# 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.Z_Dna_Generator import Z_Dna_Generator

class Z_Dna_Atomistic_Generator(Z_Dna_Generator):
    """
    Provides an atomistic model of the Z form of DNA.

    @attention: This class will never be implemented.
    """
    model = "PAM5"

    def _strandAinfo(self, baseLetter, index):
        """
        Returns parameters needed to add a base to strand A.

        @param baseLetter: The base letter.
        @type  baseLetter: str

        @param index: Base-pair index.
        @type  index: int
        """

        thetaOffset  =  0.0
        basename  =  basesDict[baseLetter]['Name']

        if (index & 1) != 0:
            # Index is odd.
            basename  +=  "-outer"
            zoffset    =  2.045
        else:
            # Index is even.
            basename  +=  '-inner'
            zoffset    =  0.0

        basefile     =  self._baseFileName(basename)
        return (basefile, zoffset, thetaOffset)

    def _strandBinfo(self, baseLetter, index):
        """
        Returns parameters needed to add a base to strand B.

        @param baseLetter: The base letter.
        @type  baseLetter: str

        @param index: Base-pair index.
        @type  index: int
        """

        thetaOffset  =  0.5 * pi
        basename     =  basesDict[baseLetter]['Name']

        if (index & 1) != 0:
            basename  +=  '-inner'
            zoffset    =  -0.055
        else:
            basename  +=  "-outer"
            zoffset    =  -2.1

        basefile     = self._baseFileName(basename)
        return (basefile, zoffset, thetaOffset)