def parseEMDStream(stream, **kwargs): """ Returns an :class:`.AtomGroup` containing EMD data parsed from a stream of EMD file. :arg stream: Any object with the method ``readlines`` (e.g. :class:`file`, buffer, stdin)""" cutoff = kwargs.get('cutoff', None) if cutoff is not None: cutoff = float(cutoff) n_nodes = kwargs.get('n_nodes', 0) num_iter = int(kwargs.get('num_iter', 20)) map = kwargs.get('map', False) make_nodes = kwargs.get('make_nodes', False) if n_nodes > 0: make_nodes = True n_nodes = int(n_nodes) if map is False and make_nodes is False: LOGGER.warn( 'At least one of map and make_nodes should be True. ' 'Setting map to False was an intentional change from the default ' 'behaviour so make_nodes has been set to True with n_nodes=1000.') make_nodes = True n_nodes = 1000 title_suffix = kwargs.get('title_suffix', '') atomgroup = AtomGroup(str(kwargs.get('title', 'Unknown')) + title_suffix) atomgroup._n_atoms = n_nodes if make_nodes: LOGGER.info( 'Building coordinates from electron density map. This may take a while.' ) LOGGER.timeit() if map: emd, atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \ num_iter=num_iter, map=map, make_nodes=make_nodes) else: atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \ num_iter=num_iter, map=map, make_nodes=make_nodes) LOGGER.report('{0} pseudoatoms were fitted in %.2fs.'.format( atomgroup.numAtoms(), atomgroup.numCoordsets())) else: emd = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \ num_iter=num_iter, map=map, make_nodes=make_nodes) if make_nodes: if map: return emd, atomgroup else: return atomgroup else: return emd
def parseEMDStream(stream, **kwargs): """ Returns an :class:`.AtomGroup` containing EMD data parsed from a stream of EMD file. :arg stream: Any object with the method ``readlines`` (e.g. :class:`file`, buffer, stdin)""" cutoff = kwargs.get('cutoff', None) if cutoff is not None: cutoff = float(cutoff) n_nodes = int(kwargs.get('n_nodes', 1000)) num_iter = int(kwargs.get('num_iter', 20)) map = kwargs.get('map',True) make_nodes = kwargs.get('make_nodes',False) if map is False and make_nodes is False: LOGGER.warn('At least one of map and make_nodes should be True. ' 'Setting map to False was an intentional change from the default ' 'behaviour so make_nodes has been set to True.') make_nodes = True title_suffix = kwargs.get('title_suffix','') atomgroup = AtomGroup(str(kwargs.get('title', 'Unknown')) + title_suffix) atomgroup._n_atoms = n_nodes if make_nodes: LOGGER.info('Building coordinates from electron density map. This may take a while.') LOGGER.timeit() if map: emd, atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \ num_iter=num_iter, map=map, make_nodes=make_nodes) else: atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \ num_iter=num_iter, map=map, make_nodes=make_nodes) LOGGER.report('{0} atoms and {1} coordinate sets were ' 'parsed in %.2fs.'.format(atomgroup.numAtoms(), atomgroup.numCoordsets())) else: emd = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \ num_iter=num_iter, map=map, make_nodes=make_nodes) if make_nodes: if map: return emd, atomgroup else: return atomgroup else: return emd
def parseEMDStream(stream, **kwargs): """Parse lines of data stream from an EMD/MRC2014 file and optionally return an :class:`.AtomGroup` containing TRN nodes based on it. :arg stream: Any object with the method ``readlines`` (e.g. :class:`file`, buffer, stdin) """ cutoff = kwargs.get('cutoff', None) min_cutoff = kwargs.get('min_cutoff', cutoff) if min_cutoff is not None: if isinstance(min_cutoff, Number): min_cutoff = float(min_cutoff) else: raise TypeError('min_cutoff should be a number or None') max_cutoff = kwargs.get('max_cutoff', None) if max_cutoff is not None: if isinstance(max_cutoff, Number): max_cutoff = float(max_cutoff) else: raise TypeError('max_cutoff should be a number or None') n_nodes = kwargs.get('n_nodes', 0) num_iter = int(kwargs.get('num_iter', 20)) map = kwargs.get('map', False) if not isinstance(n_nodes, int): raise TypeError('n_nodes should be an integer') if n_nodes > 0: make_nodes = True else: make_nodes = False map = True LOGGER.info('As n_nodes is less than or equal to 0, no nodes will be' ' made and the raw map will be returned') emd = EMDMAP(stream, min_cutoff, max_cutoff) if make_nodes: title_suffix = kwargs.get('title_suffix', '') atomgroup = AtomGroup( str(kwargs.get('title', 'Unknown')) + title_suffix) atomgroup._n_atoms = n_nodes coordinates = np.zeros((n_nodes, 3), dtype=float) atomnames = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['name'].dtype) resnames = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['resname'].dtype) resnums = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['resnum'].dtype) chainids = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['chain'].dtype) trn = TRNET(n_nodes=n_nodes) trn.inputMap(emd, sample='density') trn.run(tmax=num_iter) for i in range(n_nodes): coordinates[i, :] = trn.W[i, :] atomnames[i] = 'B' resnames[i] = 'CGB' resnums[i] = i + 1 chainids[i] = 'X' atomgroup.setCoords(coordinates) atomgroup.setNames(atomnames) atomgroup.setResnames(resnames) atomgroup.setResnums(resnums) atomgroup.setChids(chainids) if make_nodes: if map: return atomgroup, emd else: return atomgroup else: return emd