I/O¶

File readers and writers for molecular data, force fields, and trajectories.

Quick reference¶

Data files¶

Function	Format	Direction
`read_pdb` / `write_pdb`	PDB	read/write
`read_lammps_data` / `write_lammps_data`	LAMMPS data	read/write
`read_gro` / `write_gro`	GROMACS GRO	read/write
`read_mol2`	MOL2	read
`read_xyz`	XYZ	read
`XsfReader` / `XsfWriter`	XSF (crystallographic)	read/write
`read_amber_inpcrd`	AMBER inpcrd	read

Force fields¶

Function	Format	Direction
`read_xml_forcefield`	OpenMM/OPLS XML	read
`XMLForceFieldWriter`	OpenMM/OPLS XML	write
`read_lammps_forcefield`	LAMMPS `*.ff` include	read (molrs)
`write_lammps_forcefield` / `LAMMPSForceFieldWriter`	LAMMPS `*.ff` include	write (molrs; molrs units → LAMMPS `real`)
`GromacsForceFieldWriter`	GROMACS .itp	write
`read_amber`	AMBER prmtop + inpcrd	read

Trajectories¶

Function	Format	Direction
`read_lammps_trajectory`	LAMMPS dump	read (lazy)
`read_xyz_trajectory`	XYZ trajectory	read (lazy)

Logs¶

Function	Format	Direction
`read_LAMMPS_log`	LAMMPS log	read

Canonical examples¶

import molpy as mp

# Read/write structure
frame = mp.io.read_pdb("molecule.pdb")
mp.io.write_lammps_data("system.data", frame, atom_style="full")

# Read force field (XML or LAMMPS *.ff)
ff = mp.io.read_xml_forcefield("oplsaa.xml")
ff = mp.io.read_lammps_forcefield("system.ff")

# Write LAMMPS *.ff (via molrs; optional type filter)
mp.io.write_lammps_forcefield("system.ff", ff)
from molpy.io.forcefield import LAMMPSForceFieldWriter
LAMMPSForceFieldWriter("system.ff").write(ff, atom_types={"CT", "HC"})

# Read trajectory (lazy)
traj = mp.io.read_lammps_trajectory("dump.lammpstrj")
for frame in traj:
    process(frame)

# Read LAMMPS run output
log = mp.io.read_LAMMPS_log("log.lammps")
thermo = log.runs[0].thermo
print(thermo.columns)

# Write full LAMMPS system (data + ff)
mp.io.write_lammps_system("output_dir", frame, ff)

Full API¶

Factory Functions¶

readers ¶

Data file reader factory functions.

This module provides convenient factory functions for creating various data file readers. All functions return Frame objects by populating an optional frame parameter.

PathLike `module-attribute` ¶

PathLike = str | Path

LAMMPSLog `dataclass` ¶

LAMMPSLog(file, style='default')

Parsed LAMMPS log with one structured entry per run.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to a LAMMPS log file.	required
`style`	`str`	Thermo style. Only `"default"` is currently parsed.	`'default'`

read ¶

read()

Read and parse the log file. Returns self for chaining.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

_ensure_frame ¶

_ensure_frame(frame)

Ensure a Frame object exists.

read_LAMMPS_log ¶

read_LAMMPS_log(file)

Read a LAMMPS log file and return a nested dataclass result.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to LAMMPS log file	required

Returns:

Type	Description
`LAMMPSLog`	Parsed `LAMMPSLog` object.

read_amber ¶

read_amber(prmtop, inpcrd=None, frame=None)

Read AMBER prmtop and optional inpcrd files.

Parameters:

Name	Type	Description	Default
`prmtop`	`PathLike`	Path to AMBER prmtop file	required
`inpcrd`	`PathLike \| None`	Optional path to AMBER inpcrd file	`None`
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Tuple of (Frame, ForceField)

read_amber_ac ¶

read_amber_ac(file, frame=None)

Read AC file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to AC file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_amber_frcmod ¶

read_amber_frcmod(file)

Read an AMBER FRCMOD file.

FRCMOD files contain additional force field parameters generated by parmchk2.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to FRCMOD file	required

Returns:

Type	Description
`dict[str, Any]`	Dictionary with sections: 'remark', 'mass', 'bond', 'angle', 'dihe',
`dict[str, Any]`	'improper', 'nonbon', and 'raw_text'.

read_amber_inpcrd ¶

read_amber_inpcrd(inpcrd, frame=None)

Read AMBER inpcrd file and return a Frame object.

Parameters:

Name	Type	Description	Default
`inpcrd`	`PathLike`	Path to AMBER inpcrd file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_dcd_trajectory ¶

read_dcd_trajectory(file)

Read a DCD trajectory and return a lazy trajectory reader.

Backed by the molrs Rust lazy reader (O(1) random access by frame index).

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to a `.dcd` file.	required

Returns:

Type	Description
`Any`	molrs `TrajectoryReader` object.

read_gro ¶

read_gro(file, frame=None)

Read GROMACS gro file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to gro file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_lammps_data ¶

read_lammps_data(file, atom_style, frame=None)

Read a LAMMPS data file and return its explicit parse products.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to LAMMPS data file	required
`atom_style`	`str`	LAMMPS atom style (e.g., 'full', 'atomic')	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	`LammpsDataResult` with `frame`, `forcefield`, `counts`, and
`Any`	`type_labels`. Callers must select the product they consume.

read_lammps_forcefield ¶

read_lammps_forcefield(scripts)

Read a LAMMPS force-field include (*.ff) into a ForceField.

Delegates to the native molrs reader (molrs.read_lammps_forcefield), which parses the include directly into a molrs.ForceField in molrs units (Å, kcal/mol, radians, e): LAMMPS harmonic K → molrs k = 2K, angle and dihedral-phase values stay in degrees, and dihedral_style fourier maps to the molrs periodic kernel. AMBER 1-4 scaling is recorded on the force field's special bonds. Per-atom charge and mass live in the LAMMPS data file, not this include, so they are not read here.

