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# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
DnaDuplex.py -- DNA duplex generator helper classes, based on empirical data.
@author: Mark Sims
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
History:
Mark 2007-10-18:
- Created. Major rewrite of DnaGenHelper.py.
"""
import foundation.env as env
import os
from math import sin, cos, pi
from utilities.debug import print_compact_traceback, print_compact_stack
from platform_dependent.PlatformDependent import find_plugin_dir
from files.mmp.files_mmp import readmmp
from geometry.VQT import Q, V, angleBetween, cross, vlen
from utilities.Log import orangemsg
from utilities.exception_classes import PluginBug
from utilities.constants import gensym
from utilities.prefs_constants import dnaDefaultStrand1Color_prefs_key
from utilities.prefs_constants import dnaDefaultStrand2Color_prefs_key
from utilities.prefs_constants import dnaDefaultSegmentColor_prefs_key
from dna.model.Dna_Constants import getDuplexBasesPerTurn
##from dna.updater.dna_updater_prefs import pref_dna_updater_convert_to_PAM3plus5
from simulation.sim_commandruns import adjustSinglet
from model.elements import PeriodicTable
from model.Line import Line
from model.chem import Atom_prekill_prep
Element_Ae3 = PeriodicTable.getElement('Ae3')
from dna.model.Dna_Constants import basesDict, dnaDict
from dna.model.dna_model_constants import LADDER_END0
basepath_ok, basepath = find_plugin_dir("DNA")
if not basepath_ok:
env.history.message(orangemsg("The cad/plugins/DNA directory is missing."))
RIGHT_HANDED = -1
LEFT_HANDED = 1
from geometry.VQT import V, Q, norm, cross
from geometry.VQT import vlen
from Numeric import dot
from utilities.debug import print_compact_stack
from model.bonds import bond_at_singlets
from dna.generators.B_Dna_Generator import B_Dna_Generator
class B_Dna_PAM5_Generator(B_Dna_Generator):
"""
Provides a PAM5 reduced model of the B form of DNA.
"""
model = "PAM5"
def _isStartPosition(self, index):
"""
Returns True if I{index} points the first base-pair position (5').
@param index: Base-pair index.
@type index: int
@return: True if index is zero.
@rtype : bool
"""
if index == 0:
return True
else:
return False
def _isEndPosition(self, index):
"""
Returns True if I{index} points the last base-pair position (3').
@param index: Base-pair index.
@type index: int
@return: True if index is zero.
@rtype : bool
"""
if index == self.getNumberOfBasePairs() - 1:
return True
else:
return False
def _strandAinfo(self, index):
"""
Returns parameters needed to add a base, including its complement base,
to strand A.
@param index: Base-pair index.
@type index: int
"""
zoffset = 0.0
thetaOffset = 0.0
basename = "MiddleBasePair"
if self._isStartPosition(index):
basename = "StartBasePair"
if self._isEndPosition(index):
basename = "EndBasePair"
if self.getNumberOfBasePairs() == 1:
basename = "SingleBasePair"
basefile = self._baseFileName(basename)
return (basefile, zoffset, thetaOffset)
def _postProcess(self, baseList): # bruce 070414
"""
Set bond direction on the backbone bonds.
@param baseList: List of basepair chunks that make up the duplex.
@type baseList: list
"""
# This implem depends on the specifics of how the end-representations
# are terminated. If that's changed, it might stop working or it might
# start giving wrong results. In the current representation,
# baseList[0] (a chunk) has two bonds whose directions we must set,
# which will determine the directions of their strands:
# Ss5 -> Sh5, and Ss5 <- Pe5.
# Just find those bonds and set the strand directions (until such time
# as they can be present to start with in the end1 mmp file).
# (If we were instead passed all the atoms, we could be correct if we
# just did this to the first Pe5 and Sh5 we saw, or to both of each if
# setting the same direction twice is allowed.)
atoms = baseList[0].atoms.values()
Pe_list = filter( lambda atom: atom.element.symbol in ('Pe5'), atoms)
Sh_list = filter( lambda atom: atom.element.symbol in ('Sh5'), atoms)
if len(Pe_list) == len(Sh_list) == 1:
for atom in Pe_list:
assert len(atom.bonds) == 1
atom.bonds[0].set_bond_direction_from(atom, 1, propogate = True)
for atom in Sh_list:
assert len(atom.bonds) == 1
atom.bonds[0].set_bond_direction_from(atom, -1, propogate = True)
else:
#bruce 070604 mitigate bug in above code when number of bases == 1
# by not raising an exception when it fails.
msg = "Warning: strand not terminated, bond direction not set \
(too short)"
env.history.message( orangemsg( msg))
# Note: It turns out this bug is caused by a bug in the rest of the
# generator (which I didn't try to diagnose) -- for number of
# bases == 1 it doesn't terminate the strands, so the above code
# can't find the termination atoms (which is how it figures out
# what to do without depending on intimate knowledge of the base
# mmp file contents).
# print "baseList = %r, its len = %r, atoms in [0] = %r" % \
# (baseList, len(baseList), atoms)
## baseList = [<molecule 'unknown' (11 atoms) at 0xb3d6f58>],
## its len = 1, atoms in [0] = [Ax1, X2, X3, Ss4, Pl5, X6, X7, Ss8, Pl9, X10, X11]
# It would be a mistake to fix this here (by giving it that
# intimate knowledge) -- instead we need to find and fix the bug
# in the rest of generator when number of bases == 1.
return
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)
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