In process

molsysmt/basic/info.py

@@ -139,11 +139,11 @@ def info(molecular_system,
         chain_index, \
         molecule_index, molecule_type, \
         entity_index, entity_name = get(molecular_system, element=element, selection=selection,
-                                        syntax=syntax, atom_index=True, atom_id=True, atom_name=True,
-                                        atom_type=True, group_index=True, group_id=True, group_name=True,
-                                        group_type=True, component_index=True, chain_index=True,
-                                        molecule_index=True,
-                                        molecule_type=True, entity_index=True, entity_name=True,
+                                        syntax=syntax, skip_digestion=True, atom_index=True, atom_id=True,
+                                        atom_name=True, atom_type=True, group_index=True, group_id=True,
+                                        group_name=True, group_type=True, component_index=True,
+                                        chain_index=True, molecule_index=True, molecule_type=True,
+                                        entity_index=True, entity_name=True,
                                         )
 
         if not attributes_filter['atom_index']: atom_index=None
@@ -176,9 +176,9 @@ def info(molecular_system,
         chain_index, \
         molecule_index, molecule_type, \
         entity_index, entity_name = get(molecular_system, element=element, selection=selection,
-                                        syntax=syntax, group_index=True, group_id=True, group_name=True,
-                                        group_type=True, n_atoms=True, component_index=True, chain_index=True,
-                                        molecule_index=True, molecule_type=True, entity_index=True,
+                                        syntax=syntax, skip_digestion=True, group_index=True, group_id=True,
+                                        group_name=True, group_type=True, n_atoms=True, component_index=True,
+                                        chain_index=True, molecule_index=True, molecule_type=True, entity_index=True,
                                         entity_name=True)
 
         if not attributes_filter['group_index']: group_index=None
@@ -206,9 +206,9 @@ def info(molecular_system,
         chain_index, \
         molecule_index, molecule_type, \
         entity_index, entity_name = get(molecular_system, element=element, selection=selection,
-                                        syntax=syntax, component_index=True, n_atoms=True, n_groups=True,
-                                        chain_index=True, molecule_index=True, molecule_type=True,
-                                        entity_index=True, entity_name=True)
+                                        syntax=syntax, skip_digestion=True, component_index=True,
+                                        n_atoms=True, n_groups=True, chain_index=True, molecule_index=True,
+                                        molecule_type=True, entity_index=True, entity_name=True)
 
         if not attributes_filter['component_index']: component_index=None
         if not attributes_filter['n_atoms']: n_atoms=None
@@ -231,9 +231,9 @@ def info(molecular_system,
         n_atoms, n_groups, n_components, \
         molecule_index, molecule_type, \
         entity_index, entity_name = get(molecular_system, element=element, selection=selection,
-                                        syntax=syntax, chain_index=True, chain_id=True, chain_name=True,
-                                        n_atoms=True, n_groups=True, n_components=True, molecule_index=True,
-                                        molecule_type=True, entity_index=True, entity_name=True)
+                                        syntax=syntax, skip_digestion=True, chain_index=True, chain_id=True,
+                                        chain_name=True, n_atoms=True, n_groups=True, n_components=True,
+                                        molecule_index=True, molecule_type=True, entity_index=True, entity_name=True)
 
         if not attributes_filter['chain_index']: chain_index=None
         if not attributes_filter['chain_id']: chain_id=None
@@ -286,7 +286,7 @@ def info(molecular_system,
         molecule_index, molecule_name, molecule_type, \
         n_atoms, n_groups, n_components, chain_index, \
         entity_index, entity_name = get(molecular_system, element=element, selection=selection,
-                                        syntax=syntax, molecule_index=True, molecule_name=True,
+                                        syntax=syntax, skip_digestion=True, molecule_index=True, molecule_name=True,
                                         molecule_type=True, n_atoms=True, n_groups=True, n_components=True,
                                         chain_index=True, entity_index=True, entity_name=True)
 
@@ -321,8 +321,9 @@ def info(molecular_system,
         entity_index, entity_name, entity_type, \
         n_atoms, n_groups, n_components, n_chains, \
         n_molecules = get(molecular_system, element=element, selection=selection,
-                          syntax=syntax, entity_index=True, entity_name=True, entity_type=True, n_atoms=True,
-                          n_groups=True, n_components=True, n_chains=True, n_molecules=True)
+                          syntax=syntax, skip_digestion=True, entity_index=True, entity_name=True,
+                          entity_type=True, n_atoms=True, n_groups=True, n_components=True, n_chains=True,
+                          n_molecules=True)
 
         if not attributes_filter['entity_index']: entity_index=None
         if not attributes_filter['entity_name']: entity_name=None
@@ -342,7 +343,8 @@ def info(molecular_system,
 
