In process

molsysmt/basic/get.py

@@ -257,16 +257,18 @@ def _piped_molecular_system(molecular_system, element, in_attributes):
                                                                                 skip_digestion=True)
             if is_topological_attribute(in_attribute, skip_digestion=True):
                 _, aux_form = where_is_attribute(molecular_system, in_attribute, skip_digestion=True)
-                if piped_topological_attribute[aux_form] not in aux_piped_topological_attribute:
-                    aux_piped_topological_attribute.append(piped_topological_attribute[aux_form])
-                if piped_any_attribute[aux_form] not in aux_piped_any_attribute:
-                    aux_piped_any_attribute.append(piped_any_attribute[aux_form])
+                if aux_form is not None:
+                    if piped_topological_attribute[aux_form] not in aux_piped_topological_attribute:
+                        aux_piped_topological_attribute.append(piped_topological_attribute[aux_form])
+                    if piped_any_attribute[aux_form] not in aux_piped_any_attribute:
+                        aux_piped_any_attribute.append(piped_any_attribute[aux_form])
             elif is_structural_attribute(in_attribute, skip_digestion=True):
                 _, aux_form = where_is_attribute(molecular_system, in_attribute)
-                if piped_structural_attribute[aux_form] not in aux_piped_structural_attribute:
-                    aux_piped_structural_attribute.append(piped_structural_attribute[aux_form])
-                if piped_any_attribute[aux_form] not in aux_piped_any_attribute:
-                    aux_piped_any_attribute.append(piped_any_attribute[aux_form])
+                if aux_form is not None:
+                    if piped_structural_attribute[aux_form] not in aux_piped_structural_attribute:
+                        aux_piped_structural_attribute.append(piped_structural_attribute[aux_form])
+                    if piped_any_attribute[aux_form] not in aux_piped_any_attribute:
+                        aux_piped_any_attribute.append(piped_any_attribute[aux_form])
 
         n_top = len(aux_piped_topological_attribute)
         n_str = len(aux_piped_structural_attribute)

molsysmt/element/component/get_component_type.py

@@ -1,6 +1,7 @@
 from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
 import numpy as np
-
+import pandas as pd
 
 @digest()
 def get_component_type(molecular_system, element='atom', selection='all', redefine_indices=False,
@@ -15,45 +16,43 @@ def get_component_type(molecular_system, element='atom', selection='all', redefi
 
         if redefine_indices:
 
-            atom_indices = select(molecular_system, element='atom', selection=selection,
-                                  syntax=syntax, skip_digestion=True)
-
-            #if element!='atom':
-            #    aux_atom_indices = []
-            #    for aux in atom_indices:
-            #        aux_atom_indices += aux
-            #    atom_indices = aux_atom_indices
-
             component_indices = get_component_index(molecular_system, element='atom',
                                                     selection='all', redefine_indices=True,
                                                     skip_digestion=True)
 
-            unique_component_indices, first_atoms, n_atoms = np.unique(component_indices, return_index=True,
-                                                                      return_counts=True)
+            group_index_per_atom = get(molecular_system, element='atom', selection='all', group_index=True,
+                                       skip_digestion=True)
 
-            component_types={}
+            group_names, group_types = get(molecular_system, element='group', selection='all', group_name=True,
+                                           group_type=True, skip_digestion=True)
 
-            for component_index, first_atom, aux_n_atoms in zip(unique_component_indices, first_atoms, n_atoms):
+            group_names = np.array(group_names)
+            group_types = np.array(group_types)
+
+
+            aux_df = pd.DataFrame({'component_indices':component_indices, 'group_indices':group_index_per_atom})
+            aux_dict = aux_df.groupby('component_indices')['group_indices'].unique().to_dict()
+
+            component_types={}
 
-                atom_indices_component = list(np.arange(aux_n_atoms))+first_atom
-                aux_group_names, aux_group_types = get(molecular_system, element='group',
-                                                       selection='atom_index in @atom_indices_component',
-                                                       group_name=True, group_type=True,
-                                                       syntax='MolSysMT', skip_digestion=True)
+            for component_index, group_indices in aux_dict.items():
 
