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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
elements_data_PAM3.py -- data for PAM3 pseudoatom elements
@author: Mark
@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.
"""
from model.elements_data import tetra4, flat, tetra2, tetra3, onebond
from utilities.constants import MODEL_PAM3
_DIRECTIONAL_BOND_ELEMENTS_PAM3 = ('Ss3', 'Pl3', 'Sj3', 'Se3', 'Sh3', 'Hp3')
# ==
# mark 060129. New default colors for Alpha 7.
_defaultRadiusAndColor = {
"Ax3" : (4.5, [0.4, 0.4, 0.8]),
"Ss3" : (4.5, [0.4, 0.8, 0.4]),
"Sj3" : (4.5, [0.4, 0.8, 0.8]),
"Pl3" : (3.0, [0.4, 0.1, 0.5]), # (unused)
"Ae3" : (4.5, [0.1, 0.1, 0.5]),
"Se3" : (4.5, [0.4, 0.8, 0.4]),
"Sh3" : (3.0, [0.6, 0.2, 0.6]),
"Hp3" : (4.5, [0.3, 0.7, 0.3]),
"Ub3" : (2.3, [0.428, 0.812, 0.808]), #bruce 080117 guess, "light blue"
"Ux3" : (2.3, [0.428, 0.812, 0.808]), #bruce 080410 stub
"Uy3" : (2.3, [0.812, 0.428, 0.808]), #bruce 080410 stub
}
_alternateRadiusAndColor = {}
# Format of _mendeleev: see elements_data.py
_mendeleev = [
# B-DNA PAM3 v2 pseudo atoms (see also _DIRECTIONAL_BOND_ELEMENTS)
#
# Note: the bond vector lists are mainly what we want in length,
# not necessarily in geometry.
#
#bruce 071106: added option dicts; deprecated_to options are good or bad
# guesses or unfinished; the X ones might be WRONG
#bruce 080410 added Ux3 and Uy3 and updated all general comments below
# axis and strand sugar -- these make up all the PAM atoms in a simple PAM3 duplex
("Ax3", "PAM3-Axis", 300, 1.0, [[4, 200, tetra4]], dict(role = 'axis')),
("Ss3", "PAM3-Sugar", 301, 1.0, [[3, 210, flat]], dict(role = 'strand')),
# PAM3 version of Pl5 (never used, in past, present or future)
("Pl3", "PAM3-Phosphate", 302, 1.0, [[2, 210, tetra2]], dict(role = 'strand', deprecated_to = 'remove')), ### ?? unused atom?
# deprecated PAM3 elements
# (btw, some of these say None, 'sp', which is probably wrong --
# don't imitate this in new elements) [bruce 080516 comment]
("Sj3", "PAM3-Sugar-Junction", 303, 1.0, [[3, 210, flat]], dict(role = 'strand', deprecated_to = 'Ss3')),
("Ae3", "PAM3-Axis-End", 304, 1.0, [[3, 200, tetra3]], dict(role = 'axis', deprecated_to = 'Ax3')),
("Se3", "PAM3-Sugar-End", 305, 1.0, [[2, 210, tetra2]], dict(role = 'strand', deprecated_to = 'X')), # might be WRONG
# WARNING: Se3 is a confusing name, since Se with no '3' or '5' is Selenium (unrelated).
# Fortunately Se3 is one of the deprecated PAM elements, and there is no Se5. [bruce 080320]
("Sh3", "PAM3-Sugar-Hydroxyl", 306, 1.0, [[1, 210, None, 'sp']], dict(role = 'strand', deprecated_to = 'X')), # might be WRONG
("Hp3", "PAM3-Hairpin", 307, 1.0, [[2, 210, tetra2]], dict(role = 'strand', deprecated_to = 'Ss3')),
# note: 308 and 309 are not used because they correspond to PAM5 atoms
# with no PAM3 analogue.
# unpaired base elements:
# one-atom (besides backbone) unpaired base -- might be used, don't know yet
("Ub3", "PAM3-Unpaired-base", 310, 1.0, [[4, 200, tetra4]], dict(role = 'unpaired-base')),
# two-atom (besides backbone) unpaired base -- the PAM5 version of this
# (see elements_data_PAM5.py for an explanation of these element symbols
# and names, and something about their purpose)
# is a recent proposal under active development and is very likely to
# be used; the PAM3 translation is undecided, and might be a single Ub3,
# but seems a bit more likely to be a pair of these two, Ux3 and Uy3,
# because that way their positions will transform properly with no extra
# work when we rotate a set of atoms, and will define a PAM3+5 baseframe:
("Ux3", "PAM3-Unpaired-base-x", 311, 1.0, [[4, 200, tetra4]], dict(role = 'unpaired-base')), # (likely to be revised)
("Uy3", "PAM3-Unpaired-base-y", 312, 1.0, [[4, 200, tetra4]], dict(role = 'unpaired-base')), # (likely to be revised)
# note: 313 won't be used unless we decide we want a PAM3-Axis-handle,
# which is unlikely.
]
# 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
_PAM3AtomTypeData = [
["Ax3", None, 0, 8, 4, 2.00, tetra4],
["Ss3", None, 0, 6, 3, 2.10, flat],
["Pl3", None, 0, 4, 2, 2.10, tetra2],
["Sj3", None, 0, 6, 3, 2.10, flat],
["Ae3", None, 0, 6, 3, 2.00, tetra3],
["Se3", None, 0, 4, 2, 2.10, tetra2],
["Sh3", None, 0, 2, 1, 2.10, None],
["Hp3", None, 0, 4, 2, 2.10, tetra2],
["Ub3", None, 0, 8, 4, 2.00, tetra4],
["Ux3", None, 0, 8, 4, 2.00, tetra4],
["Uy3", None, 0, 8, 4, 2.00, tetra4],
]
# ==
def init_PAM3_elements( periodicTable):
periodicTable.addElements( _mendeleev,
_defaultRadiusAndColor,
_alternateRadiusAndColor,
_PAM3AtomTypeData,
_DIRECTIONAL_BOND_ELEMENTS_PAM3,
default_options = dict(pam = MODEL_PAM3)
)
return
# end
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