code stringlengths 3 6.57k |
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self.model.predict(x,batch_size) |
train(self,model) |
model.load_weights("cifar10vgg.h5") |
cifar10.load_data() |
x_train.astype('float32') |
x_test.astype('float32') |
self.normalize(x_train, x_test) |
keras.utils.to_categorical(y_train, self.num_classes) |
keras.utils.to_categorical(y_test, self.num_classes) |
lr_scheduler(epoch) |
keras.callbacks.LearningRateScheduler(lr_scheduler) |
range (degrees, 0 to 180) |
horizontally (fraction of total width) |
vertically (fraction of total height) |
datagen.fit(x_train) |
optimizers.SGD(lr=learning_rate, decay=lr_decay, momentum=0.9, nesterov=True) |
model.compile(loss='categorical_crossentropy', optimizer=sgd,metrics=['accuracy']) |
model.save_weights('cifar10vgg.h5') |
cifar10.load_data() |
x_train.astype('float32') |
x_test.astype('float32') |
keras.utils.to_categorical(y_train, 10) |
keras.utils.to_categorical(y_test, 10) |
cifar10vgg() |
model.predict(x_test) |
np.argmax(predicted_x,1) |
np.argmax(y_test,1) |
sum(residuals) |
len(residuals) |
print("the validation 0/1 loss is: ",loss) |
get_EF_atom_indices(atoms) |
NeighborList(natural_cutoffs(atoms) |
nl.update(atoms) |
np.concatenate((nl.get_neighbors(index_Al[0]) |
nl.get_neighbors(index_Al[1]) |
np.concatenate((nl.get_neighbors(index_EF_TM[0]) |
nl.get_neighbors(index_EF_TM[1]) |
list(TM_neigh_list) |
count(x) |
get_capped_cluster(atoms, folder_path, file_name, save_traj, EF_O_index) |
capping (remove all caps for now, does not need this cluster to be physical) |
cluster (the later two output index lists share the ordering) |
ExtraFrameworkAnalyzer(atoms) |
EFMaker.get_extraframework_cluster(EF_O_index) |
get_EF_atom_indices(cluster) |
cluster.get_positions() |
EFMaker.recentering_atoms(cluster, centering_pos) |
Zeolite(cluster) |
cap_atoms() |
proteindatabank.write_proteindatabank(folder_path + '/%s.pdb' % file_name, recentered_cluster) |
write(folder_path + '/%s.traj' % file_name, recentered_cluster) |
EFMaker.get_extraframework_cluster(EF_O_index) |
label_pdb(folder_path, file_name, del_unlabeled_pdb) |
file. (required step for openMM) |
open(folder_path + '/%s.pdb' % file_name, 'r') |
open(folder_path + '/%s_labeled.pdb' % file_name, 'w') |
filein.readlines() |
line.startswith('ATOM') |
line.startswith('HETATM') |
strip() |
name_list.append(name) |
str(name_list.count(name) |
name.rjust(4) |
line.replace(line[12:16], name, 1) |
fileout.writelines(line) |
filein.close() |
fileout.close() |
os.remove(folder_path + '/%s.pdb' % file_name) |
get_bonds(cluster, mult=1, excluded_index=None, excluded_pair=None) |
user (excluded_pair) |
indices (excluded_index) |
NeighborList(natural_cutoffs(cluster, mult=mult) |
nl.update(cluster) |
enumerate(Analysis(cluster, nl=nl) |
bond_list.append([count, index]) |
all(single_index not in bond for single_index in excluded_index) |
all(tuple(bond) |
list(permutations(pair) |
shortened_list.append(bond) |
get_angles(cluster, mult=1, excluded_index=None, excluded_pair=None) |
NeighborList(natural_cutoffs(cluster, mult=mult) |
nl.update(cluster) |
enumerate(Analysis(cluster, nl=nl) |
all(list(val) |
list(permutations([count, index[0], index[1]]) |
angle_list.append([count, index[0], index[1]]) |
all(single_index not in angle for single_index in excluded_index) |
all(list(value) |
list(permutations(angle, 2) |
shortened_list.append(angle) |
write_xml(atoms, bonds, save_as) |
etree.Element('ForceField') |
etree.SubElement(root, "AtomTypes") |
join(filter(lambda x: not x.isdigit() |
str(atomic_mass) |
str(atomic_mass) |
etree.SubElement(xml_section, 'Type', **properties) |
etree.SubElement(root, 'Residues') |
etree.SubElement(xml_section, 'Residue', name='MOL') |
etree.SubElement(xml_residue, 'Atom', name=atom.name, type=atom.name) |
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