Parameters:

Name	Type	Description	Default
`scripts`	`PathLike \| list[PathLike]`	Path (or list of paths) to LAMMPS force-field include(s). A list is concatenated and parsed as a single document.	required

Returns:

Type	Description
`Any`	`molpy.ForceField` (which is `molrs.ForceField`).

read_lammps_molecule ¶

read_lammps_molecule(file, frame=None)

Read LAMMPS molecule file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to LAMMPS molecule file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_lammps_trajectory ¶

read_lammps_trajectory(traj)

Read LAMMPS trajectory file and return a trajectory reader.

Backed by the molrs Rust lazy reader.

Parameters:

Name	Type	Description	Default
`traj`	`PathLike`	Path to LAMMPS trajectory file	required

Returns: molrs TrajectoryReader object

read_mol2 ¶

read_mol2(file, frame=None)

Read mol2 file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to mol2 file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_pdb ¶

read_pdb(file, frame=None)

Read PDB file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to PDB file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_pdb_trajectory ¶

read_pdb_trajectory(file)

Read every model of a (multi-frame) PDB file as a list of Frames.

Each MODEL/END-delimited block becomes one Frame. A single-model PDB yields a one-element list. Backed by the molrs Rust reader.

read_top ¶

read_top(file, forcefield=None)

Read GROMACS topology file and return a ForceField object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to GROMACS .top file	required
`forcefield`	`Any`	Optional existing ForceField to populate	`None`

Returns:

Type	Description
`Any`	Populated ForceField object

read_trr_trajectory ¶

read_trr_trajectory(file)

Read a GROMACS TRR trajectory and return a lazy trajectory reader.

Backed by the molrs Rust lazy reader (single/double precision, coordinates plus velocities/forces when present; O(1) random access).

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to a `.trr` file.	required

Returns:

Type	Description
`Any`	molrs `TrajectoryReader` object.

read_xml_forcefield ¶

read_xml_forcefield(file)

Read XML force field file and return a ForceField object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to XML force field file	required

Returns:

Type	Description
`Any`	ForceField object

read_xsf ¶

read_xsf(file, frame=None)

Read XSF file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to XSF file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_xtc_trajectory ¶

read_xtc_trajectory(file)

Read a GROMACS XTC (compressed) trajectory and return a lazy reader.

Backed by the molrs Rust lazy reader (lossy compression; accepts classic 1995 and 2023 magic; O(1) random access after a one-time index scan).

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to a `.xtc` file.	required

Returns:

Type	Description
`Any`	molrs `TrajectoryReader` object.

read_xyz ¶

read_xyz(file, frame=None)

Read XYZ file and return a Frame object.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to XYZ file	required
`frame`	`Any`	Optional existing Frame to populate	`None`

Returns:

Type	Description
`Any`	Populated Frame object

read_xyz_trajectory ¶

read_xyz_trajectory(file)

Read XYZ trajectory file and return a trajectory reader.

Backed by the molrs Rust lazy reader.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to XYZ trajectory file	required

Returns:

Type	Description
`Any`	molrs `TrajectoryReader` object

writers ¶

Data file writer factory functions.

This module provides convenient factory functions for creating various data file writers. All functions write Frame or ForceField objects to files.

PathLike `module-attribute` ¶

PathLike = str | Path

_frame_used_types ¶

_frame_used_types(frame)

Per-section set of the type names a frame actually uses (None if the section/column is absent), for whitelisting FF output to the labelmap.

A LAMMPS data file's type labels come from the frame's used types, so any coeff the FF writer emits for a type not in this set references a labelmap entry that does not exist and LAMMPS rejects it. Both the system writer and the engine writer filter against this so their coeffs match the data file.

write_amber_frcmod ¶

write_amber_frcmod(
    file,
    *,
    remark="",
    mass="",
    bond="",
    angle="",
    dihe="",
    improper="",
    nonbon="",
)

Write an AMBER FRCMOD file.

FRCMOD files contain additional force field parameters. This function creates a properly formatted file with the provided sections.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`remark`	`str`	Optional comment/remark line	`''`
`mass`	`str`	MASS section content	`''`
`bond`	`str`	BOND section content	`''`
`angle`	`str`	ANGLE section content	`''`
`dihe`	`str`	DIHEDRAL section content	`''`
`improper`	`str`	IMPROPER section content	`''`
`nonbon`	`str`	NONBON section content	`''`

write_bond_react_map ¶

write_bond_react_map(template, base_path)

Write the .map file for a LAMMPS fix bond/react template.

Thin factory over :class:~molpy.io.data.lammps_bond_react.LammpsBondReactWriter, matching the write_* convention the rest of this module uses.

write_gro ¶

write_gro(file, frame)

Write a Frame object to a GROMACS GRO file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frame`	`Any`	Frame object to write	required

write_lammps_bond_react_system ¶

write_lammps_bond_react_system(
    workdir, frame, forcefield, templates
)

Write a complete LAMMPS fix bond/react system.

Produces all files needed for a reactive MD simulation:

{stem}.data — system configuration
{stem}.ff — force field coefficients
{name}_pre.mol / {name}_post.mol — reaction templates
{name}.map — atom equivalence maps

Type numbering is unified across the system and all templates so that fix bond/react can match atom types correctly.

