In process to refactor set chain_id to atoms

molsysmt/_private/digestion/argument/chain_id.py

@@ -1,6 +1,10 @@
 from ...exceptions import ArgumentError
 from ...variables import is_all
 
+set_functions = (
+        'set.set',
+        'set_chain_id_to_atom')
+
 def digest_chain_id(chain_id, caller=None):
     """Checks if `chain_id` has the expected type and value.
 
@@ -28,7 +32,7 @@ def digest_chain_id(chain_id, caller=None):
     if caller=='molsysmt.basic.get.get':
         if isinstance(chain_id, bool):
             return chain_id
-    elif caller=='molsysmt.basic.set.set':
+    elif caller.endswith(set_functions):
         if isinstance(chain_id, str):
             return chain_id
     elif caller.startswith('molsysmt.form.') and caller.count('.to_')==2:

molsysmt/_private/digestion/digest.py

@@ -77,7 +77,6 @@ def wrapper(*args, **kwargs):
 
             all_args = argument_names_standardization(caller, all_args)
 
-
             # Digestions:
 
             digested_args = {}
@@ -102,13 +101,16 @@ def gut(arg_name):
                         not_digested_args[arg_name] = all_args[arg_name]
                 pass
 
+
             for arg_name in all_args:
                 gut(arg_name)
 
+
             for arg_name in not_digested_args:
                 if arg_name not in ['self']:
                     warnings.warn(arg_name+' from '+caller, NotDigestedArgumentWarning, stacklevel=2)
 
+
             final_args = digested_args
 
             if 'self' in all_args:

molsysmt/basic/set.py

@@ -154,7 +154,6 @@ def set(molecular_system,
                 indices = select(molecular_system, element=element, selection=selection, syntax=syntax)
 
         # doing the work here
-
         for in_attribute in in_attributes:
 
             dict_indices = {}

molsysmt/build/__init__.py

@@ -14,4 +14,5 @@
 from .solvate import solvate
 from .model_loop import model_loop
 from .mutate import mutate
+from .define_chain import define_chain
 

molsysmt/build/define_chain.py

@@ -0,0 +1,20 @@
+from molsysmt._private.digestion import digest
+import numpy as np
+
+@digest()
+def define_chain(molecular_system, selection=None, id=None, name=None, syntax='MolSysMT'):
+    """
+    To be written soon...
+    """
+
+    from molsysmt.basic import get, set
+
+    former_id, former_name = get(molecular_system, element='chain', chain_id=True)
+
+    if id in former_id:
+        raise ValueError()
+
+    set(molecular_system, element='atom', selection=selection, syntax=syntax,
+            chain_id=id, chain_name=name)
+
+    pass

molsysmt/form/molsysmt_Topology/set.py

@@ -1,4 +1,5 @@
 from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
 from molsysmt import pyunitwizard as puw
 import numpy as np
 
@@ -11,168 +12,244 @@
 @digest(form=form)
 def set_atom_index_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'atom_index']=value
+    if is_all(indices):
+        item.atoms_dataframe['atom_index']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'atom_index']=value
 
     pass
 
 @digest(form=form)
 def set_atom_name_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'atom_name']=value
+    if is_all(indices):
+        item.atoms_dataframe['atom_name']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'atom_name']=value
 
     pass
 
 @digest(form=form)
 def set_atom_id_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'atom_id']=value
+    if is_all(indices):
+        item.atoms_dataframe['atom_id']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'atom_id']=value
 
     pass
 
 @digest(form=form)
 def set_atom_type_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'atom_type']=value
+    if is_all(indices):
+        item.atoms_dataframe['atom_type']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'atom_type']=value
 
     pass
 
 @digest(form=form)
 def set_group_index_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'group_index']=value
+    if is_all(indices):
+        item.atoms_dataframe['group_index']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'group_index']=value
 
     pass
 
 @digest(form=form)
 def set_group_name_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'group_name']=value
+    if is_all(indices):
+        item.atoms_dataframe['group_name']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'group_name']=value
 