-                component_type = _get_component_type_from_group_names_and_types(aux_group_names, aux_group_types)
+                component_type = _get_component_type_from_group_names_and_types(group_names[group_indices],
+                                                                                group_types[group_indices])
 
                 component_types[component_index]=component_type
 
             if element == 'atom':
 
+                atom_indices = select(molecular_system, element='atom', selection=selection,
+                                      syntax=syntax, skip_digestion=True)
                 output = [component_types[component_indices[ii]] for ii in atom_indices]
 
             elif element == 'group':
 
                 output = []
                 group_indices = get(molecular_system, element='atom',
-                                        selection=atom_indices, group_indices=True, skip_digestion=True)
+                                        selection=selection, group_indices=True, skip_digestion=True)
                 former_index = -1
                 for ii,jj,kk in zip(group_indices, atom_indices, component_indices):
                     if ii!=former_index:
@@ -63,13 +62,16 @@ def get_component_type(molecular_system, element='atom', selection='all', redefi
 
             elif element == 'component':
 
-                output = list(component_types.values())
+                if is_all(selection):
+                    output = list(component_types.values())
+                else:
+                    raise NotImplementedError
 
             else:
 
                 raise NotImplementedError
 
-            del atom_indices, component_types, component_indices 
+            del component_types, component_indices, group_index_per_atom, group_names, group_types
 
         else:
 

molsysmt/element/molecule/get_molecule_name.py

@@ -4,7 +4,7 @@
 
 @digest()
 def get_molecule_name(molecular_system, element='atom', selection='all', redefine_molecules=False,
-                       redefine_names=False, syntax='MolSysMT'):
+                       redefine_names=False, syntax='MolSysMT', skip_digestion=False):
 
     if redefine_molecules or redefine_names:
 

molsysmt/element/molecule/get_molecule_type.py

@@ -11,10 +11,8 @@ def get_molecule_type(molecular_system, element='atom', selection='all',
 
     if redefine_indices:
 
-        print('da1')
         molecule_types_from_molecule = get_component_type(molecular_system, element='component', selection=selection,
                 redefine_indices=True, syntax=syntax)
-        print('da2')
 
         if element == 'atom':
             aux = get(molecular_system, element='atom', selection=selection, syntax=syntax,

molsysmt/form/file_prmtop/__init__.py

@@ -3,9 +3,11 @@
 form_info = ["AMBER parameter/topology file format",
              "https://ambermd.org/FileFormats.php#topology"]
 
-piped_topological_attribute = None
+piped_topological_attribute = 'molsysmt.Topology'
 piped_structural_attribute = None
 piped_any_attribute = None
+bonds_are_explicit = True
+bonds_can_be_computed = False
 
 from .is_form import is_form
 

molsysmt/form/file_prmtop/attributes.py

@@ -41,6 +41,7 @@
 attributes['n_lipids'] = True
 attributes['n_oligosaccharides'] = True
 attributes['n_saccharides'] = True
+attributes['n_entities'] = True
 
 attributes['bond_index'] = True
 attributes['bond_id'] = True

molsysmt/form/file_prmtop/to_molsysmt_MolSys.py

@@ -1,22 +1,13 @@
 from molsysmt._private.digestion import digest
 
 @digest(form='file:prmtop')
-def to_molsysmt_MolSys(item, atom_indices='all',
-        component_id=None, component_type=None, component_name=None,
-        entity_id=None, entity_type=None, entity_name=None,
-        structure_id=None, coordinates=None, velocities=None, time=None, box=None,
-        formal_charge=None, partial_charge=None, forcefield=None, non_bonded_method=None,
-        cutoff_distance=None, switch_distance=None, dispersion_correction=None, ewald_error_tolerance=None,
-        hydrogen_mass=None, constraints=None, flexible_constraints=None, water_model=None, rigid_water=None,
-        implicit_solvent=None, solute_dielectric=None, solvent_dielectric=None, salt_concentration=None,
-        kappa=None):
+def to_molsysmt_MolSys(item, atom_indices='all', skip_digestion=False):
 
     from molsysmt.native import MolSys, Structures
     from .to_molsysmt_Topology import to_molsysmt_Topology
     tmp_item = MolSys()
     tmp_item.topology = to_molsysmt_Topology(item, atom_indices=atom_indices)
     tmp_item.structures = Structures()
-    tmp_item.structures.append_structures(coordinates=coordinates)
 
     return tmp_item