Commit 27fbc86c authored by cmaffeo2's avatar cmaffeo2
Browse files

Added all-atom model

parent fca5b912
......@@ -21,7 +21,8 @@ def stringToIntTuples(string, tupleLen, offset):
class CanonicalNucleotide(Group):
# DefaultOrientation = rotationAboutAxis([0,0,1], 68)
DefaultOrientation = rotationAboutAxis([0,0,1], 68+180)
# DefaultOrientation = rotationAboutAxis([0,0,1], 68+180)
DefaultOrientation = rotationAboutAxis([0,0,1], 68+180-20)
def __init__(self, prefix, seq):
self.sequence = seq
Group.__init__(self, orientation = CanonicalNucleotide.DefaultOrientation)
......
......@@ -16,7 +16,12 @@ import pdb
"""
TODO:
+ fix handling of crossovers for atomic representation
- map to atomic representation
+ map to atomic representation
- add nicks
- shrink ssDNA
- shrink dsDNA backbone
- make orientation continuous
- sequence
- remove performance bottlenecks
- test for large systems
- assign sequence
......
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