)
def getSelectedSegments(self):
"""
Returns a list of segments whose all members are selected.
@return: A list containing the selected strand objects
within self.
@rtype: list
"""
#TODO: This is a TEMPORARY KLUDGE until Dna model is fully functional.
#Must be revised. Basically it returns a list of PeptideSegments whose
#all members are selected.
#See BuildDna_PropertyManager._currentSelectionParams() where it is used
#-- Ninad 2008-01-18
segmentList = self.getSegments()
selectedSegmentList = []
for segment in segmentList:
pickedNodes = []
unpickedNodes = []
def func(node):
if isinstance(node, self.assy.Chunk):
if not node.picked:
unpickedNodes.append(node)
else:
pickedNodes.append(node)
segment.apply2all(func)
if len(unpickedNodes) == 0 and pickedNodes:
selectedSegmentList.append(segment)
return selectedSegmentList
def getAtomList(self):
"""
Return a list of all atoms contained within this PeptideGroup
"""
atomList = []
def func(node):
if isinstance(node, self.assy.Chunk):
atomList.extend(node.atoms.itervalues())
self.apply2all(func)
return atomList
def draw_highlighted(self, glpane, color):
"""
Draw the Peptide segment chunks as highlighted. (Calls the related
methods in the chunk class)
@param: GLPane object
@param color: The highlight color
@see: Chunk.draw_highlighted()
@see: SelectChunks_GraphicsMode.draw_highlightedChunk()
@see: SelectChunks_GraphicsMode._get_objects_to_highlight()
"""
for c in self.getSegments():
c.draw_highlighted(glpane, color)
pass # end of class PeptideGroup
# ==
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