in process

devtools/requirements.yaml

@@ -15,6 +15,7 @@ production:
     - *setup_channels
   dependencies: &production_dependencies
     - *setup_dependencies
+    - h5py
     - numpy
     - numba
     - pyunitwizard

molsysmt/basic/convert.py

@@ -68,7 +68,14 @@ def _convert_one_to_one(molecular_system,
         'copy_if_all'})
 
         if len(missing_arguments)>0:
-            raise NotCompatibleConversionError(from_form, to_form, missing_arguments)
+
+            missing_arguments.discard('compression')
+            missing_arguments.discard('compression_opts')
+            missing_arguments.discard('int_precision')
+            missing_arguments.discard('float_precision')
+
+            if len(missing_arguments)>0:
+                raise NotCompatibleConversionError(from_form, to_form, missing_arguments)
 
         output = function(molecular_system, **conversion_arguments, **kwargs)
 

molsysmt/form/file_msmh5/__init__.py

@@ -0,0 +1,31 @@
+form_name = 'file:msmh5'
+form_type = 'file'
+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_MolSys import to_molsysmt_MolSys
+from .to_molsysmt_Topology import to_molsysmt_Topology
+from .to_molsysmt_Structures import to_molsysmt_Structures
+from .to_nglview_NGLWidget import to_nglview_NGLWidget
+
+_convert_to={
+        'file:msmh5': extract,
+        'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.Topology': to_molsysmt_Topology,
+        'molsysmt.Structures': to_molsysmt_Structures,
+        'nglview.NGLWidget': to_nglview_NGLWidget,
+        }
+

molsysmt/form/file_msmh5/add.py

@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmh5', to_form='file:msmh5')
+def add(to_item, item, atom_indices='all', structure_indices='all'):
+
+    raise NotImplementedMethodError()
+

molsysmt/form/file_msmh5/append_structures.py

@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmh5')
+def append_structures(item, structure_id=None, time=None, coordinates=None, box=None):
+
+    raise NotImplementedMethodError()
+

molsysmt/form/file_msmh5/attributes.py

@@ -0,0 +1,39 @@
+from molsysmt.attribute.attributes import attributes as _all_attributes
+
+attributes = {ii:False for ii in _all_attributes}
+
+attributes['atom_index'] = True
+attributes['atom_id'] = True
+attributes['atom_name'] = True
+attributes['atom_type'] = True
+attributes['bond_index'] = True
+attributes['bond_id'] = True
+attributes['bond_type'] = True
+attributes['bond_order'] = True
+attributes['group_index'] = True
+attributes['group_id'] = True
+attributes['group_name'] = True
+attributes['group_type'] = True
+attributes['component_index'] = True
+attributes['component_id'] = True
+attributes['component_name'] = True
+attributes['component_type'] = True
+attributes['molecule_index'] = True
+attributes['molecule_id'] = True
+attributes['molecule_name'] = True
+attributes['molecule_type'] = True
+attributes['chain_index'] = True
+attributes['chain_id'] = True
+attributes['chain_name'] = True
+attributes['chain_type'] = True
+attributes['entity_index'] = True
+attributes['entity_id'] = True
+attributes['entity_name'] = True
+attributes['entity_type'] = True
+attributes['coordinates'] = True
+attributes['velocities'] = True
+attributes['box'] = True
+attributes['time'] = True
+attributes['structure_id'] = True
+
+del(_all_attributes)

molsysmt/form/file_msmh5/copy.py

@@ -0,0 +1,16 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest(form='file:msmh5')
+def copy(item, output_filename=None):
+
+    if output_filename is None:
+        output_filename = item
+
+    from shutil import copy as copy_file
+    copy_file(item, output_filename)
+    tmp_item = output_filename
+
+    return tmp_item
+

molsysmt/form/file_msmh5/extract.py

@@ -0,0 +1,27 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest(form='file:msmh5')
+def extract(item, atom_indices='all', structure_indices='all', output_filename=None, copy_if_all=True):
+
+    if output_filename is None:
+        output_filename = item
+
+    if is_all(atom_indices) and is_all(structure_indices):
+
+        if copy_if_all or (output_filename!=item):
+
+            from shutil import copy as copy_file
+            copy_file(item, output_filename)
+            tmp_item = output_filename
+
+        else:
+
+            tmp_item = item
+    else:
+
+        raise NotImplementedMethodError()
+
+    return tmp_item
+