In process

molsysmt/_private/conversion_shortcuts/__init__.py

@@ -1,55 +1,40 @@
 _multiple_conversion_shortcuts = {}
 
-
 from .to_molsysmt_MolSys import molsysmt_Topology_and_molsysmt_Structures_to_molsysmt_MolSys
 from .to_molsysmt_MolSys import file_prmtop_and_file_inpcrd_to_molsysmt_MolSys
 from .to_molsysmt_MolSys import file_psf_and_file_dcd_to_molsysmt_MolSys
 from .to_molsysmt_MolSys import file_psf_and_file_crd_to_molsysmt_MolSys
 from .to_molsysmt_MolSys import file_gro_and_file_xtc_to_molsysmt_MolSys
 
-_multiple_conversion_shortcuts[tuple(sorted(('molsysmt.Topology','molsysmt.Structures')))]={
-        'molsysmt.MolSys': molsysmt_Topology_and_molsysmt_Structures_to_molsysmt_MolSys
-        }
-
-_multiple_conversion_shortcuts[tuple(sorted(('file:prmtop','file:inpcrd')))]={
-        'molsysmt.MolSys': file_prmtop_and_file_inpcrd_to_molsysmt_MolSys
-        }
-
-_multiple_conversion_shortcuts[tuple(sorted(('file:psf','file:dcd')))]={
-        'molsysmt.MolSys': file_psf_and_file_dcd_to_molsysmt_MolSys
-        }
-
-_multiple_conversion_shortcuts[tuple(sorted(('file:psf','file:crd')))]={
-        'molsysmt.MolSys': file_psf_and_file_crd_to_molsysmt_MolSys
-        }
-
-_multiple_conversion_shortcuts[tuple(sorted(('file:gro','file:xtc')))]={
-        'molsysmt.MolSys': file_gro_and_file_xtc_to_molsysmt_MolSys
-        }
-
 from .to_molsysmt_Topology import molsysmt_Topology_and_molsysmt_Structures_to_molsysmt_Topology
 from .to_molsysmt_Topology import file_prmtop_and_file_inpcrd_to_molsysmt_Topology
 from .to_molsysmt_Topology import file_psf_and_file_dcd_to_molsysmt_Topology
 from .to_molsysmt_Topology import file_psf_and_file_crd_to_molsysmt_Topology
 from .to_molsysmt_Topology import file_gro_and_file_xtc_to_molsysmt_Topology
 
+
 _multiple_conversion_shortcuts[tuple(sorted(('molsysmt.Topology','molsysmt.Structures')))]={
+        'molsysmt.MolSys': molsysmt_Topology_and_molsysmt_Structures_to_molsysmt_MolSys,
         'molsysmt.Topology': molsysmt_Topology_and_molsysmt_Structures_to_molsysmt_Topology
         }
 
 _multiple_conversion_shortcuts[tuple(sorted(('file:prmtop','file:inpcrd')))]={
+        'molsysmt.MolSys': file_prmtop_and_file_inpcrd_to_molsysmt_MolSys,
         'molsysmt.Topology': file_prmtop_and_file_inpcrd_to_molsysmt_Topology
         }
 
 _multiple_conversion_shortcuts[tuple(sorted(('file:psf','file:dcd')))]={
+        'molsysmt.MolSys': file_psf_and_file_dcd_to_molsysmt_MolSys,
         'molsysmt.Topology': file_psf_and_file_dcd_to_molsysmt_Topology
         }
 
 _multiple_conversion_shortcuts[tuple(sorted(('file:psf','file:crd')))]={
+        'molsysmt.MolSys': file_psf_and_file_crd_to_molsysmt_MolSys,
         'molsysmt.Topology': file_psf_and_file_crd_to_molsysmt_Topology
         }
 
 _multiple_conversion_shortcuts[tuple(sorted(('file:gro','file:xtc')))]={
+        'molsysmt.MolSys': file_gro_and_file_xtc_to_molsysmt_MolSys,
         'molsysmt.Topology': file_gro_and_file_xtc_to_molsysmt_Topology
         }
 

molsysmt/_private/digestion/argument/chain_id.py

@@ -1,6 +1,13 @@
 from ...exceptions import ArgumentError
 from ...variables import is_all
 
+functions_with_boolean = (
+        'molsysmt.basic.get.get',
+        'molsysmt.basic.compare.compare',
+        'molsysmt.basic.iterator.__init__',
+        'iterators.__init__',
+        )
+
 set_functions = (
         'set.set',
         'set_chain_id_to_atom')
@@ -29,7 +36,8 @@ def digest_chain_id(chain_id, caller=None):
         If the given `chain_id` has not of the correct type or value.
     """
 
-    if caller=='molsysmt.basic.get.get':
+
+    if caller.endswith(functions_with_boolean):
         if isinstance(chain_id, bool):
             return chain_id
     elif caller.endswith(set_functions):

molsysmt/_private/digestion/argument/chain_name.py

@@ -2,6 +2,14 @@
 from ...variables import is_all
 from numpy import ndarray
 
+functions_with_boolean = (
+        'molsysmt.basic.get.get',
+        'molsysmt.basic.compare.compare',
+        'molsysmt.basic.iterator.__init__',
+        'iterators.__init__',
+        )
+
+
 def digest_chain_name(chain_name, caller=None):
     """Checks if `chain_name` has the expected type and value.
 
