In process

molsysmt/data/_make/chicken_villin_HP35.py

@@ -17,15 +17,17 @@
         'mmtf/1vii.mmtf',
         'h5msm/chicken_villin_HP35.h5msm',
         'h5msm/chicken_villin_HP35_solvated.h5msm',
-        'dcd/traj_chicken_villin_HP35_solvated.dcd',
-        'h5/traj_chicken_villin_HP35_solvated.h5',
+        'dcd/traj_chicken_villin_HP35.dcd',
+        'h5/traj_chicken_villin_HP35.h5',
+        'h5msm/traj_chicken_villin_HP35.h5msm',
         ]
 
 for filename in files_to_be_purged:
     filepath = Path(data_dir, filename)
     if os.path.isfile(filepath):
         os.remove(filepath)
 
+
 # Make
 
 # 1vii pdb and mmtf files
@@ -53,11 +55,10 @@
 molsys = msm.build.solvate([molsys, {'forcefield':'AMBER14', 'water_model':'TIP3P'}],
                    box_shape='truncated octahedral', clearance='14.0 angstroms',
                    to_form='molsysmt.MolSys')
-_ = msm.convert(molsys, to_form='chicken_villin_HP35_solvated.msmpk')
+_ = msm.convert(molsys, to_form='chicken_villin_HP35_solvated.h5msm')
 shutil.move('chicken_villin_HP35_solvated.h5msm', Path(data_dir, 'h5msm/chicken_villin_HP35_solvated.h5msm'))
 
 
-
 # simulation
 print('Trajectory files...')
 modeller = msm.convert(molsys, to_form='openmm.Modeller')
@@ -73,10 +74,13 @@
     potentialEnergy=True, temperature=True, remainingTime=True, totalSteps=1000000))
 simulation.reporters.append(app.DCDReporter('traj_chicken_villin_HP35_solvated.dcd', 50000, enforcePeriodicBox=True))
 simulation.reporters.append(HDF5Reporter('traj_chicken_villin_HP35_solvated.h5', 50000))
+#simulation.reporters.append(msm.thirds.openmm.reporters.H5MSMReporter('traj_chicken_villin_HP35_solvated.h5msm', 
+#                                                                      10000000, 50000))
 simulation.step(1000000)
 simulation.reporters[2].close()
 final_positions = simulation.context.getState(getPositions=True).getPositions()
 
 shutil.move('traj_chicken_villin_HP35_solvated.dcd', Path(data_dir, 'dcd/traj_chicken_villin_HP35_solvated.dcd'))
 shutil.move('traj_chicken_villin_HP35_solvated.h5', Path(data_dir, 'h5/traj_chicken_villin_HP35_solvated.h5'))
+#shutil.move('traj_chicken_villin_HP35_solvated.h5msm', Path(data_dir, 'h5/traj_chicken_villin_HP35_solvated.h5msm'))
 

molsysmt/form/molsysmt_MolSys/__init__.py

@@ -25,6 +25,7 @@
 from .to_molsysmt_MolecularMechanicsDict import to_molsysmt_MolecularMechanicsDict
 from .to_networkx_Graph import to_networkx_Graph
 from .to_nglview_NGLWidget import to_nglview_NGLWidget
+from .to_openmm_Context import to_openmm_Context
 from .to_openmm_Topology import to_openmm_Topology
 from .to_openmm_Modeller import to_openmm_Modeller
 from .to_pdbfixer_PDBFixer import to_pdbfixer_PDBFixer
@@ -40,6 +41,7 @@
         'molsysmt.MolecularMechanicsDict': to_molsysmt_MolecularMechanicsDict,
         'networkx.Graph': to_networkx_Graph,
         'nglview.NGLWidget': to_nglview_NGLWidget,
+        'openmm.Context': to_openmm_Context,
         'openmm.Topology': to_openmm_Topology,
         'openmm.Modeller': to_openmm_Modeller,
         'pdbfixer.PDBFixer': to_pdbfixer_PDBFixer,

