In process

molsysmt/form/molsysmt_MolSys/to_nglview_NGLWidget.py

@@ -12,7 +12,6 @@ def to_nglview_NGLWidget(item, atom_indices='all', structure_indices='all', skip
     else:
         tmp_item = item
 
-
     tmp_item = show_molsysmt(tmp_item, skip_digestion=True)
 
     return tmp_item

molsysmt/form/molsysmt_MolSys/to_string_pdb_text.py

@@ -1,33 +1,123 @@
 from molsysmt._private.digestion import digest
+from molsysmt import pyunitwizard as puw
+from molsysmt._private.variables import is_all
+from datetime import datetime
 
 @digest(form='molsysmt.MolSys')
 def to_string_pdb_text(item, atom_indices='all', structure_indices='all', skip_digestion=False):
 
+    now = datetime.now()
+
+    from molsysmt.pbc import get_lengths_and_angles_from_box
+
     tmp_item = ""
 
-    tp=item.topology
-    st=item.structures
-
-    for ii in range(item.topology.atoms.shape[0]):
-        line = f"{'ATOM':<6}{[i]:>5} {tp.atoms[i]:<4}" \
-               f"{' ':1}{residue_names[i]:>3} {' ':1}{chain_ids[i]:>1}" \
-               f"{residue_numbers[i]:>4}{' ':1}   {x_coords[i]:>8.3f}" \
-               f"{y_coords[i]:>8.3f}{z_coords[i]:>8.3f}{occupancies[i]:>6.2f}" \
-               f"{temp_factors[i]:>6.2f}          {element_symbols[i]:>2}"
-        file.write(line + '\n')
-        line = f"ATOM  {atom_numbers[i]:5d} {atom_names[i]:^4}{residue_names[i]:>3} {chain_ids[i]}{residue_numbers[i]:4d}    {x_coords[i]:8.3f}{y_coords[i]:8.3f}{z_coords[i]:8.3f}{occupancies[i]:6.2f}{temp_factors[i]:6.2f}           {atom_names[i][0]}"
-        # Escribe la línea en el archivo
-        file.write(line + '\n')
-
-    from . import to_openmm_Topology
-    from . import get_coordinates_from_atom
-    from ..openmm_Topology import to_string_pdb_text as openmm_Topology_to_string_pdb_text
-
-    coordinates = get_coordinates_from_atom(item, indices=atom_indices, structure_indices=structure_indices,
-                                            skip_digestion=True)
-    tmp_item = to_openmm_Topology(item, atom_indices=atom_indices, structure_indices=structure_indices,
-                                  skip_digestion=True)
-    tmp_item = openmm_Topology_to_string_pdb_text(tmp_item, coordinates=coordinates, skip_digestion=True)
+    description = "MOLECULAR SYSTEM"
+    date = now.strftime('%d-%b-%y').upper()
+    pdb_id = ''
+
+    line = f"HEADER    {description:<40}{date:>9}   {pdb_id:<4}\n"
+    tmp_item += line
+
+
+    line = f"REMARK   1 Created by MolSysMT version 1.0 on {now.strftime('%d-%b-%Y').upper()} at {now.strftime('%H:%M:%S')}\n"
+    tmp_item += line
+
+
+    with_multiple_models = False
+
+    if is_all(structure_indices):
+        if item.structures.coordinates.shape[0]>1:
+            with_multiple_models = True
+            if item.structures.structure_id is not None:
+                model_index = item.structures.structure_id
+            else:
+                model_index = list(range(item.structures.coordinates.shape[0]))
+    else:
+        if len(structure_indices)>1:
+            with_multiple_models = True
+            if item.structures.structure_id is not None:
+                model_index = item.structures.structure_id[structure_indices]
+            else:
+                model_index = list(range(len(structure_indices)))
+
+    if item.structures.box is not None:
+
+        if is_all(structure_indices):
+            lengths, angles = get_lengths_and_angles_from_box(item.structures.box[0])
+        else:
+            lengths, angles = get_lengths_and_angles_from_box(item.structures.box[structure_indices[0]])
+
+        a,b,c = puw.get_value(lengths[0], to_unit='angstrom')
+        alpha,beta,gamma = puw.get_value(angles[0], to_unit='degrees')
+
+        line = f"CRYST1{a:>9.3f}{b:>9.3f}{c:>9.3f}{alpha:>7.2f}{beta:>7.2f}{gamma:>7.2f}\n"
+        tmp_item += line
+
+    if is_all(atom_indices):
+        aux_df = item.topology.atoms
+    else:
+        aux_df = item.topology.atoms.iloc[atom_indices]
+        aux_df.reset_index(drop=True, inplace=True)
+
+    st_ii=0
+
+    if is_all(atom_indices):
+        aux_coors = puw.get_value(item.structures.coordinates[st_ii, :, :], to_unit='angstroms')
+    else:
+        aux_coors = puw.get_value(item.structures.coordinates[st_ii, atom_indices, :], to_unit='angstroms')
+
+    if with_multiple_models:
+
+        line = f"MODEL     {model_index[st_ii]:>4}"
+        tmp_item += line
+
+    for atom in aux_df.itertuples():
+
+        head = 'ATOM'
+
+        atom_id = atom.atom_id
+        atom_name = atom.atom_name
+        group_name = item.topology.groups.iloc[atom.group_index,1]
+        group_id = item.topology.groups.iloc[atom.group_index,0]
+        chain_id = item.topology.chains.iloc[atom.chain_index,1]
+
+        x,y,z = aux_coors[atom.Index, :]
+
+        occupancy = 0.0
+        temp_factor = 0.0
+
+        element_symbol = atom.atom_type
+
+        line = (
+            f"{head:<6}"
+            f"{atom_id:>5}"
+            f"{' ':1}"
+            f"{atom_name:<4}"
+            f"{' ':1}"
+            f"{group_name:>3}"
+            f"{' ':1}"
+            f"{chain_id:>1}"
+            f"{group_id:>4}"
+            f"{' ':1}"
+            f"{x:>8.3f}"
+            f"{y:>8.3f}"
+            f"{z:>8.3f}"
+            f"{occupancy:>6.2f}"
+            f"{temp_factor:>6.2f}"
+            f"{' ':10}"
+            f"{element_symbol:>2}"
+            f"\n"
+        )
+        tmp_item += line
+
+    if with_multiple_models:
+
+        line = f"ENDMDL"
+        tmp_item += line
+
+
+    tmp_item += 'END\n'
 
     return tmp_item
 

molsysmt/form/openmm_Topology/to_molsysmt_Topology.py

@@ -119,23 +119,24 @@ def to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False):
 
     # components
 
-    tmp_item.rebuild_components()
+    tmp_item.rebuild_components(redefine_indices=True, redefine_ids=True, redefine_names=True,
+                                redefine_types=True)
 
     # molecules
 
-    tmp_item.rebuild_molecules()
+    tmp_item.rebuild_molecules(redefine_indices=True, redefine_ids=True, redefine_names=True,
+                               redefine_types=True)
 
     # chain types
 
-    tmp_item.rebuild_chain_types()
+    tmp_item.rebuild_chains(redefine_ids=True, redefine_types=True)
 
     # entity
 
-    tmp_item.rebuild_entities()
+    tmp_item.rebuild_entities(redefine_indices=True, redefine_ids=True, redefine_names=True,
+                               redefine_types=True)
 
-    # nan to None
 
-    tmp_item._fix_null_values()
     tmp_item.bonds._sort_bonds()
 
     tmp_item = tmp_item.extract(atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)