class PeptideSegment(LeafLikeGroup):
"""
Model object which represents a Peptide Segment inside a Peptide Group.
Internally, this is just a specialized Group containing a single chunk,
itself containing all the atoms of a Peptide.
"""
# 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 = ('PeptideSegment',)
Peptide = None
_endPoint1 = None
_endPoint2 = None
# TODO: undo or copy code for those attrs,
# and updating them when the underlying structure changes.
# But maybe that won't be needed, if they are replaced
# by computing them from the atom geometry as needed.
# [bruce 080227 comment]
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)
iconPath = "ui/modeltree/PeptideSegment.png"
hide_iconPath = "ui/modeltree/PeptideSegment-hide.png"
def writemmp_other_info_opengroup(self, mapping): #bruce 080507 refactoring
"""
"""
#bruce 080507 refactoring (split this out of Group.writemmp)
# (I think the following condition is always true, but I didn't
# prove this just now, so I left in the test for now.)
encoded_classifications = self._encoded_classifications()
if encoded_classifications == "PeptideSegment":
# This is a Peptide segment, so write the parameters into an info
# record so we can read and restore them in the next session.
# --Mark 2008-04-12
assert self.Peptide
mapping.write("info opengroup Peptide-parameters = %d, %d, %s, %s\n" \
% (self.Peptide.getChiralityN(),
self.Peptide.getChiralityM(),
self.Peptide.getType(),
self.Peptide.getEndings()))
pass
return
def readmmp_info_opengroup_setitem( self, key, val, interp ):
"""
[extends superclass method]
"""
#bruce 080507 refactoring (split this out of the superclass method)
if key == ['Peptide-parameters']:
# val includes all the parameters, separated by commas.
n, m, type, endings = val.split(",")
self.n = int(n)
self.m = int(m)
self.type = type.lstrip()
self.endings = endings.lstrip()
# Create the Peptide.
from cnt.model.Peptide import Peptide
self.Peptide = Peptide() # Returns a 5x5 CNT.
self.Peptide.setChirality(self.n, self.m)
self.Peptide.setType(self.type)
self.Peptide.setEndings(self.endings)
# The endpoints are recomputed every time it is edited.
else:
_superclass.readmmp_info_opengroup_setitem( self, key, val, interp)
return
def edit(self):
"""
Edit this PeptideSegment.
@see: PeptideSegment_EditCommand
"""
commandSequencer = self.assy.w.commandSequencer
commandSequencer.userEnterCommand('Peptide_SEGMENT')
assert commandSequencer.currentCommand.commandName == 'Peptide_SEGMENT'
commandSequencer.currentCommand.editStructure(self)
def getAxisVector(self, atomAtVectorOrigin = None):
"""
Returns the unit axis vector of the segment (vector between two axis
end points)
"""
# REVIEW: use common code for this method? [bruce 081217 comment]
endPoint1, endPoint2 = self.Peptide.getEndPoints()
if endPoint1 is None or endPoint2 is None:
return V(0, 0, 0)
#@see: RotateAboutAPoint command. The following code is disabled
#as it has bugs (not debugged but could be in
#self.Peptide.getEndPoints). So, rotate about a point won't work for
#rotating a Peptide. -- Ninad 2008-05-13
##if atomAtVectorOrigin is not None:
###If atomAtVectorOrigin is specified, we will return a vector that
###starts at this atom and ends at endPoint1 or endPoint2 .
###Which endPoint to choose will be dicided by the distance between
###atomAtVectorOrigin and the respective endPoints. (will choose the
###frthest endPoint
##origin = atomAtVectorOrigin.posn()
##if vlen(endPoint2 - origin ) > vlen(endPoint1 - origin):
##return norm(endPoint2 - endPoint1)
##else:
##return norm(endPoint1 - endPoint2)
return norm(endPoint2 - endPoint1)
def setProps(self, props):
"""
Sets some properties. These will be used while editing the structure.
(but if the structure is read from an mmp file, this won't work. As a
fall back, it returns some constant values)
@see: InsertPeptide_EditCommand.createStructure which calls this method.
@see: self.getProps, PeptideSegment_EditCommand.editStructure
"""
(_n, _m), _type, _endings, (_endPoint1, _endPoint2) = props
from cnt.model.Peptide import Peptide
self.Peptide = Peptide()
self.Peptide.setChirality(_n, _m)
self.Peptide.setType(_type)
self.Peptide.setEndings(_endings)
self.Peptide.setEndPoints(_endPoint1, _endPoint2)
def getProps(self):
"""
Returns Peptide parameters necessary for editing.
