In process

molsysmt/_private/common_get.py

@@ -263,7 +263,7 @@ def get_n_atoms_from_atom(item, indices='all'):
     if is_all(indices):
         output = get_n_atoms_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 
@@ -900,7 +900,7 @@ def get_n_groups_from_group(item, indices='all'):
     if is_all(indices):
         output = get_n_groups_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 
@@ -1535,7 +1535,7 @@ def get_n_components_from_component(item, indices='all'):
     if is_all(indices):
         output = get_n_components_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 
@@ -2232,7 +2232,7 @@ def get_n_molecules_from_molecule(item, indices='all'):
     if is_all(indices):
         output = get_n_molecules_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 
@@ -2935,7 +2935,7 @@ def get_n_chains_from_chain(item, indices='all'):
     if is_all(indices):
         output = get_n_chains_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 
@@ -3658,7 +3658,7 @@ def get_n_entities_from_entity(item, indices='all'):
     if is_all(indices):
         output = get_n_entities_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 
@@ -4070,7 +4070,7 @@ def get_n_bonds_from_bond(item, indices='all'):
     if is_all(indices):
         output = get_n_bonds_from_system(item)
     else:
-        output = indices.shape[0]
+        output = len(indices)
 
     return output
 

molsysmt/_private/digestion/argument/keep_ids.py

@@ -1,12 +1,15 @@
 from ...exceptions import ArgumentError
 
-def digest_keep_ids(keep_ids, caller=None):
+functions_with_boolean = (
+        'merge.merge',
+        'add.add',
+        'add_missing_terminal_cappings.add_missing_terminal_cappings'
+        )
 
-    if caller.endswith('.merge.merge'):
-        if isinstance(keep_ids, bool):
-            return keep_ids
 
-    if caller.endswith('.add.add'):
+def digest_keep_ids(keep_ids, caller=None):
+
+    if caller.endswith(functions_with_boolean):
         if isinstance(keep_ids, bool):
             return keep_ids
 

molsysmt/build/is_solvated.py

@@ -2,7 +2,7 @@
 from molsysmt import pyunitwizard as puw
 
 @digest()
-def is_solvated(molecular_system):
+def is_solvated(molecular_system, skip_digestion=False):
     """
     To be written soon...
     """
@@ -11,7 +11,7 @@ def is_solvated(molecular_system):
 
     output = False
 
-    n_waters, volume = get(molecular_system, element='system', n_waters=True, box_volume=True)
+    n_waters, volume = get(molecular_system, element='system', n_waters=True, box_volume=True, skip_digestion=True)
 
     if (n_waters>0) and (volume is not None):
 

molsysmt/build/mutate.py

@@ -40,7 +40,7 @@ def mutate(molecular_system, mutations=None, keys='group_index', selection="all"
                     aux_indices = get(molecular_system, element='group',
                             selection='group_id==@ii', mask=selection,
                             group_index=True)
-                    if aux_indices.shape[0]>1:
+                    if len(aux_indices)>1:
                         raise ValueError(f'There are multiple groups with the group_id: {ii}')
                     else:
                         group_indices.append(aux_indices[0])

molsysmt/form/molsysmt_MolSys/__init__.py

@@ -43,6 +43,8 @@
 from .to_file_h5msm import to_file_h5msm
 from .to_file_pdb import to_file_pdb
 from .to_string_pdb_text import to_string_pdb_text
+from .to_string_amino_acids_1 import to_string_amino_acids_1
+from .to_string_amino_acids_3 import to_string_amino_acids_3
 
 _convert_to={
         'molsysmt.MolSys': extract,
@@ -59,6 +61,8 @@
         'openmm.Modeller': to_openmm_Modeller,
         'pdbfixer.PDBFixer': to_pdbfixer_PDBFixer,
         'string:pdb_text': to_string_pdb_text,
+        'string:amino_acids_1': to_string_amino_acids_1,
+        'string:amino_acids_3': to_string_amino_acids_3,
         'file:msmpk': to_file_msmpk,
         'file:h5msm': to_file_h5msm,
         'file:pdb': to_file_pdb,

molsysmt/form/molsysmt_MolSys/to_string_amino_acids_1.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.MolSys')
+def to_string_amino_acids_1(item, group_indices='all', skip_digestion=False):
+
+    from . import to_molsysmt_Topology
+    from ..molsysmt_Topology import to_string_amino_acids_1 as molsysmt_Topology_to_string_amino_acids_1
+
+    tmp_item = to_molsysmt_Topology(item, skip_digestion=True)
+    tmp_item = molsysmt_Topology_to_string_amino_acids_1(tmp_item, group_indices=group_indices, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/molsysmt_MolSys/to_string_amino_acids_3.py

@@ -0,0 +1,12 @@
+from molsysmt._private.digestion import digest
+import numpy as np
+
+@digest(form='molsysmt.MolSys')
+def to_string_amino_acids_3(item, group_indices='all', skip_digestion=False):
+
+    from ..molsysmt_Topology import to_string_amino_acids_3 as molsysmt_Topology_to_string_amino_acids_3
+
+    tmp_item = molsysmt_Topology_to_string_amino_acids_3(item.topology, group_indices=group_indices, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/molsysmt_Structures/get.py

