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New Topology Format #69

Merged
merged 37 commits into from
Oct 3, 2023
Merged

New Topology Format #69

merged 37 commits into from
Oct 3, 2023

Commits on Mar 1, 2023

  1. Add an utility class to help parsing DNA/RNA topology files

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 1, 2023
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Commits on Mar 3, 2023

  1. Make it possible to use a new type of topology 

    Note that only few selected features are available if using the new
topology.
    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 3, 2023
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Commits on Mar 5, 2023

  1. Add custom-type nucleotides to and strengthen the parser

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 5, 2023
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Commits on Mar 13, 2023

  1. Add flexibility to the new way of parsing the topology file

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 13, 2023
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  2. Add another check to the new topology parser

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 13, 2023
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  3. Change the default value for the type line in the new topology file 

    From now on, if not specified the parser will assume `type=DNA`
    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 13, 2023
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Commits on Mar 19, 2023

  1. Start implementing a script to convert between the topology formats

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 19, 2023
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Commits on Mar 22, 2023

  1. Complete the conversion script

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Mar 22, 2023
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Commits on Apr 14, 2023

  1. Update pybind11 version to 2.10.0 for Python11 compatability

    @ErikPoppleton
    ErikPoppleton committed Apr 14, 2023
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  2. update python version requirements

    @ErikPoppleton
    ErikPoppleton committed Apr 14, 2023
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Commits on May 22, 2023

  1. Merge branch 'new_topology' into oat_new_top

    @ErikPoppleton
    ErikPoppleton committed May 22, 2023
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  2. linear strands work

    @ErikPoppleton
    ErikPoppleton committed May 22, 2023
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  3. circular strands work for new topology, broken for old topology

    @ErikPoppleton
    ErikPoppleton committed May 22, 2023
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Commits on May 23, 2023

  1. topology reader is fully operational

    @ErikPoppleton
    ErikPoppleton committed May 23, 2023
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  2. can now write to new top format

    @ErikPoppleton
    ErikPoppleton committed May 23, 2023
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  3. Raise error when converting topology but not configuration

    @ErikPoppleton
    ErikPoppleton committed May 23, 2023
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Commits on May 30, 2023

  1. merge new_top parsers into oat_dev

    @ErikPoppleton
    ErikPoppleton committed May 30, 2023
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  2. Make the topology converter support multi-strand configurations

    @lorenzo-rovigatti
    lorenzo-rovigatti committed May 30, 2023
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  3. merge new_topology into oat_dev

    @ErikPoppleton
    ErikPoppleton committed May 30, 2023
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  4. actually merge_new_toplogy into oat_dev

    @ErikPoppleton
    ErikPoppleton committed May 30, 2023
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Commits on Jun 2, 2023

  1. small docstring and typing update

    @ErikPoppleton
    ErikPoppleton committed Jun 2, 2023
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Commits on Jun 8, 2023

  1. fixed topology writing bug with old format in subset

    @ErikPoppleton
    ErikPoppleton committed Jun 8, 2023
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  2. fixed topology writing bug with old format in subset

    @ErikPoppleton
    ErikPoppleton committed Jun 8, 2023
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Commits on Jun 16, 2023

  1. update typing for distance

    @ErikPoppleton
    ErikPoppleton committed Jun 16, 2023
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  2. added scaling page to the docs

    @ErikPoppleton
    ErikPoppleton committed Jun 16, 2023
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  3. move scaling in TOC

    @ErikPoppleton
    ErikPoppleton committed Jun 16, 2023
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Commits on Sep 15, 2023

  1. fixed error in oxDNA_PDB CLI parser

    @ErikPoppleton
    ErikPoppleton committed Sep 15, 2023
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  2. updated documentation to reflect the problem with base conda environm… 

    …ents
    @ErikPoppleton
    ErikPoppleton committed Sep 15, 2023
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  3. Merge branch 'master' into update_pybind

    @ErikPoppleton
    ErikPoppleton committed Sep 15, 2023
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Commits on Sep 18, 2023

  1. changed oxpy python version to match oat's so that errors are emitted… 

    … at cmake phase
    @ErikPoppleton
    ErikPoppleton committed Sep 18, 2023
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Commits on Sep 20, 2023

  1. Merge branch 'update_pybind' into oat_dev

    @ErikPoppleton
    ErikPoppleton committed Sep 20, 2023
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  2. added stiff_rate to mutual_trap and updated documentation to include … 

    …both rate and stiff_rate
    @ErikPoppleton
    ErikPoppleton committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. Merge branch 'master' into oat_dev

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Sep 21, 2023
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Commits on Sep 22, 2023

  1. Make the topology converter more flexible

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Sep 22, 2023
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  2. Add info about the new topology to the docs

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Sep 22, 2023
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Commits on Sep 23, 2023

  1. Add documentation and an example for the new topology format

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Sep 23, 2023
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Commits on Sep 25, 2023

  1. bump oat version and update lots of documentation

    @ErikPoppleton
    ErikPoppleton committed Sep 25, 2023
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