In process

molsysmt/_private/digestion/argument/copy_if_None.py

@@ -0,0 +1,9 @@
+from molsysmt._private.exceptions import ArgumentError
+
+def digest_copy_if_None(copy_if_None, caller=None):
+
+    if isinstance(copy_if_None, bool):
+        return copy_if_None
+
+    raise ArgumentError('copy_if_None', value=copy_if_None, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/n_atoms.py

@@ -22,6 +22,9 @@ def digest_n_atoms(n_atoms, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_atoms, int):
             return n_atoms
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_atoms, int):
+            return n_atoms
 
     raise ArgumentError('n_atoms', value=n_atoms, caller=caller, message=None)
 

molsysmt/_private/digestion/argument/n_bonds.py

@@ -11,5 +11,8 @@ def digest_n_bonds(n_bonds, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_bonds, int):
             return n_bonds
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_bonds, int):
+            return n_bonds
 
     raise ArgumentError('n_entities', value=n_entities, caller=caller, message=None)

molsysmt/_private/digestion/argument/n_chains.py

@@ -22,6 +22,9 @@ def digest_n_chains(n_chains, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_chains, int):
             return n_chains
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_chains, int):
+            return n_chains
 
     raise ArgumentError('n_chains', value=n_chains, caller=caller, message=None)
 

molsysmt/_private/digestion/argument/n_components.py

@@ -22,6 +22,9 @@ def digest_n_components(n_components, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_components, int):
             return n_components
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_components, int):
+            return n_components
 
     raise ArgumentError('n_components', value=n_components, caller=caller, message=None)
 

molsysmt/_private/digestion/argument/n_entities.py

@@ -22,6 +22,9 @@ def digest_n_entities(n_entities, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_entities, int):
             return n_entities
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_entities, int):
+            return n_entities
 
     raise ArgumentError('n_entities', value=n_entities, caller=caller, message=None)
 

molsysmt/_private/digestion/argument/n_groups.py

@@ -22,6 +22,9 @@ def digest_n_groups(n_groups, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_groups, int):
             return n_groups
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_groups, int):
+            return n_groups
 
     raise ArgumentError('n_groups', value=n_groups, caller=caller, message=None)
 

molsysmt/_private/digestion/argument/n_molecules.py

@@ -22,6 +22,9 @@ def digest_n_molecules(n_molecules, caller=None):
     elif caller=='molsysmt.native.topology.__init__':
         if isinstance(n_molecules, int):
             return n_molecules
+    elif caller=='molsysmt.native.molsys.__init__':
+        if isinstance(n_molecules, int):
+            return n_molecules
 
     raise ArgumentError('n_molecules', value=n_molecules, caller=caller, message=None)
 

molsysmt/element/group/__init__.py

@@ -10,6 +10,7 @@
 
 from .is_group_type import is_group_type
 from .get_group_type import get_group_type, get_group_type_from_group_name
+from .get_bonded_atom_pairs import get_bonded_atom_pairs
 
 _group_types = [
         'water',

molsysmt/element/group/get_bonded_atom_pairs.py

@@ -0,0 +1,54 @@
+import numpy as np
+
+def get_bonded_atom_pairs(group_name, atom_names, atom_indices=None, sorted=True):
+
+    from .get_group_type import get_group_type_from_group_name
+    from amino_acid import get_bonded_atom_pairs as get_bonded_atom_pairs_from_amino_acid
+    from ion import get_bonded_atom_pairs as get_bonded_atom_pairs_from_ion
+    from small_molecule import get_bonded_atom_pairs as get_bonded_atom_pairs_from_small_molecule
+    from terminal_capping import get_bonded_atom_pairs as get_bonded_atom_pairs_from_terminal_capping
+    from water import get_bonded_atom_pairs as get_bonded_atom_pairs_from_water
+
+    group_type = get_group_type_from_group_name(group_name)
+
+    bonds = None
+
+    match group_type:
+
+         case 'amino acid':
+             bonds = get_bonded_atom_pairs_from_amino_acid(group_name, atom_names, atom_indices=atom_indices,
+                                                           sorted=sorted)
+
+         case 'ion':
+             bonds = get_bonded_atom_pairs_from_ion(group_name, atom_names, atom_indices=atom_indices, sorted=sorted)
+
+         case 'lipid':
+             pass
+
+         case 'nucleotide':
+             pass
+
+         case 'oligosaccharide':
+             pass
+
+         case 'saccharide':
+             pass
+
+         case 'small molecule':
+             bonds = get_bonded_atom_pairs_from_small_molecule(group_name, atom_names, atom_indices=atom_indices,
+                                                               sorted=sorted)
+
+         case 'terminal capping':
+             bonds = get_bonded_atom_pairs_from_terminal_capping(group_name, atom_names, atom_indices=atom_indices,
+                                                                 sorted=sorted)
+
+         case 'water':
+             bonds = get_bonded_atom_pairs_from_water(atom_names, atom_indices=atom_indices, sorted=sorted)
+
+
+    if bonds is None:
+        print(f'Warning! The amino acid {group_name} has no template.')
+        raise ValueError
+
+    return bonds
+