@@ -218,9 +218,6 @@ def get_box_volume_from_system(item, structure_indices='all', skip_digestion=Fal
     if structure_indices is None:
         return None
 
-    if item.time is None:
-        return None
-
     from molsysmt.pbc import get_volume_from_box
     output = None
     box = get_box_from_system(item, structure_indices=structure_indices, skip_digestion=True)

molsysmt/form/pdbfixer_PDBFixer/__init__.py

@@ -5,6 +5,8 @@
 piped_topological_attribute = None
 piped_structural_attribute = None
 piped_any_attribute = None
+bonds_are_explicit = True
+bonds_can_be_computed = True
 
 from .is_form import is_form
 

molsysmt/form/string_pdb_id/get_structural_attributes.py

@@ -163,6 +163,17 @@ def get_n_bioassemblies_from_system(item, skip_digestion=False):
 
     return output
 
+@digest(form=form)
+def get_alternate_location_from_system (item, skip_digestion=False):
+
+    from . import to_mmtf_MMTFDecoder
+    from ..mmtf_MMTFDecoder import get_alternate_location_from_system as aux_get
+
+    tmp_item = to_mmtf_MMTFDecoder(item, skip_digestion=True)
+    output = aux_get(tmp_item, skip_digestion=True)
+
+    return output
+
 
 # List of functions to be imported
 

molsysmt/pbc/get_angles_from_box.py

@@ -3,7 +3,7 @@
 from molsysmt import lib as msmlib
 
 @digest()
-def get_angles_from_box(box):
+def get_angles_from_box(box, skip_digestion=False):
     """
     To be written soon...
     """

molsysmt/pbc/get_lengths_from_box.py

@@ -3,7 +3,7 @@
 from molsysmt import lib as msmlib
 
 @digest()
-def get_lengths_from_box(box):
+def get_lengths_from_box(box, skip_digestion=False):
     """
     To be written soon...
     """

molsysmt/pbc/get_shape_from_box.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 @digest()
-def get_shape_from_box(box):
+def get_shape_from_box(box, skip_digestion=False):
     """
     To be written soon...
     """
@@ -15,6 +15,6 @@ def get_shape_from_box(box):
         return None
     else:
 
-        lengths, angles = get_lengths_and_angles_from_box(box)
-        return get_shape_from_lengths_and_angles(lengths, angles)
+        lengths, angles = get_lengths_and_angles_from_box(box, skip_digestion=True)
+        return get_shape_from_lengths_and_angles(lengths, angles, skip_digestion=True)
 

molsysmt/pbc/get_shape_from_lengths_and_angles.py

@@ -3,7 +3,7 @@
 from molsysmt import pyunitwizard as puw
 
 @digest()
-def get_shape_from_lengths_and_angles(box_lengths, box_angles):
+def get_shape_from_lengths_and_angles(box_lengths, box_angles, skip_digestion=False):
     """
     To be written soon...
     """

molsysmt/pbc/has_pbc.py

@@ -1,14 +1,14 @@
 from molsysmt._private.digestion import digest
 
 @digest()
-def has_pbc(molecular_system):
+def has_pbc(molecular_system, skip_digestion=False):
     """
     To be written soon...
     """
 
     from molsysmt import get
 
-    box = get(molecular_system, structure_indices=0, box=True)
+    box = get(molecular_system, structure_indices=0, box=True, skip_digestion=True)
 
     output = True
 

molsysmt/pbc/unwrap.py

@@ -7,7 +7,7 @@
 
 @digest()
 def unwrap(molecular_system, selection='all', structure_indices='all',
-        syntax='MolSysMT', engine='MolSysMT', in_place=False):
+        syntax='MolSysMT', engine='MolSysMT', in_place=False, skip_digestion=False):
     """
     To be written soon...
     """
@@ -16,10 +16,10 @@ def unwrap(molecular_system, selection='all', structure_indices='all',
 
         from molsysmt.basic import select, get, set, extract, copy
 
-        coordinates= get(molecular_system, element='atom', selection=selection, coordinates=True)
+        coordinates= get(molecular_system, element='atom', selection=selection, coordinates=True, skip_digestion=True)
         n_structures = coordinates.shape[0]
         n_atoms = coordinates.shape[1]
-        box = get(molecular_system, element='system', structure_indices=structure_indices, box=True)
+        box = get(molecular_system, element='system', structure_indices=structure_indices, box=True, skip_digestion=True)
 
         coordinates, length_units = puw.get_value_and_unit(coordinates)
         box = puw.get_value(box, to_unit=length_units)
@@ -35,18 +35,18 @@ def unwrap(molecular_system, selection='all', structure_indices='all',
     if in_place:
 
         set(molecular_system, selection=selection, structure_indices=structure_indices,
-            syntax=syntax, coordinates=coordinates)
+            syntax=syntax, coordinates=coordinates, skip_digestion=True)
 
         del(coordinates, box)
 
         gc.collect()
 
     else:
 
