def insertBaseFromMmp(filename, subgroup, tfm, position=position):
"""
Insert the atoms for a nucleic acid base from an MMP file into
a single chunk.
- If atomistic, the atoms for each base are in a separate chunk.
- If PAM5, the pseudo atoms for each base-pair are together in a
chunk.
@param filename: The mmp filename containing the base
(or base-pair).
@type filename: str
@param subgroup: The part group to add the atoms to.
@type subgroup: L{Group}
@param tfm: Transform applied to all new base atoms.
@type tfm: V
@param position: The origin in space of the DNA duplex, where the
3' end of strand A is 0, 0, 0.
@type position: L{V}
"""
try:
ok, grouplist = readmmp(assy, filename, isInsert=True)
except IOError:
raise PluginBug("Cannot read file: " + filename)
if not grouplist:
raise PluginBug("No atoms in DNA base? " + filename)
viewdata, mainpart, shelf = grouplist
for member in mainpart.members:
# 'member' is a chunk containing a set of base-pair atoms.
for atm in member.atoms.values():
atm._posn = tfm(atm._posn) + position
if atm.element.symbol in ('Se3', 'Ss3', 'Ss5'):
if atm.getDnaBaseName() == "a":
baseLetter = currentBaseLetter
else:
try:
baseLetter = \
basesDict[currentBaseLetter]['Complement']
except:
# If complement not found, just assign same
# letter.
baseLetter = currentBaseLetter
if 0:
print "Ss(%r) being set to %r." \
% (atm.getDnaBaseName(), baseLetter)
atm.setDnaBaseName(baseLetter)
member.name = currentBaseLetter
subgroup.addchild(member)
baseList.append(member)
# Clean up.
del viewdata
shelf.kill()
def build_struct(self, name, params, position):
"""
Build the DNA helix based on parameters in the UI.
@param name: The name to assign the node in the model tree.
@type name: str
@param params: The list of parameters gathered from the PM.
@type params: tuple
@param position: The position in 3d model space at which to
create the DNA strand. This is always 0, 0, 0.
@type position: position
"""
# No error checking in build_struct, do all your error
# checking in gather_parameters
numberOfBases, \
dnaForm, \
basesPerTurn, \
endPoint1, \
endPoint2 = params
if Veq(endPoint1, endPoint2):
raise CadBug("DNA endpoints cannot be the same point.")
if numberOfBases < 1:
msg = redmsg("Cannot to preview/insert a DNA duplex with 0 bases.")
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
self.dna = None # Fixes bug 2530. Mark 2007-09-02
return None
if dnaForm == 'B-DNA':
dna = B_Dna_PAM3()
else:
raise PluginBug("Unsupported DNA Form: " + dnaForm)
self.dna = dna # needed for done msg
# Create the model tree group node.
dnaGroup = Group(self.name, self.win.assy, self.win.assy.part.topnode)
try:
# Make the DNA duplex. <dnaGroup> will contain three chunks:
# - Strand1
# - Strand2
# - Axis
dna.make(dnaGroup, numberOfBases, basesPerTurn, endPoint1,
endPoint2)
return dnaGroup
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
rawDnaGroup.kill()
raise PluginBug(
"Internal error while trying to create DNA duplex.")
pass
def _create_atomLists_for_regrouping(self, dnaGroup):
"""
Creates and returns the atom lists that will be used to regroup the
chunks within the DnaGroup.
@param dnaGroup: The DnaGroup whose atoms will be filtered and put into
individual strand A or strandB or axis atom lists.
@return: Returns a tuple containing three atom lists
-- two atom lists for strand chunks and one for axis chunk.
@see: self._regroup()
"""
_strandA_list = []
_strandB_list = []
_axis_list = []
# Build strand and chunk atom lists.
for m in dnaGroup.members:
for atom in m.atoms.values():
if atom.element.symbol in ('Pl5', 'Pe5'):
if atom.getDnaStrandId_for_generators() == 'Strand1':
_strandA_list.append(atom)
# Following makes sure that the info record
#'dnaStrandId_for_generators' won't be written for
#this atom that the dna generator outputs. i.e.
