In process

molsysmt/_private/digestion/argument/bond_indices.py

@@ -0,0 +1,41 @@
+from ...exceptions import ArgumentError
+from ...variables import is_all
+import numpy as np
+
+def digest_bond_indices(bond_indices, caller=None):
+    """ Checks if bond_indices has the expected type and value.
+
+    Parameters
+    ----------
+    indices : str or int or list or tuple or range.
+        The indices
+
+    caller: str, optional
+        Name of the function or method that is being digested.
+        For debugging purposes.
+
+    Returns
+    -------
+    str or ndarray or None
+        Either None, 'all' or an numpy array of integers with the indices.
+
+    Raises
+    -------
+    ArgumentError
+        If the given indices are not of the correct type.
+    """
+
+    if bond_indices is None:
+        return None
+    elif is_all(bond_indices):
+        return 'all'
+    elif isinstance(bond_indices, (int, np.int64, np.int32)):
+        return np.array([bond_indices], dtype='int64')
+    elif isinstance(bond_indices, (np.ndarray, list, tuple, range)):
+        if all(isinstance(ii, (int, np.int64, np.int32)) for ii in bond_indices):
+            return np.array(bond_indices, dtype='int64')
+        else:
+            return [digest_bond_indices(ii) for ii in bond_indices]
+
+    raise ArgumentError('bond_indices', caller=caller, message=None)
+

molsysmt/build/__init__.py

@@ -19,4 +19,5 @@
 from .define_new_chain import define_new_chain
 from .make_water_box import make_water_box
 from .remove_overlapping_molecules import remove_overlapping_molecules
+from .remove_bonds import remove_bonds
 

molsysmt/build/remove_bonds.py

@@ -0,0 +1,22 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest()
+def remove_bonds(molecular_system, bond_indices='all', in_place=True, skip_digestion=False):
+
+    from molsysmt.basic import where_is_attribute
+    from molsysmt.form import _dict_modules
+
+    if in_place:
+
+        item, form = where_is_attribute(molecular_system, 'bond_index', check_if_None=False,
+                                        skip_digestion=True)
+
+        add_bonds_function = getattr(_dict_modules[form], f'remove_bonds')
+        add_bonds_function(item, bond_indices, skip_digestion=True)
+
+    else:
+
+        raise NotImplementedMethodError
+

molsysmt/element/entity/get_entity_index.py

@@ -3,7 +3,8 @@
 
 @digest()
 def get_entity_index(molecular_system, element='atom', selection='all',
-        redefine_molecules=False, redefine_indices=False, syntax='MolSysMT'):
+                     redefine_molecules=False, redefine_indices=False, syntax='MolSysMT',
+                     skip_digestion=False):
 
     if redefine_molecules or redefine_indices:
 
@@ -12,18 +13,20 @@ def get_entity_index(molecular_system, element='atom', selection='all',
         if redefine_molecules:
 
             molecule_name_from_molecules = get_molecule_name(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=True, syntax=syntax)
+                    selection=selection, redefine_molecules=True, syntax=syntax, skip_digestion=True)
 
             molecule_type_from_molecules = get_molecule_type(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=True, syntax=syntax)
+                    selection=selection, redefine_molecules=True, syntax=syntax, skip_digestion=True)
 
         else:
 
             molecule_name_from_molecules = get_molecule_name(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=False, redefine_names=False, syntax=syntax)
+                    selection=selection, redefine_molecules=False, redefine_names=False, syntax=syntax,
+                                                            skip_digestion=True)
 
             molecule_type_from_molecules = get_molecule_type(molecular_system, element='molecule',
-                    selection=selection, redefine_molecules=False, redefine_types=False, syntax=syntax)
+                    selection=selection, redefine_molecules=False, redefine_types=False, syntax=syntax,
+                                                            skip_digestion=True)
 
         count = 0
         output = []
@@ -87,7 +90,7 @@ def get_entity_index(molecular_system, element='atom', selection='all',
 
         from molsysmt import get
         output = get(molecular_system, element=element, selection=selection, syntax=syntax,
-                     entity_index=True)
+                     entity_index=True, skip_digestion=True)
 
     return output
 

molsysmt/form/molsysmt_MolSys/__init__.py

@@ -15,14 +15,16 @@
 from .copy import copy
 from .add import add
 from .merge import merge
-from .add_bonds import add_bonds
 from .append_structures import append_structures
 from .get_topological_attributes import *
 from .get_structural_attributes import *
 from .get_mechanical_attributes import *
 from .set import *
 from .iterators import StructuresIterator, TopologyIterator
 
