In process

molsysmt/_private/digestion/argument/box.py

@@ -67,8 +67,7 @@ def digest_box(box, caller=None):
         else:
             raise ArgumentError('box', value=box, caller=caller, message=None)
 
-        box = puw.quantity(box_value, box_unit)
-        box = puw.standardize(box)
+        box = puw.quantity(box_value, box_unit, standardized=True)
 
         return box
 

molsysmt/_private/digestion/argument/box_angles.py

@@ -36,5 +36,24 @@ def digest_box_angles(box_angles, caller=None):
         if not puw.check(box_angles, dimensionality={}):
             raise ArgumentError('box_angles', value=box_angles, caller=caller, message=None)
 
-        return puw.standardize(box_angles)
+        value, unit = puw.get_value_and_unit(box_angles)
+
+        if not isinstance(value, np.ndarray):
+            value = np.array(value)
+
+        shape = value.shape
+
+        if len(shape) == 1:
+            if shape[0] != 3:
+                raise ArgumentError('box_angles', caller=caller, message=None)
+            value = np.expand_dims(value, axis=0)
+        elif len(shape) == 2:
+            if shape[1] != 3:
+                raise ArgumentError('box_angles', value=box_angles, caller=caller, message=None)
+        else:
+            raise ArgumentError('box_angles', value=box_angles, caller=caller, message=None)
+
+        box_angles = puw.quantity(value, unit, standardized=True)
+
+        return box_angles
 

molsysmt/_private/digestion/argument/box_lengths.py

@@ -36,5 +36,24 @@ def digest_box_lengths(box_lengths, caller=None):
         if not puw.check(box_lengths, dimensionality={'[L]':1}):
             raise ArgumentError('box_lengths', value=box_lengths, caller=caller, message=None)
 
-        return puw.standardize(box_lengths)
+        value, unit = puw.get_value_and_unit(box_lengths)
+
+        if not isinstance(value, np.ndarray):
+            value = np.array(value)
+
+        shape = value.shape
+
+        if len(shape) == 1:
+            if shape[0] != 3:
+                raise ArgumentError('box_lengths', caller=caller, message=None)
+            value = np.expand_dims(value, axis=0)
+        elif len(shape) == 2:
+            if shape[1] != 3:
+                raise ArgumentError('box_lengths', value=box_lengths, caller=caller, message=None)
+        else:
+            raise ArgumentError('box_lengths', value=box_lengths, caller=caller, message=None)
+
+        box_lengths = puw.quantity(value, unit, standardized=True)
+
+        return box_lengths
 

molsysmt/form/file_pdb/to_molsysmt_MolSys.py

@@ -1,16 +1,17 @@
 from molsysmt._private.digestion import digest
 
 @digest(form='file:pdb')
-def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', get_missing_bonds=False,
+                       skip_digestion=False):
 
-    from molsysmt.native import MolSys
-    from . import to_molsysmt_Topology
-    from . import to_molsysmt_Structures
+    from . import to_molsysmt_PDBFileHandler
+    from ..molsysmt_PDBFileHandler import to_molsysmt_MolSys as molsysmt_PDBFileHandler_to_molsysmt_MolSys
 
-    tmp_item = MolSys()
-    tmp_item.topology = to_molsysmt_Topology(item, atom_indices=atom_indices, skip_digestion=True)
-    tmp_item.structures = to_molsysmt_Structures(item, atom_indices=atom_indices,
-                                                 structure_indices=structure_indices, skip_digestion=True)
+    tmp_item = to_molsysmt_PDBFileHandler(item, skip_digestion=True)
+    tmp_item = molsysmt_PDBFileHandler_to_molsysmt_MolSys(tmp_item, atom_indices=atom_indices,
+                                                          structure_indices=structure_indices,
+                                                          get_missing_bonds=get_missing_bonds,
+                                                          skip_digestion=True)
 
     return tmp_item
 

molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_MolSys.py

@@ -70,6 +70,8 @@ def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', get_mi
     occupancy_array = np.array(occupancy_array, dtype=float)
     alternate_location_array = np.array(alternate_location_array, dtype=str)
 
+    coordinates_array = np.array(coordinates_array, dtype=float)
+
     alt_atom_indices = np.where(alternate_location_array!=' ')[0]
     aux_dict = {}
 
@@ -132,9 +134,15 @@ def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', get_mi
     cryst1 = item.entry.crystallographic_and_coordinate_transformation.cryst1
     box_lengths = puw.quantity([[cryst1.a, cryst1.b, cryst1.c]], 'angstroms')
     box_angles = puw.quantity([[cryst1.alpha, cryst1.beta, cryst1.gamma]], 'degrees')
-    print(box_lengths, box_angles)
-    box = get_box_from_lengths_and_angles(box_lengths, box_angles)
-    print(box)
+    box = get_box_from_lengths_and_angles(box_lengths, box_angles, skip_digestion=True)
+
+    coordinates = puw.quantity(coordinates_array, 'angstroms')
+    tmp_item.structures.append(coordinates=coordinates, box=box)
+
+    del(coordinates_array, box, box_lengths, box_angles)
+    del(atom_id_array, atom_name_array, group_index_array, chain_index_array,
+        group_id_array, group_name_array, chain_name_array, occupancy_array,
+        alternate_location_array, alt_atom_indices, aux_dict)
 
     if get_missing_bonds:
 
@@ -145,6 +153,8 @@ def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', get_mi
         tmp_item.topology.bonds.atom1_index=bonds[:,0]
         tmp_item.topology.bonds.atom2_index=bonds[:,1]
 
+        del(bonds)
+
         tmp_item.topology.rebuild_components()
         tmp_item.topology.rebuild_molecules()
         tmp_item.topology.rebuild_chains(redefine_ids=False, redefine_types=True)