#the info record 'dnaStrandId_for_generators' is only
#required while generating the dna from scratch
#(by reading in the strand base files in 'cad/plugins'
#see more comments in Atom.getDnaStrandId_for_generators
atom.setDnaStrandId_for_generators('')
elif atom.getDnaStrandId_for_generators() == 'Strand2':
atom.setDnaStrandId_for_generators('')
_strandB_list.append(atom)
if atom.element.symbol in ('Ss5', 'Sh5'):
if atom.getDnaBaseName() == 'a':
_strandA_list.append(atom)
#Now reset the DnaBaseName for the added atom
# to 'unassigned' base i.e. 'X'
atom.setDnaBaseName('X')
elif atom.getDnaBaseName() == 'b':
_strandB_list.append(atom)
#Now reset the DnaBaseName for the added atom
# to 'unassigned' base i.e. 'X'
atom.setDnaBaseName('X')
else:
msg = "Ss5 or Sh5 atom not assigned to strand 'a' or 'b'."
raise PluginBug(msg)
elif atom.element.symbol in ('Ax5', 'Ae5', 'Gv5', 'Gr5'):
_axis_list.append(atom)
return (_strandA_list, _strandB_list, _axis_list)
def gather_parameters(self):
"""
Return the parameters from the property manager UI.
@return: All the parameters:
- dnaSequence
- dnaType
- basesPerTurn
- chunkOption
@rtype: tuple
"""
if not basepath_ok:
raise PluginBug("The cad/plugins/DNA directory is missing.")
dnaModel = str(self.modelComboBox.currentText())
dnaType = str(self.conformationComboBox.currentText())
assert dnaType in ('B-DNA')
# Get bases per turn.
basesPerTurnString = str(self.basesPerTurnComboBox.currentText())
basesPerTurn = float(basesPerTurnString)
chunkOption = str(self.createComboBox.currentText())
resolve_random = False
# Later this flag may depend on a new checkbox in that case;
# for now it doesn't matter, since sequence info is
# discarded for reduced bases anyway.
(dnaSequence, allKnown) = \
self._getSequence( resolve_random = resolve_random)
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
endpoint1 = V(x1, y1, z1)
endpoint2 = V(x2, y2, z2)
return (dnaSequence, dnaModel, dnaType, basesPerTurn, chunkOption,
endpoint1, endpoint2)
def _createStructure(self):
"""
creates and returns the structure (in this case a L{Group} object that
contains the DNA strand and axis chunks.
@return : group containing that contains the DNA strand and axis chunks.
@rtype: L{Group}
@note: This needs to return a DNA object once that model is implemented
"""
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix,
self.win.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
# Create the model tree group node.
# Make sure that the 'topnode' of this part is a Group (under which the
# DNa group will be placed), if the topnode is not a group, make it a
# a 'Group' (applicable to Clipboard parts).See part.py
# --Part.ensure_toplevel_group method. This is an important line
# and it fixes bug 2585
self.win.assy.part.ensure_toplevel_group()
dnaGroup = DnaGroup(self.name,
self.win.assy,
self.win.assy.part.topnode,
editCommand=self)
try:
self.win.assy.place_new_geometry(dnaGroup)
return dnaGroup
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
dnaGroup.kill()
raise PluginBug(
"Internal error while trying to create DNA duplex.")
def build_struct(self, name, params, position):
"""
Same API as in GeneratorBaseClass (though we are not its subclass).
On error, raise an exception.
"""
# get executable, append exe, ensure it exists
program = self.executable_path
# make command line args from params
args, outfiles = self.command_line_args_and_outfiles(params, name)
# makes param args and outputfile args;
# args is a list of strings (including outfile names);
# outfiles is a list of full pathnames of files this command might create
# run executable using the way we run the sim
exitcode = self.run_command(program, args)
#e look at exitcode?
if exitcode and debug_run():
print "generator exitcode: %r" % (exitcode, )
if exitcode:
# treat this as a fatal error for this run [to test, use an invalid chirality with m > n]
msg = "Plugin %r exitcode: %r" % (self.plugin_name, exitcode)
## not needed, GBC UserError will do it, more or less: env.history.message(redmsg(msg))
###e should: self.remove_outfiles(outfiles, complain_if_missing = False)
raise UserError(
msg
) # this prints a redmsg; maybe we'd rather do that ourselves, and raise SilentUserError (nim)??
# look for outfiles
# (if there are more than one specified, for now just assume all of them need to be there)
for outfile in outfiles:
if not os.path.exists(outfile):
###e should: self.remove_outfiles(outfiles, complain_if_missing = False)
raise PluginBug(
"generator output file should exist but doesn't: [%s]" %
(outfile, ))
# insert file contents, rename the object in it, return that (see dna generator)
thing = self.insert_output(outfiles, params, name)
# we pass params, since some params might affect insertion (or postprocessing)
# other than by affecting the command output
###@@@ WARNING: the following repositioning code is not correct for all kinds of "things",
# only for single-chunk things like for CoNTub
# (and also it probably belongs inside insert_output, not here):
for atom in thing.atoms.values():
atom.setposn(atom.posn() + position)
self.remove_outfiles(outfiles)
return thing
def _createStructure(self):
"""
Returns the current NanotubeSegment being edited with a new nanotube
chunk.
@return : Nanotube segment that include the new nanotube chunk.
@rtype: L{NanotubeSegment}
"""
try:
# Create a new nanotube chunk using new params.
n, m, type, endings, endPoint1, endPoint2 = self._gatherParameters()
from cnt.model.NanotubeParameters import NanotubeParameters
self.nanotube = NanotubeParameters()
nanotube = self.nanotube
nanotube.setChirality(n, m)
nanotube.setType(type)
nanotube.setEndings(endings)
nanotube.setEndPoints(endPoint1, endPoint2)
position = V(0.0, 0.0, 0.0)
ntChunk = nanotube.build(self.struct.name, self.win.assy, position)
nanotube.computeEndPointsFromChunk(ntChunk) # Needed.
self.struct.addchild(ntChunk)
#WARNING 2008-03-05:
#When we actually permit modifying a nanotube without recreating it,
#then the following properties must be set in self._modifyStructure
#as well. Needs more thought.
props =(nanotube.getChirality(),
nanotube.getType(),
nanotube.getEndings(),
nanotube.getEndPoints())
self.struct.setProps(props)
return self.struct
except (PluginBug, UserError):
self.struct.kill()
raise PluginBug("Internal error while trying to recreate a NanotubeSegment.")
return None
def _create_atomLists_for_regrouping(self, dnaGroup):
"""
Creates and returns the atom lists that will be used to regroup the
chunks within the DnaGroup.
@param dnaGroup: The DnaGroup whose atoms will be filtered and put into
individual strand A or strandB or axis atom lists.
@return: Returns a tuple containing three atom lists
-- two atom lists for strand chunks and one for axis chunk.
@see: self._regroup()
"""
_strandA_list = []
_strandB_list = []
_axis_list = []
# Build strand and chunk atom lists.
for m in dnaGroup.members:
for atom in m.atoms.values():
if atom.element.symbol in ('Ss3'):
if atom.getDnaBaseName() == 'a':
_strandA_list.append(atom)
#Now reset the DnaBaseName for the added atom
# to 'unassigned' base i.e. 'X'
atom.setDnaBaseName('X')
elif atom.getDnaBaseName() == 'b':
_strandB_list.append(atom)
#Now reset the DnaBaseName for the added atom
# to 'unassigned' base i.e. 'X'
atom.setDnaBaseName('X')
else:
msg = "Ss3 atom not assigned to strand 'a' or 'b'."
raise PluginBug(msg)
elif atom.element.symbol in ('Ax3', 'Ae3'):
_axis_list.append(atom)
return (_strandA_list, _strandB_list, _axis_list)
def build_struct(self, name, params, position):
"""
Build the DNA helix based on parameters in the UI.
@param name: The name to assign the node in the model tree.
@type name: str
@param params: The list of parameters gathered from the PM.
@type params: tuple
@param position: The position in 3d model space at which to
create the DNA strand. This is always 0, 0, 0.
@type position: position
"""
# No error checking in build_struct, do all your error
# checking in gather_parameters
theSequence, \
dnaModel, \
dnaType, \
basesPerTurn, \
chunkOption, \
endpoint1, \
endpoint2 = params
if Veq(endpoint1, endpoint2):
raise CadBug("Dna endpoints cannot be the same point.")
return
if len(theSequence) < 1:
msg = redmsg("Enter a strand sequence to preview/insert DNA")
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
self.dna = None # Fixes bug 2530. Mark 2007-09-02
return None
if dnaModel == 'PAM3':
dna = B_Dna_PAM3()
else:
dna = B_Dna_PAM5()
self.dna = dna # needed for done msg
# Create the model tree group node.
rawDnaGroup = Group(self.name, self.win.assy,
self.win.assy.part.topnode)
try:
# Make the DNA duplex. <rawDnaGroup> returns a different
# grouping arrangement for atomistic vs. PAM5. This 'issue'
# is resolved when we regroup the atoms into strand chunks
# below.
dna.make(rawDnaGroup, theSequence, basesPerTurn)
self._orientRawDnaGroup(rawDnaGroup, endpoint1, endpoint2)
# Now group the DNA atoms based on the grouping option selected
# (i.e. "Strand chunks" or "Single Chunk").
dnaGroup = self._makePAMStrandAndAxisChunks(rawDnaGroup)
if chunkOption == 'Single chunk':
return self._makeDuplexChunk(dnaGroup)
return dnaGroup
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
rawDnaGroup.kill()
raise PluginBug(
"Internal error while trying to create DNA duplex.")
return None
def _createStructure(self):
"""
Creates and returns the structure (in this case a L{Group} object that
contains the DNA strand and axis chunks.
@return : group containing that contains the DNA strand and axis chunks.
@rtype: L{Group}
@note: This needs to return a DNA object once that model is implemented
"""
params = self._gatherParameters()
# No error checking in build_struct, do all your error
# checking in gather_parameters
number_of_basePairs_from_struct,\
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
endPoint1, \
endPoint2, \
color_junk = params
#Note: color_junk is not used. Ideally it should do struct.setColor(color)
#but the color combobox in the PM directly sets the color of the
#structure to the specified one when the current index in the combobx
#changes
#If user enters the number of basepairs and hits preview i.e. endPoint1
#and endPoint2 are not entered by the user and thus have default value
#of V(0, 0, 0), then enter the endPoint1 as V(0, 0, 0) and compute
#endPoint2 using the duplex length.
#Do not use '==' equality check on vectors! its a bug. Use same_vals
# or Veq instead.
if Veq(endPoint1, endPoint2) and Veq(endPoint1, V(0, 0, 0)):
endPoint2 = endPoint1 + \
self.win.glpane.right*getDuplexLength('B-DNA',
numberOfBases)
if numberOfBases < 1:
msg = redmsg("Cannot preview/insert a DNA duplex with 0 bases.")