molsysmt/form/molsysmt_MolSys/to_openmm_Context.py

@@ -0,0 +1,26 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.MolSys')
+def to_openmm_Context(item, atom_indices='all', structure_indices='all',
+        forcefield='AMBER14', water_model=None, implicit_solvent=None,
+        non_bonded_method='no cutoff', constraints='hbonds', switch_distance=None,
+        dispersion_correction=False, ewald_error_tolerance=0.0005,
+        integrator='Langevin', temperature='300.0 kelvin', friction='1.0/picoseconds', time_step='2 femtoseconds',
+        platform='CUDA', skip_digestion=False):
+
+    from . import to_openmm_Topology
+    from . import get_coordinates_from_atom
+    from ..openmm_Topology import to_openmm_Context as openmm_Topology_to_openmm_Context
+
+    tmp_item = to_openmm_Topology(item, atom_indices=atom_indices, structure_indices=structure_indices, skip_digestion=True)
+    coordinates = get_coordinates_from_atom(item, indices=atom_indices, structure_indices=structure_indices, skip_digestion=True)
+
+    tmp_item = openmm_Topology_to_openmm_Context(tmp_item, coordinates=coordinates,
+            forcefield=forcefield, water_model=water_model, implicit_solvent=implicit_solvent,
+            non_bonded_method=non_bonded_method, constraints=constraints, switch_distance=switch_distance,
+            dispersion_correction=dispersion_correction, ewald_error_tolerance=ewald_error_tolerance,
+            integrator=integrator, temperature=temperature, friction=friction, time_step=time_step,
+            platform=platform, skip_digestion=True)
+
+    return tmp_item
+

molsysmt/form/molsysmt_Topology/__init__.py

@@ -16,13 +16,21 @@
 from .set import *
 from .iterators import TopologyIterator
 
-from .to_file_h5msm import to_file_h5msm
+from .to_string_aminoacids3 import to_string_aminoacids3
+from .to_string_aminoacids1 import to_string_aminoacids1
+from .to_string_pdb_text import to_string_pdb_text
+from .to_file_h5msm import to_file_h5msm, dump_topology_to_h5msm
 from .to_networkx_Graph import to_networkx_Graph
 from .to_openmm_Topology import to_openmm_Topology
+from .to_parmed_Structure import to_parmed_Structure
 
 _convert_to={
         'molsysmt.Topology': extract,
+        'string:aminoacids1': to_string_aminoacids1,
+        'string:aminoacids3': to_string_aminoacids3,
+        'string:pdb_text': to_string_pdb_text,
         'file:h5msm': to_file_h5msm,
         'networkx.Graph': to_networkx_Graph,
         'openmm.Topology': to_openmm_Topology,
+        'parmed.Structure': to_parmed_Structure,
         }

molsysmt/form/molsysmt_Topology/to_file_h5msm.py

@@ -18,7 +18,7 @@ def to_file_h5msm(item, atom_indices='all', coordinates=None, output_filename=No
 
     return output_filename
 
-def _add_topology_to_h5msm(item, file, atom_indices='all'):
+def dump_topology_to_h5msm(item, file, atom_indices='all'):
 
     from h5py._hl.files import File as h5py_File
     from molsysmt.native import H5MSMFileHandler

molsysmt/form/molsysmt_Topology/to_parmed_Structure.py

@@ -0,0 +1,12 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.Topology')
+def to_parmed_Structure(item, atom_indices='all', skip_digestion=False):
+
+    from .to_openmm_Topology import to_openmm_Topology as molsysmt_Topology_to_openmm_Topology
+    from ..openmm_Topology import to_parmed_Structure as openmm_Topology_to_parmed_Structure
+
+    tmp_item = molsysmt_Topology_to_openmm_Topology(item, atom_indices=atom_indices)
+    tmp_item = openmm_Topology_to_parmed_Structure(tmp_item)
+    return tmp_item
+

molsysmt/form/molsysmt_Topology/to_string_aminoacids1.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.Topology')
+def to_string_aminoacids1(item, group_indices='all', skip_digestion=False):
+
+    from . import to_string_aminoacids3
+    from ..string_aminoacids3 import to_string_aminoacids1 as string_aminoacids3_to_string_aminoacids1
+
+    tmp_item = to_string_aminoacids3(item, group_indices=group_indices)
+    tmp_item = string_aminoacids3_to_string_aminoacids1(tmp_item)
+
+    return tmp_item
+

molsysmt/form/molsysmt_Topology/to_string_aminoacids3.py

@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+import numpy as np
+
+@digest(form='molsysmt.Topology')
+def to_string_aminoacids3(item, group_indices='all', skip_digestion=False):
+
+    from . import get_group_name_from_group
+
+    group_names = get_group_name_from_group(item, indices=group_indices)
+    tmp_item = ''.join([ii.title() for ii in group_names])
+
+    return tmp_item
+

