semvec/pypi-packages huggingface dataset:
novemberff 0.6.1
Custom implementation of the AMBER forcefield, focused on simplicity and verbose outputs.
License: MIT
Requires Python: >=3.10
Keywords: Amber Forcefield MolecularDynamics MD Simulation

# NOVEMBERFF
**NovemberFF** (implemeNtatiOn of VErbose aMBER ForceField) is a custom implementation of the AMBER forcefield, inspired by [OpenMM](https://github.com/openmm/openmm)'s C++ source. NovemberFF's aim is not to be performant, but rather to be compact and easy to modify/customize. It also provides by default the option to obtain verbose outputs, i.e. the energies of every singular molecular interaction in arrays (instead of their sum).

* Current outputs supported:
    * Bonded energies
    * Angle energies
    * Dihedral (Torsion) energies
    * LennardJones energies
    * Coulomb energies

* Current forcefield formats supported:
    * XML

* Current forcefields packed along NovemberFF (at `novemberff/_data`):
    * `RNA.OL3.xml` for RNA
    * `amber99sb.xml` for protein
    * `amber99sb-ucb.xml` for protein

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# Requirements
* currently depends on `MDAnalysis` for parsing the PDB structures

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# Examples
* display energy sums:
```python3 main.py rna  testdata/1ato.pdb```
```python3 main.py prot testdata/prot.pdb```

* save energy arrays:
```python3 main.py rna  testdata/1ato.pdb testdata/output/1ato```
```python3 main.py prot testdata/prot.pdb testdata/output/prot```


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# TODO
* improve CLI.
* add documentation.
* add more forcefields.
* improve performance.
    * remove MDAnalysis dependency for PDB parsing.
    * improve `bond_graphs`'s graph data structure.
* improve the residue/atom labels fixing procedures.
* finish refactoring of parser base class and `forcefield.from_xml` (i.e. should be Parser's responsability to yield the needed data, not Forcefield).
* allow to specify the forcefield to use in `main.py`.
* improve the option for saving the molecule's topology features (bonds, angles, etc), as well as their geometry values. Add it to the CLI.  Add tests.
* allow the XML parser to deal with files were new lines are missing.
* improve `Utils.solve_forcefield_path`