Parameters:

Name	Type	Description	Default
`workdir`	`PathLike`	Output directory (created if missing).	required
`frame`	`Any`	Packed system Frame.	required
`forcefield`	`Any`	ForceField object.	required
`templates`	`dict[str, Any] \| Sequence[Any]`	Either a `{name: BondReactTemplate}` dict, or a sequence of templates (named `rxn1`, `rxn2`, …).	required

Example::

mp.io.write_lammps_bond_react_system(
    "output", packed_frame, ff,
    templates={"rxn1": template},
)

write_lammps_data ¶

write_lammps_data(
    file,
    frame,
    atom_style="full",
    *,
    type_labels=None,
    forcefield=None,
)

Write a Frame object to a LAMMPS data file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frame`	`Any`	Frame object to write	required
`atom_style`	`str`	LAMMPS atom style (default: 'full')	`'full'`
`type_labels`	`dict[str, list[str]] \| None`	Format-owned label inventory, including unused types.	`None`
`forcefield`	`Any`	Optional ForceField whose coefficients belong in this data file.	`None`

write_lammps_forcefield ¶

write_lammps_forcefield(
    file,
    forcefield,
    precision=6,
    skip_pair_style=False,
    frame=None,
)

Write a ForceField object to a LAMMPS force field file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`forcefield`	`Any`	ForceField object to write	required
`precision`	`int`	Number of decimal places for floating point values	`6`
`skip_pair_style`	`bool`	If True, omit the `pair_style` line so the calling LAMMPS input script can set it independently (e.g. to switch between `lj/cut/coul/cut` for minimisation and `lj/cut/coul/long` for MD).	`False`
`frame`	`Any`	When given, restrict emitted coeffs to the types the frame actually uses — so a force field carrying extra types (e.g. cap artifacts from region parameterisation) does not emit a coeff for a type absent from the data file's labelmap (which LAMMPS rejects).	`None`

write_lammps_molecule ¶

write_lammps_molecule(file, frame, format_type='native')

Write a Frame object to a LAMMPS molecule file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frame`	`Any`	Frame object to write	required
`format_type`	`str`	Format type (default: 'native')	`'native'`

write_lammps_system ¶

write_lammps_system(workdir, frame, forcefield)

Write a complete LAMMPS system (data + forcefield) to a directory.

Parameters:

Name	Type	Description	Default
`workdir`	`PathLike`	Output directory path	required
`frame`	`Any`	Frame object containing structure	required
`forcefield`	`Any`	ForceField object containing parameters	required

Returns:

Type	Description
`dict[str, Path]`	Dict with keys `"data"` and `"ff"` pointing to the written files.

write_lammps_trajectory ¶

write_lammps_trajectory(file, frames, atom_style='full')

Write frames to a LAMMPS trajectory file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frames`	`list`	List of Frame objects to write	required
`atom_style`	`str`	LAMMPS atom style (default: 'full')	`'full'`

write_pdb ¶

write_pdb(file, frame)

Write a Frame object to a PDB file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frame`	`Any`	Frame object to write	required

write_top ¶

write_top(file, frame)

Write a Frame object to a GROMACS topology file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frame`	`Any`	Frame object to write	required

write_trr ¶

write_trr(file, frames)

Write frames to a GROMACS TRR trajectory (single precision).

Thin delegation to the native molrs writer. Each frame needs x/y/ z (nm); optional vx/vy/vz and fx/fy/fz are written when present.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path.	required
`frames`	`list`	List of Frame objects to write.	required

write_xsf ¶

write_xsf(file, frame)

Write a Frame object to an XSF file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frame`	`Any`	Frame object to write	required

write_xtc ¶

write_xtc(file, frames)

Write frames to a GROMACS XTC (compressed) trajectory.

Thin delegation to the native molrs writer. Each frame needs x/y/ z (nm); quantization precision comes from frame.meta['precision'] when present, else 1000 (0.001 nm).

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path.	required
`frames`	`list`	List of Frame objects to write.	required

write_xyz_trajectory ¶

write_xyz_trajectory(file, frames)

Write frames to an XYZ trajectory file.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Output file path	required
`frames`	`list`	List of Frame objects to write	required

ForceField Modules¶

Base¶

base ¶

Abstract base classes for force field readers and writers.

ForceFieldReader ¶

ForceFieldReader(path)

Bases: ABC

Base class for force field file readers.

read `abstractmethod` ¶

read(forcefield=None)

Read force field data from file.

Parameters:

Name	Type	Description	Default
`forcefield`	`ForceField \| None`	Optional existing ForceField to populate.	`None`

Returns:

Type	Description
`ForceField`	Populated ForceField object.

ForceFieldWriter ¶

ForceFieldWriter(path)

Bases: ABC

Base class for force field file writers.

write `abstractmethod` ¶

write(forcefield)

Write force field data to file.

Parameters:

Name	Type	Description	Default
`forcefield`	`ForceField`	ForceField object to serialize.	required

LAMMPS¶

lammps ¶

LAMMPS force-field include (*.ff) I/O.

Read/write of the AMBER/GAFF-style include is implemented in molrs (:func:molrs.read_lammps_forcefield, :func:molrs.write_lammps_forcefield). This module exposes the molpy entry points and parameter formatters for specialized pair styles (CL&Pol Thole / Tang−Toennies).

LAMMPSForceFieldWriter ¶

LAMMPSForceFieldWriter(fpath, precision=6)

Write a :class:~molpy.ForceField to a LAMMPS *.ff include.

Parameters:

Name	Type	Description	Default
`fpath`	`str \| Path \| TextIO`	Output path or file-like object.	required
`precision`	`int`	Decimal places for floating-point coefficients.	`6`

write ¶

write(
    forcefield,
    atom_types=None,
    bond_types=None,
    angle_types=None,
    dihedral_types=None,
    improper_types=None,
    skip_pair_style=False,
)

Write forcefield (molrs units) as a LAMMPS include.

Parameters:

Name	Type	Description	Default
`forcefield`	`ForceField`	Force field to write.	required
`atom_types`	`set[str] \| None`	Optional atom-type whitelist for pair coeffs.	`None`
`bond_types`	`set[str] \| None`	Optional bond type-name whitelist.	`None`
`angle_types`	`set[str] \| None`	Optional angle type-name whitelist.	`None`
`dihedral_types`	`set[str] \| None`	Optional dihedral type-name whitelist.	`None`
`improper_types`	`set[str] \| None`	Optional improper type-name whitelist.	`None`
`skip_pair_style`	`bool`	If True, omit the `pair_style` line.	`False`

LammpsForceFieldFormatter ¶

Bases: LammpsFieldFormatter, ForceFieldFormatter

Parameter formatters for LAMMPS pair styles beyond the AMBER/GAFF set.

