amber/md format

amber/md format#

Aliases#

amber/md

Implementation: AmberMDFormat

Overview#

AMBER molecular-dynamics trajectory and label files.

AMBER is a suite of biomolecular simulation programs for molecular dynamics simulations and analysis.

Coordinates and topology are read from .nc and .parm7 files. Labeled loading additionally requires the .mdfrc force trajectory and takes energies from either the .mden or the .mdout file. The parmed optional dependency is required.

Quick examples#

The examples use the preferred alias amber/md; any alias listed above is equivalent.

import dpdata

# Geometry-only data
system = dpdata.System("trajectory_prefix", fmt="amber/md")

# Data with energies and forces
labeled_system = dpdata.LabeledSystem("trajectory_prefix", fmt="amber/md")

Conversions#

Convert from this format to System#

dpdata.System(file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None, fmt: Literal['amber/md'] = None, **kwargs) → dpdata.system.System

dpdata.System.from_amber_md(file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None, **kwargs) → dpdata.system.System

Load an unlabeled AMBER trajectory.

Parameters:

file_namestr, optional: Common prefix used to infer <prefix>.parm7 and <prefix>.nc.
parm7_filestr, optional: Explicit AMBER topology file. Overrides the inferred path.
nc_filestr, optional: Explicit NetCDF trajectory file. Overrides the inferred path.
use_element_symbolslist[int] or str, optional: Atoms whose element symbols are used instead of AMBER atom types, given either as a list of atom indexes or as an AMBER mask string selecting them.
**kwargsdict: Additional format arguments accepted for API compatibility.

Returns:

System: converted system

Convert from this format to LabeledSystem#

dpdata.LabeledSystem(file_name=None, parm7_file=None, nc_file=None, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None, fmt: Literal['amber/md'] = None, **kwargs) → dpdata.system.LabeledSystem

dpdata.LabeledSystem.from_amber_md(file_name=None, parm7_file=None, nc_file=None, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None, **kwargs) → dpdata.system.LabeledSystem

Load a labeled AMBER trajectory.