- 04 Sep, 2018 7 commits
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cmaffeo2 authored
Updated algorithm that fits splines into beads to extend farther into intrahelically connected segments, and to use linear interpolation for quaternions, resulting in better all-atom models
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cmaffeo2 authored
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cmaffeo2 authored
Updated bead model potentials to work with antiparallel DNA; also made terminal_crossovers bond shorter at 1.2 nm (vs 1.85)
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
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- 29 Aug, 2018 1 commit
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cmaffeo2 authored
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- 28 Aug, 2018 7 commits
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cmaffeo2 authored
Added type_ argument to SingleStrandedSegment.add_crossover() for compatibility with DoubleStrandedSegment
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
Updated imports to be compatible with new package structure; updated paths to resources to use new get_resource_path() function
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cmaffeo2 authored
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- 24 Aug, 2018 2 commits
- 21 Aug, 2018 1 commit
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cmaffeo2 authored
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- 20 Aug, 2018 1 commit
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cmaffeo2 authored
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- 17 Aug, 2018 4 commits
- 13 Aug, 2018 1 commit
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cmaffeo2 authored
Made bond potentials longer ranged (120 vs 50 nm), and removed unneeded 'continue' statement that was attempting to prevent double-counting when placing initial beads
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- 10 Aug, 2018 1 commit
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cmaffeo2 authored
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- 23 Jul, 2018 1 commit
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cmaffeo2 authored
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- 20 Jul, 2018 3 commits
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cmaffeo2 authored
Fixed spring constant for dihedral that spans crossovers, keeping helices parallel (note this differs from prototyped web service where 90 degree angle potentials were used) Changed dna bead type clustering to have higher resolution Streamlined some small parts of the code
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cmaffeo2 authored
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cmaffeo2 authored
Moved run_simulate_protocols outside of cadnano_segments since more modular; increased density of coarsest DNA model
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- 18 Jul, 2018 1 commit
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cmaffeo2 authored
Made intrahelical connections remove any existing connections; important for intrahelical "crossovers"
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- 17 Jul, 2018 2 commits
- 16 Jul, 2018 1 commit
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cmaffeo2 authored
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- 13 Jul, 2018 4 commits
- 10 Jul, 2018 3 commits