XML¶

xml ¶

XML force field parser for atomistic force fields.

AngleUnitWarning ¶

Bases: UserWarning

An angle value looks inconsistent with its declared angle_unit.

OPLSAAForceFieldReader ¶

OPLSAAForceFieldReader(filepath, *, angle_unit='radian')

Bases: XMLForceFieldReader

Specialized reader for OPLS-AA force field with LAMMPS unit conversions.

This reader extends XMLForceFieldReader to: 1. Use lj/cut/coul/long pair style instead of lj/cut/coul/cut 2. Convert epsilon: kJ/mol → kcal/mol (÷4.184) 3. Convert sigma: nm → Å (×10) 4. Convert bond K: kJ/mol/nm² → kcal/mol/Å² (÷(4.184×100), both use 0.5 factor in formula) 5. Convert angle K: kJ/mol/rad² → kcal/mol/deg² (direct to LAMMPS format) Formula: k_lammps = (0.5 * k_opls / 4.184) * (π/180)² Stored internally in LAMMPS format, so no conversion needed when writing 6. Convert dihedral K: kJ/mol → kcal/mol (÷4.184)

XMLForceFieldReader ¶

XMLForceFieldReader(filepath, *, angle_unit='radian')

XML force field parser for atomistic force fields.

Parses XML-formatted force field files (e.g., OPLS-AA) and populates a ForceField object with atom types, bond parameters, angle parameters, dihedral parameters, and nonbonded interactions.

The parser handles: - AtomTypes section: atom type definitions - HarmonicBondForce: harmonic bond parameters - HarmonicAngleForce: harmonic angle parameters - RBTorsionForce: Ryckaert-Bellemans dihedral parameters - NonbondedForce: LJ and Coulomb parameters

Initialize the XML force field reader.

Parameters:

Name	Type	Description	Default
`filepath`	`str \| Path`	Path to the XML force field file, or filename for built-in files (e.g., "oplsaa.xml" will load from molpy/data/forcefield/)	required
`angle_unit`	`str`	Unit of angle equilibria (`"angle"`/phase) in the input file — `"radian"` (default, the OpenMM/OPLS XML convention) or `"degree"`. Values are converted to the internal degrees representation on read, so the rest of the pipeline is unit-consistent.	`'radian'`

read ¶

read(forcefield=None, layer=0)

Read and parse the XML force field file.

Parameters:

Name	Type	Description	Default
`forcefield`	`ForceField \| None`	Optional existing force field to populate. If None, creates new one.	`None`
`layer`	`int`	Overlay level for this read. `0` (default) is the base force field; a positive value marks every atom type parsed here as an overlay that overrides the base during SMARTS typing (higher layer wins). Used to stack `oplsaa.xml` (layer 0) → `clp.xml` (layer 1) → `clpol.xml` (layer 2).	`0`

Returns:

Type	Description
`ForceField`	Populated ForceField object

XMLForceFieldWriter ¶

XMLForceFieldWriter(
    filepath, precision=6, *, angle_unit="radian"
)

Write a ForceField to OpenMM-style XML.

The output is roundtrip-compatible with :class:XMLForceFieldReader.

Parameters:

Name	Type	Description	Default
`filepath`	`str \| Path`	Destination path.	required
`precision`	`int`	Number of decimal digits for floating-point values.	`6`

write ¶

write(forcefield)

Serialize forcefield to XML.

read_oplsaa_forcefield ¶

read_oplsaa_forcefield(filepath, forcefield=None, layer=0)

Read OPLS-AA force field with proper unit conversions for LAMMPS.

This function uses OPLSAAForceFieldReader which: - Uses lj/cut/coul/long pair style - Converts epsilon: epsilon_lammps = epsilon_opls / 4.184 (kJ/mol to kcal/mol) - Converts sigma: sigma_lammps = sigma_opls * 10.0 (nm to Angstrom)

Parameters:

Name	Type	Description	Default
`filepath`	`str \| Path`	Path to the OPLS-AA XML file, or "oplsaa.xml" for built-in	required
`forcefield`	`ForceField \| None`	Optional existing force field to populate	`None`

Returns:

Type	Description
`ForceField`	Populated ForceField object with LAMMPS-compatible units

Example

ff = read_oplsaa_forcefield("oplsaa.xml")

read_xml_forcefield ¶

read_xml_forcefield(filepath, forcefield=None, layer=0)

Convenience function to read an XML force field file.

Parameters:

Name	Type	Description	Default
`filepath`	`str \| Path`	Path to the XML force field file, or filename for built-in files (e.g., "oplsaa.xml" will load from molpy/data/forcefield/)	required
`forcefield`	`ForceField \| None`	Optional existing force field to populate	`None`
`layer`	`int`	Overlay level (0 = base, >0 = overlay that overrides the base during SMARTS typing). Pass `layer=1` when stacking `clp.xml` onto an already-loaded `oplsaa.xml` so CL&P types win conflicts.	`0`

Returns:

Type	Description
`ForceField`	Populated ForceField object

Example

Load built-in OPLS-AA force field¶

ff = read_xml_forcefield("oplsaa.xml")

Overlay CL&P on top of OPLS-AA (CL&P overrides where it matches)¶

ff = read_xml_forcefield("clp.xml", ff, layer=1)

write_xml_forcefield ¶

write_xml_forcefield(filepath, forcefield)

Convenience function to write a force field to XML.

Parameters:

Name	Type	Description	Default
`filepath`	`str \| Path`	Output path.	required
`forcefield`	`ForceField`	Force field to serialize.	required

GROMACS Topology¶

top ¶

GromacsForceFieldWriter ¶

GromacsForceFieldWriter(filepath, precision=6)

Write a ForceField to GROMACS .top / .itp format.

The output is roundtrip-compatible with :class:GromacsTopReader.

Parameters:

Name	Type	Description	Default
`filepath`	`str \| Path`	Destination path.	required
`precision`	`int`	Number of decimal digits for floating-point values.	`6`

write ¶

write(forcefield)

Serialize forcefield to GROMACS topology format.