molsysmt/form/molsysmt_Topology/to_string_pdb_text.py

@@ -0,0 +1,17 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='molsysmt.Topology')
+def to_string_pdb_text(item, atom_indices='all', coordinates=None, box=None, skip_digestion=False):
+
+    from molsysmt.native import MolSys, Structures
+    from . import extract
+    from ..molsysmt_MolSys import to_string_pdb_text as molsysmt_MolSys_to_string_pdb_text
+
+    tmp_item =  MolSys()
+    tmp_item.topology = extract(item, atom_indices=atom_indices, copy_if_all=False, skip_digestion=True)
+    tmp_item.structures.append(coordinates=coordinates, box=box, skip_digestion=True)
+    tmp_item = molsysmt_MolSys_to_string_pdb_text(tmp_item, skip_digestion=True)
+
+    return tmp_item
+
+

molsysmt/form/openmm_Topology/to_openmm_Context.py

@@ -4,7 +4,7 @@
 def to_openmm_Context(item, atom_indices='all', coordinates=None, forcefield='AMBER14', water_model=None,
         implicit_solvent=None, non_bonded_method='no cutoff', constraints='hbonds', switch_distance=None,
         dispersion_correction=False, ewald_error_tolerance=0.0005, integrator='Langevin', temperature=None,
-        friction='1.0/picoseconds', time_step='2 femtoseconds', platform='CUDA'):
+        friction='1.0/picoseconds', time_step='2 femtoseconds', platform='CUDA', skip_digestion=False):
 
 
     from . import to_openmm_System
@@ -14,10 +14,10 @@ def to_openmm_Context(item, atom_indices='all', coordinates=None, forcefield='AM
             water_model=water_model, implicit_solvent=implicit_solvent,
             non_bonded_method=non_bonded_method, constraints=constraints,
             switch_distance=switch_distance, dispersion_correction=dispersion_correction,
-            ewald_error_tolerance=ewald_error_tolerance)
+            ewald_error_tolerance=ewald_error_tolerance, skip_digestion=True)
     context = openmm_System_to_openmm_Context(system, coordinates=coordinates,
             integrator=integrator, temperature=temperature, friction=friction,
-            time_step=time_step, platform=platform)
+            time_step=time_step, platform=platform, skip_digestion=True)
 
     return context
 

molsysmt/molecular_mechanics/forcefields.py

@@ -157,7 +157,7 @@
 }
 
 
-def forcefield_to_engine(forcefield, implicit_solvent=None, water_model=None, engine='OpenMM'):
+def forcefield_to_engine(forcefield, implicit_solvent=None, water_model=None, engine='OpenMM', skip_digestion=False):
 
     forcefield_out = None
 

molsysmt/native/h5msm_file_handler.py

@@ -45,11 +45,11 @@ def write_topology(self, topology, selection='all', syntax='MolSysMT'):
 
         try:
             topology_form = get_form(topology)
-            _dict_modules[topology_form].write_topology_in_h5msm(topology, file=self.file,
+            _dict_modules[topology_form].dump_topology_to_h5msm(topology, file=self.file,
                     atom_indices=atom_indices)
         except:
             aux_topology = convert(topology, to_form='molsysmt.Topology', selection=atom_indices)
-            _dict_modules['molsysmt.Topology'].write_topology_in_h5msm(aux_topology, file=self.file,
+            _dict_modules['molsysmt.Topology'].dump_topology_to_h5msm(aux_topology, file=self.file,
                     atom_indices=atom_indices)
             del(aux_topology)
 

molsysmt/systems.py

@@ -51,13 +51,13 @@ def path(package, file):
 
 # Villin HP35
 
-#systems['chicken villin HP35'] = {}
-#systems['chicken villin HP35']['1vii.pdb'] = path('molsysmt.data.pdb', '1vii.pdb')
-#systems['chicken villin HP35']['1vii.mmtf'] = path('molsysmt.data.mmtf', '1vii.mmtf')
-#systems['chicken villin HP35']['chicken_villin_HP35.msmpk'] = path('molsysmt.data.msmpk', 'chicken_villin_HP35.msmpk')
-#systems['chicken villin HP35']['chicken_villin_HP35_solvated.msmpk'] = path('molsysmt.data.msmpk', 'chicken_villin_HP35_solvated.msmpk')
-#systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.dcd'] = path('molsysmt.data.dcd', 'traj_chicken_villin_HP35_solvated.dcd')
-#systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5'] = path('molsysmt.data.h5', 'traj_chicken_villin_HP35_solvated.h5')
+systems['chicken villin HP35'] = {}
+systems['chicken villin HP35']['1vii.pdb'] = path('molsysmt.data.pdb', '1vii.pdb')
+systems['chicken villin HP35']['1vii.mmtf'] = path('molsysmt.data.mmtf', '1vii.mmtf')
+systems['chicken villin HP35']['chicken_villin_HP35.h5msm'] = path('molsysmt.data.h5msm', 'chicken_villin_HP35.h5msm')
+systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'] = path('molsysmt.data.h5msm', 'chicken_villin_HP35_solvated.h5msm')
+systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.dcd'] = path('molsysmt.data.dcd', 'traj_chicken_villin_HP35_solvated.dcd')
+systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5'] = path('molsysmt.data.h5', 'traj_chicken_villin_HP35_solvated.h5')
 
 
 # T4 Lysozyme L99A

sandbox/Tests.ipynb

@@ -28,7 +28,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8b87277e2fb54c069e290543ded39aff",
+       "model_id": "68d1b5acc00648fba4dbed24dea654e3",
        "version_major": 2,
        "version_minor": 0
       },
@@ -56,31 +56,25 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "f1048ba3-4aa0-4ed5-a30f-cd54dabb4c64",
+   "id": "5976ffbc-590e-4fc1-a7b9-30e11f4f17ca",
    "metadata": {},
-   "outputs": [],
-   "source": [
-    "molsys_A = msm.convert(systems['T4 lysozyme L99A']['t4_lysozyme_L99A.h5msm'], to_form='molsysmt.MolSys')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "7c13929f-61f7-471f-b713-4cf7c32d77fa",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "molsys_B = msm.convert(systems['T4 lysozyme L99A']['t4_lysozyme_L99A.h5msm'], to_form='molsysmt.MolSys')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "0fe83988-232e-438e-8c90-7d442b263baf",
-   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NotImplementedConversionError",
+     "evalue": "Error in conversion from file:mmtf to openmm.Modeller",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNotImplementedConversionError\u001b[0m             Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m molsys_A \u001b[38;5;241m=\u001b[39m \u001b[43mmsm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43msystems\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mT4 lysozyme L99A\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m181l.mmtf\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mto_form\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mopenmm.Modeller\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:122\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    120\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(all_args[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n\u001b[1;32m    121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 122\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/basic/convert.py:554\u001b[0m, in \u001b[0;36mconvert\u001b[0;34m(molecular_system, to_form, selection, structure_indices, syntax, verbose, skip_digestion, **kwargs)\u001b[0m\n\u001b[1;32m    552\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(from_form)\u001b[38;5;241m==\u001b[39m\u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m    553\u001b[0m         from_form\u001b[38;5;241m=\u001b[39mfrom_form[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 554\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m NotImplementedConversionError(from_form, to_form)\n\u001b[1;32m    556\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(output, (\u001b[38;5;28mlist\u001b[39m, \u001b[38;5;28mtuple\u001b[39m)):\n\u001b[1;32m    557\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(output) \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n",
+      "\u001b[0;31mNotImplementedConversionError\u001b[0m: Error in conversion from file:mmtf to openmm.Modeller"
+     ]
+    }
+   ],
    "source": [
-    "output = msm.compare(molsys_A, molsys_B, attributes_type='topological', coordinates=True, box=True)"
+    "molsys_A = msm.convert(systems['T4 lysozyme L99A']['181l.mmtf'], to_form='openmm.Modeller')"
    ]
   },
   {
@@ -89,7 +83,12 @@
    "id": "825cfd0e-bce4-4af7-b33e-03f34a2f3b5d",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "    molsys_A = msm.convert(systems['T4 lysozyme L99A']['181l.mmtf'], to_form='openmm.Modeller')\n",
+    "    molsys_B = msm.convert(molsys_A, to_form='molsysmt.MolSys')\n",
+    "    output = msm.compare(molsys_A, molsys_B)\n",
+    "    assert output == True\n"
+   ]
   }
  ],
  "metadata": {