@see: PeptideSegment_EditCommand.editStructure where it is used.
@see: PeptideSegment_PropertyManager.getParameters
@see: PeptideSegmentEditCommand._createStructure
"""
# Recompute the endpoints in case this Peptide was read from
# MMP file (which means this Peptide doesn't have endpoint
# parameters yet).
self.Peptide.computeEndPointsFromChunk(self.members[0])
return self.Peptide.getParameters()
def getPeptideGroup(self):
"""
Return the PeptideGroup we are contained in, or None if we're not
inside one.
"""
return self.parent_node_of_class( self.assy.PeptideGroup)
def isAncestorOf(self, obj):
"""
Checks whether the object <obj> is contained within the PeptideSegment
Example: If the object is an Atom, it checks whether the
atom's chunk is a member of this PeptideSegment (chunk.dad is self)
It also considers all the logical contents of the PeptideSegment to determine
whether self is an ancestor. (returns True even for logical contents)
@see: self.get_all_content_chunks()
@see: PeptideSegment_GraphicsMode.leftDrag
"""
# see my comments in the NanotubeSegment version [bruce 081217]
c = None
if isinstance(obj, Atom):
c = obj.molecule
elif isinstance(obj, Bond):
chunk1 = obj.atom1.molecule
chunk2 = obj.atom1.molecule
if chunk1 is chunk2:
c = chunk1
elif isinstance(obj, Chunk):
c = obj
if c is not None:
if c in self.get_all_content_chunks():
return True
#NOTE: Need to check if the isinstance checks are acceptable (apparently
#don't add any import cycle)
if isinstance(obj, Atom):
chunk = obj.molecule
if chunk.dad is self:
return True
else:
return False
elif isinstance(obj, Bond):
chunk1 = obj.atom1.molecule
chunk2 = obj.atom1.molecule
if (chunk1.dad is self) or (chunk2.dad is self):
return True
elif isinstance(obj, Chunk):
if obj.dad is self:
return True
return False
def node_icon(self, display_prefs):
# REVIEW: use common code for this method? [bruce 081217 comment]
del display_prefs
if self.all_content_is_hidden():
return imagename_to_pixmap( self.hide_iconPath)
else:
return imagename_to_pixmap( self.iconPath)
def permit_as_member(self, node, pre_updaters = True, **opts):
"""
[friend method for enforce_permitted_members_in_groups and subroutines]
Does self permit node as a direct member,
when called from enforce_permitted_members_in_groups with
the same options as we are passed?
@rtype: boolean
[extends superclass method]
"""
# this method was copied from DnaStrandOrSegment and edited for this class
if not LeafLikeGroup.permit_as_member(self, node, pre_updaters, **opts):
# reject if superclass would reject [bruce 081217]
return False
del opts
assy = self.assy
res = isinstance( node, assy.Chunk) #@ NEEDS SOMETHING MORE.
return res
pass # end of class PeptideSegment
class PeptideSegment(Group):
"""
Model object which represents a Peptide Segment inside a Peptide Group.
Internally, this is just a specialized Group containing a single chunk,
itself containing all the atoms of a Peptide.
"""
# 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 = ('PeptideSegment',)
Peptide = None
_endPoint1 = None
_endPoint2 = None
# TODO: undo or copy code for those attrs,
# and updating them when the underlying structure changes.
# But maybe that won't be needed, if they are replaced
# by computing them from the atom geometry as needed.
# [bruce 080227 comment]
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)
iconPath = "ui/modeltree/PeptideSegment.png"
hide_iconPath = "ui/modeltree/PeptideSegment-hide.png"
def __init__(self, name, assy, dad, members = (), editCommand = None):
Group.__init__(self,
name,
assy,
dad,
members = members,
editCommand = editCommand)
###BUG: not all callers pass an editCommand. It would be better
# to figure out on demand which editCommand would be appropriate.
# [bruce 080227 comment]
return
def writemmp_other_info_opengroup(self, mapping): #bruce 080507 refactoring
"""
"""
#bruce 080507 refactoring (split this out of Group.writemmp)
# (I think the following condition is always true, but I didn't
# prove this just now, so I left in the test for now.)
encoded_classifications = self._encoded_classifications()
if encoded_classifications == "PeptideSegment":
# This is a Peptide segment, so write the parameters into an info
# record so we can read and restore them in the next session.
# --Mark 2008-04-12
assert self.Peptide
mapping.write("info opengroup Peptide-parameters = %d, %d, %s, %s\n" \
% (self.Peptide.getChiralityN(),
self.Peptide.getChiralityM(),
self.Peptide.getType(),
self.Peptide.getEndings()))
pass
return
def readmmp_info_opengroup_setitem( self, key, val, interp ):
"""
[extends superclass method]
"""
#bruce 080507 refactoring (split this out of the superclass method)
if key == ['Peptide-parameters']:
# val includes all the parameters, separated by commas.
n, m, type, endings = val.split(",")
self.n = int(n)
self.m = int(m)
self.type = type.lstrip()
self.endings = endings.lstrip()
# Create the Peptide.
from cnt.model.Peptide import Peptide
self.Peptide = Peptide() # Returns a 5x5 CNT.
