This release is a pre-release and may not be stable for production use.
molcrafts-molrs
Python bindings for the molrs molecular modeling toolkit.
This package is the first public preview of the Python API. Install with
pip install molcrafts-molrs and import it as molrs.
Full documentation lives at https://molcrafts.github.io/molrs/. The Python API reference is rendered at https://molcrafts.github.io/molrs/reference/python/.
Install
pip install molcrafts-molrs
Quick start
import numpy as np
import molrs
# Parse SMILES and generate 3D coordinates
ir = molrs.parse_smiles("CCO")
mol = ir.to_atomistic()
result = molrs.generate_3d(mol, molrs.EmbedOptions(speed="fast", seed=42))
frame = result.mol.to_frame()
# Build a system from scratch
frame = molrs.Frame()
atoms = molrs.Block()
atoms.insert("x", np.array([0.0, 0.96, -0.24], dtype=np.float64))
atoms.insert("y", np.array([0.0, 0.0, 0.93], dtype=np.float64))
atoms.insert("z", np.zeros(3, dtype=np.float64))
atoms.insert("element", ["O", "H", "H"])
frame["atoms"] = atoms
Support
- Python 3.9+
pip install molcrafts-molrsimport molrs- Offline API help is available with
help(molrs.Frame)and related symbols
API
Data model
Frame— dict-like container of namedBlocks + optionalBoxBlock— column store backed by numpy arraysBox— simulation box with periodic boundaries
I/O
molrs.read_pdb(path)/molrs.read_xyz(path)→Framemolrs.parse_smiles(smiles)→SmilesIR→.to_frame()
Neighbor search and analysis
nq = molrs.NeighborQuery(box, positions, cutoff=5.0)
nlist = nq.query_self()
from molrs.compute.density import RDF
rdf = RDF(100, 5.0)
result = rdf.compute(frame, nlist)
Force field
typifier = molrs.MMFFTypifier()
potentials = typifier.build(atomistic)
Development
maturin build
pip install target/wheels/*.whl
pytest -q
| Component | Version |
|---|---|
| Python | 3.9+ |
| PyO3 | Managed by molrs-python/Cargo.toml |
| maturin | 1.x |
License
BSD-3-Clause
Metadata
Release files for molcrafts-molrs-nightly 0.6.0.dev202607031404
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| molcrafts_molrs_nightly-0.6.0.dev202607031404-cp312-abi3-win_amd64.whl | CPython 3.12 | abi3 | Windows x86-64 | Details |
| molcrafts_molrs_nightly-0.6.0.dev202607031404-cp312-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.12 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| molcrafts_molrs_nightly-0.6.0.dev202607031404-cp312-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl | CPython 3.12 | abi3 | macOS 10.12+ x86-64, macOS 10.12+ universal2 (ARM64, x86-64), macOS 11.0+ ARM64 | Details |
Total release size: 19.1 MB
Release files / molcrafts_molrs_nightly-0.6.0.dev202607031404-cp312-abi3-win_amd64.whl
| Download URL | molcrafts_molrs_nightly-0.6.0.dev202607031404-cp312-abi3-win_amd64.whl |
|---|---|
| Size | 4.5 MB |
| Tags | CPython 3.12 Windows x86-64 abi3 |
|
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| Size | 5.2 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 abi3 |
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| Download URL | molcrafts_molrs_nightly-0.6.0.dev202607031404-cp312-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 9.4 MB |
| Tags | CPython 3.12 abi3 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
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