+from .add_bonds import add_bonds
+from .remove_bonds import remove_bonds
+
 from .to_mdtraj_Topology import to_mdtraj_Topology
 from .to_mdtraj_Trajectory import to_mdtraj_Trajectory
 from .to_molsysmt_Topology import to_molsysmt_Topology

molsysmt/form/molsysmt_MolSys/remove_bonds.py

@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest(form='molsysmt.MolSys')
+def remove_bonds(item, bond_indices='all', skip_digestion=False):
+
+    return item.topology.remove_bonds(bond_indices=bond_indices, skip_digestion=True)

molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_Topology.py

@@ -1,16 +1,16 @@
 from molsysmt._private.digestion import digest
 from molsysmt._private.variables import is_all
+from molsysmt import pyunitwizard as puw
 import pandas as pd
 import numpy as np
 
 @digest(form='molsysmt.PDBFileHandler')
 def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_missing_bonds=True,
                          skip_digestion=False):
 
-    from molsysmt.native import Topology
-    from molsysmt.build import get_missing_bonds as _get_missing_bonds
+    from molsysmt.native import MolSys
 
-    tmp_item = Topology()
+    tmp_item = MolSys()
 
     atom_id_array = []
     atom_name_array = []
@@ -22,6 +22,7 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
 
     occupancy_array = []
     alternate_location_array = []
+    coordinates_array = []
 
     group_index = -1
     former_group_id = None
@@ -30,8 +31,6 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
     former_chain_name = None
     aux_dict_chain = {}
 
-
-
     for atom_record in item.entry.coordinate.model[0].record:
 
         atom_id_array.append(atom_record.serial)
@@ -58,6 +57,8 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
 
         chain_index_array.append(chain_index)
 
+        coordinates_array.append([atom_record.x, atom_record.y, atom_record.z])
+
     atom_id_array = np.array(atom_id_array, dtype=int)
     atom_name_array = np.array(atom_name_array, dtype=str)
     group_index_array = np.array(group_index_array, dtype=int)
@@ -69,6 +70,8 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
     occupancy_array = np.array(occupancy_array, dtype=float)
     alternate_location_array = np.array(alternate_location_array, dtype=str)
 
+    coordinates_array = np.array(coordinates_array, dtype=float)
+
     alt_atom_indices = np.where(alternate_location_array!=' ')[0]
     aux_dict = {}
 
@@ -96,51 +99,72 @@ def to_molsysmt_Topology(item, atom_indices='all', structure_indices=0, get_miss
             chosen = np.argmax(alt_occupancy)
         chosen = same_atoms.pop(chosen)
         atoms_to_be_removed_with_alt_loc += same_atoms
-    
+
     atom_id_array = np.delete(atom_id_array, atoms_to_be_removed_with_alt_loc)
     atom_name_array = np.delete(atom_name_array, atoms_to_be_removed_with_alt_loc)
     group_index_array = np.delete(group_index_array, atoms_to_be_removed_with_alt_loc)
     chain_index_array = np.delete(chain_index_array, atoms_to_be_removed_with_alt_loc)
 
+    if len(atoms_to_be_removed_with_alt_loc):
+        coordinates_array = np.delete(coordinates_array, atoms_to_be_removed_with_alt_loc)
+
     n_atoms = atom_id_array.shape[0]
     n_groups = group_name_array.shape[0]
     n_chains = chain_name_array.shape[0]
 
