def _add_angles(self): try: angles = guessers.guess_angles(self.bonds) self._topology.add_TopologyAttr(topologyattrs.Angles(angles)) self._generate_from_topology() except AttributeError: pass
def test_guess_impropers(): u = make_starshape() ag = u.atoms[:5] u.add_TopologyAttr(Angles(guessers.guess_angles(ag.bonds))) vals = guessers.guess_improper_dihedrals(ag.angles) assert_equal(len(vals), 12)
def test_guess_impropers(): u = make_starshape() ag = u.atoms[:5] u.add_TopologyAttr(Angles(guessers.guess_angles(ag.bonds))) vals = guessers.guess_improper_dihedrals(ag.angles) assert_equal(len(vals), 12)
def coarse_grain(universe, residue_list, simulation_name='simulation_name', export=False): # ============== Misc Initiation ============== # with open('src/mapping_dict.json', "r") as f: mapping_dict = load(f) with open('src/abrev_dict.json', "r") as f: abrev_dict = load(f) u = universe # ================= Execution ================= # print('Calculating Bond connections...') resnames = ' '.join(residue_list) original_bond_count = len(u.bonds) u.select_atoms(f'resname {resnames}').guess_bonds(vdwradii=config.vdw_radi) print( f'Original file contained {original_bond_count} bonds. {len(u.bonds) - original_bond_count} additional bonds infered.' ) print(f'Begining Coarse-Graining process...') bead_data = [] cg_beads = [] dummy_parents = {} non_water_atoms = u.select_atoms('not resname WAT') for residue in non_water_atoms.residues: # loops thu each matching residue id resid = residue.resid # store int id resname = residue.resname if resname in residue_list: # if resname == "PHOSPHATE" or resname == "RIBOSE": # resname_atoms = u.atoms.select_atoms('resname DA DT DG DC DU') # else: # resname_atoms = u.atoms.select_atoms(f'resname {resname}') # selects all resname-specific atoms if len(resname) == 4 and resname[0] == 'D': # for D-varants resname_key = resname[1:] else: resname_key = resname try: segments = mapping_dict[resname_key].keys() for segment in segments: # loops thru each segment of each residue params = 'name ' + ' '.join( mapping_dict[resname_key][segment] ['atoms']) # generates param # selects all atoms in a given residue segment atms = residue.atoms.select_atoms(params) dummy = atms[0] # names dummy atom in propper format dummy.name = str(abrev_dict[resname_key]) + str( segment[0]) + str(resid) dummy.type = mapping_dict[resname_key][segment]['name'] dummy.charge = mapping_dict[resname_key][segment]['charge'] bead_data.append((dummy, atms)) cg_beads.append(dummy) for atm in atms: dummy_parents[atm.ix] = dummy except KeyError: print( f'{resname_key} was not found in mapping/abrev_dict, skipping coarse grain. Please add its parameters to the dictionary. (See README section A3. for help)' ) new_bonds = [] # for residue in residue_list: # for mapping in mapping_dict[residue]["Bonds"]: # first_code = mapping[0] # segment, resid offset, resname # seccond_code = mapping[1] if isinstance(mapping[1], list) else [mapping[1], 0, residue] # type_params = list(mapping_dict[residue]["Mapping"].keys())[first_code] # first_atoms = cg_beads.select_atoms(f'resname {residue} and type {type_params}') # for first_atom in first_atoms: # type_params = list(mapping_dict[residue]["Mapping"].keys())[seccond_code[0]] # segment # seccond_atom_resid = int(first_atom.resid) + int(seccond_code[1]) # try: # seccond_atom = cg_beads.atoms.select_atoms(f'resname {seccond_code[2]} and type {type_params} and resid {seccond_atom_resid}') # except IndexError: # pass # if isinstance(seccond_atom, mda.core.groups.AtomGroup): # closest = seccond_atom[0] # closest_dist = mda.AtomGroup([first_atom, seccond_atom[0]]).bond.length() # for atom in seccond_atom: # dist = mda.AtomGroup([first_atom, atom]).bond.length() # if dist < closest_dist: # closest = atom # closest_dist = dist # seccond_atom = closest # new_bonds.append([first_atom.index, seccond_atom.index]) # new_bonds = [] for dummy, atms in bead_data: # connect all parents with connected children for atom in atms: for bond in atom.bonds: for bonded_atom in bond.atoms: if bonded_atom not in atms: # make more efficent if atms were a set # by the end of all these loops and ifs, every bonded_atom that gets to this point is an atom connected to the edge of the cluster of atoms assigned to the coarse grain dummy bead in question try: new_bonds.append([ cg_beads.index(dummy), cg_beads.index(dummy_parents[bonded_atom.ix]) ]) # type is used to store the cluster dummy except KeyError: # raises if atom does not belong to a coarse grain bead pass # try: # new_bonds.append([cg_beads.index(dummy), cg_beads.index(bonded_atom)]) # adds the bond between the dummies # except ValueError: # if the other atom is just an atom withouot a coarse grain bead parent, ignore it # pass cg_beads = mda.AtomGroup(cg_beads) # TODO: EXPORT NEW_U INSTEAD OF OLD U # TODO: EXPORT NEW_U TO HAVE APPROPRIATE FRAMES # TODO: SHIFT THE DEFINITION OF CENTERS IN THE UNIVERSE EVEN IF NOT EXPORTING # TODO: AUTOTUNE THE CURVE TO FIND THE RIGHT STEP progress(0) number_of_frames = len(u.trajectory) for frame in u.trajectory: # loops tru each frame f = frame.frame # positions a dummy atoms at cluster center of mass for dummy, atms in bead_data: dummy.position = AtomGroup(atms).center_of_mass() progress(f / number_of_frames) progress(1) print() for dummy, atms in bead_data: dummy.mass = AtomGroup(atms).masses.sum() # purge existing reminant bonds u.delete_bonds(u.bonds) u.delete_angles(u.angles) u.delete_dihedrals(u.dihedrals) print(f'Building new coarse-grained universe...') coordinates = AnalysisFromFunction(lambda ag: ag.positions.copy(), cg_beads).run().results new_u = mda.Merge(cg_beads) new_u.load_new(coordinates, format=MemoryReader) new_u.add_TopologyAttr('bonds', new_bonds) new_u.add_TopologyAttr('angles', guess_angles(new_u.bonds)) new_u.add_TopologyAttr('dihedrals', guess_dihedrals(new_u.angles)) print( f'Built universe with {len(new_u.atoms)} coarse-grained beads, {len(new_u.bonds)} bonds, {len(new_u.angles)} angles, and {len(new_u.dihedrals)} dihedrals' ) if export: print('Writing Output Files...') out_file = f'outputs/CoarseGrain/{simulation_name}_CG.pdb' with open(out_file, 'w+') as _: new_u.atoms.write(out_file, bonds='all') print(f'Topology written to {simulation_name}_CG.pdb!') is_multiframe = number_of_frames > 1 with mda.Writer(f'outputs/CoarseGrain/{simulation_name}_CG.dcd', new_u.atoms.n_atoms, multiframe=is_multiframe, bonds='all') as w: for frame in new_u.trajectory[1:]: # loops tru each frame w.write(new_u.atoms) print('Generated All Coarse Grained Molecules!') print(f'Trajectory written to {simulation_name}_CG.dcd!') # for dummy, atms in bead_data: # dummy.type = '' print(f'Reduced {len(u.atoms)} atoms to {len(new_u.atoms)} beads!') print('Coarse Graining Task complete!') return new_u