In process

molsysmt/form/file_gro/__init__.py

@@ -20,6 +20,9 @@
 from .to_mdtraj_Trajectory import to_mdtraj_Trajectory
 from .to_mdtraj_Topology import to_mdtraj_Topology
 from .to_mdtraj_GroTrajectoryFile import to_mdtraj_GroTrajectoryFile
+from .to_molsysmt_MolSys import to_molsysmt_MolSys
+from .to_molsysmt_Topology import to_molsysmt_Topology
+from .to_molsysmt_Structures import to_molsysmt_Structures
 from .to_molsysmt_MolSysOld import to_molsysmt_MolSysOld
 from .to_molsysmt_TopologyOld import to_molsysmt_TopologyOld
 from .to_molsysmt_StructuresOld import to_molsysmt_StructuresOld
@@ -33,6 +36,9 @@
         'mdtraj.Trajectory': to_mdtraj_Trajectory,
         'mdtraj.Topology': to_mdtraj_Topology,
         'mdtraj.GroTrajectoryFile': to_mdtraj_GroTrajectoryFile,
+        'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.Topology': to_molsysmt_Topology,
+        'molsysmt.Structures': to_molsysmt_Structures,
         'molsysmt.MolSysOld': to_molsysmt_MolSysOld,
         'molsysmt.TopologyOld': to_molsysmt_TopologyOld,
         'molsysmt.StructuresOld': to_molsysmt_StructuresOld,
@@ -41,3 +47,4 @@
         'openmm.GromacsGroFile': to_openmm_GromacsGroFile,
         'nglview.NGLWidget': to_nglview_NGLWidget,
         }
+

molsysmt/form/file_gro/to_molsysmt_MolSys.py

@@ -0,0 +1,14 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:gro')
+def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from . import to_mdtraj_Trajectory
+    from ..mdtraj_Trajectory import to_molsysmt_MolSys as mdtraj_Trajectory_to_molsysmt_MolSys
+
+    tmp_item = to_mdtraj_Trajectory(item, skip_digestion=True)
+    tmp_item = mdtraj_Trajectory_to_molsysmt_MolSys(tmp_item, atom_indices=atom_indices,
+                                                    structure_indices=structure_indices, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/file_gro/to_molsysmt_Structures.py

@@ -0,0 +1,15 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:gro')
+def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from . import to_openmm_GromacsGroFile
+    from ..openmm_GromacsGroFile import to_molsysmt_Structures as openmm_GromacsGroFile_to_molsysmt_Structures
+
+    tmp_item = to_openmm_GromacsGroFile(item, skip_digestion=True)
+    tmp_item = openmm_GromacsGroFile_to_molsysmt_Structures(tmp_item, atom_indices=atom_indices,
+                                                            structure_indices=structure_indices,
+                                                            skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/file_gro/to_molsysmt_Topology.py

@@ -0,0 +1,33 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:gro')
+def to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False):
+
+    #from . import to_mdtraj_Topology
+    #from ..mdtraj_Topology import to_molsysmt_Topology as mdtraj_Topology_to_molsysmt_Topology
+
+    #tmp_item = to_mdtraj_Topology(item, atom_indices=atom_indices, skip_digestion=True)
+    #tmp_item = mdtraj_Topology_to_molsysmt_Topology(tmp_item, skip_digestion=True)
+
+    from molsysmt.native import Topology
+    from ..molsysmt_Topology import extract
+
+    tmp_item = Topology()
+
+    n_atoms = item.n_atoms
+    n_groups = item.n_residues
+    n_chains = item.n_chains
+    n_bonds = item.n_bonds
+
+
+    # atoms
+
+    atom_name_array = np.empty(n_atoms, dtype=object)
+    atom_id_array = np.empty(n_atoms, dtype=int)
+    atom_type_array = np.empty(n_atoms, dtype=object)
+    group_index_array = np.empty(n_atoms, dtype=int)
+    chain_index_array = np.empty(n_atoms, dtype=int)
+
+
+    return tmp_item
+

molsysmt/form/mdtraj_Topology/__init__.py

@@ -22,6 +22,7 @@
 from .to_mdtraj_Trajectory import to_mdtraj_Trajectory
 from .to_parmed_Structure import to_parmed_Structure
 from .to_parmed_GromacsTopologyFile import to_parmed_GromacsTopologyFile
+from .to_molsysmt_Topology import to_molsysmt_Topology
 from .to_molsysmt_TopologyOld import to_molsysmt_TopologyOld
 from .to_openmm_Topology import to_openmm_Topology
 
@@ -33,6 +34,7 @@
         'mdtraj_Trajectory': to_mdtraj_Trajectory,
         'parmed_Structure': to_parmed_Structure,
         'parmed_GromacsTopologyFile': to_parmed_GromacsTopologyFile,
+        'molsysmt_Topology': to_molsysmt_Topology,
         'molsysmt_TopologyOld': to_molsysmt_TopologyOld,
         'openmm_Topology': to_openmm_Topology,
         }

molsysmt/form/mdtraj_Topology/to_molsysmt_Topology.py

@@ -0,0 +1,135 @@
+from molsysmt._private.digestion import digest
+from molsysmt.element.group.get_group_type import _get_group_type_from_group_name
+
+@digest(form='mdtraj.Topology')
+def to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False):
+
+    #from ..openmm_Topology import to_molsysmt_Topology as openmm_Topology_to_molsysmt_Topology
+
+    #tmp_item = item.to_openmm()
+    #tmp_item = openmm_Topology_to_molsysmt_Topology(tmp_item, atom_indices=atom_indices, skip_digestion=True)
+
+    from molsysmt.native import Topology
+    from ..molsysmt_Topology import extract
+
+    tmp_item = Topology()
+
+    n_atoms = item.n_atoms
+    n_groups = item.n_residues
+    n_chains = item.n_chains
+    n_bonds = item.n_bonds
+
+    # atoms
+
+    atom_name_array = np.empty(n_atoms, dtype=object)
+    atom_id_array = np.empty(n_atoms, dtype=int)
+    atom_type_array = np.empty(n_atoms, dtype=object)
+    group_index_array = np.empty(n_atoms, dtype=int)
+    chain_index_array = np.empty(n_atoms, dtype=int)
+
+    for atom_index, atom in enumerate(item.atoms):
+
+        atom_name_array[atom_index] = atom.name
+        atom_id_array[atom_index] = atom.serial
+        atom_type_array[atom_index] = atom.element
+        group_index_array[atom_index] = atom.residue.index
+        chain_index_array[chain_index] = atom.residue.chain.index
+
+    tmp_item.atoms["atom_name"] = atom_name_array
+    tmp_item.atoms["atom_id"] = atom_id_array
+    tmp_item.atoms["atom_type"] = atom_type_array
+    tmp_item.atoms["group_index"] = group_index_array
+    tmp_item.atoms["chain_index"] = chain_index_array
+
+    del atom_name_array, atom_id_array, atom_type_array
+    del group_index_array, chain_index_array
+
+    # groups
+
+    group_name_array = np.empty(n_groups, dtype=object)
+    group_id_array = np.empty(n_groups, dtype=int)
+
+    aux_dict = {}
+
+    for group_index, residue in enumerate(item.residues):
+
+        group_name_array[group_index] = residue.name
+        group_id_array[group_index] = residue.resSeq
+
+        if residue.name not in aux_dict:
+            aux_dict[residue.name] = _get_group_type_from_group_name(residue.name)
+
+    tmp_item.groups["group_id"] = group_id_array
+    tmp_item.groups["group_name"] = group_name_array
+    tmp_item.groups["group_type"] = np.array([aux_dict[ii] for ii in group_name_array], dtype=object)
+
+    del group_name_array, group_id_array
+
+    # chains
+
+    chain_name_array = np.empty(n_chains, dtype=object)
+
+    index = 0
+
+    for chain in item.chains():
+
+        chain_name_array[index] = chain.chain_id
+
+    tmp_item.chains["chain_name"] = chain_name_array
+    tmp_item.chains["chain_id"] = tmp_item.chains.index
+
+    del chain_name_array
+
+    # bonds
+
+    bond_atom1_array = np.empty(n_bonds, dtype=int)
+    bond_atom2_array = np.empty(n_bonds, dtype=int)
+    bond_type_array = np.empty(n_bonds, dtype=object)
+    bond_order_array = np.empty(n_bonds, dtype=object)
+
+    for bond in item.bonds():
+
+        bond_atom1_array[index] = bond.atom1.index
+        bond_atom2_array[index] = bond.atom2.index
+        bond_order_array[index] = bond.order
+        bond_type_array[index] = bond.type
+
+    tmp_item.bonds["atom1_index"] = bond_atom1_array
+    tmp_item.bonds["atom2_index"] = bond_atom2_array
+    tmp_item.bonds["order"] = bond_order_array
+    tmp_item.bonds["type"] = bond_type_array
+
+    del bond_atom1_array, bond_atom2_array
+    del bond_order_array, bond_type_array
+
+    if tmp_item.bonds["order"].isnull().all():
+        tmp_item.bonds.drop("order", axis=1, inplace=True)
+
+    if tmp_item.bonds["type"].isnull().all():
+        tmp_item.bonds.drop("type", axis=1, inplace=True)
+
+    # components
+
+    tmp_item.rebuild_components()
+
+    # molecules
+
+    tmp_item.rebuild_molecules()
+
+    # chain types
+
+    tmp_item.rebuild_chain_types()
+
+    # entity
+
+    tmp_item.rebuild_entities()
+
+    # nan to None
+
+    tmp_item._fix_null_values()
+    tmp_item.bonds._sort_bonds()
+
+    tmp_item = tmp_item.extract(atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/mdtraj_Trajectory/__init__.py

@@ -24,6 +24,9 @@
 from .to_openmm_Topology import to_openmm_Topology
 from .to_openmm_Modeller import to_openmm_Modeller
 from .to_pdbfixer_PDBFixer import to_pdbfixer_PDBFixer
+from .to_molsysmt_MolSys import to_molsysmt_MolSys
+from .to_molsysmt_Structures import to_molsysmt_Structures
+from .to_molsysmt_Topology import to_molsysmt_Topology
 from .to_molsysmt_MolSysOld import to_molsysmt_MolSysOld
 from .to_molsysmt_StructuresOld import to_molsysmt_StructuresOld
 from .to_molsysmt_TopologyOld import to_molsysmt_TopologyOld
@@ -44,6 +47,9 @@
         'openmm.Topology': to_openmm_Topology,
         'openmm.Modeller': to_openmm_Modeller,
         'pdbfixer.PDBFixer': to_pdbfixer_PDBFixer,
+        'molsysmt.MolSys': to_molsysmt_MolSys,
+        'molsysmt.Structures': to_molsysmt_Structures,
+        'molsysmt.Topology': to_molsysmt_Topology,
         'molsysmt.MolSysOld': to_molsysmt_MolSysOld,
         'molsysmt.StructuresOld': to_molsysmt_StructuresOld,
         'molsysmt.TopologyOld': to_molsysmt_TopologyOld,

molsysmt/form/mdtraj_Trajectory/to_molsysmt_MolSys.py

@@ -0,0 +1,17 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='mdtraj.Trajectory')
+def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from molsysmt.native.molsys import MolSys
+    from . import to_molsysmt_Topology
+    from . import to_molsysmt_Structures
+
+    tmp_item = MolSys()
+    tmp_item.topology = to_molsysmt_Topology(item, atom_indices=atom_indices, skip_digestion=True)
+    tmp_item.structures = to_molsysmt_Structures(item, atom_indices=atom_indices,
+            structure_indices=structure_indices, skip_digestion=True)
+
+    return tmp_item
+
+

molsysmt/form/mdtraj_Trajectory/to_molsysmt_Structures.py

@@ -0,0 +1,20 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='mdtraj.Trajectory')
+def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from molsysmt.native.structures import Structures
+    from . import get_coordinates_from_atom, get_time_from_system, get_structure_id_from_system, get_box_from_system
+
+    tmp_item = Structures()
+
+    coordinates = get_coordinates_from_atom(item, indices=atom_indices, structure_indices=structure_indices,
+                                            skip_digestion=True)
+    time = get_time_from_system(item, structure_indices=structure_indices, skip_digestion=True)
+    structure_id = get_structure_id_from_system(item, structure_indices=structure_indices, skip_digestion=True)
+    box = get_box_from_system(item, structure_indices=structure_indices, skip_digestion=True)
+
+    tmp_item.append(structure_id=structure_id, time=time, box=box, coordinates=coordinates)
+
+    return tmp_item
+

molsysmt/form/mdtraj_Trajectory/to_molsysmt_Topology.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='mdtraj.Trajectory')
+def to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False):
+
+    from . import to_mdtraj_Topology
+    from ..mdtraj_Topology import to_molsysmt_Topology as mdtraj_Topology_to_molsysmt_Topology
+
+    tmp_item = to_mdtraj_Topology(item, skip_digestion=True)
+    tmp_item = mdtraj_Topology_to_molsysmt_Topology(tmp_item, atom_indices=atom_indices, skip_digestion=True)
+
+    return tmp_item
+