     pass
 
 @digest(form=form)
 def set_group_id_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'group_id']=value
+    if is_all(indices):
+        item.atoms_dataframe['group_id']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'group_id']=value
 
     pass
 
 @digest(form=form)
 def set_group_type_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'group_type']=value
+    if is_all(indices):
+        item.atoms_dataframe['group_type']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'group_type']=value
 
     pass
 
 @digest(form=form)
 def set_component_index_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'component_index']=value
+    if is_all(indices):
+        item.atoms_dataframe['component_index']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'component_index']=value
 
     pass
 
 @digest(form=form)
 def set_component_name_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'component_name']=value
+    if is_all(indices):
+        item.atoms_dataframe['component_name']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'component_name']=value
 
     pass
 
 @digest(form=form)
 def set_component_id_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'component_id']=value
+    if is_all(indices):
+        item.atoms_dataframe['component_id']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'component_id']=value
 
     pass
 
 @digest(form=form)
 def set_component_type_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'component_type']=value
+    if is_all(indices):
+        item.atoms_dataframe['component_type']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'component_type']=value
 
     pass
 
 @digest(form=form)
 def set_molecule_index_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'molecule_index']=value
+    if is_all(indices):
+        item.atoms_dataframe['molecule_index']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'molecule_index']=value
 
     pass
 
 @digest(form=form)
 def set_molecule_name_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'molecule_name']=value
+    if is_all(indices):
+        item.atoms_dataframe['molecule_name']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'molecule_name']=value
 
     pass
 
 @digest(form=form)
 def set_molecule_id_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'molecule_id']=value
+    if is_all(indices):
+        item.atoms_dataframe['molecule_id']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'molecule_id']=value
 
     pass
 
 @digest(form=form)
 def set_molecule_type_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'molecule_type']=value
+    if is_all(indices):
+        item.atoms_dataframe['molecule_type']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'molecule_type']=value
 
     pass
 
 @digest(form=form)
 def set_chain_index_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'chain_index']=value
+    if is_all(indices):
+        item.atoms_dataframe['chain_index']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'chain_index']=value
 
     pass
 
 @digest(form=form)
 def set_chain_name_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'chain_name']=value
+    if is_all(indices):
+        item.atoms_dataframe['chain_name']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'chain_name']=value
 
     pass
 
 @digest(form=form)
 def set_chain_id_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'chain_id']=value
+    if is_all(indices):
+        item.atoms_dataframe['chain_id']=value
+        item.atoms_dataframe['chain_index']=0
+    else:
+        item.atoms_dataframe.loc[indices, 'chain_id']=value
+        aux_list = item.atoms_dataframe['chain_id'].unique()
+        for new_index, id for enumerate(aux_list):
+            item[item['chain_id']==id]=new_index
 
     pass
 
 @digest(form=form)
 def set_chain_type_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'chain_type']=value
+    if is_all(indices):
+        item.atoms_dataframe['chain_type']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'chain_type']=value
 
     pass
 
 @digest(form=form)
 def set_entity_index_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'entity_index']=value
+    if is_all(indices):
+        item.atoms_dataframe['entity_index']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'entity_index']=value
 
     pass
 
 @digest(form=form)
 def set_entity_name_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'entity_name']=value
+    if is_all(indices):
+        item.atoms_dataframe['entity_name']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'entity_name']=value
 
     pass
 
 @digest(form=form)
 def set_entity_id_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'entity_id']=value
+    if is_all(indices):
+        item.atoms_dataframe['entity_id']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'entity_id']=value
 
     pass
 
 @digest(form=form)
 def set_entity_type_to_atom(item, indices='all', value=None):
 
-    item.atoms_dataframe.loc[indices, 'entity_type']=value
+    if is_all(indices):
+        item.atoms_dataframe['entity_type']=value
+    else:
+        item.atoms_dataframe.loc[indices, 'entity_type']=value
 
     pass