GromacsTopReader ¶

GromacsTopReader(file, include=False)

Utility to read a Gromacs .top/.itp topology file into a dictionary.

The returned mapping contains a key for every section header encountered (e.g. atomtypes, moleculetype), mapping to the raw content lines (with inline comments stripped) that appear under that section in the order they occur.

read ¶

read(forcefield, *, strip_comments=True, recursive=True)

Parse the topology file.

Parameters¶

forcefield: Optional object providing a base_dir or path attribute used to resolve relative #include statements that point inside the force-field directory (e.g. ff/amber14sb.ff/ions.itp). strip_comments: Whether to remove text following a ; (Gromacs comment delimiter). Leading/trailing whitespace is always removed. recursive: If True (default) #included files are parsed recursively. The content of an included file is merged into the dictionary being built; if the same section appears multiple times its content is extended in occurrence order.

Returns¶

dict[str, list[str]] Mapping from lower‑case section name to list of raw content lines.

AMBER¶

amber ¶

AmberPrmtopReader ¶

AmberPrmtopReader(file)

get_bond_with_H ¶

get_bond_with_H()

Return list of bonded atom pairs, K, and Rmin for each bond with a hydrogen

get_bond_without_H ¶

get_bond_without_H()

Return list of bonded atom pairs, K, and Rmin for each bond with no hydrogen

parse_angle_params ¶

parse_angle_params()

Return list of atom triplets, K, and ThetaMin for each bond angle

parse_dihedral_params ¶

parse_dihedral_params()

Return list of atom quads, K, phase and periodicity for each dihedral angle

parse_nonbond_params ¶

parse_nonbond_params(atoms)

Return list of all rVdw, epsilon pairs for each atom. If off-diagonal elements of the Lennard-Jones A and B coefficient matrices are found, NbfixPresent exception is raised

Data Modules¶

LAMMPS¶

lammps ¶

Modern LAMMPS data file I/O using Block.from_csv.

This module provides a clean, imperative approach to reading and writing LAMMPS data files using the Block.from_csv functionality.

LammpsDataReader ¶

LammpsDataReader(path, atom_style='full')

Bases: DataReader[LammpsDataResult]

Modern LAMMPS data file reader using Block.from_csv.

read ¶

read(frame=None)

Read a LAMMPS data file into explicit frame and format products.

LammpsDataResult `dataclass` ¶

LammpsDataResult(frame, forcefield, counts, type_labels)

Explicit products of parsing one LAMMPS data file.

LammpsDataWriter ¶

LammpsDataWriter(
    path,
    atom_style="full",
    *,
    type_labels=None,
    forcefield=None,
)

Bases: DataWriter

Modern LAMMPS data file writer using Block.to_csv approach.

Important Requirements: - Atoms in the frame must have an 'id' field. This field is required to map atom indices to atom IDs for LAMMPS output. - Connectivity data (bonds, angles, dihedrals) in the frame uses atom indices (0-based from to_frame()). The writer automatically converts these indices to atom IDs using the index->ID mapping from the atoms 'id' field.

Frame Structure: - Atoms: Must include 'id' field. Other required fields depend on atom_style. - Bonds/Angles/Dihedrals: Use atom indices in 'atomi', 'atomj', 'atomk', 'atoml' (from to_frame()). These are 0-based indices that will be converted to 1-based atom IDs.

write ¶

write(frame)

Write Frame to LAMMPS data file.

Parameters:

Name	Type	Description	Default
`frame`	`Frame`	Frame containing atoms and optionally bonds/angles/dihedrals. Atoms must have 'id' field.	required

Raises:

Type	Description
`ValueError`	If atoms are missing 'id' field.

LammpsFieldFormatter ¶

Bases: FieldFormatter

LAMMPS-specific field name translation.

Maps LAMMPS atom_style column names to canonical field names::

"q"   → "charge"
"mol" → "mol_id"

lammps_molecule ¶

LAMMPS molecule file I/O.

This module provides readers and writers for LAMMPS molecule template files, supporting both native format and JSON format as described in the LAMMPS documentation.

LammpsMoleculeReader ¶

LammpsMoleculeReader(path)

Bases: DataReader

LAMMPS molecule file reader supporting both native and JSON formats.

read ¶

read(frame=None)

Read LAMMPS molecule file into a Frame.

LammpsMoleculeWriter ¶

LammpsMoleculeWriter(path, format_type='native')

Bases: DataWriter

LAMMPS molecule file writer supporting both native and JSON formats.

write ¶

write(frame)

Write Frame to LAMMPS molecule file.

lammps_bond_react ¶

LAMMPS fix bond/react template serialization.

A fix bond/react template is a pre-reaction subgraph, the same subgraph after the reaction, and the atom map between them. That is an IO artifact, not reaction machinery: it is one serialization of the local environment a graph edit disturbed. It used to live in molpy.reacter because a Reacter subclass produced it; nothing produces it now but the caller, so it lives with the writer that consumes it.

File format references

LAMMPS fix bond/react: https://docs.lammps.org/fix_bond_react.html
REACTER methodology: https://www.reacter.org (Gissinger, Jensen & Wise, Polymer 128, 211-217 (2017); Macromolecules 53, 9953-9961 (2020))

BondReactTemplate `dataclass` ¶

BondReactTemplate(
    pre,
    post,
    initiator_atoms,
    edge_atoms,
    deleted_atoms,
    pre_react_id_to_atom,
    post_react_id_to_atom,
)

The pre/post subgraph pair fix bond/react needs, plus its atom map.

Serialized into {name}_pre.mol, {name}_post.mol and {name}.map.