@@ -26,7 +34,7 @@ def digest_chain_name(chain_name, caller=None):
         If the given `chain_name` has not of the correct type or value.
     """
 
-    if caller=='molsysmt.basic.get.get':
+    if caller.endswith(functions_with_boolean):
         if isinstance(chain_name, bool):
             return chain_name
     elif caller.startswith('molsysmt.form.') and caller.count('.to_')==2:

molsysmt/_private/digestion/argument/chain_type.py

@@ -2,6 +2,14 @@
 from ...variables import is_all
 from numpy import ndarray
 
+functions_with_boolean = (
+        'molsysmt.basic.get.get',
+        'molsysmt.basic.compare.compare',
+        'molsysmt.basic.iterator.__init__',
+        'iterators.__init__',
+        )
+
+
 def digest_chain_type(chain_type, caller=None):
     """Checks if `chain_type` has the expected type and value.
 
@@ -26,7 +34,7 @@ def digest_chain_type(chain_type, caller=None):
         If the given `chain_type` has not of the correct type or value.
     """
 
-    if caller=='molsysmt.basic.get.get':
+    if caller.endswith(functions_with_boolean):
         if isinstance(chain_type, bool):
             return chain_type
     elif caller.startswith('molsysmt.form.') and caller.count('.to_')==2:

molsysmt/_private/digestion/argument/keep_ids.py

@@ -2,8 +2,12 @@
 
 def digest_keep_ids(keep_ids, caller=None):
 
-    if isinstance(keep_ids, bool):
-        return keep_ids
+    if caller.endswith('.merge.merge'):
+        if isinstance(keep_ids, bool):
+            return keep_ids
 
-    raise ArgumentError('keep_ids', value=keep_ids, caller=caller, message=None)
+    if caller.endswith('.add.add'):
+        if isinstance(keep_ids, bool):
+            return keep_ids
 
+    raise ArgumentError('keep_ids', value=keep_ids, caller=caller, message=None)

molsysmt/basic/add.py

@@ -4,7 +4,7 @@
 
 @digest()
 def add(to_molecular_system, from_molecular_system, selection='all', structure_indices='all',
-        syntax='MolSysMT'):
+        keep_ids=True, syntax='MolSysMT'):
     """
     Adding elements of a molecular system into another molecular system.
 

molsysmt/basic/merge.py

@@ -6,6 +6,7 @@
 def merge(molecular_systems,
           selections='all',
           structure_indices='all',
+          keep_ids = True,
           syntax='MolSysMT',
           to_form=None,
           skip_digestion=False
@@ -171,6 +172,7 @@ def merge(molecular_systems,
         merge_arguments['structure_indices']=aux_structure_indices
 
     merge_arguments['skip_digestion']=True
+    merge_arguments['keep_ids']=keep_ids
 
     output = merge_function(aux_molecular_systems, **merge_arguments)
 

molsysmt/element/chain/get_chain_type.py

@@ -20,6 +20,10 @@ def get_chain_type(molecular_system, element='atom', selection='all',
                                                       redefine_indices=redefine_molecule_indices,
                                                       redefine_types=redefine_molecule_types)
 
+        for ii in range(len(molecule_types_from_chain)):
+            if isinstance(molecule_types_from_chain[ii], str):
+                molecule_types_from_chain[ii]=[molecule_types_from_chain[ii]]
+
         n_molecules = get_n_molecules(molecular_system, redefine_molecules=redefine_molecule_indices)
 
         chain_types_from_chain = []

molsysmt/element/group/amino_acid/get_bonded_atom_pairs.py

@@ -47,6 +47,7 @@ def get_bonded_atom_pairs(group_name, atom_names, atom_indices=None, sorted=True
             else:
                 return bonds
 
+
     if group_name in ['HIS']:
         for aux_group_name in group_names:
             try:
@@ -75,6 +76,8 @@ def get_bonded_atom_pairs(group_name, atom_names, atom_indices=None, sorted=True
             except:
                 pass
 
+    print(f'Warning! The amino acid {group_name} has no template.')
+    raise ValueError
 
     return None
 

molsysmt/form/molsysmt_MolSys/add.py

@@ -4,9 +4,10 @@
 import numpy as np
 
 @digest(to_form='molsysmt.MolSys', from_form='molsysmt.MolSys')
-def add(to_item, from_item, atom_indices='all', structure_indices='all', skip_digestion=False):
+def add(to_item, from_item, atom_indices='all', structure_indices='all', keep_ids=True, skip_digestion=False):
 
-    to_item.add(from_item, atom_indices=atom_indices, structure_indices=structure_indices, skip_digestion=True)
+    to_item.add(from_item, atom_indices=atom_indices, structure_indices=structure_indices, keep_ids=keep_ids,
+                skip_digestion=True)
 
     pass
 

molsysmt/form/molsysmt_MolSys/merge.py

@@ -3,7 +3,7 @@
 from molsysmt._private.variables import is_all
 
 @digest(form='molsysmt.MolSys')
-def merge(items, atom_indices='all', structure_indices='all', skip_digestion=False):
+def merge(items, atom_indices='all', structure_indices='all', keep_ids=True, skip_digestion=False):
 
     from molsysmt.native import MolSys
     from ..molsysmt_Topology import merge as merge_molsysmt_Topology
@@ -26,7 +26,7 @@ def merge(items, atom_indices='all', structure_indices='all', skip_digestion=Fal
 
     output = MolSys()
     output.topology = merge_molsysmt_Topology([ii.topology for ii in items], atom_indices=atom_indices,
-                                              skip_digestion=True)
+                                              keep_ids=keep_ids, skip_digestion=True)
     output.structures = merge_molsysmt_Structures([ii.structures for ii in items],
             atom_indices=atom_indices, structure_indices=structure_indices, skip_digestion=True)
     output.molecular_mechanics = merge_molsysmt_MolecularMechanics([ii.molecular_mechanics for ii in items],