self.propMgr.updateMessage(msg)
self.dna = None # Fixes bug 2530. Mark 2007-09-02
return None
if dnaForm == 'B-DNA':
if dnaModel == 'PAM3':
dna = B_Dna_PAM3_Generator()
elif dnaModel == 'PAM5':
dna = B_Dna_PAM5_Generator()
else:
print "bug: unknown dnaModel type: ", dnaModel
else:
raise PluginBug("Unsupported DNA Form: " + dnaForm)
self.dna = dna # needed for done msg
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix,
self.win.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
# Create the model tree group node.
# Make sure that the 'topnode' of this part is a Group (under which the
# DNa group will be placed), if the topnode is not a group, make it a
# a 'Group' (applicable to Clipboard parts).See part.py
# --Part.ensure_toplevel_group method. This is an important line
# and it fixes bug 2585
self.win.assy.part.ensure_toplevel_group()
dnaSegment = DnaSegment(self.name,
self.win.assy,
self.win.assy.part.topnode,
editCommand=self)
try:
# Make the DNA duplex. <dnaGroup> will contain three chunks:
# - Strand1
# - Strand2
# - Axis
dna.make(dnaSegment, numberOfBases, basesPerTurn, duplexRise,
endPoint1, endPoint2)
#set some properties such as duplexRise and number of bases per turn
#This information will be stored on the DnaSegment object so that
#it can be retrieved while editing this object.
#This works with or without dna_updater. Now the question is
#should these props be assigned to the DnaSegment in
#dnaDuplex.make() itself ? This needs to be answered while modifying
#make() method to fit in the dna data model. --Ninad 2008-03-05
#WARNING 2008-03-05: Since self._modifyStructure calls
#self._createStructure()
#If in the near future, we actually permit modifying a
#structure (such as dna) without actually recreating the whole
#structre, then the following properties must be set in
#self._modifyStructure as well. Needs more thought.
props = (duplexRise, basesPerTurn)
dnaSegment.setProps(props)
return dnaSegment
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
dnaSegment.kill()
raise PluginBug(
"Internal error while trying to create DNA duplex.")
def _createStructure(self):
"""
Creates and returns the structure (in this case a L{Group} object that
contains the nanotube chunk.
@return : group containing the nanotube chunk.
@rtype: L{Group}
@note: This needs to return a CNT object once that model is implemented
"""
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix,
self.win.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
# Create the model tree group node.
# Make sure that the 'topnode' of this part is a Group (under which the
# Nanotube group will be placed), if the topnode is not a group, make it
# a 'Group' (applicable to Clipboard parts). See part.py
# --Part.ensure_toplevel_group method. This is an important line
# and it fixes bug 2585
self.win.assy.part.ensure_toplevel_group()
ntSegment = NanotubeSegment(self.name,
self.win.assy,
self.win.assy.part.topnode,
editCommand=self)
try:
# Make the nanotube. <ntGroup> will contain one chunk:
# - Axis (Segment)
# No error checking here; do all error checking in _gatherParameters().
nanotube = self._gatherParameters()
position = V(0.0, 0.0, 0.0)
self.nanotube = nanotube # needed for done msg #@
ntChunk = nanotube.build(self.name, self.win.assy, position)
ntSegment.addchild(ntChunk)
#set some properties such as ntRise and its two endpoints.
#This information will be stored on the NanotubeSegment object so that
#it can be retrieved while editing this object.
#WARNING 2008-03-05: Since self._modifyStructure calls
#self._createStructure() If in the near future, we actually permit
#modifying a
#structure (such as a nanotube) without actually recreating the
#entire structure, then the following properties must be set in
#self._modifyStructure as well. Needs more thought.
#props =(nanotube.getChirality(),
# nanotube.getType(),
# nanotube.getEndings(),
# nanotube.getEndPoints())
ntSegment.setProps(nanotube.getParameters())
return ntSegment
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
self._segmentList.remove(ntSegment)
ntSegment.kill_with_contents()
raise PluginBug("Internal error while trying to create Nanotube.")
def _strandBinfo(self, sequence, index):
"""
Raise exception since A-DNA is not support.
"""
raise PluginBug("A-DNA is not yet implemented.")
def _strandAinfo(self, baseLetter, index):
"""
Raise exception since A-DNA is not support.
"""
raise PluginBug("A-DNA is not yet implemented.")