-        tmp_molecular_system = copy(molecular_system)
+        tmp_molecular_system = copy(molecular_system, skip_digestion=True)
 
         set(tmp_molecular_system, selection=selection, structure_indices=structure_indices,
-            syntax='MolSysMT', coordinates=coordinates)
+            syntax='MolSysMT', coordinates=coordinates, skip_digestion=True)
 
         del(coordinates, box)
 

molsysmt/pbc/wrap_to_mic.py

@@ -9,7 +9,7 @@
 def wrap_to_mic(molecular_system, selection='all', structure_indices='all',
                 center_coordinates='[0,0,0] nanometers', center_of_selection=None, weights=None,
                 center_at_origin=True, keep_covalent_bonds=False,
-                syntax='MolSysMT', engine='MolSysMT', in_place=False):
+                syntax='MolSysMT', engine='MolSysMT', in_place=False, skip_digestion=False):
     """
     To be written soon...
     """
@@ -19,16 +19,16 @@ def wrap_to_mic(molecular_system, selection='all', structure_indices='all',
         from molsysmt.basic import select, get, set, extract, copy
         from molsysmt.structure import get_center
 
-        atom_indices = select(molecular_system, selection=selection, syntax=syntax)
+        atom_indices = select(molecular_system, selection=selection, syntax=syntax, skip_digestion=True)
 
-        coordinates= get(molecular_system, element='atom', selection=atom_indices, coordinates=True)
-        box = get(molecular_system, element='system', structure_indices=structure_indices, box=True)
+        coordinates= get(molecular_system, element='atom', selection=atom_indices, coordinates=True, skip_digestion=True)
+        box = get(molecular_system, element='system', structure_indices=structure_indices, box=True, skip_digestion=True)
 
         if center_of_selection is not None:
 
             center_coordinates = get_center(molecular_system, selection=center_of_selection,
                                 weights=weights, structure_indices=structure_indices,
-                                syntax=syntax, engine='MolSysMT')
+                                syntax=syntax, engine='MolSysMT', skip_digestion=True)
 
         coordinates, length_units = puw.get_value_and_unit(coordinates)
         box = puw.get_value(box, to_unit=length_units)
@@ -47,7 +47,7 @@ def wrap_to_mic(molecular_system, selection='all', structure_indices='all',
     if in_place:
 
         set(molecular_system, selection='atom_index in @atom_indices', structure_indices=structure_indices,
-            syntax=syntax, coordinates=coordinates)
+            syntax=syntax, coordinates=coordinates, skip_digestion=True)
 
         del(coordinates, atom_indices, structure_indices)
 
@@ -57,9 +57,9 @@ def wrap_to_mic(molecular_system, selection='all', structure_indices='all',
 
     else:
 
-        tmp_molecular_system = copy(molecular_system)
+        tmp_molecular_system = copy(molecular_system, skip_digestion=True)
         set(tmp_molecular_system, selection='atom_index in @atom_indices', structure_indices=structure_indices,
-            syntax=syntax, coordinates=coordinates)
+            syntax=syntax, coordinates=coordinates, skip_digestion=True)
 
         del(coordinates, atom_indices, structure_indices)
 

molsysmt/tests/build/add_missing_terminal_cappings/test_add_missing_terminal_cappings.py

@@ -4,7 +4,7 @@
 
 # Import package, test suite, and other packages as needed
 import molsysmt as msm
-from molsysmt.systems import tests as tests_systems
+from molsysmt import systems
 import numpy as np
 import os
 

molsysmt/tests/build/build_peptide/test_build_peptide_molsysmt_MolSys.py

@@ -12,7 +12,7 @@
 def test_build_peptide_molsysmt_MolSys_1():
     seq = 'TyrGlyGlyPheMet'
     molsys = msm.build.build_peptide(seq, to_form='molsysmt.MolSys')
-    seq_2 = msm.convert(molsys, to_form='string:aminoacids3')
+    seq_2 = msm.convert(molsys, to_form='string:amino_acids_3')
     assert seq.lower()==seq_2.lower()
 
 #def test_build_peptide_molsysmt_MolSys_2():

molsysmt/tests/build/is_solvated/test_is_solvated_molsysmt_MolSys.py

@@ -6,13 +6,13 @@
 # Import package, test suite, and other packages as needed
 import pytest
 import molsysmt as msm
-from molsysmt.systems import tests as tests_systems
+from molsysmt import systems
 import numpy as np
 
 # Distance between atoms in space and time
 
 def test_is_solvate_molsysmt_MolSys_1():
-    molsys = msm.convert(tests_systems['Met-enkephalin']['met_enkephalin.pdb'], to_form='molsysmt.MolSys')
+    molsys = msm.convert(systems['Met-enkephalin']['met_enkephalin.pdb'], to_form='molsysmt.MolSys')
     molsys = msm.build.add_missing_terminal_cappings(molsys)
     molsys = msm.build.add_missing_hydrogens(molsys)
     output_before = msm.build.is_solvated(molsys)