in process

molsysmt/form/file_msmh5/is_form.py

@@ -1,5 +1,6 @@
 from pathlib import PosixPath
 import h5py
+import os
 
 def is_form(item):
 
@@ -11,9 +12,16 @@ def is_form(item):
     if isinstance(item, str):
         if item.endswith('.msmh5'):
 
-            with h5py.File(item, "r") as file:
-                if 'type' in file.attrs:
-                    output = (file.attrs['type']=='msmh5')
+            if os.path.isfile(item):
+
+                with h5py.File(item, "r") as file:
+                    if 'type' in file.attrs:
+                        output = (file.attrs['type']=='msmh5')
+
+            else:
+
+                output = True
 
     return output
 
+

molsysmt/form/file_msmh5/to_molsysmt_Structures.py

@@ -3,4 +3,12 @@
 @digest(form='file:msmh5')
 def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all'):
 
-    raise NotImplementedError
+    from . import to_molsysmt_MSMH5FileHandler
+    from ..molsysmt_MSMH5FileHandler import to_molsysmt_Structures as molsysmt_MSMH5FileHandler_to_molsysmt_Structures
+
+    handler = to_molsysmt_MSMH5FileHandler(item)
+    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_Structures(handler, atom_indices=atom_indices,
+            structure_indices=structure_indices)
+    handler.close()
+
+    return tmp_item

molsysmt/form/molsysmt_MSMH5FileHandler/to_molsysmt_Structures.py

@@ -1,6 +1,110 @@
 from molsysmt._private.digestion import digest
+from molsysmt import pyunitwizard as puw
+import numpy as np
 
 @digest(form='molsysmt.MSMH5FileHandler')
 def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all'):
 
-    raise NotImplementedError
+    from molsysmt.native import Structures
+
+    structures_ds = item.file['structures']
+
+    n_atoms = structures_ds.attrs['n_atoms']
+    n_structures = structures_ds.attrs['n_structures']
+
+    length_unit = puw.unit(structures_ds.attrs['length_unit'])
+    time_unit = puw.unit(structures_ds.attrs['time_unit'])
+    energy_unit = puw.unit(structures_ds.attrs['energy_unit'])
+    temperature_unit = puw.unit(structures_ds.attrs['temperature_unit'])
+
+    standard_length_unit = puw.get_standard_units(length_unit)
+    standard_time_unit = puw.get_standard_units(time_unit)
+    standard_energy_unit = puw.get_standard_units(energy_unit)
+    standard_temperature_unit = puw.get_standard_units(temperature_unit)
+
+    tmp_item = Structures()
+
+    tmp_item.n_atoms = n_atoms
+    tmp_item.n_structures = n_structures
+
+    # Coordinates
+
+    if structures_ds['coordinates'].shape[0]>0:
+
+        tmp_item.coordinates = puw.quantity(np.zeros([n_structures, n_atoms, 3], dtype='float64'),
+                standard_length_unit)
+        tmp_item.coordinates[:,:,:] = puw.quantity(structures_ds['coordinates'][:,:,:],
+                length_unit)
+
+    else:
+
+        tmp_item.coordinates = None
+
+    # Velocities
+
+    if structures_ds['velocities'].shape[0]>0:
+
+        tmp_item.velocities = puw.quantity(np.zeros([n_structures, n_atoms, 3], dtype='float64'),
+                standard_length_unit/standard_time_unit)
+        tmp_item.velocities[:,:,:] = puw.quantity(structures_ds['velocities'][:,:,:],
+                length_unit/time_unit)
+
+    else:
+
+        tmp_item.velocities = None
+
+    # Box
+
+    if structures_ds['box'].shape[0]>0:
+
+        tmp_item.box = puw.quantity(np.zeros([n_structures, 3, 3], dtype='float64'),
+                standard_length_unit)
+        tmp_item.box[:,:,:] = puw.quantity(structures_ds['box'][:,:,:],
+                length_unit)
+
+    else:
+
+        tmp_item.box = None
+
+    # Kinetic Energy
+
+    if structures_ds['kinetic_energy'].shape[0]>0:
+
+        tmp_item.kinetic_energy = puw.quantity(np.zeros([n_structures], dtype='float64'),
+                standard_energy_unit)
+        tmp_item.kinetic_energy[:] = puw.quantity(structures_ds['kinetic_energy'][:],
+                energy_unit)
+
+    else:
+
+        tmp_item.kinetic_energy = None
+
+    # Potential Energy
+
+    if structures_ds['potential_energy'].shape[0]>0:
+
+        tmp_item.potential_energy = puw.quantity(np.zeros([n_structures], dtype='float64'),
+                standard_energy_unit)
+        tmp_item.potential_energy[:] = puw.quantity(structures_ds['potential_energy'][:],
+                energy_unit)
+
+    else:
+
+        tmp_item.potential_energy = None
+
+    # Temperature
+
+    if structures_ds['temperature'].shape[0]>0:
+
+        tmp_item.temperature = puw.quantity(np.zeros([n_structures], dtype='float64'),
+                standard_temperature_unit)
+        tmp_item.temperature[:] = puw.quantity(structures_ds['temperature'][:],
+                temperature_unit)
+
+    else:
+
+        tmp_item.temperature = None
+
+
+    return tmp_item
+