self.Peptide.setChirality(self.n, self.m)
self.Peptide.setType(self.type)
self.Peptide.setEndings(self.endings)
# The endpoints are recomputed every time it is edited.
else:
Group.readmmp_info_opengroup_setitem( self, key, val, interp)
return
def edit(self):
"""
Edit this PeptideSegment.
@see: PeptideSegment_EditCommand
"""
commandSequencer = self.assy.w.commandSequencer
if commandSequencer.currentCommand.commandName != "Peptide_SEGMENT":
commandSequencer.userEnterTemporaryCommand('Peptide_SEGMENT')
assert commandSequencer.currentCommand.commandName == 'Peptide_SEGMENT'
commandSequencer.currentCommand.editStructure(self)
#Following methods are likely to be revised in a fully functional dna data
# model. These methods are mainly created to get working many core UI
# operations for Rattlesnake. -- Ninad 2008-02-01
def get_all_content_chunks(self):
"""
Return all the chunks contained within this PeptideSegment.
@note: there is only one chunk inside this group.
"""
all_content_chunk_list = []
for member in self.members:
if isinstance(member, Chunk):
all_content_chunk_list.append(member)
return all_content_chunk_list
def getAxisVector(self, atomAtVectorOrigin = None):
"""
Returns the unit axis vector of the segment (vector between two axis
end points)
"""
endPoint1, endPoint2 = self.Peptide.getEndPoints()
if endPoint1 is None or endPoint2 is None:
return V(0, 0, 0)
#@see: RotateAboutAPoint command. The following code is disabled
#as it has bugs (not debugged but could be in
#self.Peptide.getEndPoints). So, rotate about a point won't work for
#rotating a Peptide. -- Ninad 2008-05-13
##if atomAtVectorOrigin is not None:
###If atomAtVectorOrigin is specified, we will return a vector that
###starts at this atom and ends at endPoint1 or endPoint2 .
###Which endPoint to choose will be dicided by the distance between
###atomAtVectorOrigin and the respective endPoints. (will choose the
###frthest endPoint
##origin = atomAtVectorOrigin.posn()
##if vlen(endPoint2 - origin ) > vlen(endPoint1 - origin):
##return norm(endPoint2 - endPoint1)
##else:
##return norm(endPoint1 - endPoint2)
return norm(endPoint2 - endPoint1)
def setProps(self, props):
"""
Sets some properties. These will be used while editing the structure.
(but if the structure is read from an mmp file, this won't work. As a
fall back, it returns some constant values)
@see: InsertPeptide_EditCommand.createStructure which calls this method.
@see: self.getProps, PeptideSegment_EditCommand.editStructure
"""
(_n, _m), _type, _endings, (_endPoint1, _endPoint2) = props
from cnt.model.Peptide import Peptide
self.Peptide = Peptide()
self.Peptide.setChirality(_n, _m)
self.Peptide.setType(_type)
self.Peptide.setEndings(_endings)
self.Peptide.setEndPoints(_endPoint1, _endPoint2)
def getProps(self):
"""
Returns Peptide parameters necessary for editing.
@see: PeptideSegment_EditCommand.editStructure where it is used.
@see: PeptideSegment_PropertyManager.getParameters
@see: PeptideSegmentEditCommand._createStructure
"""
# Recompute the endpoints in case this Peptide was read from
# MMP file (which means this Peptide doesn't have endpoint
# parameters yet).
self.Peptide.computeEndPointsFromChunk(self.members[0])
return self.Peptide.getParameters()
def getPeptideGroup(self):
"""
Return the PeptideGroup we are contained in, or None if we're not
inside one.
