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# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaDuplexGenerator.py
@author: Mark Sims
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
History:
Mark 2007-10-18:
- Created. Major rewrite of DnaGenerator.py.
"""
from foundation.Group import Group
from utilities.Log import redmsg, greenmsg
from geometry.VQT import V, Veq
from dna.commands.BuildDuplex.DnaDuplex import B_Dna_PAM3
from command_support.GeneratorBaseClass import GeneratorBaseClass
from utilities.exception_classes import CadBug, PluginBug, UserError
from dna.commands.BuildDuplex.DnaDuplexPropertyManager import DnaDuplexPropertyManager
############################################################################
# DnaDuplexPropertyManager must come BEFORE GeneratorBaseClass in this list
class DnaDuplexGenerator(DnaDuplexPropertyManager, GeneratorBaseClass):
cmd = greenmsg("Build DNA: ")
sponsor_keyword = 'DNA'
prefix = 'DNA-' # used for gensym
# Generators for DNA, nanotubes and graphene have their MT name
# generated (in GeneratorBaseClass) from the prefix.
create_name_from_prefix = True
# pass window arg to constructor rather than use a global, wware 051103
def __init__(self, win):
DnaDuplexPropertyManager.__init__(self)
GeneratorBaseClass.__init__(self, win)
self._random_data = []
# ##################################################
# How to build this kind of structure, along with
# any necessary helper functions.
def gather_parameters(self):
"""
Return the parameters from the property manager UI.
@return: All the parameters:
- numberOfBases
- dnaForm
- basesPerTurn
- endPoint1
- endPoint2
@rtype: tuple
"""
numberOfBases = self.numberOfBasesSpinBox.value()
dnaForm = str(self.conformationComboBox.currentText())
basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
# First endpoint (origin) of DNA duplex
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of DNA duplex.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
endPoint1 = V(x1, y1, z1)
endPoint2 = V(x2, y2, z2)
return (numberOfBases,
dnaForm,
basesPerTurn,
endPoint1,
endPoint2)
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
###################################################
# The done message
#@ THIS SHOULD BE REMOVED. Mark
def done_msg(self):
if not self.dna: # Mark 2007-06-01
return "No DNA added."
return "Done creating a strand of %s." % (self.dna.form)
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