dpdata.formats.amber package

Submodules

dpdata.formats.amber.mask module

Amber mask.

dpdata.formats.amber.mask.load_param_file(param_file)

dpdata.formats.amber.mask.pick_by_amber_mask(param, maskstr, coords=None)

Pick atoms by amber masks.

Parameters:

paramstr or parmed.Structure

filename of Amber param file or parmed.Structure

maskstrstr

Amber masks

coordsnp.ndarray (optional)

frame coordinates, shape: N*3

dpdata.formats.amber.md module

dpdata.formats.amber.md.cell_lengths_angles_to_cell(cell_lengths: ndarray, cell_angles: ndarray) → ndarray

Convert cell lengths and angles to cell vectors.

Parameters:

cell_lengths

Cell lengths with shape (..., 3) where the last dimension is a, b, c.

cell_angles

Cell angles in degrees with shape (..., 3) where the last dimension is alpha, beta, gamma.

Returns:

np.ndarray

Cell vectors with shape (..., 3, 3).

dpdata.formats.amber.md.read_amber_traj(parm7_file, nc_file, mdfrc_file=None, mden_file=None, mdout_file=None, use_element_symbols=None, labeled=True)

The amber trajectory includes: * nc, NetCDF format, stores coordinates * mdfrc, NetCDF format, stores forces * mden (optional), text format, stores energies * mdout (optional), text format, may store energies if there is no mden_file * parm7, text format, stores types.

Parameters:

parm7_file, nc_file, mdfrc_file, mden_file, mdout_file:

filenames

use_element_symbolsNone or list or str

If use_element_symbols is a list of atom indexes, these atoms will use element symbols instead of amber types. For example, a ligand will use C, H, O, N, and so on instead of h1, hc, o, os, and so on. IF use_element_symbols is str, it will be considered as Amber mask.

labeledbool

Whether to return labeled data

dpdata.formats.amber.sqm module

dpdata.formats.amber.sqm.make_sqm_in(data, fname: FileType | None = None, frame_idx=0, **kwargs)

dpdata.formats.amber.sqm.parse_sqm_out(fname: FileType)

Read atom symbols, charges and coordinates from ambertools sqm.out file.