Third-Party Attributions & Licenses¶
MolPy is distributed under the BSD 3-Clause License
(Copyright © 2024–2025, Roy Kid). It ports or adapts code and reference data from
the projects listed here. Numerical kernels executed through the molrs Rust
backend are attributed in
molrs docs/attribution.md;
this page covers what MolPy's own Python layer copies.
External tools that MolPy merely invokes as a subprocess or imports as a library (Packmol, AmberTools, LAMMPS, CP2K, RDKit, OpenBabel, …) are runtime dependencies, not copied code, and are not listed here.
Ported / adapted — permissive licenses¶
| Project | SPDX | Copyright | Used in | Upstream |
|---|---|---|---|---|
| foyer | MIT |
© 2015 Vanderbilt University | typifier.graph (SMARTSGraph), typifier.matcher, typifier.atomistic (OPLS SMARTS atom-typing engine); data/forcefield/oplsaa.xml, tip3p.xml |
mosdef-hub/foyer |
| OpenMM | MIT (openmm/app/element.py) |
Stanford University and the Authors | core.element — element name/symbol/mass table |
openmm/openmm |
| moltemplate | MIT |
© 2013 Andrew Jewett, UC Santa Barbara | parser.moltemplate.*, cli.moltemplate — .lt format reader/writer & ltemplify |
jewettaij/moltemplate |
| tame | BSD-3-Clause |
© Yunqi Shao | compute.mcd, compute.pmsd, compute.time_series, compute.jacf, compute.onsager, compute.persist |
yqshao-archive/tame (archived) |
tamedeclareslicense = "BSD-3-Clause"in itspyproject.toml(it ships no standaloneLICENSEfile). It is an archived third-party project by Yunqi Shao.
Bundled parameter data¶
| Data file | Origin | License |
|---|---|---|
data/forcefield/oplsaa.xml, tip3p.xml |
OPLS-AA / TIP3P force-field XML from foyer | MIT (foyer) |
data/forcefield/clp.xml |
CL&P ionic-liquid force field, subset from paduagroup/clandp (il.ff) |
Academic; DOI 10.1021/jp0362133 |
data/forcefield/alpha.ff, clpol_fragments.ff |
paduagroup/clandpol CL&Pol polarizable data (A. Padua, K. Goloviznina) | Academic; DOI 10.1021/acs.jctc.9b00689 |
Kernels via the molrs backend¶
Analyses such as RDF, Steinhardt/hexatic/nematic order, radical Voronoi,
structure factor, and PMFT run through molrs, whose backend ports freud
(BSD-3-Clause), voro++ (BSD-3-Clause-LBNL), and RDKit
(BSD-3-Clause, MMFF). See the
molrs attribution file.
Specifications implemented (cite, not license)¶
Grammars under parser/grammar/ and parser/smiles/grammars/ implement public
notation specifications, not another project's code:
| Specification | Cited as | Implemented in |
|---|---|---|
| OpenSMILES | opensmiles.org community specification | smiles.lark, base.lark |
| Daylight SMILES/SMARTS | Daylight Theory Manual (© Daylight C.I.S. — proprietary documentation, cited only) | smarts.lark |
| BigSMILES | Lin et al., ACS Cent. Sci. 5, 1523 (2019), DOI 10.1021/acscentsci.9b00476 | bigsmiles.lark |
| G-BigSMILES | generative-BigSMILES extension | gbigsmiles.lark, gbigsmiles_new.lark |
| CGSmiles | Grünewald et al. (2025) | cgsmiles.lark |