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Optional external tools

pip install molcrafts-molpy is enough for the default path: parse, build, embed, typify, pack, export, and analyze on the default MolPy stack (plus molpack for packing). No system scientific binaries are required.

Anything that shells out to another package or executable is optional. This page is the only place those integrations are documented as prerequisites.

Default path

Task Use
Parse SMILES / SMARTS mp.SmilesIR, mp.SmartsPattern
3D coordinates mp.Conformer
Polymer assembly mp.Assembler on a CGsmiles site graph (native); see Polymer Topologies
Pack a box molpack (molcrafts-molpack, installed separately)
OPLS-AA / MMFF94 typing molpy.typifier
Trajectory analysis molpy.compute (kernels)
Files (PDB, LAMMPS data, XML FF, …) molpy.io

Workflow guides and the Quickstart assume only this path.

AmberTools (GAFF parameters)

Kept for GAFF types and charges. Each monomer is typed once as a complete molecule; a polymer is assembled by MolPy from the typed monomers and finished by tleap. tleap never changes types or charges, so choose each monomer so its leaving groups mimic the chain neighbour:

Surface Role
molpy.typifier.AntechamberTypifier antechamber (types + charges) → parmchk2 → tleap for one complete molecule; net charge from the atoms' formal charges
molpy.typifier.TLeapTypifier tleap only, for a graph whose atoms already carry AMBER types and charges (an assembled chain); junction terms from the leaprc
molpy.wrapper (AntechamberWrapper, Parmchk2Wrapper, PrepgenWrapper, TLeapWrapper, SanderWrapper) Thin subprocess wrappers

Install AmberTools in its own conda env (example):

conda create -n AmberTools25 -c conda-forge ambertools=25
conda activate AmberTools25
which antechamber tleap prepgen parmchk2

Pass the env into the typifier when you construct it:

# docs: skip — needs AmberTools; typifiers unit-tested with the executables faked
import molpy as mp

mol, _ = mp.Conformer(add_hydrogens=True, seed=42).generate(
    mp.io.read_smiles("CCO")
)  # antechamber needs 3D coordinates
ante = mp.typifier.AntechamberTypifier(
    atom_type="gaff2", charge_method="bcc",
    work_dir="amber_work", env="AmberTools25", env_manager="conda",
)
typed = ante.typify(mol)  # GAFF2 types, BCC charges, bonded terms
ff = ante.forcefield()  # the parameters of the types just assigned

End-to-end recipes that use this path:

Unit tests never shell out to antechamber/tleap — wrappers are mocked under tests/test_wrapper and the typifiers under tests/test_typifier. Offline recipes in the user guide mark those blocks with # docs: skip so the doc gate does not re-run them.

MD engines (input decks and optional run)

molpy.engine always writes input for LAMMPS, CP2K, and OpenMM. Launching a binary is optional:

Engine Generate Run
LAMMPSEngine control script + data/ff you already wrote lmp / lmp_serial on PATH
CP2KEngine CP2K input cp2k on PATH
OpenMMEngine PDB + XML + simulate.py Python with openmm importable for run / serialize_system 
from molpy.engine import LAMMPSEngine

engine = LAMMPSEngine(check_executable=False) # generate / write only
# engine.run(script, workdir="run") # needs a LAMMPS binary

See Simulation Engines.

Pip extras (not system tools)

These are Python package groups, not scientific executables:

Extra Command Role
dev pip install molcrafts-molpy[dev] pytest, ruff, ty, tox
doc pip install molcrafts-molpy[doc] zensical + theme for docs builds

See also