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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
elements_data_PAM5.py -- data for PAM5 pseudoatom elements
@author: Mark, Eric D
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 071105 revised init code, and split PAM3 and PAM5 data
out of elements_data.py into separate files.
Bruce 080108 added Gv5 for use in Eric D's forthcoming PAM5 revision.
"""
from model.elements_data import tetra4, flat, tetra2, onebond
from utilities.constants import MODEL_PAM5
_DIRECTIONAL_BOND_ELEMENTS_PAM5 = ('Ss5', 'Pl5', 'Sj5', 'Pe5', 'Sh5', 'Hp5')
# ==
# mark 060129. New default colors for Alpha 7.
_defaultRadiusAndColor = {
"Ax5" : (5.0, [0.4, 0.4, 0.8]),
"Ss5" : (4.0, [0.4, 0.8, 0.4]),
"Pl5" : (3.2, [0.4, 0.1, 0.5]),
"Sj5" : (4.0, [0.4, 0.8, 0.8]),
"Ae5" : (3.5, [0.4, 0.4, 0.8]),
"Pe5" : (3.0, [0.4, 0.1, 0.5]),
"Sh5" : (2.5, [0.4, 0.8, 0.4]),
"Hp5" : (4.0, [0.3, 0.7, 0.3]),
"Gv5" : (5.0, [156./255, 83./255, 8./255]), #bruce 080108
"Gr5" : (5.0, [156./255, 83./255, 8./255]),
"Ub5" : (2.5, [0.428, 0.812, 0.808]), #bruce 080117 guess, "light blue"
"Ux5" : (2.5, [0.428, 0.812, 0.808]), #bruce 080410 stub
"Uy5" : (2.5, [0.812, 0.428, 0.808]), #bruce 080410 stub
"Ah5" : (2.5, [0.8, 0.8, 0.8]), #bruce 080515 guess, "very light gray"
}
_alternateRadiusAndColor = {
}
# Format of _mendeleev: see elements_data.py
_mendeleev = [
# B-DNA PAM5 pseudo atoms (see also _DIRECTIONAL_BOND_ELEMENTS)
# Note: the bond vector lists are mainly what we want in length,
# not necessarily in geometry.
#
#bruce 070415: End->Hydroxyl per Eric D email, in "Sh5" == "PAM5-Sugar-Hydroxyl"
#bruce 071106: added option dicts; deprecated_to options are good guesses but are untested
#bruce 080410 added Ux5 and Uy5 and updated all general comments below
# axis element (old, only semi-supported, not generated anymore)
("Ax5", "PAM5-Axis", 200, 1.0, [[4, 200, tetra4]], dict(role = 'axis')), # todo: convert to Gv5, moving it as you do
# strand elements
("Ss5", "PAM5-Sugar", 201, 1.0, [[3, 210, flat]], dict(role = 'strand')),
("Pl5", "PAM5-Phosphate", 202, 1.0, [[2, 210, tetra2]], dict(role = 'strand')),
# deprecated axis and strand elements
# (btw, some of these say None, 'sp', which is probably wrong --
# don't imitate this in new elements) [bruce 080516 comment]
("Sj5", "PAM5-Sugar-Junction", 203, 1.0, [[3, 210, flat]], dict(role = 'strand', deprecated_to = 'Ss5')),
("Ae5", "PAM5-Axis-End", 204, 1.0, [[1, 200, None, 'sp']], dict(role = 'axis', deprecated_to = 'X')),
("Pe5", "PAM5-Phosphate-End", 205, 1.0, [[1, 210, None, 'sp']], dict(role = 'strand', deprecated_to = 'Pl5')), #bruce 080129 X->Pl5; UNCONFIRMED
("Sh5", "PAM5-Sugar-Hydroxyl", 206, 1.0, [[1, 210, None, 'sp']], dict(role = 'strand', deprecated_to = 'X')),
("Hp5", "PAM5-Hairpin", 207, 1.0, [[2, 210, tetra2]], dict(role = 'strand', deprecated_to = 'Ss5')), # REVIEW: Ss or Pl?
# major groove (used instead of axis for PAM5, bonded same as axis)
("Gv5", "PAM5-Major-Groove", 208, 1.0, [[4, 200, tetra4]], dict(role = 'axis')), #bruce 080108
("Gr5", "PAM5-Major-Groove-End",209,1.0, [[3, 210, flat]], dict(role = 'axis', deprecated_to = 'Gv5')),
# unpaired base components (experimental and mostly stubs as of 080410):
# old one-atom (besides backbone) unpaired base (never used, may or may not end up being useful,
# mainly retained since the corresponding PAM3 element is more likely to be useful)
("Ub5", "PAM5-Unpaired-base", 210, 1.0, [[4, 200, tetra4]], dict(role = 'unpaired-base')),
# newly proposed two-atom (besides backbone) unpaired base (never yet used but under active development):
#
# Ux means "unpaired base x-point" and is in the same direction from the
# sugar (roughly) as the major groove or axis in a basepair
#
# Uy means "unpaired base y-point" and is in the same direction from the
# sugar as the other sugar in a basepair (exactly)
#
# The mnemonic is that the sugar-Uy line is the "PAM3+5 baseframe Y axis"
# and the sugar-Ux line is then enough to define the X axis
# (though its actual direction is a combination of Y and X).
#
("Ux5", "PAM5-Unpaired-base-x",211, 1.0, [[4, 200, tetra4]], dict(role = 'unpaired-base')), # (likely to be revised)
("Uy5", "PAM5-Unpaired-base-y",212, 1.0, [[4, 200, tetra4]], dict(role = 'unpaired-base')), # (likely to be revised)
# basepair axis handle (defined as PAM5 to make it more convenient to permit its bonding with Gv5)
# (see also: elements_data_other.py)
("Ah5", "PAM5-Axis-handle", 213, 1.0, [[1, 200, onebond]], dict(role = 'handle')), #bruce 080515, revised 080516
]
# Since these are not real chemical bonds, the electron accounting
# need not be based on filled shells. We just specify that each atom
# provides the same number of electrons as the bond count, and that it
# needs twice that many.
# symbol name
# hybridization name
# formal charge
# number of electrons needed to fill shell
# number of valence electrons provided
# covalent radius (pm)
# geometry (array of vectors, one for each available bond)
# symb hyb FC need prov c-rad geometry
_PAM5AtomTypeData = [
["Ax5", None, 0, 8, 4, 2.00, tetra4],
["Ss5", None, 0, 6, 3, 2.10, flat],
["Pl5", None, 0, 4, 2, 2.10, tetra2],
["Sj5", None, 0, 6, 3, 2.10, flat],
["Ae5", None, 0, 2, 1, 2.00, None],
["Pe5", None, 0, 2, 1, 2.10, None],
["Sh5", None, 0, 2, 1, 2.10, None],
["Hp5", None, 0, 4, 2, 2.10, tetra2],
["Gv5", None, 0, 8, 4, 2.00, tetra4],
["Gr5", None, 0, 6, 3, 2.10, flat],
["Ub5", None, 0, 8, 4, 2.00, tetra4],
["Ux5", None, 0, 8, 4, 2.00, tetra4],
["Uy5", None, 0, 8, 4, 2.00, tetra4],
["Ah5", None, 0, 2, 1, 2.00, onebond],
]
# ==
def init_PAM5_elements( periodicTable):
periodicTable.addElements( _mendeleev,
_defaultRadiusAndColor,
_alternateRadiusAndColor,
_PAM5AtomTypeData,
_DIRECTIONAL_BOND_ELEMENTS_PAM5,
default_options = dict(pam = MODEL_PAM5)
)
return
# end
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