-    tmp_item.reset_atoms(n_atoms=n_atoms)
-    tmp_item.reset_groups(n_groups=n_groups)
-    tmp_item.reset_chains(n_chains=n_chains)
+    tmp_item.topology.reset_atoms(n_atoms=n_atoms)
+    tmp_item.topology.reset_groups(n_groups=n_groups)
+    tmp_item.topology.reset_chains(n_chains=n_chains)
 
-    tmp_item.atoms.atom_id = atom_id_array
-    tmp_item.atoms.atom_name = atom_name_array
-    tmp_item.atoms.group_index = group_index_array
-    tmp_item.atoms.chain_index = chain_index_array
+    tmp_item.topology.atoms.atom_id = atom_id_array
+    tmp_item.topology.atoms.atom_name = atom_name_array
+    tmp_item.topology.atoms.group_index = group_index_array
+    tmp_item.topology.atoms.chain_index = chain_index_array
 
-    tmp_item.rebuild_atoms(redefine_ids=False, redefine_types=True)
+    tmp_item.topology.rebuild_atoms(redefine_ids=False, redefine_types=True)
 
-    tmp_item.groups.group_id = group_id_array
-    tmp_item.groups.group_name = group_name_array
+    tmp_item.topology.groups.group_id = group_id_array
+    tmp_item.topology.groups.group_name = group_name_array
 
-    tmp_item.rebuild_groups(redefine_ids=False, redefine_types=True)
+    tmp_item.topology.rebuild_groups(redefine_ids=False, redefine_types=True)
 
-    tmp_item.chains.chain_name = chain_name_array
+    tmp_item.topology.chains.chain_name = chain_name_array
 
-    tmp_item.rebuild_chains(redefine_ids=True, redefine_types=False )
+    tmp_item.topology.rebuild_chains(redefine_ids=True, redefine_types=False )
+
+    del(atom_id_array, atom_name_array,
+        group_index_array, group_id_array, group_name_array,
+        chain_index_array, chain_name_array,
+        occupancy_array, alternate_location_array, alt_atom_indices, aux_dict)
 
     if get_missing_bonds:
 
+        from molsysmt.build import get_missing_bonds as _get_missing_bonds
+        from molsysmt.pbc import get_box_from_lengths_and_angles
+
+        cryst1 = item.entry.crystallographic_and_coordinate_transformation.cryst1
+        box_lengths = puw.quantity([[cryst1.a, cryst1.b, cryst1.c]], 'angstroms')
+        box_angles = puw.quantity([[cryst1.alpha, cryst1.beta, cryst1.gamma]], 'degrees')
+        box = get_box_from_lengths_and_angles(box_lengths, box_angles, skip_digestion=True)
+
+        coordinates = puw.quantity(coordinates_array, 'angstroms')
+        tmp_item.structures.append(coordinates=coordinates, box=box)
+
+        del(coordinates_array, box, box_lengths, box_angles)
+
         bonds = _get_missing_bonds(tmp_item, skip_digestion=True)
         bonds = np.array(bonds)
-        tmp_item.reset_bonds(n_bonds=bonds.shape[0])
-        tmp_item.bonds.drop(['order', 'type'], axis=1, inplace=True)
-        tmp_item.bonds.atom1_index=bonds[:,0]
-        tmp_item.bonds.atom2_index=bonds[:,1]
+        tmp_item.topology,reset_bonds(n_bonds=bonds.shape[0])
+        tmp_item.topology.bonds.drop(['order', 'type'], axis=1, inplace=True)
+        tmp_item.topology.bonds.atom1_index=bonds[:,0]
+        tmp_item.topology.bonds.atom2_index=bonds[:,1]
 
-        tmp_item.rebuild_components()
-        tmp_item.rebuild_molecules()
-        tmp_item.rebuild_chains(redefine_ids=False, redefine_types=True)
-        tmp_item.rebuild_entities()
+        tmp_item.topology.rebuild_components()
+        tmp_item.topology.rebuild_molecules()
+        tmp_item.topology.rebuild_chains(redefine_ids=False, redefine_types=True)
+        tmp_item.topology.rebuild_entities()
 
