in process

molsysmt/_private/digestion/argument/compression.py

@@ -0,0 +1,12 @@
+from molsysmt._private.exceptions import ArgumentError
+
+def digest_compression(compression, caller=None):
+
+    if isinstance(compression, str):
+
+        if caller.endswith('to_file_msmh5'):
+            if compression in ['gzip', 'lzf', 'szip']:
+                return compression
+
+    raise ArgumentError('compression', value=compression, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/compression_opts.py

@@ -0,0 +1,12 @@
+from molsysmt._private.exceptions import ArgumentError
+
+def digest_compression_opts(compression_opts, caller=None):
+
+    if isinstance(compression_opts, int):
+
+        if caller.endswith('to_file_msmh5'):
+            if 0<=compression_opts<=9:
+                return compression_opts
+
+    raise ArgumentError('compression_opts', value=compression_opts, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/float_precision.py

@@ -0,0 +1,12 @@
+from molsysmt._private.exceptions import ArgumentError
+
+def digest_float_precision(float_precision, caller=None):
+
+    if isinstance(float_precision, str):
+
+        if caller.endswith('to_file_msmh5'):
+            if float_precision in ['single', 'double']:
+                return float_precision
+
+    raise ArgumentError('float_precision', value=float_precision, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/int_precision.py

@@ -0,0 +1,12 @@
+from molsysmt._private.exceptions import ArgumentError
+
+def digest_int_precision(int_precision, caller=None):
+
+    if isinstance(int_precision, str):
+
+        if caller.endswith('to_file_msmh5'):
+            if int_precision in ['single', 'double']:
+                return int_precision
+
+    raise ArgumentError('int_precision', value=int_precision, caller=caller, message=None)
+

molsysmt/form/file_msmh5/__init__.py

@@ -16,13 +16,15 @@
 from .set import *
 from .iterators import StructuresIterator, TopologyIterator
 
+from .to_molsysmt_MSMH5FileHandler import to_molsysmt_MSMH5FileHandler
 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.MSMH5FileHandler': to_molsysmt_MSMH5FileHandler,
         'molsysmt.MolSys': to_molsysmt_MolSys,
         'molsysmt.Topology': to_molsysmt_Topology,
         'molsysmt.Structures': to_molsysmt_Structures,

molsysmt/form/file_msmh5/to_molsysmt_MSMH5FileHandler.py

@@ -0,0 +1,8 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmh5')
+def to_molsysmt_MSMH5FileHandler(item, atom_indices='all'):
+
+    from molsysmt.native import MSMH5FileHandler
+
+    return MSMH5FileHandler(item, io_mode='r')

molsysmt/form/file_msmh5/to_molsysmt_Topology.py

@@ -3,4 +3,11 @@
 @digest(form='file:msmh5')
 def to_molsysmt_Topology(item, atom_indices='all'):
 
-    raise NotImplementedError
+    from . import to_molsysmt_MSMH5FileHandler
+    from ..molsysmt_MSMH5FileHandler import to_molsysmt_Topology as molsysmt_MSMH5FileHandler_to_molsysmt_Topology
+
+    handler = to_molsysmt_MSMH5FileHandler(item)
+    tmp_item = molsysmt_MSMH5FileHandler_to_molsysmt_Topology(handler, atom_indices=atom_indices)
+    handler.close()
+
+    return tmp_item

molsysmt/form/molsysmt_MSMH5FileHandler/__init__.py

@@ -0,0 +1,31 @@
+form_name = 'molsysmt.MSMH5FileHandler'
+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_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={
+        'molsysmt.MSMH5FileHandler': extract,
+        'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.Topology': to_molsysmt_Topology,
+        'molsysmt.Structures': to_molsysmt_Structures,
+        'nglview.NGLWidget': to_nglview_NGLWidget,
+        }
+

molsysmt/form/molsysmt_MSMH5FileHandler/add.py

@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.MSMH5FileHandler', to_form='molsysmt.MSMH5FileHandler')
+def add(to_item, item, atom_indices='all', structure_indices='all'):
+
+    raise NotImplementedMethodError()
+

molsysmt/form/molsysmt_MSMH5FileHandler/append_structures.py

@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.MSMH5FileHandler')
+def append_structures(item, structure_id=None, time=None, coordinates=None, box=None):
+
+    raise NotImplementedMethodError()
+

molsysmt/form/molsysmt_MSMH5FileHandler/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/molsysmt_MSMH5FileHandler/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='molsysmt.MSMH5FileHandler')
+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/molsysmt_MSMH5FileHandler/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='molsysmt.MSMH5FileHandler')
+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
+