Source code for MDAnalysis.coordinates.DMS

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DESRES file format --- :mod:`MDAnalysis.coordinates.DMS`

Classes to read DESRES_ Molecular Structure file format (DMS_)
coordinate files (as used by the Desmond_ MD package).

.. _Desmond:
.. _DMS:
import numpy as np
import sqlite3

from . import base
from .core import triclinic_box

[docs]class DMSReader(base.SingleFrameReaderBase): """ Reads both coordinates and velocities. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based """ format = 'DMS' units = {'time': None, 'length': 'A', 'velocity': 'A/ps'} def get_coordinates(self, cur): cur.execute('SELECT * FROM particle') particles = cur.fetchall() return [(p['x'], p['y'], p['z']) for p in particles] def get_particle_by_columns(self, cur, columns=None): if columns is None: columns = ['x', 'y', 'z'] cur.execute('SELECT * FROM particle') particles = cur.fetchall() return [tuple([p[c] for c in columns]) for p in particles] def get_global_cell(self, cur): cur.execute('SELECT * FROM global_cell') rows = cur.fetchall() assert len(rows) == 3 x = [row["x"] for row in rows] y = [row["y"] for row in rows] z = [row["z"] for row in rows] return {'x': x, 'y': y, 'z': z} def _read_first_frame(self): coords_list = None velocities_list = None def dict_factory(cursor, row): d = {} for idx, col in enumerate(cursor.description): d[col[0]] = row[idx] return d with sqlite3.connect(self.filename) as con: # This will return dictionaries instead of tuples, when calling cur.fetch() or fetchall() con.row_factory = dict_factory cur = con.cursor() coords_list = self.get_coordinates(cur) velocities_list = self.get_particle_by_columns(cur, columns=['vx', 'vy', 'vz']) unitcell = self.get_global_cell(cur) if not coords_list: raise IOError("Found no coordinates") self.n_atoms = len(coords_list) velocities = np.array(velocities_list, dtype=np.float32) if not velocities.any(): velocities = None self.ts = self._Timestep.from_coordinates( np.array(coords_list, dtype=np.float32), velocities=velocities, **self._ts_kwargs) self.ts.frame = 0 # 0-based frame number self.ts.dimensions = triclinic_box(unitcell['x'], unitcell['y'], unitcell['z']) if self.convert_units: self.convert_pos_from_native(self.ts._pos) # in-place ! if self.ts.dimensions is not None: self.convert_pos_from_native(self.ts.dimensions[:3]) # in-place ! if self.ts.has_velocities: # converts nm/ps to A/ps units self.convert_velocities_from_native(self.ts._velocities)