Attributes:

Name	Type	Description
`pre`	`Atomistic`	Pre-reaction subgraph (the local environment before the edit).
`post`	`Atomistic`	Post-reaction subgraph (same atoms, new topology).
`initiator_atoms`	`list[Atom]`	The pair of atoms that trigger the reaction (LAMMPS `InitiatorIDs`). Exactly two.
`edge_atoms`	`list[Atom]`	Boundary atoms bonded to topology outside the template (LAMMPS `EdgeIDs`).
`deleted_atoms`	`list[Atom]`	Atoms the reaction removes (LAMMPS `DeleteIDs`).
`pre_react_id_to_atom`	`dict`	`react_id` → atom in `pre`.
`post_react_id_to_atom`	`dict`	`react_id` → atom in `post`.

assign_atom_ids ¶

assign_atom_ids()

Assign deterministic 1-based id values to the pre/post atoms.

Insertion order defines the template-local indices the .map file uses, so writers call this before serializing.

LammpsBondReactWriter ¶

LammpsBondReactWriter(base_path)

Serialize a :class:BondReactTemplate into the files LAMMPS reads.

The .map file is purely topological and independent of type numbering. The unified type maps, by contrast, must be shared between the system data file and every template, which is what lets fix bond/react match template atoms against the system.

apply_type_maps `staticmethod` ¶

apply_type_maps(frame, type_maps, template_name='')

Convert string type columns to unified numeric IDs, in place.

Rows whose type is absent from the mapping (boundary topology with untyped terms) are dropped with a warning. The numeric IDs must match the system data file for template matching.

collect_type_maps `staticmethod` ¶

collect_type_maps(frames)

Build unified string-type → 1-based ID mappings across frames.

Scans the type column of every topology section in every frame, keeps named types (skipping empty strings, "None" placeholders, and purely numeric labels that are already IDs), sorts them, and assigns 1-based integer IDs.

Returns:

Type	Description
`dict[str, list[str]]`	`(labels, type_maps)`: `labels` maps data-writer label keys
`dict[str, dict[str, int]]`	(`"atom_types"`, …) to sorted type-name lists; `type_maps` maps
`tuple[dict[str, list[str]], dict[str, dict[str, int]]]`	section names (`"atoms"`, …) to `{type_name: 1-based id}`.

write_map ¶

write_map(template)

Write {base_path}.map.

Raises:

Type	Description
`ValueError`	if `pre` and `post` do not carry the same set of `react_id` atoms, if an initiator atom is unresolvable in `pre`, or if there are not exactly two initiators.

PDB¶

pdb ¶

PDBReader ¶

PDBReader(file, **kwargs)

Bases: DataReader

Minimal-yet-robust PDB reader.

ATOM / HETATM parsed per PDB v3.3 fixed columns
CRYST1 -> frame.box
CONECT -> bond list

read ¶

read(frame=None)

Read a single PDB model via the molrs Rust backend.

Multi-MODEL / multi-frame PDBs are read one model at a time; use :func:molpy.io.read_pdb_trajectory for all models.

PDBWriter ¶

PDBWriter(path)

Bases: DataWriter

Robust PDB file writer that creates properly formatted PDB files.

Features: - Writes ATOM/HETATM records with proper formatting - Handles missing fields with sensible defaults - Writes CRYST1 records from box information - Writes CONECT records for bonds - Ensures PDB format compliance

write ¶

write(frame)

Write frame to PDB file.

Required fields in frame["atoms"]: - x, y, z: coordinates (float, required) - id: atom ID (int, optional, defaults to index+1)

Optional fields in frame["atoms"]: - name: atom name (str) - resName: residue name (str) - element: element symbol (str) - resSeq: residue sequence number (int) - chainID: chain identifier (str) - occupancy: occupancy (float) - tempFactor: temperature factor (float)

Optional typed metadata: - elements: space-separated string of element symbols (one per atom) - name: frame name (str)

The optional CRYST1 cell is read from frame.box.

Raises:

Type	Description
`ValueError`	If required fields (x, y, z) are missing or contain None

GRO¶

gro ¶

GROMACS .gro file I/O — molrs (Rust) backend.

Reader/writer delegate to :mod:molrs.io (parsing + field canonicalization in Rust). :class:GroFieldFormatter is retained for the formatter hierarchy.

GroFieldFormatter ¶

Bases: FieldFormatter

GROMACS .gro field name translation.

GroReader ¶

GroReader(path, **kwargs)

Bases: DataReader

Read GRO files via the molrs Rust backend.

GroWriter ¶

GroWriter(path, **kwargs)

Bases: DataWriter

Write GRO files via the molrs Rust backend.

Mol2¶

mol2 ¶

Mol2Reader ¶

Mol2Reader(file)

Bases: DataReader

Robust MOL2 file reader following TRIPOS MOL2 format specification.

Features: - Parses MOLECULE, ATOM, BOND, and SUBSTRUCTURE sections - Handles various atom types and bond types - Robust error handling for malformed files - Supports partial files with missing sections - Assigns atomic numbers from atom names/types

read ¶

read(frame)

Read MOL2 file and populate frame.

sanitizer `staticmethod` ¶

sanitizer(line)

Clean up line by stripping whitespace.

Amber¶

amber ¶

AmberInpcrdReader ¶

AmberInpcrdReader(file, **kwargs)

Bases: DataReader

Reader for AMBER ASCII *.inpcrd (old-style) coordinate files.

Coordinates: 12.7/12.8 format, 6 numbers per line
Optional velocities section (same length as coordinates)
Optional final box line (3-6 floats)

AC¶

ac ¶

Antechamber (AC) file format reader.

Reads Antechamber .ac files containing atom and bond information with force field types and charges.

AcFieldFormatter ¶

Bases: FieldFormatter

Antechamber .ac field name translation.

AcReader ¶

AcReader(file)

Bases: DataReader

Reader for Antechamber .ac format files.

Parses ATOM and BOND sections from Antechamber output files, extracting coordinates, charges, atom types, and connectivity.

Parameters:

Name	Type	Description	Default
`file`	`str \| Path`	Path to .ac file	required

assign_atomic_numbers ¶

assign_atomic_numbers(atoms)

Assign atomic numbers by guessing from atom names/types.

read ¶

read(frame)

Read .ac file and populate Frame with atoms and bonds.

