Martini3 SAXS formfactors - #1429
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New MARTINI_FF keyword selects the Martini form-factor generation: 2 (default, existing Martini 2.2) or 3 (Martini 3 proteins). v3 adds getMartiniFFparam_v3 with per-bead degree-6 polynomials and the M3 bead->type mapping (new beads ALA_SC1, TRP_SC5, TYR_SC4). Includes regtest rt-saxs-martini3 (4LZT lysozyme) and changelog entry.
…actors # Conflicts: # CHANGES/v2.11.md
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@mlund thanks for your contribution, to me this is fine to be merged as is. I'll wait for you setting it as ready |
Add the runtime plumed.cite() reference (ChemRxiv, doi:10.26434/chemrxiv.15006205/v1) printed when MARTINI_FF=3 is selected, and point the manual page at it from the MARTINI_FF description.
Add explanatory comments describing the two halves of the function (the per-bead form-factor coefficient table and the MOLINFO-based bead->index mapping), clearing the CodeQL "poorly documented large function" warning. No functional change.
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Thanks, I was waiting for the ChemRxiv DOI which is now added. It's under review. |
mlund
marked this pull request as ready for review
July 20, 2026 07:51
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Description
This pull request adds support for using Martini 3 protein form factors in the
SAXSaction, allowing users to select between Martini 2.2 (the previous default) and Martini 3 form-factor sets via a newMARTINI_FFkeyword.MARTINI_FFkeyword to theSAXSaction, allowing users to choose between Martini 2.2 (MARTINI_FF=2, default) and Martini 3 (MARTINI_FF=3) protein form factors. The code validates the keyword and applies the correct parameter set. (src/isdb/SAXS.cpp) [1] [2] [3]getMartiniFFparam_v3to provide the Martini 3 protein bead form-factor coefficients and updated the bead enumeration to include new beads present only in Martini 3. (src/isdb/SAXS.cpp) [1] [2]MARTINI_FFoption and its behavior. (src/isdb/SAXS.cpp,CHANGES/v2.11.md) [1] [2]SAXSaction with Martini 3 form factors, including configuration, reference output, and input files. (regtest/isdb/rt-saxs-martini3/)These changes ensure users can now select the latest Martini 3 protein form factors for SAXS calculations in PLUMED, with appropriate documentation and testing.
Target release
I would like my code to appear in release v2.11
Type of contribution
Copyright
I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.
the module I added or modified contains a
COPYRIGHTfile with the correct license information. Code should be released under an open source license. I also used the commandcd src && ./header.sh mymodulenamein order to make sure the headers of the module are correct.Tests