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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

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ErikPoppleton
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This pull request includes the following major updates to all systems:

  • The new topology format with correct DNA strand orientation
  • Updates to oat to work with the new topology format

And the following minor update to oxDNA:

  • Implement rate for stiff as well as for r0 for mutual_trap

And the following minor updates to oxDNA_analysis_tools:

  • Update external force system to work with the rate parameters above
  • Fixed bug in oxDNA2PDB CLI parser
  • Updates to typing and docstrings

lorenzo-rovigatti and others added 30 commits March 1, 2023 09:37
@lorenzo-rovigatti
Add an utility class to help parsing DNA/RNA topology files
3e843f9
@lorenzo-rovigatti
Make it possible to use a new type of topology
0040414 
Note that only few selected features are available if using the new
topology.
@lorenzo-rovigatti
Add custom-type nucleotides to and strengthen the parser
cd2e2db
@lorenzo-rovigatti
Add flexibility to the new way of parsing the topology file
04c4cef
@lorenzo-rovigatti
Add another check to the new topology parser
53bd29b
@lorenzo-rovigatti
Change the default value for the type line in the new topology file
526e2e3 
From now on, if not specified the parser will assume `type=DNA`
@lorenzo-rovigatti
Start implementing a script to convert between the topology formats
619d142
@lorenzo-rovigatti
Complete the conversion script
c47d45f
@ErikPoppleton
Update pybind11 version to 2.10.0 for Python11 compatability
1100ef4
@ErikPoppleton
update python version requirements
c65dfd6
@ErikPoppleton
Merge branch 'new_topology' into oat_new_top
6325f4d
@ErikPoppleton
linear strands work
0b48d67
@ErikPoppleton
circular strands work for new topology, broken for old topology
1548c78
@ErikPoppleton
topology reader is fully operational
838008c
@ErikPoppleton
can now write to new top format
3269bda
@ErikPoppleton
Raise error when converting topology but not configuration
ba40b9c
@ErikPoppleton
merge new_top parsers into oat_dev
54f4033
@lorenzo-rovigatti
Make the topology converter support multi-strand configurations
732331a
@ErikPoppleton
merge new_topology into oat_dev
471c751
@ErikPoppleton
actually merge_new_toplogy into oat_dev
4debb78
@ErikPoppleton
small docstring and typing update
d49cad7
@ErikPoppleton
fixed topology writing bug with old format in subset
fbdc2fa
@ErikPoppleton
fixed topology writing bug with old format in subset
466b345
@ErikPoppleton
update typing for distance
00cd6f2
@ErikPoppleton
added scaling page to the docs
c0dee6c
@ErikPoppleton
move scaling in TOC
1fff467
@ErikPoppleton
fixed error in oxDNA_PDB CLI parser
23d4c8b
@ErikPoppleton
updated documentation to reflect the problem with base conda environm…
ecba8d1 
…ents
@ErikPoppleton
Merge branch 'master' into update_pybind
61afa46
@ErikPoppleton
changed oxpy python version to match oat's so that errors are emitted…
3664f94 
… at cmake phase
@ErikPoppleton
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Note that update_pybind was already merged into this branch, so maybe I should wait until that's merged in and resubmit this.

@lorenzo-rovigatti
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I have added an example and some documentation. Can you have a look when you have some spare time? If you like it we can merge the branch (and maybe make a new release?)

@ErikPoppleton
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I haven't looked at the example yet, but I just took a pass at the documentation and added a bunch more of my own to the oat subdirectory.

@lorenzo-rovigatti lorenzo-rovigatti merged commit a6214b9 into master Oct 3, 2023
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@lorenzo-rovigatti lorenzo-rovigatti Awaiting requested review from lorenzo-rovigatti

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2 participants
@ErikPoppleton @lorenzo-rovigatti