in process

molsysmt/_private/digestion/argument/file.py

@@ -0,0 +1,26 @@
+from ...exceptions import ArgumentError
+
+def digest_file(file, caller=None):
+
+    if caller.endswith('write_topology_in_msmh5'):
+
+        from h5py._hl.files import File as h5py_File
+        from molsysmt.native import MSMH5FileHandler
+
+        if isinstance(file, h5py_File):
+            if 'type' in file.attrs:
+                return file
+
+        elif isinstance(file, MSMH5FileHandler):
+                return file
+
+        else:
+
+            from molsysmt.form.file_msmh5.is_form import is_form as is_file_msmh5_form
+            file_is_msmh5 = is_file_msmh5_form(file)
+            if file_is_msmh5:
+                return file
+
+
+    raise ArgumentError('file', value=file, caller=caller, message=None)
+

molsysmt/form/openmm_Simulation/__init__.py

@@ -17,6 +17,7 @@
 from .iterators import StructuresIterator, TopologyIterator
 
 from .to_file_pdb import to_file_pdb
+from .to_file_msmpk import to_file_msmpk
 from .to_molsysmt_Topology import to_molsysmt_Topology
 from .to_openmm_Context import to_openmm_Context
 from .to_openmm_Topology import to_openmm_Topology
@@ -28,6 +29,7 @@
 _convert_to={
         'openmm.Simulation': extract,
         'file:pdb': to_file_pdb,
+        'file:msmpk': to_file_msmpk,
         'molsysmt.Topology': to_molsysmt_Topology,
         'openmm.Context': to_openmm_Context,
         'openmm.Topology': to_openmm_Topology,

molsysmt/form/openmm_Simulation/is_form.py

@@ -1,6 +1,6 @@
 def is_form(item):
 
-    item_fullname = item.__class__.__module__+'.'+item.__class__.__name__
+    from openmm.app.simulation import Simulation
 
-    return 'openmm.Simulation'==item_fullname
+    return isinstance(item, Simulation)
 

molsysmt/form/openmm_Simulation/to_file_msmpk.py

@@ -0,0 +1,15 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='openmm.Simulation')
+def to_file_msmpk(item, atom_indices='all', structure_indices='all', output_filename=None):
+
+    from . import to_molsysmt_MolSys as openmm_Simulation_to_molsysmt_MolSys
+    from ..molsysmt_MolSys import to_file_msmpk as molsysmt_MolSys_to_file_msmpk
+
+    tmp_item = openmm_Simulation_to_molsysmt_MolSys(item, atom_indices=atom_indices,
+            structure_indices=structure_indices)
+
+    tmp_item = molsysmt_MolSys_to_file_msmpk(tmp_item, output_filename=output_filename)
+
+    return tmp_item
+

molsysmt/form/openmm_Simulation/to_molsysmt_MolSys.py

@@ -9,7 +9,7 @@ def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all'):
 
     tmp_item = MolSys()
     tmp_item.topology = openmm_Simulation_to_molsysmt_Topology(item, atom_indices=atom_indices)
-    tmp_item.trajectory = openmm_Simulation_to_molsysmt_Structures(item, atom_indices=atom_indices, structure_indices=structure_indices)
+    tmp_item.structures = openmm_Simulation_to_molsysmt_Structures(item, atom_indices=atom_indices, structure_indices=structure_indices)
 
     return tmp_item
 

molsysmt/form/openmm_Simulation/to_openmm_Topology.py

@@ -3,7 +3,7 @@
 @digest(form='openmm.Simulation')
 def to_openmm_Topology(item, atom_indices='all'):
 
-    from molsysmt.form.openmm_Topology import extract_openmm_Topology
+    from molsysmt.form.openmm_Topology import extract as extract_openmm_Topology
 
     tmp_item = item.topology
     tmp_item = extract_openmm_Topology(tmp_item, atom_indices=atom_indices)

molsysmt/form/openmm_Topology/__init__.py

@@ -16,10 +16,11 @@
 from .set import *
 from .iterators import TopologyIterator
 
+from .write_topology_in_msmh5 import write_topology_in_msmh5
+
 from .to_string_pdb_text import to_string_pdb_text
 from .to_file_pdb import to_file_pdb
 from .to_file_psf import to_file_psf
-from .to_file_msmh5 import to_file_msmh5
 from .to_molsysmt_MolSys import to_molsysmt_MolSys
 from .to_molsysmt_Topology import to_molsysmt_Topology
 from .to_mdtraj_Topology import to_mdtraj_Topology
@@ -39,7 +40,6 @@
         'string:pdb_text': to_string_pdb_text,
         'file:pdb': to_file_pdb,
         'file:psf': to_file_psf,
-        'file:msmh5': to_file_msmh5,
         'molsysmt.MolSys': to_molsysmt_MolSys,
         'molsysmt.Topology': to_molsysmt_Topology,
         'mdtraj.Topology': to_mdtraj_Topology,

molsysmt/form/openmm_Topology/write_topology_in_msmh5.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='openmm.Topology')
+def write_topology_in_msmh5(item, file, atom_indices='all'):
+
+    from . import to_molsysmt_Topology as openmm_Topology_to_molsysmt_Topology
+    from ..molsysmt_Topology import write_topology_in_msmh5 as write_molsysmt_Topology_in_msmh5
+
+    molsysmt_Topology = openmm_Topology_to_molsysmt_Topology(item, atom_indices=atom_indices)
+    write_molsysmt_Topology_in_msmh5(molsysmt_Topology, file)
+
+    pass
+

molsysmt/native/msmh5_file_handler.py

@@ -31,10 +31,11 @@ def __init__(self, filename, io_mode='r', creator='MolSysMT', compression="gzip"
         if closed:
             self.file.close()
 