Parameters:

Name	Type	Description	Default
`frame`	`Frame`	Frame to populate	required

Returns:

Type	Description
`Frame`	Frame with atoms and bonds data

Top¶

top ¶

GROMACS topology file reader for Frame objects.

This module provides a reader for GROMACS topology files that extracts structural information (atoms, bonds, angles, dihedrals, pairs) and creates Frame objects with Block containers.

TopReader ¶

TopReader(file, **open_kwargs)

Bases: DataReader

Read GROMACS topology files and create Frame objects.

This reader parses GROMACS .top files and extracts structural information from sections like [atoms], [bonds], [angles], [dihedrals], and [pairs].

Examples:

>>> reader = TopReader("molecule.top")
>>> frame = reader.read()
>>> frame["atoms"]  # Block with atom data
>>> frame["bonds"]  # Block with bond data

Initialize GROMACS topology reader.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to GROMACS .top file	required
`**open_kwargs`	`Any`	Additional arguments passed to file open.	`{}`

read ¶

read(frame=None)

Read GROMACS topology file and populate Frame.

Parameters:

Name	Type	Description	Default
`frame`	`Frame \| None`	Optional existing Frame to populate. If None, creates a new one.	`None`

Returns:

Type	Description
`Frame`	Frame object with atoms, bonds, angles, dihedrals, and pairs blocks.

TopWriter ¶

TopWriter(file, **open_kwargs)

Bases: DataWriter

Write GROMACS topology files from Frame objects.

Produces a minimal .top file with [ moleculetype ], [ atoms ], [ bonds ], and optional [ pairs ], [ angles ], [ dihedrals ] sections, followed by [ system ] and [ molecules ].

Examples:

>>> writer = TopWriter("molecule.top")
>>> writer.write(frame)

write ¶

write(frame)

Write Frame to GROMACS topology file.

Parameters:

Name	Type	Description	Default
`frame`	`Frame`	Frame object containing `"atoms"` and optionally `"bonds"`, `"pairs"`, `"angles"`, `"dihedrals"` blocks.	required

XYZ¶

xyz ¶

XYZ file I/O — molrs (Rust) backend.

Reader/writer delegate to :mod:molrs.io. The reader normalizes molrs output to molpy conventions (merge split multi-columns, species→element, atomic numbers); the writer ensures separate x/y/z coordinate columns.

XYZReader ¶

XYZReader(path, **kwargs)

Bases: DataReader

Read XYZ files via the molrs Rust backend.

XYZWriter ¶

XYZWriter(path, **kwargs)

Bases: DataWriter

Write XYZ files via the molrs Rust backend.

XSF¶

xsf ¶

XSF (XCrySDen Structure File) format reader and writer.

XSF is a format for crystal structure visualization, supporting both periodic and non-periodic structures. It can contain atomic coordinates, unit cell parameters, and other structural information.

XsfReader ¶

XsfReader(file)

Bases: DataReader

Parse an XSF file into a Frame.

XSF format supports both crystal structures (with unit cell) and molecular structures. The format can contain: - CRYSTAL or MOLECULE keyword - PRIMVEC or CONVVEC for unit cell vectors - PRIMCOORD for atomic coordinates - Optional comment lines starting with #

read ¶

read(frame=None)

Read XSF file and return Frame.

Returns¶

Frame Frame with: - frame containing atomic data - box: unit cell for CRYSTAL, Free Box for MOLECULE

XsfWriter ¶

XsfWriter(file)

Bases: DataWriter

Write Frame to XSF format.

Features: - Supports both CRYSTAL and MOLECULE structures - Writes PRIMVEC for unit cell vectors - Writes PRIMCOORD for atomic coordinates - Automatically determines structure type based on presence of box

write ¶

write(frame)

Write Frame to XSF file.

Parameters¶

frame : Frame Frame containing atomic data and optional box information

Trajectory Modules¶

Base¶

base ¶

BaseTrajectoryReader ¶

BaseTrajectoryReader(fpath, *, must_exist=True)

Bases: BaseReader, Iterable['Frame']

Pure, storage-agnostic trajectory reader: a lazy Iterable[Frame].

Subclasses implement only read_frame(index) and the n_frames property; the random-access and iteration API (__iter__, __getitem__, slicing, read_frames / read_range / read_all, __len__) is derived entirely from those two and involves no files.

n_frames `abstractmethod` `property` ¶

n_frames

Total number of frames in the trajectory.

read_all ¶

read_all()

Read every frame in the trajectory.

read_frame `abstractmethod` ¶

read_frame(index)

Read and return the frame at index (negative indices allowed).

read_frames ¶

read_frames(indices)

Read the frames at indices.

Parameters:

Name	Type	Description	Default
`indices`	`list[int]`	Frame indices to read.	required

Returns:

Type	Description
`list[Frame]`	The frames, in the order requested.

read_range ¶

read_range(start, stop, step=1)

Read frames start (inclusive) to stop (exclusive) by step.

TrajectoryWriter ¶

TrajectoryWriter(fpath)

Bases: BaseReader

Base class for all trajectory file writers.

write_frame `abstractmethod` ¶

write_frame(frame)

Write a single frame to the file.

LAMMPS¶

lammps ¶

LammpsTrajectoryWriter ¶

LammpsTrajectoryWriter(fpath, atom_style='full')

Bases: TrajectoryWriter

Writer for LAMMPS trajectory files.

write_frame ¶

write_frame(frame, timestep=None)

Write a single frame to the file.

XYZ¶

xyz ¶

XYZTrajectoryWriter ¶

XYZTrajectoryWriter(fpath)

Bases: TrajectoryWriter

Writer for XYZ trajectory files.

close ¶

close()

Close the file.

write_frame ¶

write_frame(frame)

Write a single frame to the XYZ file.

write_traj ¶

write_traj(trajectory)

Write multiple frames to the XYZ file.

Log Modules¶

LAMMPS¶

lammps ¶

LAMMPS log file parser.

This module parses the standard LAMMPS run output structure documented in Run_output.html: thermo tables, loop timing, performance summaries, CPU/MPI timing, load-balance statistics, neighbor statistics, and warnings. Unrecognized lines are preserved so callers can still inspect information that does not yet have a structured representation.

LAMMPSCPUUse `dataclass` ¶

LAMMPSCPUUse(percent, MPI_tasks, OMP_threads, raw_line)

% CPU use summary line.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSLoadBalance `dataclass` ¶

LAMMPSLoadBalance(
    name, average, maximum, minimum, histogram, raw_lines
)

LAMMPS load-balance statistic plus optional histogram.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSLog `dataclass` ¶

LAMMPSLog(file, style='default')

Parsed LAMMPS log with one structured entry per run.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to a LAMMPS log file.	required
`style`	`str`	Thermo style. Only `"default"` is currently parsed.	`'default'`

read ¶

read()

Read and parse the log file. Returns self for chaining.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSLogHeader `dataclass` ¶

LAMMPSLogHeader(lines)

Header text before the first parsed LAMMPS run block.

raw_text `property` ¶

raw_text

Header lines joined by newlines.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSLoopTime `dataclass` ¶

LAMMPSLoopTime(seconds, procs, steps, atoms, raw_line)

Loop time summary line.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSMemoryUsage `dataclass` ¶

LAMMPSMemoryUsage(
    minimum, average, maximum, units, raw_line
)

Per MPI rank memory allocation line.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSNeighborStatistics `dataclass` ¶

LAMMPSNeighborStatistics(
    total_neighbors,
    ave_neighs_per_atom,
    ave_special_neighs_per_atom,
    neighbor_list_builds,
    dangerous_builds,
    raw_lines,
)

Neighbor-list statistics emitted after a run.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSPerformance `dataclass` ¶

LAMMPSPerformance(
    ns_per_day,
    hours_per_ns,
    timesteps_per_second,
    atom_steps_per_second,
    atom_steps_units,
    raw_line,
)

LAMMPS Performance summary line.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSRun `dataclass` ¶

LAMMPSRun(
    index,
    setup_log,
    memory,
    thermo,
    loop_time,
    performance,
    CPU_use,
    MPI_task_timing,
    thread_timing,
    load_balance,
    neighbor_statistics,
    warnings,
    unparsed_log,
    raw_text,
)

One LAMMPS run output block.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSThermo `dataclass` ¶

LAMMPSThermo(columns, data, raw_lines)

LAMMPS thermo table with dynamic columns.

n_rows `property` ¶

n_rows

Number of thermo rows.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSTimingBreakdown `dataclass` ¶

LAMMPSTimingBreakdown(title, rows, raw_lines)

MPI task timing breakdown or thread timing table.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSTimingRow `dataclass` ¶

LAMMPSTimingRow(
    section,
    min_time,
    avg_time,
    max_time,
    percent_varavg,
    percent_total,
    raw_line,
)

One row from a LAMMPS timing breakdown table.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

LAMMPSWarning `dataclass` ¶

LAMMPSWarning(
    message, raw_line, line_number=None, run_index=None
)

A warning line from the LAMMPS log.

to_dict ¶

to_dict()

Return a JSON-friendly representation.

read_LAMMPS_log ¶

read_LAMMPS_log(file)

Read a LAMMPS log file into a nested dataclass result.

Parameters:

Name	Type	Description	Default
`file`	`PathLike`	Path to the LAMMPS log file.	required

Returns:

Type	Description
`LAMMPSLog`	Parsed `LAMMPSLog` object.

I/O¶

Quick reference¶

Data files¶

Force fields¶

Trajectories¶

Logs¶

Canonical examples¶

Related¶

Full API¶

Factory Functions¶

readers ¶

PathLike module-attribute ¶

LAMMPSLog dataclass ¶

read ¶

to_dict ¶

_ensure_frame ¶

read_LAMMPS_log ¶

read_amber ¶

read_amber_ac ¶

read_amber_frcmod ¶

read_amber_inpcrd ¶

read_dcd_trajectory ¶

read_gro ¶

read_lammps_data ¶

read_lammps_forcefield ¶

read_lammps_molecule ¶

read_lammps_trajectory ¶

read_mol2 ¶

read_pdb ¶

read_pdb_trajectory ¶

read_top ¶

read_trr_trajectory ¶

read_xml_forcefield ¶

read_xsf ¶

read_xtc_trajectory ¶

read_xyz ¶

read_xyz_trajectory ¶

writers ¶

PathLike module-attribute ¶

_frame_used_types ¶

write_amber_frcmod ¶

write_bond_react_map ¶

write_gro ¶

write_lammps_bond_react_system ¶

write_lammps_data ¶

write_lammps_forcefield ¶

write_lammps_molecule ¶

write_lammps_system ¶

write_lammps_trajectory ¶

write_pdb ¶

write_top ¶

write_trr ¶

write_xsf ¶

write_xtc ¶

write_xyz_trajectory ¶

ForceField Modules¶

Base¶

base ¶

ForceFieldReader ¶

read abstractmethod ¶

ForceFieldWriter ¶

write abstractmethod ¶

LAMMPS¶

lammps ¶

LAMMPSForceFieldWriter ¶

write ¶

LammpsForceFieldFormatter ¶

XML¶

xml ¶

AngleUnitWarning ¶

OPLSAAForceFieldReader ¶

XMLForceFieldReader ¶

read ¶

XMLForceFieldWriter ¶

write ¶

read_oplsaa_forcefield ¶

read_xml_forcefield ¶

Load built-in OPLS-AA force field¶

Overlay CL&P on top of OPLS-AA (CL&P overrides where it matches)¶

write_xml_forcefield ¶

PathLike `module-attribute` ¶

LAMMPSLog `dataclass` ¶

PathLike `module-attribute` ¶

read `abstractmethod` ¶

write `abstractmethod` ¶

LammpsDataResult `dataclass` ¶

BondReactTemplate `dataclass` ¶

apply_type_maps `staticmethod` ¶

collect_type_maps `staticmethod` ¶

sanitizer `staticmethod` ¶