In process

molsysmt/_version.py

@@ -1 +1 @@
-__version__ = "0.8.3+17.gcda3efaf.dirty"
+__version__ = "0.8.3+19.g38a19d1b.dirty"

molsysmt/form/file_msmh5/__init__.py

@@ -18,18 +18,22 @@
 
 from .to_molsysmt_MSMH5FileHandler import to_molsysmt_MSMH5FileHandler
 from .to_molsysmt_MolSys import to_molsysmt_MolSys
+from .to_molsysmt_MolSysNEW import to_molsysmt_MolSysNEW
 from .to_molsysmt_Topology import to_molsysmt_Topology
-from .to_molsysmt_Topology2 import to_molsysmt_Topology2
+from .to_molsysmt_TopologyNEW import to_molsysmt_TopologyNEW
 from .to_molsysmt_Structures import to_molsysmt_Structures
+from .to_molsysmt_StructuresNEW import to_molsysmt_StructuresNEW
 from .to_nglview_NGLWidget import to_nglview_NGLWidget
 
 _convert_to={
         'file:msmh5': extract,
         'molsysmt.MSMH5FileHandler': to_molsysmt_MSMH5FileHandler,
         'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.MolSysNEW': to_molsysmt_MolSysNEW,
         'molsysmt.Topology': to_molsysmt_Topology,
-        'molsysmt.Topology2': to_molsysmt_Topology2,
+        'molsysmt.TopologyNEW': to_molsysmt_TopologyNEW,
         'molsysmt.Structures': to_molsysmt_Structures,
+        'molsysmt.StructuresNEW': to_molsysmt_StructuresNEW,
         'nglview.NGLWidget': to_nglview_NGLWidget,
         }
 

molsysmt/form/file_msmh5/to_molsysmt_MolSys.py

@@ -3,5 +3,13 @@
 @digest(form='file:msmh5')
 def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all'):
 
-    raise NotImplementedError
+    from . import to_molsysmt_MSMH5FileHandler
+    from ..molsysmt_MSMH5FileHandler import to_molsysmt_MolSys as molsysmt_MSMH5FileHandler_to_molsysmt_MolSys
+
+    handler = to_molsysmt_MSMH5FileHandler(item)
+    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_MolSys(handler, atom_indices=atom_indices,
+                                                           structure_indices=structure_indices)
+    handler.close()
+
+    return tmp_item
 

molsysmt/form/file_msmh5/to_molsysmt_MolSysNEW.py

@@ -0,0 +1,15 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmh5')
+def to_molsysmt_MolSysNEW(item, atom_indices='all', structure_indices='all'):
+
+    from . import to_molsysmt_MSMH5FileHandler
+    from ..molsysmt_MSMH5FileHandler import to_molsysmt_MolSysNEW as molsysmt_MSMH5FileHandler_to_molsysmt_MolSys
+
+    handler = to_molsysmt_MSMH5FileHandler(item)
+    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_MolSysNEW(handler, atom_indices=atom_indices,
+                                                           structure_indices=structure_indices)
+    handler.close()
+
+    return tmp_item
+

molsysmt/form/file_msmh5/to_molsysmt_StructuresNEW.py

@@ -0,0 +1,14 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmh5')
+def to_molsysmt_StructuresNEW(item, atom_indices='all', structure_indices='all'):
+
+    from . import to_molsysmt_MSMH5FileHandler
+    from ..molsysmt_MSMH5FileHandler import to_molsysmt_StructuresNEW as molsysmt_MSMH5FileHandler_to_molsysmt_StructuresNEW
+
+    handler = to_molsysmt_MSMH5FileHandler(item)
+    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_StructuresNEW(handler, atom_indices=atom_indices,
+            structure_indices=structure_indices)
+    handler.close()
+
+    return tmp_item

molsysmt/form/file_msmh5/to_molsysmt_Topology2.py → molsysmt/form/file_msmh5/to_molsysmt_TopologyNEW.py

@@ -1,13 +1,13 @@
 from molsysmt._private.digestion import digest
 
 @digest(form='file:msmh5')
-def to_molsysmt_Topology2(item, atom_indices='all'):
+def to_molsysmt_TopologyNEW(item, atom_indices='all'):
 
     from . import to_molsysmt_MSMH5FileHandler
-    from ..molsysmt_MSMH5FileHandler import to_molsysmt_Topology2 as molsysmt_MSMH5FileHandler_to_molsysmt_Topology2
+    from ..molsysmt_MSMH5FileHandler import to_molsysmt_TopologyNEW as molsysmt_MSMH5FileHandler_to_molsysmt_TopologyNEW
 
     handler = to_molsysmt_MSMH5FileHandler(item)
-    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_Topology2(handler, atom_indices=atom_indices)
+    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_TopologyNEW(handler, atom_indices=atom_indices)
     handler.close()
 
     return tmp_item

molsysmt/form/molsysmt_MSMH5FileHandler/__init__.py

@@ -17,17 +17,21 @@
 from .iterators import StructuresIterator, TopologyIterator
 
 from .to_molsysmt_MolSys import to_molsysmt_MolSys
+from .to_molsysmt_MolSysNEW import to_molsysmt_MolSysNEW
 from .to_molsysmt_Topology import to_molsysmt_Topology
-from .to_molsysmt_Topology2 import to_molsysmt_Topology2
+from .to_molsysmt_TopologyNEW import to_molsysmt_TopologyNEW
 from .to_molsysmt_Structures import to_molsysmt_Structures
+from .to_molsysmt_StructuresNEW import to_molsysmt_StructuresNEW
 from .to_nglview_NGLWidget import to_nglview_NGLWidget
 
