In process

molsysmt/element/group/get_group_type.py

@@ -64,14 +64,14 @@ def _get_group_type_from_group_name(group_name):
         output = 'water'
     elif is_ion(group_name):
         output = 'ion'
-    elif is_small_molecule(group_name):
-        output = 'small molecule'
     elif is_amino_acid(group_name):
         output = 'amino acid'
     elif is_terminal_capping(group_name):
         output = 'terminal capping'
     elif is_nucleotide(group_name):
         output = 'nucleotide'
+    elif is_small_molecule(group_name):
+        output = 'small molecule'
     elif is_lipid(group_name):
         output = 'lipid'
     elif is_saccharide(group_name):

molsysmt/element/group/small_molecule/make_components_pkl.py

@@ -0,0 +1,15 @@
+# wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
+
+from molsysmt.native import CIFFileHandler
+import pickle
+
+handler = CIFFileHandler('components.cif')
+cif_entries = handler.parse()
+output = {}
+
+for value, key in cif_entries.items():
+    output[key['_chem_comp']['three_letter_code']]=key['_chem_comp']['name']
+
+with open('components.pkl', 'wb') as fp:
+    pickle.dump(output, fp)
+

molsysmt/element/group/small_molecule/small_molecule_names.py

@@ -1,5 +1,18 @@
-small_molecule_names = [
-        'HED', # PDBID 181L
-        'BNZ', # PDBID 181L
-        ]
+import pickle
+import sys
+
+if sys.version_info[1]==10:
+    from importlib.resources import files
+    def path(package, file):
+        return files(package).joinpath(file)
+elif sys.version_info[1] in (8,9):
+    from pathlib import PurePath
+    parent = PurePath(__file__).parent
+    def path(package, file):
+        data_dir = package.split('.')[-1]
+        return parent.joinpath('../data/'+data_dir+'/'+file).__str__()
+
+
+with open(path('molsysmt.data.databases','components.pkl'), 'rb') as fff:
+    small_molecule_names = pickle.load(fff)
 

molsysmt/form/file_cif/__init__.py

@@ -16,6 +16,10 @@
 from .set import *
 from .iterators import StructuresIterator, TopologyIterator
 
+from .to_molsysmt_CIFFileHandler import to_molsysmt_CIFFileHandler
+
 _convert_to={
+        'file:cif': extract,
+        'molsysmt.CIFFileHandler': to_molsysmt_CIFFileHandler,
         }
 

molsysmt/form/file_pdb/__init__.py

@@ -27,6 +27,9 @@
 from .to_mdtraj_PDBTrajectoryFile import to_mdtraj_PDBTrajectoryFile
 from .to_mdtraj_Topology import to_mdtraj_Topology
 from .to_mdtraj_Trajectory import to_mdtraj_Trajectory
+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
@@ -50,6 +53,9 @@
         'mdtraj.PDBTrajectoryFile': to_mdtraj_PDBTrajectoryFile,
         'mdtraj.Topology': to_mdtraj_Topology,
         'mdtraj.Trajectory': to_mdtraj_Trajectory,
+        '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,

molsysmt/form/file_pdb/to_molsysmt_MolSys.py

@@ -0,0 +1,16 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:pdb')
+def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False):
+
+    from molsysmt.native 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/file_pdb/to_molsysmt_Structures.py

@@ -0,0 +1,18 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:pdb')
+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_box_from_system
+
+    tmp_item = Structures()
+
+    coordinates = get_coordinates_from_atom(item, indices=atom_indices, structure_indices=structure_indices,
+                                            skip_digestion=True)
+    box = get_box_from_system(item, structure_indices=structure_indices, skip_digestion=True)
+
+    tmp_item.append_structures(coordinates=coordinates, box=box)
+
+    return tmp_item
+

molsysmt/form/file_pdb/to_molsysmt_Topology.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='file:pdb')
+def to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False):
+
+    from . import to_openmm_PDBFile
+    from ..openmm_PDBFile import to_molsysmt_Topology as openmm_PDBFile_to_molsysmt_Topology
+
+    tmp_item = to_openmm_PDBFile(item, skip_digestion=True)
+    tmp_item = openmm_PDBFile_to_molsysmt_Topology(tmp_item, atom_indices=atom_indices, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/mmtf_MMTFDecoder/to_molsysmt_MolSys.py

@@ -12,8 +12,8 @@ def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_d
     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)
-    tmp_item.molecular_mechanics = to_molsysmt_MolecularMechanics(item, atom_indices=atom_indices,
-                                                                  skip_digestion=True)
+    #tmp_item.molecular_mechanics = to_molsysmt_MolecularMechanics(item, atom_indices=atom_indices,
+    #                                                              skip_digestion=True)
 
     return tmp_item
 

molsysmt/form/mmtf_MMTFDecoder/to_molsysmt_Structures.py

@@ -6,8 +6,8 @@
 @digest(form='mmtf.MMTFDecoder')
 def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False):
 
-    from molsysmt.native.structures_old import StructuresOld
-    from molsysmt.form.molsysmt_StructuresOld import extract as extract_molsysmt_StructuresOld
+    from molsysmt.native.structures import Structures
+    from molsysmt.form.molsysmt_Structures import extract as extract_molsysmt_Structures
     from molsysmt.pbc import get_box_from_lengths_and_angles
 
     n_atoms = item.num_atoms
@@ -150,12 +150,12 @@ def to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', sk
 
         bioassembly[aux_bioassembly['name']] = aux
 
-    tmp_item = StructuresOld(structure_id=structure_id, time=time, coordinates=coordinates, box=box,
+    tmp_item = Structures(structure_id=structure_id, time=time, coordinates=coordinates, box=box,
             occupancy=occupancy, b_factor=b_factor, alternate_location=alternate_location, bioassembly=bioassembly)
 
     if not is_all(atom_indices)*is_all(structure_indices):
 
-        tmp_item = extract_molsysmt_StructuresOld(tmp_item, atom_indices=atom_indices,
+        tmp_item = extract_molsysmt_Structures(tmp_item, atom_indices=atom_indices,
                                                   structure_indices=structure_indices, skip_digestion=True)
 
     return tmp_item