"""
return self.parent_node_of_class( self.assy.PeptideGroup)
def isAncestorOf(self, obj):
"""
Checks whether the object <obj> is contained within the PeptideSegment
Example: If the object is an Atom, it checks whether the
atom's chunk is a member of this PeptideSegment (chunk.dad is self)
It also considers all the logical contents of the PeptideSegment to determine
whether self is an ancestor. (returns True even for logical contents)
@see: self.get_all_content_chunks()
@see: PeptideSegment_GraphicsMode.leftDrag
"""
# TODO: this needs cleanup (it looks like it's made of two alternative
# implems, one after the other), and speedup. [bruce 080507 comment]
c = None
if isinstance(obj, Atom):
c = obj.molecule
elif isinstance(obj, Bond):
chunk1 = obj.atom1.molecule
chunk2 = obj.atom1.molecule
if chunk1 is chunk2:
c = chunk1
elif isinstance(obj, Chunk):
c = obj
if c is not None:
if c in self.get_all_content_chunks():
return True
#NOTE: Need to check if the isinstance checks are acceptable (apparently
#don't add any import cycle) Also this method needs to be revised
#after we completely switch to dna data model.
if isinstance(obj, Atom):
chunk = obj.molecule
if chunk.dad is self:
return True
else:
return False
elif isinstance(obj, Bond):
chunk1 = obj.atom1.molecule
chunk2 = obj.atom1.molecule
if (chunk1.dad is self) or (chunk2.dad is self):
return True
elif isinstance(obj, Chunk):
if obj.dad is self:
return True
return False
def node_icon(self, display_prefs):
del display_prefs # unused
if self.all_content_is_hidden():
return imagename_to_pixmap( self.hide_iconPath)
else:
return imagename_to_pixmap( self.iconPath)
# =======================================================================
# These methods were copied from DnaStrandOrSegment and edited for
# this class.
def permits_ungrouping(self):
"""
Should the user interface permit users to dissolve this Group
using self.ungroup?
[overridden from Group]
"""
return self._show_all_kids_for_debug() # normally False
# note: modelTree should modify menu text for Ungroup to say "(unsupported)",
# but this is broken as of before 080318 since it uses a self.is_block() test.
def _show_all_kids_for_debug(self):
#bruce 080207 in deprecated class Block 080318
classname_short = self.__class__.__name__.split('.')[-1]
debug_pref_name = "Model Tree: show content of %s?" % classname_short
# typical examples (for text searches to find them here):
# Model Tree: show content of DnaStrand?
# Model Tree: show content of DnaSegment?
return debug_pref( debug_pref_name, Choice_boolean_False )
def permit_as_member(self, node, pre_updaters = True, **opts):
"""
[friend method for enforce_permitted_members_in_groups and subroutines]
Does self permit node as a direct member,
when called from enforce_permitted_members_in_groups with
the same options as we are passed?
@rtype: boolean
[overrides Group method]
"""
#bruce 080319
# someday, reject if superclass would reject -- so far, it never does
del opts
assy = self.assy
res = isinstance( node, assy.Chunk) #@ NEEDS SOMETHING MORE.
return res
def _f_wants_to_be_killed(self, pre_updaters = True, **opts): # in DnaStrandOrSegment
"""
[friend method for enforce_permitted_members_in_groups and subroutines]
Does self want to be killed due to members that got ejected
by _f_move_nonpermitted_members (or due to completely invalid structure
from before then, and no value in keeping self even temporarily)?
@rtype: boolean
[overrides Group method]
"""
#bruce 080319
del opts, pre_updaters
return not self.members
def MT_DND_can_drop_inside(self): #bruce 080317, revised 080318
"""
Are ModelTree Drag and Drop operations permitted to drop nodes
inside self?
[overrides Node/Group method]
"""
return self._show_all_kids_for_debug() # normally False
def openable(self): # overrides Node.openable()
"""
whether tree widgets should permit the user to open/close their view of this node
"""
# if we decide this depends on the tree widget or on somet for thing about it,
# we'll have to pass in some args... don't do that unless/until we need to.
#If there are no MT_kids (subnodes visible in MT under this group) then
#don't make this node 'openable'. This makes sure that expand/ collapse
#pixmap next to the node is not shown for this type of Group with 0
#MT_kids
#Examples of such groups include empty groups, DnaStrand Groups,
#DnaSegments etc -- Ninad 2008-03-15
return len(self.MT_kids()) != 0
def _raw_MT_kids(self, display_prefs = {}):
"""
DnaStrand or DnaSegment groups (subclasses of this class) should not
show any MT kids.
@see: Group._raw__MT_kids()
@see: Group.MT_kids()
"""
if self._show_all_kids_for_debug(): # normally False
# bruce 080318
return self.members
return ()
pass # end of class PeptideSegment