 _convert_to={
         'molsysmt.MSMH5FileHandler': extract,
         'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.MolSysNEW': to_molsysmt_MolSysNEW,
         'molsysmt.Topology': to_molsysmt_Topology,
-        'molsysmt.Topology2': to_molsysmt_Topology2,
+        'molsysmt.TopologyNEW': to_molsysmt_TopologyNEW,
         'molsysmt.Structures': to_molsysmt_Structures,
+        'molsysmt.StructuresNEW': to_molsysmt_StructuresNEW,
         'nglview.NGLWidget': to_nglview_NGLWidget,
         }
 

molsysmt/form/molsysmt_MSMH5FileHandler/to_molsysmt_MolSys.py

@@ -3,5 +3,13 @@
 @digest(form='molsysmt.MSMH5FileHandler')
 def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all'):
 
-    raise NotImplementedError
+    from .to_molsysmt_Topology import to_molsysmt_Topology
+    from .to_molsysmt_Structures import to_molsysmt_Structures
+    from molsysmt.native import MolSys
+
+    tmp_item = MolSys()
+    tmp_item.topology = to_molsysmt_Topology(item, atom_indices=atom_indices)
+    tmp_item.structures = to_molsysmt_Structures(item, atom_indices=atom_indices, structure_indices=structure_indices)
+
+    return tmp_item
 

molsysmt/form/molsysmt_MSMH5FileHandler/to_molsysmt_MolSysNEW.py

@@ -0,0 +1,15 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.MSMH5FileHandler')
+def to_molsysmt_MolSysNEW(item, atom_indices='all', structure_indices='all'):
+
+    from .to_molsysmt_TopologyNEW import to_molsysmt_TopologyNEW
+    from .to_molsysmt_StructuresNEW import to_molsysmt_StructuresNEW
+    from molsysmt.native import MolSysNEW
+
+    tmp_item = MolSysNEW()
+    tmp_item.topology = to_molsysmt_TopologyNEW(item, atom_indices=atom_indices)
+    tmp_item.structures = to_molsysmt_StructuresNEW(item, atom_indices=atom_indices, structure_indices=structure_indices)
+
+    return tmp_item
+

molsysmt/form/molsysmt_MSMH5FileHandler/to_molsysmt_StructuresNEW.py

@@ -0,0 +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_StructuresNEW(item, atom_indices='all', structure_indices='all'):
+
+    from molsysmt.native import StructuresNEW
+
+    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 = StructuresNEW()
+
+    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
+

molsysmt/form/molsysmt_MSMH5FileHandler/to_molsysmt_Topology2.py → molsysmt/form/molsysmt_MSMH5FileHandler/to_molsysmt_TopologyNEW.py

@@ -3,13 +3,13 @@
 import numpy as np
 
 @digest(form='molsysmt.MSMH5FileHandler')
-def to_molsysmt_Topology2(item, atom_indices='all'):
+def to_molsysmt_TopologyNEW(item, atom_indices='all'):
 
-    from molsysmt.native import Topology2
+    from molsysmt.native import TopologyNEW
 
     topology_ds = item.file['topology']
 
-    tmp_item = Topology2()
+    tmp_item = TopologyNEW()
 
     # Atoms
 

molsysmt/form/molsysmt_MolSysNEW/__init__.py

@@ -0,0 +1,33 @@
+form_name = 'molsysmt.MolSysNEW'
+form_type = 'class'
+form_info = ["", ""]
+
+from .is_form import is_form
+
+from .attributes import attributes
+from .has_attribute import has_attribute
+
+from .extract import extract
+from .copy import copy
+from .add import add
+from .merge import merge
+from .append_structures import append_structures
+from .get import *
+from .set import *
+from .iterators import StructuresIterator, TopologyIterator
+
+from .to_molsysmt_TopologyNEW import to_molsysmt_TopologyNEW
+from .to_molsysmt_StructuresNEW import to_molsysmt_StructuresNEW
+from .to_molsysmt_MolecularMechanics import to_molsysmt_MolecularMechanics
+from .to_molsysmt_MolecularMechanicsDict import to_molsysmt_MolecularMechanicsDict
+from .to_file_msmpk import to_file_msmpk
+
+_convert_to={
+        'molsysmt.MolSysNEW': extract,
+        'molsysmt.TopologyNEW': to_molsysmt_TopologyNEW,
+        'molsysmt.StructuresNEW': to_molsysmt_StructuresNEW,
+        'molsysmt.MolecularMechanics': to_molsysmt_MolecularMechanics,
+        'molsysmt.MolecularMechanicsDict': to_molsysmt_MolecularMechanicsDict,
+        'file:msmpk': to_file_msmpk,
+        }
+

molsysmt/form/molsysmt_MolSysNEW/add.py

@@ -0,0 +1,12 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt import pyunitwizard as puw
+import numpy as np
+
+@digest(form='molsysmt.MolSysNEW', to_form='molsysmt.MolSysNEW')
+def add(to_item, item, atom_indices='all', structure_indices='all'):
+
+    to_item.add(item)
+
+    pass
+

molsysmt/form/molsysmt_MolSysNEW/append_structures.py

@@ -0,0 +1,12 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.MolSysNEW')
+def append_structures(item, structure_id=None, time=None, coordinates=None, velocities=None,
+        box=None):
+
+    item.structures.append_structures(structure_id=structure_id, time=time, coordinates=coordinates,
+            velocities=velocities, box=box)
+
+    pass
+