-    tmp_item = tmp_item.extract(atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)
+    tmp_item = tmp_item.topology.extract(atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)
 
     return tmp_item
 

molsysmt/form/molsysmt_Topology/__init__.py

@@ -20,6 +20,9 @@
 from .set import *
 from .iterators import TopologyIterator
 
+from .add_bonds import add_bonds
+from .remove_bonds import remove_bonds
+
 from .to_string_amino_acids_3 import to_string_amino_acids_3
 from .to_string_amino_acids_1 import to_string_amino_acids_1
 from .to_string_pdb_text import to_string_pdb_text

molsysmt/form/molsysmt_Topology/add_bonds.py

@@ -0,0 +1,10 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt import pyunitwizard as puw
+import numpy as np
+
+@digest(form='molsysmt.Topology')
+def add_bonds(item, bonded_atom_pairs, skip_digestion=False):
+
+    item.add_bonds(bonded_atom_pairs, skip_digestion=True)
+

molsysmt/form/molsysmt_Topology/remove_bonds.py

@@ -0,0 +1,8 @@
+from molsysmt._private.exceptions import NotImplementedMethodError
+from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
+
+@digest(form='molsysmt.Topology')
+def remove_bonds(item, bond_indices='all', skip_digestion=False):
+
+    return item.remove_bonds(bond_indices=bond_indices, skip_digestion=True)

molsysmt/form/openmm_Modeller/__init__.py

@@ -2,9 +2,9 @@
 form_type = 'class'
 form_info = ["", ""]
 
-piped_topological_attribute = None
-piped_structural_attribute = None
-piped_any_attribute = None
+piped_topological_attribute = 'molsysmt.Topology'
+piped_structural_attribute = 'molsysmt.Structures'
+piped_any_attribute = 'molsysmt.MolSys'
 
 from .is_form import is_form
 

molsysmt/native/topology.py

@@ -334,8 +334,46 @@ def add_bonds(self, bonded_atom_pairs, skip_digestion=False):
         self.bonds._sort_bonds()
         self.bonds._remove_empty_columns()
 
+        self.rebuild_components()
+        self.rebuild_molecules()
+        self.rebuild_entities()
+
         del(df_concatenado, aux_bonds_dataframe)
 
+    def remove_bonds(self, bond_indices='all', skip_digestion=False):
+
+        if is_all(bond_indices):
+
+            self.bonds = Bonds_DataFrame(n_bonds=0)
+
+        else:
+
+            tmp_dataframe = self.bonds.drop(bond_indices)
+
+            n_bonds = bonded_atom_pairs.shape[0]
+
+            self.bonds = Bonds_DataFrame(n_bonds=n_bonds)
+            self.bonds.atom1_index=tmp_dataframe.atom1_index
+            self.bonds.atom2_index=tmp_dataframe.atom2_index
+
+            if 'order' in tmp_dataframe:
+                self.bonds['order'] = tmp_dataframe['order']
+            else:
+                del self.bonds['order']
+
+            if 'type' in tmp_dataframe:
+                self.bonds['type'] = tmp_dataframe['type']
+            else:
+                del self.bonds['type']
+
+            self.bonds._sort_bonds()
+
+            del(tmp_dataframe)
+
+        self.rebuild_components()
+        self.rebuild_molecules()
+        self.rebuild_entities()
+
 
     def add_missing_bonds(self, selection='all', syntax='MolSysMT', skip_digestion=False):
 
@@ -347,6 +385,10 @@ def add_missing_bonds(self, selection='all', syntax='MolSysMT', skip_digestion=F
 
         self.add_bonds(bonds, skip_digestion=True)
 
+        self.rebuild_components()
+        self.rebuild_molecules()
+        self.rebuild_entities()
+
     def rebuild_atoms(self, redefine_ids=True, redefine_types=True):
 
         if redefine_ids: