- 18 Feb, 2020 3 commits
- 12 Feb, 2020 1 commit
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cmaffeo2 authored
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- 08 Feb, 2020 2 commits
- 07 Feb, 2020 4 commits
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cmaffeo2 authored
a) some intrinsic flexibility associated with the first crossover b) the spring for the twist of the helix c) intrinsic flexibility associated with the second crossover
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cmaffeo2 authored
1) Proper accounting for a single bond representing a double crossover 2) Parallel-helix dihedral angle spring constant is now computed from three "springs" placed in series that represent: a) the flexibility of the bond on one side of the crossover b) the intrinsic flexibility of the crossover c) the flexibility of the bond on the other side of the crossover
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cmaffeo2 authored
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cmaffeo2 authored
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- 24 Jan, 2020 2 commits
- 22 Jan, 2020 1 commit
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- 07 Jan, 2020 1 commit
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- 02 Jan, 2020 1 commit
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cmaffeo2 authored
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- 12 Dec, 2019 1 commit
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cmaffeo2 authored
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- 06 Dec, 2019 1 commit
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cmaffeo2 authored
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- 18 Nov, 2019 1 commit
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cmaffeo2 authored
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- 31 Oct, 2019 1 commit
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cmaffeo2 authored
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- 27 Sep, 2019 2 commits
- 26 Sep, 2019 6 commits
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cmaffeo2 authored
Added test to check that model_from_basepair_stack_3prime works with circular ssDNA; removed warnings and made function work with lists instead of numpy arrays
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cmaffeo2 authored
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cmaffeo2 authored
Fixed polygon_mesh reader so that it works with user-generated .ma files, not just autogenerated ones
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cmaffeo2 authored
find_stacks routine moved to segmentmodel_from_lists using only coordinates and transforms; generate stacks automatically if None kept old find_stacks routine in segmentmodel_from_pdb as find_stacks_mdanalysis
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cmaffeo2 authored
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cmaffeo2 authored
1) Passthrough of mrdna.segmentmodel arguments 2) Improved input validation 3) Stacks are removed unless stack[bp[stack]] == stack 4) Cleaner code for assigning ends of terminally-connected "segments"
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- 25 Sep, 2019 4 commits
- 05 Sep, 2019 1 commit
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cmaffeo2 authored
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- 04 Sep, 2019 1 commit
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cmaffeo2 authored
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- 27 Aug, 2019 1 commit
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cmaffeo2 authored
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- 20 Aug, 2019 5 commits
- 13 Aug, 2019 1 commit
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cmaffeo2 authored
Prepared code structure in potential section so that dsDNA and ssDNA are treated using separate defs
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