-    def write_topology(topology, selection='all', syntax='MolSysMT'):
+    def write_topology(self, topology, selection='all', syntax='MolSysMT'):
 
         from molsysmt.basic import get_form, select, convert
         from molsysmt._private.variables import is_all
+        from molsysmt.form import _dict_modules
 
         if is_all(selection):
             atom_indices = 'all'
@@ -43,11 +44,11 @@ def write_topology(topology, selection='all', syntax='MolSysMT'):
 
         try:
             topology_form = get_form(topology)
-            _dict_modules[topology_form].write_topology_in_msmh5(topology, self.file,
+            _dict_modules[topology_form].write_topology_in_msmh5(topology, file=self.file,
                     atom_indices=atom_indices)
         except:
             aux_topology = convert(topology, to_form='molsysmt.Topology', selection=atom_indices)
-            _dict_modules['molsysmt.Topology'].write_topology_in_msmh5(aux_topology, self.file,
+            _dict_modules['molsysmt.Topology'].write_topology_in_msmh5(aux_topology, file=self.file,
                     atom_indices=atom_indices)
             del(aux_topology)
 
@@ -73,38 +74,36 @@ def _new_msmfile(filename, creator='MolSysMT', compression="gzip", compression_o
     file.attrs['int_precision'] = int_precision
     file.attrs['float_precision'] = int_precision
 
-    structures_sd=file['structures']
-
     if length_unit is None:
-        structures_sd.attrs['length_unit']=puw.get_standard_units(dimensionality={'[L]':1}, form='string')
+        file.attrs['length_unit']=puw.get_standard_units(dimensionality={'[L]':1}, form='string')
     else:
-        structures_sd.attrs['length_unit']=puw.get_unit(length_unit, to_form='string')
+        file.attrs['length_unit']=puw.get_unit(length_unit, to_form='string')
 
     if time_unit is None:
-        structures_sd.attrs['time_unit']=puw.get_standard_units(dimensionality={'[T]':1}, form='string')
+        file.attrs['time_unit']=puw.get_standard_units(dimensionality={'[T]':1}, form='string')
     else:
-        structures_sd.attrs['time_unit']=puw.get_unit(time_unit, to_form='string')
+        file.attrs['time_unit']=puw.get_unit(time_unit, to_form='string')
 
     if energy_unit is None:
-        structures_sd.attrs['energy_unit']=puw.get_standard_units(dimensionality={'[L]':2, '[M]':1,
+        file.attrs['energy_unit']=puw.get_standard_units(dimensionality={'[L]':2, '[M]':1,
             '[T]':-2, '[mol]':-1}, form='string')
     else:
-        structures_sd.attrs['energy_unit']=puw.get_unit(energy_unit, to_form='string')
+        file.attrs['energy_unit']=puw.get_unit(energy_unit, to_form='string')
 
     if temperature_unit is None:
-        structures_sd.attrs['temperature_unit']=puw.get_standard_units(dimensionality={'[K]':1}, form='string')
+        file.attrs['temperature_unit']=puw.get_standard_units(dimensionality={'[K]':1}, form='string')
     else:
-        structures_sd.attrs['temperature_unit']=puw.get_unit(temperature_unit, to_form='string')
+        file.attrs['temperature_unit']=puw.get_unit(temperature_unit, to_form='string')
 
     if temperature_unit is None:
-        structures_sd.attrs['charge_unit']=puw.get_standard_units(dimensionality={'[A]':1, '[T]':1}, form='string')
+        file.attrs['charge_unit']=puw.get_standard_units(dimensionality={'[A]':1, '[T]':1}, form='string')
     else:
-        structures_sd.attrs['charge_unit']=puw.get_unit(temperature_unit, to_form='string')
+        file.attrs['charge_unit']=puw.get_unit(temperature_unit, to_form='string')
 
     if temperature_unit is None:
-        structures_sd.attrs['mass_unit']=puw.get_standard_units(dimensionality={'[M]':1}, form='string')
+        file.attrs['mass_unit']=puw.get_standard_units(dimensionality={'[M]':1}, form='string')
     else:
-        structures_sd.attrs['mass_unit']=puw.get_unit(mass_unit, to_form='string')
+        file.attrs['mass_unit']=puw.get_unit(mass_unit, to_form='string')
 
     global_dataset_options = {
             'compression':compression,
@@ -193,15 +192,16 @@ def _new_msmfile(filename, creator='MolSysMT', compression="gzip", compression_o
 
     # Structures
 
-    structures_sd = file.create_group("structures_sd")
+    structures_sd = file.create_group("structures")
     structures_sd.attrs['n_atoms'] = 0
-    structures_sd.attrs['n_structures_sd'] = 0
-    structures_sd.attrs['n_structures_sd_to_be_written'] = 0
+    structures_sd.attrs['n_structures'] = 0
+    structures_sd.attrs['n_structures_written'] = 0
     structures_sd.attrs['constant_time_step']=False
     structures_sd.attrs['time_step']=0.0
     structures_sd.attrs['constant_id_step']=False
     structures_sd.attrs['id_step']=0
     structures_sd.attrs['constant_box']=False
+    structures_sd.attrs['pbc']='pbc' # none, cell, mic, continuous
 
     structures_sd.create_dataset('id', (0,), dtype=int_type, maxshape=(None,), **global_dataset_options)
     structures_sd.create_dataset('time', (0,), dtype=float_type, maxshape=(None,), **global_dataset_options)