in process

molsysmt/form/openmm_Topology/to_molsysmt_Topology.py

@@ -18,7 +18,6 @@ def to_molsysmt_Topology(item, atom_indices='all'):
     atom_name_array = empty(n_atoms, dtype=object)
     atom_id_array = empty(n_atoms, dtype=int)
     atom_type_array = empty(n_atoms, dtype=object)
-    atom_bonded_atom_indices_array = empty(n_atoms, dtype=object)
 
     group_index_array = empty(n_atoms, dtype=int)
     group_name_array = empty(n_atoms, dtype=object)

molsysmt/form/parmed_Structure/to_molsysmt_Topology.py

@@ -3,11 +3,119 @@
 @digest(form='parmed.Structure')
 def to_molsysmt_Topology(item, atom_indices='all'):
 
-    from . import to_openmm_Topology
-    from ..openmm_Topology import to_molsysmt_Topology
+    from molsysmt.native import Topology
+    from numpy import empty, array, arange, reshape, where, unique, nan, sort, zeros
+    from molsysmt.element.group import get_group_type_from_group_name
+    from ..molsysmt_Topology import extract
 
-    tmp_item = to_openmm_Topology(item)
-    tmp_item = openmm_Topology_to_molsysmt_Topology(tmp_item, atom_indices=atom_indices)
+    tmp_item = Topology()
+
+    n_atoms = len(item.atoms)
+
+    # atoms, groups and chains
+
+    atom_index_array = empty(n_atoms, dtype=int)
+    atom_name_array = empty(n_atoms, dtype=object)
+    atom_id_array = empty(n_atoms, dtype=int)
+    atom_type_array = empty(n_atoms, dtype=object)
+    atom_partial_charge_array = empty(n_atoms, dtype=object)
+    atom_formal_charge_array = empty(n_atoms, dtype=object)
+
+    group_index_array = empty(n_atoms, dtype=int)
+    group_name_array = empty(n_atoms, dtype=object)
+    group_id_array = empty(n_atoms, dtype=int)
+    group_type_array = empty(n_atoms, dtype=object)
+
+    chain_index_array = empty(n_atoms, dtype=int)
+    chain_name_array = empty(n_atoms, dtype=object)
+    chain_id_array = empty(n_atoms, dtype=object)
+    chain_type_array = empty(n_atoms, dtype=object)
+
+    atom_index = 0
+
+    for atom in item.atoms:
+
+        atom_index_array[atom_index] = atom._idx
+        atom_name_array[atom_index] = atom.name
+        atom_id_array[atom_index] = atom.idx
+        atom_type_array[atom_index] = None
+        atom_partial_charge_array[atom_index] = atom.charge
+        atom_formal_charge_array[atom_index] = atom.formal_charge
+
+        group_index_array[atom_index] = atom.residue._idx
+        group_name_array[atom_index] = atom.residue.name
+        group_id_array[atom_index] = atom.residue.idx
+        group_type_array[atom_index] = get_group_type_from_group_name(atom.residue.name)
+
+        chain_index_array[atom_index] = 0
+        chain_id_array[atom_index] = None
+
+        atom_index+=1
+
+
+    tmp_item.atoms_dataframe["atom_index"] = atom_index_array
+    tmp_item.atoms_dataframe["atom_name"] = atom_name_array
+    tmp_item.atoms_dataframe["atom_id"] = atom_id_array
+    tmp_item.atoms_dataframe["atom_type"] = atom_type_array
+    tmp_item.atoms_dataframe["formal_charge"] = atom_formal_charge_array
+    tmp_item.atoms_dataframe["partial_charge"] = atom_partial_charge_array
+    del(atom_index_array, atom_name_array, atom_id_array, atom_type_array)
+    del(atom_formal_charge_array, atom_partial_charge_array)
+
+    tmp_item.atoms_dataframe["group_index"] = group_index_array
+    tmp_item.atoms_dataframe["group_name"] = group_name_array
+    tmp_item.atoms_dataframe["group_id"] = group_id_array
+    tmp_item.atoms_dataframe["group_type"] = group_type_array
+    del(group_index_array, group_id_array, group_name_array, group_type_array)
+
+    tmp_item.atoms_dataframe["chain_index"] = chain_index_array
+    tmp_item.atoms_dataframe["chain_id"] = chain_id_array
+    del(chain_index_array, chain_id_array, chain_name_array, chain_type_array)
+
+    # bonds
+
+    n_bonds = len(item.bonds)
+
+    bond_atom1_array = empty(n_bonds, dtype=int)
+    bond_atom2_array = empty(n_bonds, dtype=int)
+    bond_type_array = empty(n_bonds, dtype=object)
+    bond_order_array = empty(n_bonds, dtype=object)
+
+    bond_index = 0
+
+    for bond in item.bonds:
+
+        bond_atom1_array[bond_index] = bond.atom1._idx
+        bond_atom2_array[bond_index] = bond.atom2._idx
+        bond_order_array[bond_index] = bond.order
+        bond_type_array[bond_index] = bond.type
+
+        bond_index +=1
+
+    tmp_item.bonds_dataframe["atom1_index"] = bond_atom1_array
+    tmp_item.bonds_dataframe["atom2_index"] = bond_atom2_array
+    tmp_item.bonds_dataframe["order"] = bond_order_array
+    tmp_item.bonds_dataframe["type"] = bond_type_array
+
+    # components
+
+    tmp_item._build_components()
+
+    ## molecules
+
+    tmp_item._build_molecules()
+
+    ## entity
+
+    tmp_item._build_entities()
+
+    ## nan to None
+
+    tmp_item._nan_to_None()
+
+    ## extract if atom_indices is not 'all'
+
+    tmp_item = extract(tmp_item, atom_indices=atom_indices, copy_if_all=False)
 
     return tmp_item
 

molsysmt/form/parmed_Structure/to_openmm_Topology.py

@@ -5,7 +5,7 @@ def to_openmm_Topology(item, atom_indices='all'):
 
     from ..openmm_Topology import extract as extract_openmm_Topology
 
-    tmp_item = tmp_item.topology
+    tmp_item = item.topology
     tmp_item = extract_openmm_Topology(tmp_item, atom_indices=atom_indices, copy_if_all=False)
 
     return tmp_item