         n_atoms, n_groups, n_components, n_chains, n_molecules, n_entities, n_structures, \
         n_ions, n_waters, n_small_molecules, n_peptides, n_proteins, n_dnas, \
-        n_rnas, n_lipids, n_oligosaccharides, n_saccharides = get(molecular_system, element=element, n_atoms=True, n_groups=True,
+        n_rnas, n_lipids, n_oligosaccharides, n_saccharides = get(molecular_system, element=element, skip_digestion=True,
+                n_atoms=True, n_groups=True,
                 n_components=True, n_chains=True, n_molecules=True, n_entities=True, n_structures=True, n_ions=True,
                 n_waters=True, n_small_molecules=True, n_peptides=True, n_proteins=True, n_dnas=True,
                 n_rnas=True, n_lipids=True, n_oligosaccharides=True, n_saccharides=True)

molsysmt/basic/merge.py

@@ -8,6 +8,7 @@ def merge(molecular_systems,
           structure_indices='all',
           syntax='MolSysMT',
           to_form=None,
+          skip_digestion=False
           ):
 
     """
@@ -150,11 +151,11 @@ def merge(molecular_systems,
             if is_all(tmp_selection):
                 aux_atom_indices.append(tmp_selection)
             else:
-                aux_atom_indices.append(selection(tmp_molecular_system, selection=selection, syntax=syntax))
+                aux_atom_indices.append(selection(tmp_molecular_system, selection=selection, syntax=syntax, skip_digestion=True))
             aux_structure_indices.append(tmp_structure_indices)
         else:
             aux = convert(tmp_molecular_system, to_form=to_form, selection=tmp_selection,
-                    structure_indices=tmp_structure_indices)
+                    structure_indices=tmp_structure_indices, skip_digestion=True)
             aux_molecular_systems.append(aux)
             aux_atom_indices.append('all')
             aux_structure_indices.append('all')
@@ -169,6 +170,8 @@ def merge(molecular_systems,
     if 'structure_indices' in input_arguments:
         merge_arguments['structure_indices']=aux_structure_indices
 
+    merge_arguments['skip_digestion']=True
+
     output = merge_function(aux_molecular_systems, **merge_arguments)
 
     return output

molsysmt/form/file_msmpk/__init__.py

@@ -18,13 +18,19 @@
 
 from .update_file import update_file
 
+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_molsysmt_MolSysOld import to_molsysmt_MolSysOld
 from .to_molsysmt_TopologyOld import to_molsysmt_TopologyOld
 from .to_molsysmt_StructuresOld import to_molsysmt_StructuresOld
 from .to_nglview_NGLWidget import to_nglview_NGLWidget
 
 _convert_to={
         'file:msmpk': extract,
+        'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.Topology': to_molsysmt_Topology,
+        'molsysmt.Structures': to_molsysmt_Structures,
         'molsysmt.MolSysOld': to_molsysmt_MolSysOld,
         'molsysmt.TopologyOld': to_molsysmt_TopologyOld,
         'molsysmt.StructuresOld': to_molsysmt_StructuresOld,

molsysmt/form/file_msmpk/to_molsysmt_MolSys.py

@@ -0,0 +1,14 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmpk')
+def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from .to_molsysmt_MolSysOld import to_molsysmt_MolSysOld
+    from ..molsysmt_MolSysOld import to_molsysmt_MolSys as molsysmt_MolSysOld_to_molsysmt_MolSys
+
+    tmp_item = to_molsysmt_MolSysOld(item, atom_indices=atom_indices, structure_indices=structure_indices,
+                                     skip_digestion=True)
+    tmp_item = molsysmt_MolSysOld_to_molsysmt_MolSys(tmp_item)
+
+    return tmp_item
+

molsysmt/form/file_msmpk/to_molsysmt_MolSysOld.py

@@ -9,25 +9,42 @@ def to_molsysmt_MolSysOld(item, atom_indices='all', structure_indices='all', ski
     import bz2
 
     fff = bz2.BZ2File(item,'rb')
-    tmp_item = pickle.load(fff)
+    aux_item = pickle.load(fff)
     fff.close()
 
     # lengths with nm values and time in ps
 
-    if tmp_item.structures.coordinates is not None:
-        value = tmp_item.structures.coordinates
+    if aux_item.structures.coordinates is not None:
+        value = aux_item.structures.coordinates
         quantity = puw.quantity(value, 'nm')
-        tmp_item.structures.coordinates = puw.standardize(quantity)
+        aux_item.structures.coordinates = puw.standardize(quantity)
 
-    if tmp_item.structures.box is not None:
-        value = tmp_item.structures.box
+    if aux_item.structures.box is not None:
+        value = aux_item.structures.box
         quantity = puw.quantity(value, 'nm')
-        tmp_item.structures.box = puw.standardize(quantity)
+        aux_item.structures.box = puw.standardize(quantity)
 
-    if tmp_item.structures.time is not None:
-        value = tmp_item.structures.time
+    if aux_item.structures.time is not None:
+        value = aux_item.structures.time
         quantity = puw.quantity(value, 'ps')
-        tmp_item.structures.time = puw.standardize(quantity)
+        aux_item.structures.time = puw.standardize(quantity)
+
+    from molsysmt.native import MolSysOld
+    from copy import deepcopy
+
+    tmp_item = MolSysOld()
+
+    tmp_item.topology.atoms_dataframe = deepcopy(aux_item.topology.atoms_dataframe)
+    tmp_item.topology.bonds_dataframe = deepcopy(aux_item.topology.bonds_dataframe)
+
+    tmp_item.structures.n_atoms = aux_item.structures.n_atoms
+    tmp_item.structures.n_structures = aux_item.structures.n_structures
+
+    tmp_item.structures.coordinates = deepcopy(aux_item.structures.coordinates)
+    tmp_item.structures.box = deepcopy(aux_item.structures.box)
+    tmp_item.structures.time = deepcopy(aux_item.structures.time)
+
+    del aux_item
 
     tmp_item = extract_molsysmt_MolSysOld(tmp_item, atom_indices=atom_indices,
             structure_indices=structure_indices, copy_if_all=False, skip_digestion=True)

molsysmt/form/file_msmpk/to_molsysmt_Structures.py

@@ -0,0 +1,14 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmpk')
+def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from . import to_molsysmt_MolSys
+    from ..molsysmt_MolSys import to_molsysmt_Structures as molsysmt_MolSys_to_molsysmt_Structures
+
+    tmp_item = to_molsysmt_MolSys(item, atom_indices=atom_indices, structure_indices=structure_indices,
+                                     skip_digestion=True)
+    tmp_item = molsysmt_MolSys_to_molsysmt_Structures(tmp_item, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/file_msmpk/to_molsysmt_Topology.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:msmpk')
+def to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False):
+
+    from . import to_molsysmt_MolSys
+    from ..molsysmt_MolSys import to_molsysmt_Topology as molsysmt_MolSys_to_molsysmt_Topology
+
+    tmp_item = to_molsysmt_MolSys(item, skip_digestion=True)
+    tmp_item = molsysmt_MolSys_to_molsysmt_Topology(tmp_item, atom_indices=atom_indices, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/molsysmt_MolSysOld/__init__.py

@@ -16,6 +16,7 @@
 from .set import *
 from .iterators import StructuresIterator, TopologyIterator
 
+from .to_molsysmt_MolSys import to_molsysmt_MolSys
 from .to_molsysmt_TopologyOld import to_molsysmt_TopologyOld
 from .to_molsysmt_StructuresOld import to_molsysmt_StructuresOld
 from .to_molsysmt_MolecularMechanics import to_molsysmt_MolecularMechanics
@@ -44,6 +45,7 @@
 
 _convert_to={
         'molsysmt.MolSysOld': extract,
+        'molsysmt.MolSys': to_molsysmt_MolSys,
         'molsysmt.TopologyOld': to_molsysmt_TopologyOld,
         'molsysmt.StructuresOld': to_molsysmt_StructuresOld,
         'molsysmt.MolecularMechanics': to_molsysmt_MolecularMechanics,

molsysmt/form/molsysmt_MolSysOld/add.py

@@ -4,7 +4,7 @@
 import numpy as np
 
 @digest(form='molsysmt.MolSysOld', to_form='molsysmt.MolSysOld')
-def add(to_item, item, atom_indices='all', structure_indices='all'):
+def add(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False):
 
     to_item.add(item)
 

molsysmt/form/molsysmt_MolSysOld/append_structures.py

@@ -3,7 +3,7 @@
 
 @digest(form='molsysmt.MolSysOld')
 def append_structures(item, structure_id=None, time=None, coordinates=None, velocities=None,
-        box=None):
+        box=None, skip_digestion=True):
 
     item.structures.append_structures(structure_id=structure_id, time=time, coordinates=coordinates,
             velocities=velocities, box=box)

molsysmt/form/molsysmt_MolSysOld/copy.py

@@ -1,7 +1,7 @@
 from molsysmt._private.digestion import digest
 
 @digest(form='molsysmt.MolSysOld')
-def copy(item):
+def copy(item, skip_digestion=False):
 
     return item.copy()
 

molsysmt/form/molsysmt_MolSysOld/extract.py

@@ -2,7 +2,7 @@
 from molsysmt._private.variables import is_all
 
 @digest(form='molsysmt.MolSysOld')
-def extract(item, atom_indices='all', structure_indices='all', copy_if_all=True):
+def extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False):
 
     if is_all(atom_indices) and is_all(structure_indices):
         if copy_if_all: