DNA-RNA hybrids #72

lorenzo-rovigatti · 2023-10-08T08:51:22Z

Add the possibility of simulating DNA-RNA hybrids (by @eryykr )

This reverts commit b867624.

…MC backend" This reverts commit 7ec2968.

This reverts commit b09640c.

Added an interaction type for relaxing systems containing both DNA and RNA.

Fixed bugs caused by double inheritance (i think), updated function for checking input sanity to accommodate for both DNA and RNA in the system.

Interaction type with modified backbone potential for relaxing systems containing both DNA and RNA.

…dna-rna-hybrids into double-inheritance

Adding the new topology format to the hybrid model

Trying to fix (suspected) undefined behaviour

Version of hybrid model which uses inheritance

Add the DNA-RNA hybrid model

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

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

src/Interactions/DNAInteraction.cpp

src/Interactions/DRHInteraction_relax.cpp

src/defs.h

lorenzo-rovigatti · 2023-10-08T10:55:46Z

src/Particles/BaseParticle.h

+
+	/// Needed for DNA-RNA interactions
+	char acid_type;


@eryykr Can we do this bookkeeping in the DRH interaction rather than here? Do you foresee any issues?

I think we could so long as there is a way of distinguishing between DNA and RNA nucleotides without acid_type

OK! Have a look at my changes in b695623 and let me know if you agree with them.

Looks good!

* 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 · 2023-10-09T11:33:26Z

While working on this branch, yesterday I have also added a few more tests that check the values of the energy terms present in a nicked double strand as computed by the DNA2, RNA2 and DNA_RNA force fields. These are run automatically every time a push is performed, but you can also run them manually with make test_run.
Pinging @ErikPoppleton @sulcgroup: if you collaborate with someone who works on the code you can tell them to run the tests locally and check that their changes do not impact the core code.

These tests will end up in master as soon as we merge the branch (which will happen soon, hopefully)

eryykr and others added 30 commits March 9, 2023 21:45

Update model.h

9f792d7

Update BaseParticle.cpp

a4d180c

Update BaseParticle.h

3a5c797

Update DNANucleotide.cpp

8b72e27

Update RNANucleotide.cpp

1f4fc62

Add files via upload

e632f2c

Update InteractionFactory.cpp

fefbf53

Update CMakeLists.txt

c84b315

Update VMMC_CPUBackend.cpp

0b6a06f

Update defs.h

689be17

Update defs.h

e8836e1

Update Utils.cpp

c9bb227

Update Utils.h

601a2f2

Add files via upload

77110c9

Add files via upload

b0ceada

Update CMakeLists.txt

15103c6

Update InteractionFactory.cpp

501656c

Update model.h

3bb1c68

Update DNAwithRNAInteraction.h

d0a8e1c

Revert "Add a pivot move to the MC2 backend"

b09640c

This reverts commit b867624.

Revert "Remove some unnecessary checks on the required keys from the …

a5b4c3c

…MC backend" This reverts commit 7ec2968.

Revert "Revert "Add a pivot move to the MC2 backend""

5bb203e

This reverts commit b09640c.

Update model.h

0b90c31

Add files via upload

98d8496

Updating interaction strengths

94cf566

Merge branch 'master' of https://github.com/eryykr/oxDNA-dna-rna-hybrids

3311446

Update hybrid_sequence_dependent_parameters.txt

5b1e049

DNAwithRNA_relax interaction type

a5c3468

Added an interaction type for relaxing systems containing both DNA and RNA.

Merge branch 'master' of https://github.com/eryykr/oxDNA-dna-rna-hybrids

524ce04

Fixing sequence-dependent parameter bug

2667b73

eryykr and others added 22 commits May 23, 2023 16:15

Update to DRH code

720d3d2

Fixed bugs caused by double inheritance (i think), updated function for checking input sanity to accommodate for both DNA and RNA in the system.

Update DRHInteraction.cpp

faac6b3

DRHInteraction_relax

f4c90d1

Interaction type with modified backbone potential for relaxing systems containing both DNA and RNA.

Merge branch 'double-inheritance' of https://github.com/eryykr/oxDNA-…

0fa5134

…dna-rna-hybrids into double-inheritance

New Topology

150ffec

Adding the new topology format to the hybrid model

Updating DRH+protein interaction class

5529064

DNA and RNA interactions with new topology

11f8f3d

Seq-dep file keys

2f8581b

Update VMMC_CPUBackend.cpp

12566dd

Fixed FFS with ANM bug

4826c55

Update drh_model.h

f145a31

Updating DRHInteraction

10c5525

Trying to fix (suspected) undefined behaviour

Cleaning up inheritance of _custom_f4

b653b53

Small changes to DNANM

d8554ae

Merge pull request #1 from eryykr/double-inheritance

da13f09

Version of hybrid model which uses inheritance

Dropping some unneeded stuff

58e6843

Cleaning up analysis/tests/

ac080cc

Resolving conflict in MC backend

325c61e

Removing old protein model stuff

1b88ac5

Merge pull request #68 from eryykr/master

1b88844

Add the DNA-RNA hybrid model

Add new tests

da82d07

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

Remove a private member from the DNA and RNA classes

acad5d6

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 commented Oct 8, 2023

View reviewed changes

Clean up some code

b695623

* 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 added 3 commits October 9, 2023 13:37

Update the test docs

1292c20

Update the docs with info about the DRH interaction

43ccf6f

Update the README

aed4a01

lorenzo-rovigatti merged commit 7c97406 into master Oct 9, 2023
3 checks passed

lorenzo-rovigatti deleted the dna_rna branch October 9, 2023 15:02

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DNA-RNA hybrids #72

DNA-RNA hybrids #72

lorenzo-rovigatti commented Oct 8, 2023

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eryykr Oct 9, 2023

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eryykr Oct 9, 2023

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DNA-RNA hybrids #72

DNA-RNA hybrids #72

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