def calculate_ss(msaName, chain):
# msaName = "1FM0_E_1FM0_D"
array = pdb2biotite(msaName)
array = array[array.hetero == False] # filters out hetatoms
# Estimate secondary structure
if len(chain) > 1:
sse = []
for ch in chain:
sse.append(struc.annotate_sse(array, chain_id=ch))
return np.append(sse[0], sse[1])
else:
return struc.annotate_sse(array, chain_id=chain)
def test_sse():
array = strucio.load_structure(join(data_dir("structure"), "3o5r.mmtf"))
sse = struc.annotate_sse(array, "A")
sse_str = "".join(sse.tolist())
assert sse_str == ("caaaaaacccccccccccccbbbbbccccccbbbbccccccccccccccc"
"ccccccccccccbbbbbbcccccccaaaaaaaaaccccccbbbbbccccc"
"ccccccccccccbbbbbbbccccccccc")
def psea_sec(file):
array = mmtf.get_structure(file, model=1)
tk_dimer = array[struc.filter_amino_acids(array)]
tk_mono = tk_dimer[tk_dimer.chain_id == "A"]
sse = struc.annotate_sse(array, chain_id="A")
return sse
def pdb2Gdata(dirName, fileName, saveDir=False):
# print(os.path.join(dirName, fileName))
array = strucio.load_structure(
os.path.join(dirName, fileName),
# extra_fields=['atom_id', 'b_factor', 'occupancy', 'charge'],
extra_fields=['b_factor', 'occupancy'],
model=1)
# if type(array) == biotite.structure.AtomArrayStack:
# array = array[0]
# ca = array[array.atom_name == "CA"]
# cell_list = struc.CellList(ca, cell_size=self.threshold)
chain_id = []
for chain in array.chain_id:
if chain not in chain_id:
chain_id.append(chain)
sseDict = dict([(chain, struc.annotate_sse(array, chain_id=chain))
for chain in chain_id])
sseMaskDict = {}
for key, value in sseDict.items():
mask = array[(array.chain_id == key)
& (array.atom_name == 'CA')].res_id
tmp = mask.shape[0] - value.shape[0]
if tmp > 0:
sseDict[key] = np.append(value, ['Null'] * tmp)
sseMaskDict[key] = {}
for maskId, sseId in zip(mask, sseDict[key]):
sseMaskDict[key][maskId] = sseId
cell_list = struc.CellList(array, cell_size=cfg.threshold)
adj_matrix = cell_list.create_adjacency_matrix(cfg.threshold)
# (adj_matrix[adj_matrix == True].shape[0] - 5385) / 2
edge_index = [[], []]
nodeFeatures = []
arrayShp = array.shape[0]
for i in range(arrayShp - 1):
for j in range(i + 1, arrayShp):
if adj_matrix[i][j]:
edge_index[0].append(i)
edge_index[1].append(j)
nodeFeatures.append(
list(array.coord[i]) +
[atomsDict.get(array.atom_name[i], atomsDict['Null'])] +
[elementsDict.get(array.element[i], elementsDict['Null'])] +
[array.res_id[i]] +
[residualesDict.get(array.res_name[i], residualesDict['Null'])] +
[float(array.hetero[i])] + [array.occupancy[i]] +
[array.b_factor[i]] + [
ssesTypeDict.get(
sseMaskDict[array.chain_id[i]].get(
array.res_id[i], 'Null'), ssesTypeDict['Null'])
])
nodeFeatures.append(
list(array.coord[arrayShp - 1]) +
[atomsDict.get(array.atom_name[arrayShp - 1], atomsDict['Null'])] +
[elementsDict.get(array.element[arrayShp - 1], elementsDict['Null'])] +
[array.res_id[arrayShp - 1]] + [
residualesDict.get(array.res_name[arrayShp -
1], residualesDict['Null'])
] + [float(array.hetero[arrayShp - 1])] +
[array.occupancy[arrayShp - 1]] + [array.b_factor[arrayShp - 1]] + [
ssesTypeDict.get(
sseMaskDict[array.chain_id[arrayShp - 1]].get(
array.res_id[arrayShp - 1], 'Null'), ssesTypeDict['Null'])
])
nodeFeaturesT = torch.tensor(nodeFeatures, dtype=torch.float)
edge_indexT = torch.tensor(edge_index, dtype=torch.long)
data = Data(x=nodeFeaturesT, edge_index=edge_indexT)
if saveDir:
torch.save(data, os.path.join(saveDir, fileName))
return data
feature_plotters=[HelixPlotter(), SheetPlotter()])
fig.tight_layout()
# Visualize seconday structure array
# Sine the residues may not start at 1,
# provide the actual first residue ID
visualize_secondary_structure(sse, tk_mono.res_id[0])
########################################################################
# Almost the same result can be achieved, when we calculate the
# secondary structure ourselves using the DSSP software,
# as the content in ``'secStructList'`` is also calculated by the RCSB.
sse = dssp.DsspApp.annotate_sse(tk_mono)
sse = np.array([dssp_to_abc[e] for e in sse], dtype="U1")
visualize_secondary_structure(sse, tk_mono.res_id[0])
# sphinx_gallery_thumbnail_number = 4
########################################################################
# The one and only difference is that the second helix is slightly
# shorter.
# This is probably caused by different versions of DSSP.
#
# Last but not least we calculate the secondary structure using
# *Biotite*'s built-in method, based on the P-SEA algorithm.
sse = struc.annotate_sse(array, chain_id="A")
visualize_secondary_structure(sse, tk_mono.res_id[0])
plt.show()
