def test_guess_bonds(): u = mda.Universe(two_water_gro) bonds = guessers.guess_bonds(u.atoms, u.atoms.positions, u.dimensions) assert_equal(bonds, ((0, 1), (0, 2), (3, 4), (3, 5)))
def test_guess_bonds_peptide(): u = mda.Universe(datafiles.PSF_NAMD, datafiles.PDB_NAMD) u.atoms.types = guessers.guess_types(u.atoms.names) bonds = bond_sort(guessers.guess_bonds(u.atoms, u.atoms.positions)) assert_equal(np.sort(u.bonds.indices, axis=0), np.sort(bonds, axis=0))
def test_guess_bonds_water(): u = mda.Universe(datafiles.two_water_gro) bonds = bond_sort( guessers.guess_bonds(u.atoms, u.atoms.positions, u.dimensions)) assert_equal(bonds, ((0, 1), (0, 2), (3, 4), (3, 5)))
def test_guess_bonds_Error(): u = make_Universe(trajectory=True) with pytest.raises(ValueError): guessers.guess_bonds(u.atoms[:4], u.atoms.positions[:5])
def time_guessbonds(self, num_atoms): """Benchmark for guessing bonds""" guessers.guess_bonds(self.ag, self.ag.positions, box=self.ag.dimensions, vdwradii=self.vdwradii)
def test_guess_bonds_adk(): u = mda.Universe(datafiles.PSF, datafiles.DCD) u.atoms.types = guessers.guess_types(u.atoms.names) bonds = guessers.guess_bonds(u.atoms, u.atoms.positions) assert_equal(np.sort(u.bonds.indices, axis=0), np.sort(bonds, axis=0))
def test_guess_bonds(): u = mda.Universe(two_water_gro) bonds = guessers.guess_bonds(u.atoms, u.atoms.positions, u.dimensions) assert_equal(bonds, ((0, 1), (0, 2), (3, 4), (3, 5)))
def create_full_trajectory(*, nCycles, path, filetype, output): ## some setup getFilenameTop, getFilenameTrj = helper.make_get_filename(FILETYPE=filetype, PATH=path) getReactiveAtomIndices = helper.make_get_reactive_atoms(FILETYPE=filetype, PATH=path) frameCounter = 0 write_frame = helper.make_get_write(filename=output) FILE = open(output, 'w') ## get initial data from cycle 0 universe = mda.Universe( getFilenameTop(0), getFilenameTrj(0) ) atomNames = universe.atoms.names resNames = universe.atoms.resnames resIDs = universe.atoms.resnums atomOrder = universe.atoms.ix dt = universe.trajectory.dt ## important: sort topology such that resnames are in alphabetical order (because rs@md does this, too...) # first: sort resnames alphabetically and adapt resIDs, atomNames sortedIndices = resNames.argsort(kind='stable') atomNames = atomNames[sortedIndices] resNames = resNames[sortedIndices] resIDs = resIDs[sortedIndices] atomOrderRearrangedAlphabetically = atomOrder[sortedIndices] # second: renumber residues counterResID = 1 newResIDs = resIDs.copy() for ix in range(len(resIDs)-1): newResIDs[ix] = counterResID if resIDs[ix] != resIDs[ix+1]: counterResID += 1 resIDs = newResIDs ## create initial coordination file where all residues have been unwrapped and save it to file #for res in universe.atoms.residues: # ag = res.atoms # transform = mdatrans.unwrap(ag) # universe.trajectory.add_transformations(transform) if not hasattr(universe, 'bonds'): guessed_bonds = mdaguess.guess_bonds(universe.atoms, universe.atoms.positions, universe.trajectory[0].dimensions) universe.add_TopologyAttr('bonds', guessed_bonds) transform = mdatrans.unwrap(universe.atoms) universe.trajectory.add_transformations(transform) outputinitial = 'initial' + '.' + output.split('.')[-1] initialFile = open(outputinitial, 'w') box = universe.trajectory[0].dimensions positions = universe.atoms.positions sortedPositions = positions[sortedIndices] write_frame(filestream=initialFile, title=f'rs@md t={0:9.2f} step= {0}', resnames=resNames, resnums=resIDs, names=atomNames, positions=sortedPositions, box=box) initialFile.close() print(f'-> initial frame has been written to {outputinitial}') ## write trajectory to file frame by frame for ts in universe.trajectory: positions = universe.atoms.positions box = ts.dimensions ## sort positions before writing them sortedPositions = positions[sortedIndices] write_frame(filestream=FILE, title=f'rs@md t={frameCounter*dt:9.2f} step= {frameCounter}', resnames=resNames, resnums=resIDs, names=atomNames, positions=sortedPositions, box=box) frameCounter += 1 ## loop through all files and record remaining data firstReactiveCycle = True for cycle in np.arange(1, nCycles+1): topfile = getFilenameTop(cycle) trjfile = getFilenameTrj(cycle) if os.path.isfile( trjfile ): ## get reaction infos reactantsIx, productsIx = getReactiveAtomIndices(cycle) ## attention if firstReactiveCycle: their might have been a change in atomOrder between cycles 0 -> cycle ## due to reordering molecules in alphabetical order ## need to account for that by translating reactantsIx accordingly if firstReactiveCycle: reactantsIx = np.array( [np.argwhere(atomOrderRearrangedAlphabetically == rix)[0,0] for rix in reactantsIx] ) firstReactiveCycle = False ## important: you need to go through all transitions in an ordered fashion with respect to the product indices ## (from small to larger iy) sortedIndices = productsIx.argsort() reactantsIx = reactantsIx[sortedIndices] productsIx = productsIx[sortedIndices] ## apply reactions to atomOrder ## i.e. change positions of reactants to products ## ... first: get entries at reactant positions and remove them from list reactantEntries = [ atomOrder[x] for x in reactantsIx ] for entry in reactantEntries: atomOrder = np.delete(atomOrder, np.argwhere(atomOrder==entry), axis=0) ## ... second: put entries back at new positions given by product positions for iy, entry in zip(productsIx, reactantEntries): atomOrder = np.insert(atomOrder, iy, entry, axis=0) ## get sorted indices for new atomOrder sortedIndices = atomOrder.argsort() ## import trajectory: .tpr, .gro/.xtc/... universe = mda.Universe(topfile, trjfile) ## write trajectory to file frame by frame for ts in universe.trajectory[1:]: positions = universe.atoms.positions box = ts.dimensions ## sort positions before writing them sortedPositions = positions[sortedIndices] write_frame(filestream=FILE, title=f'rs@md t={frameCounter*dt:9.2f} step= {frameCounter}', resnames=resNames, resnums=resIDs, names=atomNames, positions=sortedPositions, box=box) frameCounter += 1 else: continue FILE.close() print(f'-> a total of {frameCounter} frames have been written to {output}')
def test_guess_bonds_Error(): u = make_Universe(trajectory=True) with pytest.raises(ValueError): guessers.guess_bonds(u.atoms[:4], u.atoms.positions[:5])