1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
|
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_model_constants.py -- constants for dna_model internals
(not the same as Dna_Constants.py, which is about DNA itself)
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
# Codes for ladder ends (used privately or passed to other-ladder friend methods)
# or chain ends.
#
# WARNING: they don't correspond in these uses! That is, strand2 of a ladder
# has chain-ends in the order 1,0, but has ladder-ends in the order 0,1.
# So I'll introduce different names for these uses. But there might be
# helper methods which accept either kind -- not sure. For now,
# assume that it's required for the two sets to have identical values.
# [bruce 080116]
LADDER_ENDS = (0, 1)
LADDER_END0 = LADDER_ENDS[0] # "left" for ladder
LADDER_END1 = LADDER_ENDS[1] # "right" for ladder
LADDER_OTHER_END = [1, 0] # 1 - end
LADDER_BOND_DIRECTION_TO_OTHER_AT_END_OF_STRAND1 = [-1, 1] # not correct for strand2 of a ladder
LADDER_STRAND1_BOND_DIRECTION = LADDER_BOND_DIRECTION_TO_OTHER_AT_END_OF_STRAND1[LADDER_END1]
CHAIN_ENDS = LADDER_ENDS
CHAIN_END0 = CHAIN_ENDS[0] # "5' end" for strand
CHAIN_END1 = CHAIN_ENDS[1] # "3' end" for strand
CHAIN_OTHER_END = [1, 0] # 1 - end
CHAIN_BOND_DIRECTION_TO_OTHER_AT_END_OF_STRAND = [-1, 1]
MAX_LADDER_LENGTH = 500 # @@@@ TODO: also use this to split long ladders
# MAX_LADDER_LENGTH limits the length of a DnaLadder that we will create
# by merging (this is implemented, and ran at 20 for a long time),
# and (not yet implemented) causes us to split DnaLadders that are longer
# than this (when encountered by the dna updater).
#
# When it's fully implemented, the best value should be determined based
# on performance (eg of graphics), and might be 20 or lower (splitting
# would be fairly common for 20).
#
# Right now, since it's only partly implemented, and since
# some display or UI ops may not yet handle split ladders ideally,
# make it a large enough value that failure to split
# (resulting in history-dependence of final state) will be rare.
#
# [bruce 080314]
# end
|
