acellera-modrna-params 0.1.0__py3-none-any.whl

acellera_modrna_params-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: acellera-modrna-params
+Version: 0.1.0
+Summary: OL3-consistent AMBER force-field parameters for modified RNA residues, generated with modXNA
+Author: Acellera
+License-Expression: GPL-3.0-only
+Project-URL: Homepage, https://github.com/Acellera/acellera-modrna-params
+Keywords: amber,rna,force-field,modified-nucleotides,modxna
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: parmed; extra == "test"
+Provides-Extra: amber
+Requires-Dist: ambertools-unofficial>=26.0.0; extra == "amber"
+Dynamic: license-file
+
+# acellera-modrna-params
+
+OL3-consistent AMBER force-field parameters for modified RNA residues,
+generated with [modXNA](https://github.com/modxna/modxna).
+
+This is a standalone GPL-3.0 package (see "Licensing"). It ships pre-generated
+AMBER OFF libraries plus the shared `frcmod.modxna`, so downstream tools can
+depend on it and load the files without needing modXNA or a generation step.
+
+## Supported residues
+
+Nine PDB residues, each in three chain-context forms (internal, 5'-terminal,
+3'-terminal), following OL3's `G` / `G5` / `G3` convention. Unit names are the
+PDB code with a `5`/`3` suffix for the terminal forms (e.g. `5MC`, `5MC5`,
+`5MC3`).
+
+| PDB | modXNA base | note |
+|-----|-------------|------|
+| 5MC | M5C | |
+| PSU | PUU | modXNA `PSU` is a thiouracil; real pseudouridine is `PUU` |
+| 5MU | M5U | |
+| 2MG | M2G | modXNA `2MG` is N2,N2-dimethyl; mono-methyl is `M2G` |
+| 1MG | M1G | |
+| 2MA | M2A | |
+| 1MA | M1A | |
+| 4AC | A4C | |
+| 6IA | I6A | |
+
+## Install
+
+```bash
+pip install acellera-modrna-params
+```
+
+## Usage
+
+```python
+import modrna_params as mp
+
+mp.RESIDUES                     # supported PDB codes
+mp.frcmod_path()                # path to frcmod.modxna
+mp.lib_path("5MC")              # internal form
+mp.lib_path("5MC", "5prime")    # 5'-terminal form
+mp.leaprc_lines()               # tleap loadamberparams/loadoff lines
+```
+
+In tleap:
+
+```
+source leaprc.RNA.OL3
+loadamberparams <frcmod_path()>
+loadoff <lib_path("5MC")>
+x = sequence { G5 5MC G3 }
+```
+
+## Charge consistency with OL3
+
+Internal residues are OL3-consistent: backbone and sugar atom charges match
+OL3's standard nucleotides to ~0.001 e; only the glycosidic-junction atoms
+(C1'/H1') shift, as expected for a base modification. Terminal caps carry
+modXNA's own fitted charges and do not match OL3 per-atom. modXNA's terminal
+split (5' = -0.320348, 3' = -0.679652) sums to -1.000, so a strand with the
+modified residue internal, or modified at both termini, is integral; a strand
+that mixes a modXNA-modified terminus with a standard OL3 terminus is
+non-integral by ~0.012 e (it still builds; downstream neutralization handles
+it).
+
+## Licensing
+
+The `.lib` files are derivative works of modXNA's GPL-3.0 fragment library and
+`frcmod.modxna` is redistributed verbatim, so this package is GPL-3.0-only. See
+`LICENSE` and `NOTICE`. Please cite modXNA (J. Chem. Theory Comput. 2024,
+doi:10.1021/acs.jctc.4c01164).

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acellera_modrna_params-0.1.0.dist-info/WHEEL

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+Generator: setuptools (83.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
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