This release is a pre-release and may not be stable for production use.
molcrafts-molrs
Python bindings for the molrs molecular modeling toolkit.
Install with pip install molcrafts-molrs and import molrs. Full docs:
https://docs.molcrafts.org/molrs/.
Install
pip install molcrafts-molrs
Requires Python 3.12+.
Quick start
import molrs
# SMILES → atomistic graph (class API under molrs.io)
mol = molrs.io.smiles.read_smiles("CCO").to_atomistic()
# 3D coordinates
from molrs.conformer import Conformer
mol, report = Conformer().generate(mol)
# Force field: typify → pairs → potentials
from molrs.ff.typifier import Mmff94Typifier
from molrs.ff.potential import intramolecular_pairs
from molrs.ff.compile import PotentialCompiler
typifier = Mmff94Typifier()
typed = typifier.typify(mol)
frame = typed.to_frame()
ff = typifier.forcefield() # a copy of exactly the types typify assigned
frame["pairs"] = intramolecular_pairs(frame, ff)
pots = PotentialCompiler(ff).compile(frame)
energy, forces = pots.evaluate(frame)
assert forces.shape == (frame["atoms"].n_rows, 3)
Package layout
The top level is the subsystems, plus the core data classes a user handles
directly (molrs.Frame is molrs.core.Frame: Frame,
Block, Trajectory, Box, MolGraph, Atomistic, CoarseGrain, the
entity classes, Element, Topology). Everything else has one path, named
after its Rust owner.
| Import | Owns |
|---|---|
molrs.core |
Frame, Block, Trajectory, frame metadata; Box and its Cell, neighbour search, regions, TriMesh, Trace; MolGraph, Atomistic, CoarseGrain and their live views, Element, Topology; Unit, Quantity, UnitPreset, UnitRegistry |
molrs.core.keys / .schema / .constants |
the column vocabulary, its specifications, and every physical and engine constant |
molrs.io |
Every file reader and writer: one door per format and direction, read_<fmt>(source) / write_<fmt>(sink, frame) (a source is a pathlib.Path, bytes or molrs.io.Text; a sink a pathlib.Path or a bytearray); each format's classes in its own submodule — the multi-frame <Fmt>Reader / <Fmt>Writer of io.pdb, io.xyz, io.gro, io.mol2, io.cif, io.sdf, io.dcd, io.trr, io.xtc, io.lammps, and the force-field reader / writer classes of io.lammps, io.gromacs, io.amber, io.openmm_xml; io.smiles, io.cgsmiles, io.mrec |
molrs.io.mrec |
*.mrec store pieces: MrecFile (per-section reads), streaming SequenceSchema, MrecWriter, MrecReader, ForceFieldSection, pack_mrec_zip, validation (a whole record is written by molrs.io.write_mrec) |
molrs.ff.* |
forcefield, potential, typifier, charge, ir, params, clpol_scaling |
molrs.optimize |
Lbfgs, OptimizationReport |
molrs.md |
Integrators and the MD driver |
molrs.compute |
One class per molrs::compute type, under its core name (flat): RDF, MSD, correlations, fits, spectra, order, clusters, … |
molrs.conformer |
3D generation |
molrs.perceive |
Rings, aromaticity, SMARTS, reactions |
molrs.builder |
Structure builders, site-graph assembly, Coarsener |
An analysis is configured when it is built and given its data when it
computes: Steinhardt(l=[6]) then .compute(...). The constructor takes
configuration only, every optional setting is None unless given (all
defaults live in the core; Msd.spec() lists them), and compute takes the
data as keyword arguments named after the core input's fields. Msd, Vacf
and Rdf are streams, as in the core: acc = Msd(max_lag).accumulator(),
acc.push(positions, dt=...) per frame, then acc.finish(). A result is a read-only object that the next compute accepts as is —
LinearFit(0.2, 0.8).compute(correlation=msd_result, channel=0).
Kernels take dt in the time unit of your trajectory, and time-valued
results come back in that unit. MSD needs unwrapped coordinates
(Unwrap produces them). VACF is the unbiased (C(\tau)) used for
Green–Kubo D and VDOS.
Development
maturin develop --release
pytest -q
Metadata
Release files for molcrafts-molrs-nightly 0.19.0.dev202610220838
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| molcrafts_molrs_nightly-0.19.0.dev202610220838-cp312-abi3-win_amd64.whl | CPython 3.12 | abi3 | Windows x86-64 | Details |
| molcrafts_molrs_nightly-0.19.0.dev202610220838-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-0.19.0.dev202610220838-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 11.0+ ARM64, macOS 10.12+ universal2 (ARM64, x86-64) | Details |
Total release size: 42.1 MB
Release files / molcrafts_molrs_nightly-0.19.0.dev202610220838-cp312-abi3-win_amd64.whl
| Download URL | molcrafts_molrs_nightly-0.19.0.dev202610220838-cp312-abi3-win_amd64.whl |
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| Size | 11.3 MB |
| Tags | CPython 3.12 Windows x86-64 abi3 |
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| Size | 19.9 MB |
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