- Sep 05, 2018
- Sep 04, 2018
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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
Added support for having multiple intrahelical connections from a single "location" in a segment; allows two ssDNA strands to emerge from the ends of a dsDNA segment
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cmaffeo2 authored
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cmaffeo2 authored
Code now always places a ssDNA bead when an ssDNA segment is between two dsDNA segments. Code now more robustly places a bead and intrahelical junctions
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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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- Aug 29, 2018
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cmaffeo2 authored
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- Aug 28, 2018
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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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- Aug 24, 2018
- Aug 21, 2018
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cmaffeo2 authored
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- Aug 20, 2018
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cmaffeo2 authored
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- Aug 17, 2018
- Aug 13, 2018
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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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- Aug 10, 2018
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cmaffeo2 authored
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- Jul 23, 2018
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cmaffeo2 authored
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- Jul 20, 2018
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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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