def test_sorting(self):
# Generate a few structures
struct_n = 5
aselist = []
for n in range(struct_n):
aselist.append(Atoms())
testcoll = AtomsCollection(aselist)
testcoll.set_array('sorter', np.array(range(struct_n, 0, -1)))
testcoll.set_array('sorted', np.array(range(1, struct_n + 1)))
testcoll = testcoll.sorted_byarray('sorter')
self.assertTrue(
np.all(testcoll.get_array('sorted') == range(struct_n, 0, -1)))
print aColl.all.info, '\n\n'
# Collections can also be sliced like Numpy arrays for convenience
aColl02 = aColl[0:2]
aColl25 = aColl[2:5]
# Then join them together
aColl05 = aColl02 + aColl25
print "---- Collection slice lengths ---- \n"
print "aColl02 = {0}\taColl25 = {1}\taColl05 = {2}\n\n".format(
aColl02.length, aColl25.length, aColl05.length)
# Collections can also store "arrays" of data, similarly to Atoms objects in ase
# These arrays' elements are tied each to one structure, and can be used to sort them
arr = range(10, 0,
-1) # Let's use this array to reverse the order of a collection
aColl.set_array('reversed_range', arr)
aCollSorted = aColl.sorted_byarray('reversed_range')
print "---- Getting an array from a collection ---- \n"
print "Unsorted: ", aColl.get_array('reversed_range'), "\n"
print "Sorted: ", aCollSorted.get_array('reversed_range'), "\n\n"
# And to make sure
print "---- First vs. last elements ---- \n"
print aColl.structures[0].get_positions(), "\n"
print aCollSorted.structures[-1].get_positions()
# Then create an AtomsCollection
if not args.pkl:
aC = AtomsCollection(args.input_files,
info={'name': args.seedname},
cell_reduce=True,
progress=True)
else:
aC = AtomsCollection([])
for f in args.input_files:
aC += AtomsCollection.load(f)
# Take only n lowest energies if required
if (args.n is not None):
# Sort by energy
CalcEnergy.get(aC, store_array=True)
aC = aC.sorted_byarray('calc_energy')[:args.n]
#discard_Z = args.Z is not None
# Calculate genomes
nrange = (0, 1) if args.gene_clamp else (None, None)
ndist = 1.0 if args.gene_clamp else None
pC = PhylogenCluster(aC, genes=[], norm_range=nrange, norm_dist=ndist)
pC.set_genes(gene_list, load_arrays=True)
if args.savepkl is not None:
# Save the structure
pC.save_collection(os.path.join(args.savepkl, args.seedname + '.pkl'))
# And now for the output
if args.genomes:
def __main__():
# So, first parse the command line arguments
parser = ap.ArgumentParser()
# Main argument
parser.add_argument('seedname',
type=str,
default=None,
help="Seedname of the job")
parser.add_argument('input_files',
type=str,
nargs='+',
default=None,
help="Files to load and analyse")
# Optional arguments
# Boolean args
parser.add_argument('-pkl',
action='store_true',
default=False,
help="Input is one or more AtomsCollections"
" in PICKLE format")
parser.add_argument('-tree',
action='store_true',
default=False,
help="Create JSON tree file")
parser.add_argument('-distmat',
action='store_true',
default=False,
help="Save a distance matrix file")
parser.add_argument('-forcemat',
action='store_true',
default=False,
help="Create JSON distance matrix file for force "
"layout")
parser.add_argument('-genomes',
action='store_true',
default=False,
help="Save genomes text file")
parser.add_argument('-gene_png',
action='store_true',
default=False,
help="Save genomes png file")
parser.add_argument('-gene_clamp',
action='store_true',
default=True,
help="Clamp genes between 0 and 1")
# Value args
parser.add_argument('-n',
type=int,
default=None,
help="Number of lowest energy structures to keep")
# parser.add_argument('-Z', type=int, default=None,
# help="Expected numbers of molecules in cell (discard structures "
# "that don't agree)")
parser.add_argument('-corrmat_minforce',
type=float,
default=0.01,
help="Correlation matrix minimum force")
parser.add_argument('-corrmat_maxforce',
type=float,
default=1.0,
help="Correlation matrix maximum force")
parser.add_argument('-savepkl',
type=str,
default=None,
help="Directory to save collection as pickle file")
args = parser.parse_args()
# First, parse the gene list
gene_list = load_genefile(args.seedname + '.gene')
# Then create an AtomsCollection
if not args.pkl:
aC = AtomsCollection(args.input_files,
info={'name': args.seedname},
cell_reduce=True,
progress=True)
else:
aC = AtomsCollection([])
for f in args.input_files:
aC += AtomsCollection.load(f)
# Take only n lowest energies if required
if (args.n is not None):
# Sort by energy
CalcEnergy.get(aC, store_array=True)
aC = aC.sorted_byarray('calc_energy')[:args.n]
#discard_Z = args.Z is not None
# Calculate genomes
nrange = (0, 1) if args.gene_clamp else (None, None)
ndist = 1.0 if args.gene_clamp else None
pC = PhylogenCluster(aC, genes=[], norm_range=nrange, norm_dist=ndist)
pC.set_genes(gene_list, load_arrays=True)
if args.savepkl is not None:
# Save the structure
pC.save_collection(os.path.join(args.savepkl, args.seedname + '.pkl'))
# And now for the output
if args.genomes:
with open(args.seedname + "_genomes.dat", 'w') as ofile:
genvec, legend = pC.get_genome_vectors()
# Create a header
header = ('Structure\t'
'{0}\n').format('\t'.join([
'\t'.join([
'{0}_{1}'.format(l[0], i + 1)
for i in range(l[1])
]) for l in legend
]))
ofile.write(header)
try:
for i, gen in enumerate(genvec):
ofile.write(aC.structures[i].info['name'] + '\t' +
' '.join([str(x) for x in gen]) + '\n')
except KeyError:
# Someone has no name!
raise RuntimeError('Not all structures have a name, '
'can\'t print out genomes as table')
if args.gene_png and _has_matplotlib:
with open(args.seedname + "_genomes.png", 'w') as ofile:
genomes2png(aC, pC, ofile)
if args.tree:
tree = pC.get_hier_tree()
with open(args.seedname + "_tree.json", 'w') as ofile:
json.dump(tree2json(aC, pC), ofile)
