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DNA-RNA hybrids #72

Merged
merged 69 commits into from
Oct 9, 2023
Merged

DNA-RNA hybrids #72

merged 69 commits into from
Oct 9, 2023

Commits on Mar 9, 2023

  1. Update model.h

    @eryykr
    eryykr authored Mar 9, 2023
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  2. Update BaseParticle.cpp

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    eryykr authored Mar 9, 2023
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  3. Update BaseParticle.h

    @eryykr
    eryykr authored Mar 9, 2023
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  4. Update DNANucleotide.cpp

    @eryykr
    eryykr authored Mar 9, 2023
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  5. Update RNANucleotide.cpp

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    eryykr authored Mar 9, 2023
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  6. Add files via upload

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    eryykr authored Mar 9, 2023
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  7. Update InteractionFactory.cpp

    @eryykr
    eryykr authored Mar 9, 2023
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  8. Update CMakeLists.txt

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    eryykr authored Mar 9, 2023
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  9. Update VMMC_CPUBackend.cpp

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    eryykr authored Mar 9, 2023
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Commits on Mar 10, 2023

  1. Update defs.h

    @eryykr
    eryykr authored Mar 10, 2023
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  2. Update defs.h

    @eryykr
    eryykr authored Mar 10, 2023
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  3. Update Utils.cpp

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    eryykr authored Mar 10, 2023
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  4. Update Utils.h

    @eryykr
    eryykr authored Mar 10, 2023
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  5. Add files via upload

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    eryykr authored Mar 10, 2023
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  6. Add files via upload

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  7. Update CMakeLists.txt

    @eryykr
    eryykr authored Mar 10, 2023
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  8. Update InteractionFactory.cpp

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    eryykr authored Mar 10, 2023
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  9. Update model.h

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    eryykr authored Mar 10, 2023
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Commits on Mar 17, 2023

  1. Update DNAwithRNAInteraction.h

    @eryykr
    eryykr committed Mar 17, 2023
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  2. Revert "Add a pivot move to the MC2 backend" 

    This reverts commit b867624.
    @eryykr
    eryykr committed Mar 17, 2023
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  3. Revert "Remove some unnecessary checks on the required keys from the … 

    …MC backend"

This reverts commit 7ec2968.
    @eryykr
    eryykr committed Mar 17, 2023
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  4. Revert "Revert "Add a pivot move to the MC2 backend"" 

    This reverts commit b09640c.
    @eryykr
    eryykr committed Mar 17, 2023
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Commits on Mar 23, 2023

  1. Update model.h

    @eryykr
    eryykr committed Mar 23, 2023
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Commits on Mar 24, 2023

  1. Add files via upload

    @eryykr
    eryykr authored Mar 24, 2023
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  2. Updating interaction strengths

    @eryykr
    eryykr committed Mar 24, 2023
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  3. Merge branch 'master' of https://github.com/eryykr/oxDNA-dna-rna-hybrids

    @eryykr
    eryykr committed Mar 24, 2023
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  4. Update hybrid_sequence_dependent_parameters.txt

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    eryykr authored Mar 24, 2023
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Commits on Mar 29, 2023

  1. DNAwithRNA_relax interaction type 

    Added an interaction type for relaxing systems containing both DNA and RNA.
    @eryykr
    eryykr committed Mar 29, 2023
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  2. Merge branch 'master' of https://github.com/eryykr/oxDNA-dna-rna-hybrids

    @eryykr
    eryykr committed Mar 29, 2023
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Commits on Apr 5, 2023

  1. Fixing sequence-dependent parameter bug

    @eryykr
    eryykr authored Apr 5, 2023
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Commits on Apr 13, 2023

  1. Update hybrid_sequence_dependent_parameters.txt

    @eryykr
    eryykr authored Apr 13, 2023
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Commits on Apr 22, 2023

  1. Update DNAwithRNAInteraction.cpp

    @eryykr
    eryykr authored Apr 22, 2023
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  2. Update DNAwithRNAInteraction.cpp

    @eryykr
    eryykr committed Apr 22, 2023
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  3. Merge branch 'master' of https://github.com/eryykr/oxDNA-dna-rna-hybrids

    @eryykr
    eryykr committed Apr 22, 2023
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  4. Update DNAwithRNAInteraction.cpp

    @eryykr
    eryykr committed Apr 22, 2023
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Commits on Apr 26, 2023

  1. Update hybrid_sequence_dependent_parameters.txt

    @eryykr
    eryykr authored Apr 26, 2023
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  2. Update model.h

    @eryykr
    eryykr authored Apr 26, 2023
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Commits on May 6, 2023

  1. Separate file for hybrid model parameters

    @eryykr
    eryykr committed May 6, 2023
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  2. Merge branch 'master' of https://github.com/eryykr/oxDNA-dna-rna-hybrids

    @eryykr
    eryykr committed May 6, 2023
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  3. Update model.h

    @eryykr
    eryykr committed May 6, 2023
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Commits on May 10, 2023

  1. Hybrid interaction with inheritance 

    Rewriting the DNA/RNA hybrid interaction to inherit from the DNA2 and RNA2 interactions.
    @eryykr
    eryykr committed May 10, 2023
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  2. Update DRHInteraction.cpp

    @eryykr
    eryykr committed May 10, 2023
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  3. Update DRHInteraction.cpp

    @eryykr
    eryykr committed May 10, 2023
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Commits on May 23, 2023

  1. Update to DRH code 

    Fixed bugs caused by double inheritance (i think), updated function for checking input sanity to accommodate for both DNA and RNA in the system.
    @eryykr
    eryykr committed May 23, 2023
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  2. Update DRHInteraction.cpp

    @eryykr
    eryykr authored May 23, 2023
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Commits on May 25, 2023

  1. DRHInteraction_relax 

    Interaction type with modified backbone potential for relaxing systems containing both DNA and RNA.
    @eryykr
    eryykr committed May 25, 2023
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  2. Merge branch 'double-inheritance' of https://github.com/eryykr/oxDNA-… 

    …dna-rna-hybrids into double-inheritance
    @eryykr
    eryykr committed May 25, 2023
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Commits on May 29, 2023

  1. New Topology 

    Adding the new topology format to the hybrid model
    @eryykr
    eryykr committed May 29, 2023
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  2. Updating DRH+protein interaction class

    @eryykr
    eryykr committed May 29, 2023
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  3. DNA and RNA interactions with new topology

    @eryykr
    eryykr committed May 29, 2023
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Commits on Jun 4, 2023

  1. Seq-dep file keys

    @eryykr
    eryykr committed Jun 4, 2023
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Commits on Jun 16, 2023

  1. Update VMMC_CPUBackend.cpp

    @eryykr
    eryykr committed Jun 16, 2023
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Commits on Jul 14, 2023

  1. Fixed FFS with ANM bug

    @eryykr
    eryykr committed Jul 14, 2023
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  2. Update drh_model.h

    @eryykr
    eryykr committed Jul 14, 2023
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  3. Updating DRHInteraction 

    Trying to fix (suspected) undefined behaviour
    @eryykr
    eryykr committed Jul 14, 2023
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Commits on Jul 15, 2023

  1. Cleaning up inheritance of _custom_f4

    @eryykr
    eryykr committed Jul 15, 2023
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Commits on Sep 19, 2023

  1. Small changes to DNANM

    @eryykr
    eryykr committed Sep 19, 2023
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  2. Merge pull request #1 from eryykr/double-inheritance 

    Version of hybrid model which uses inheritance
    @eryykr
    eryykr authored Sep 19, 2023
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  3. Dropping some unneeded stuff

    @eryykr
    eryykr committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Cleaning up analysis/tests/

    @eryykr
    eryykr committed Sep 20, 2023
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  2. Resolving conflict in MC backend

    @eryykr
    eryykr committed Sep 20, 2023
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Commits on Sep 25, 2023

  1. Removing old protein model stuff

    @eryykr
    eryykr committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Merge pull request #68 from eryykr/master 

    Add the DNA-RNA hybrid model
    @lorenzo-rovigatti
    lorenzo-rovigatti authored Sep 26, 2023
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Commits on Oct 8, 2023

  1. Add new tests 

    This commit adds 6 more tests to the `run` level. These tests check that the DNA, RNA and DRH interactions compute the right energies for a short nicked duplex
    @lorenzo-rovigatti
    lorenzo-rovigatti committed Oct 8, 2023
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  2. Remove a private member from the DNA and RNA classes 

    The member was used to check in the RNA and DNA classes whether the instance of the interaction was actually a DRH interaction. We now check this with a local variable since we need this information only at the very beginning
    @lorenzo-rovigatti
    lorenzo-rovigatti committed Oct 8, 2023
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Commits on Oct 9, 2023

  1. Clean up some code 

    * Remove some unusued define's
* Turn a char[] into a std::string
* Move the information about the type of each nucleotide (R or D) from BaseParticle to the DRHInteraction
    @lorenzo-rovigatti
    lorenzo-rovigatti committed Oct 9, 2023
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  2. Update the test docs

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Oct 9, 2023
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  3. Update the docs with info about the DRH interaction

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Oct 9, 2023
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  4. Update the README

    @lorenzo-rovigatti
    lorenzo-rovigatti committed Oct 9, 2023
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