def download_pdb(
pdb_download_button_clicked, sequence_alignment_data, caretta_class
):
if pdb_download_button_clicked and sequence_alignment_data and caretta_class:
sequence_alignment = app_helper.decompress_object(
sequence_alignment_data, suite
)
if not sequence_alignment:
return ""
msa_class = app_helper.decompress_object(caretta_class, suite)
msa_class.write_files(
write_pdb=True,
write_fasta=False,
write_class=False,
write_features=False,
)
output_filename = f"{msa_class.output_folder}/superposed_pdbs.zip"
pdb_zip_file = ZipFile(output_filename, mode="w")
for pdb_file in (Path(msa_class.output_folder) / "superposed_pdbs").glob(
"*.pdb"
):
pdb_zip_file.write(
str(pdb_file), arcname=f"{pdb_file.stem}{pdb_file.suffix}"
)
return app_layout.get_download_string(output_filename)
else:
return ""
def display_feature(
display_feature_button_clicked,
feature_selection_dropdown_value,
feature_alignment_data,
):
if (display_feature_button_clicked and feature_selection_dropdown_value
and feature_alignment_data):
feature_alignment_dict = app_helper.decompress_object(
feature_alignment_data, suite)
chosen_feature_data = feature_alignment_dict[
feature_selection_dropdown_value]
feature_line_component = dcc.Graph(
figure=app_helper.line(chosen_feature_data),
id="feature-line-graph")
feature_heatmap_component = dcc.Graph(
figure=app_helper.heatmap(chosen_feature_data),
id="feature-heatmap-graph",
)
return feature_line_component, feature_heatmap_component
else:
return (
dcc.Graph(
figure=app_helper.empty_dict(),
id="feature-line-graph",
style={"display": "none"},
),
dcc.Graph(
figure=app_helper.empty_dict(),
id="feature-heatmap-graph",
style={"display": "none"},
),
)
def download_alignment(fasta_download_button_clicked,
sequence_alignment_data, caretta_class):
if fasta_download_button_clicked and sequence_alignment_data and caretta_class:
sequence_alignment = app_helper.decompress_object(
sequence_alignment_data, suite)
if not sequence_alignment:
return ""
msa_class = app_helper.decompress_object(caretta_class, suite)
msa_class.write_files(
write_pdb=False,
write_fasta=True,
write_class=False,
write_features=False,
write_matrix=False,
)
return app_layout.get_download_string(
str(Path(msa_class.output_folder) / "result.fasta"))
else:
return ""
def download_features(
export_feature_button_clicked,
export_all_features_button_clicked,
feature_selection_dropdown_value,
feature_alignment_data,
caretta_class,
):
output_string = ""
if feature_alignment_data and caretta_class:
feature_alignment_dict = app_helper.decompress_object(
feature_alignment_data, suite
)
msa_class = app_helper.decompress_object(caretta_class, suite)
protein_names = [s.name for s in msa_class.structures]
if (
export_feature_button_clicked and feature_selection_dropdown_value
) and not export_all_features_button_clicked:
output_filename = f"{msa_class.output_folder}/{'-'.join(feature_selection_dropdown_value.split())}.csv"
app_helper.write_feature_as_tsv(
feature_alignment_dict[feature_selection_dropdown_value],
protein_names,
output_filename,
)
output_string = app_layout.get_download_string(output_filename)
elif (
export_all_features_button_clicked and not export_feature_button_clicked
):
output_filename = f"{msa_class.output_folder}/features.zip"
features_zip_file = ZipFile(output_filename, mode="w")
for feature in feature_alignment_dict:
feature_file = (
f"{msa_class.output_folder}/{'-'.join(feature.split())}.csv"
)
app_helper.write_feature_as_tsv(
feature_alignment_dict[feature], protein_names, feature_file
)
features_zip_file.write(
str(feature_file), arcname=f"{'-'.join(feature.split())}.csv"
)
output_string = app_layout.get_download_string(output_filename)
return output_string, app_layout.get_export_feature_buttons()
def align_structures(
align_button,
user_input,
proteins_selection_dropdown,
gap_open_dropdown,
gap_extend_dropdown,
unique_id,
):
if align_button and user_input and proteins_selection_dropdown:
pdb_entries = [
app_helper.decompress_object(x, suite)
for x in proteins_selection_dropdown
]
if not gap_open_dropdown:
gap_open_dropdown = 1
if not gap_extend_dropdown:
gap_extend_dropdown = 0.01
pdb_files = []
for p in pdb_entries:
try:
pdb_files.append(p.get_pdb()[1])
except (OSError, AttributeError, pyparsing.ParseException):
continue
msa_class = multiple_alignment.StructureMultiple.from_pdb_files(
pdb_files,
multiple_alignment.DEFAULT_SUPERPOSITION_PARAMETERS,
output_folder=f"static/results_{app_helper.decompress_object(unique_id, suite)}",
)
if len(msa_class.structures) > 2:
pw_matrix = msa_class.make_pairwise_shape_matrix()
sequence_alignment = msa_class.align(
pw_matrix,
gap_open_penalty=gap_open_dropdown,
gap_extend_penalty=gap_extend_dropdown,
)
else:
sequence_alignment = msa_class.align(
pw_matrix=None,
gap_open_penalty=gap_open_dropdown,
gap_extend_penalty=gap_extend_dropdown,
)
msa_class.superpose()
fasta = app_helper.to_fasta_str(sequence_alignment)
dssp_dir = msa_class.output_folder / ".caretta_tmp"
if not dssp_dir.exists():
dssp_dir.mkdir()
features = msa_class.get_aligned_features(dssp_dir, num_threads=4, only_dssp=False)
caretta_class = app_helper.compress_object(msa_class, suite)
sequence_alignment_data = app_helper.compress_object(
sequence_alignment, suite
)
feature_alignment_data = app_helper.compress_object(features, suite)
sequence_alignment_component = dash_bio.AlignmentChart(
id="sequence-alignment-graph",
data=fasta,
showconsensus=False,
showconservation=False,
overview=None,
height=300,
colorscale="hydrophobicity",
)
structure_alignment_component = dcc.Graph(
figure=app_helper.scatter3D(
{s.name: s.coordinates for s in msa_class.structures}
),
id="scatter-plot",
)
feature_selection_dropdown = [{"label": x, "value": x} for x in features]
loading_indicator_output = ""
return (
caretta_class,
sequence_alignment_data,
feature_alignment_data,
sequence_alignment_component,
structure_alignment_component,
feature_selection_dropdown,
loading_indicator_output,
)
else:
return (
app_helper.empty_object(suite),
app_helper.empty_object(suite),
app_helper.empty_object(suite),
"",
"",
[{"label": "no alignment present", "value": "no alignment"}],
"",
)
def update_interactive_panels(
scatter_plot_clickdata,
feature_line_clickdata,
feature_line_graph,
scatter_plot,
structure_alignment_selected_residue,
feature_alignment_selected_residue,
sequence_alignment_data,
):
if feature_line_graph and scatter_plot:
changed = None
clickdata = None
if (
feature_line_clickdata
and app_helper.compress_object(
(
feature_line_clickdata["points"][0]["pointNumber"],
feature_line_clickdata["points"][0]["curveNumber"],
),
suite,
)
!= feature_alignment_selected_residue
):
clickdata = feature_line_clickdata
changed = "feature-panel"
elif (
scatter_plot_clickdata
and app_helper.compress_object(
(
scatter_plot_clickdata["points"][0]["pointNumber"],
scatter_plot_clickdata["points"][0]["curveNumber"],
),
suite,
)
!= structure_alignment_selected_residue
):
clickdata = scatter_plot_clickdata
changed = "structure-panel"
if changed is not None and clickdata is not None:
# Save new clicked index
aln_index = clickdata["points"][0]["pointNumber"]
protein_index = clickdata["points"][0]["curveNumber"]
if changed == "feature-panel":
feature_alignment_selected_residue = app_helper.compress_object(
(aln_index, protein_index), suite
)
elif changed == "structure-panel":
structure_alignment_selected_residue = app_helper.compress_object(
(aln_index, protein_index), suite
)
sequence_alignment = app_helper.decompress_object(
sequence_alignment_data, suite
)
number_of_structures = len(sequence_alignment)
try:
maxim, minim = (
np.max(feature_line_graph["data"][0]["y"]),
np.min(feature_line_graph["data"][0]["y"]),
)
except KeyError:
return (
structure_alignment_selected_residue,
feature_alignment_selected_residue,
feature_line_graph,
scatter_plot,
)
if len(feature_line_graph["data"]) > 2:
feature_line_graph["data"] = feature_line_graph["data"][:-1]
if len(scatter_plot["data"]) > number_of_structures:
scatter_plot["data"] = scatter_plot["data"][:-1]
if changed == "feature-panel":
aln_positions = app_helper.aln_index_to_protein(
aln_index, sequence_alignment
)
feature_line_graph["data"] += [
dict(
y=[minim, maxim],
x=[aln_index, aln_index],
type="scatter",
mode="lines",
name="selected residue",
)
]
to_add = []
for i in range(len(scatter_plot["data"])):
p = aln_positions[scatter_plot["data"][i]["name"]]
if p is not None:
x, y, z = (
scatter_plot["data"][i]["x"][p],
scatter_plot["data"][i]["y"][p],
scatter_plot["data"][i]["z"][p],
)
to_add.append((x, y, z))
else:
continue
scatter_plot["data"] += [
dict(
x=[x[0] for x in to_add],
y=[y[1] for y in to_add],
z=[z[2] for z in to_add],
type="scatter3d",
mode="markers",
name="selected residues",
)
]
elif changed == "structure-panel":
aligned_sequence = list(sequence_alignment.values())[protein_index]
aln_index = app_helper.protein_to_aln_index(
aln_index, aligned_sequence
)
x, y, z = (
clickdata["points"][0]["x"],
clickdata["points"][0]["y"],
clickdata["points"][0]["z"],
)
feature_line_graph["data"] += [
dict(
y=[minim, maxim],
x=[aln_index, aln_index],
type="scatter",
mode="lines",
name="selected_residue",
)
]
scatter_plot["data"] += [
dict(
y=[y],
x=[x],
z=[z],
type="scatter3d",
mode="markers",
name="selected residue",
)
]
return (
structure_alignment_selected_residue,
feature_alignment_selected_residue,
feature_line_graph,
scatter_plot,
)