def use_upload(
contents,
demostr,
mol_style,
color_style,
mt,
custom_colors
):
if demostr is not None:
copy2(demostr, './str.pdb')
fname = './str.pdb'
elif contents is not None and demostr is None:
try:
content_type, content_string = str(contents).split(',')
decoded_contents = base64.b64decode(
content_string).decode("UTF-8")
f = tempfile.NamedTemporaryFile(
suffix=".pdb", delete=False, mode='w+')
f.write(decoded_contents)
fname = f.name
f.close()
except AttributeError:
pass
else:
return 'demostr and contents are none'
# Create the model data from the decoded contents
modata = parser.create_data(fname)
fmodel = files_data_style(modata)
with open(fmodel) as fm:
mdata = json.load(fm)
# Create the cartoon style from the decoded contents
datstyle = sparser.create_style(fname, mol_style, color_style, **custom_colors)
fstyle = files_data_style(datstyle)
with open(fstyle) as sf:
data_style = json.load(sf)
# Delete all the temporary files that were created
for x in [fname, fmodel, fstyle]:
if os.path.isfile(x):
os.unlink(x)
else:
pass
# Return the new molecule visualization container
return dash_bio.Molecule3dViewer(
id='mol-3d',
selectionType='atom',
modelData=mdata,
styles=data_style,
selectedAtomIds=[],
backgroundOpacity='0',
atomLabelsShown=False,
)
import dash
import dash_bio
import dash_html_components as html
from dash_bio_utils import pdb_parser as parser, styles_parser as sparser
from common_features import simple_app_layout, simple_app_callback
_model_data = None
_styles_data = None
_model_data = json.loads(
parser.create_data(
'tests/dashbio_demos/dash-molecule-3d-viewer/data/1bna.pdb'))
_styles_data = json.loads(
sparser.create_style(
'tests/dashbio_demos/dash-molecule-3d-viewer/data/1bna.pdb', 'cartoon',
'atom'))
_COMPONENT_ID = 'test-mol3d'
def test_dbm3001_selection_type(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(
dash_bio.Molecule3dViewer(id=_COMPONENT_ID,
modelData=_model_data,
styles=_styles_data)))
fdat.write(content)
dataFile = fdat.name
fdat.close()
return dataFile
fname = 'data/Figure-To-Manipulate.pdb'
# Create the model data from the decoded contents
modata = parser.create_data(fname)
fmodel = files_data_style(modata)
with open(fmodel) as fm:
mdata = json.load(fm)
# Create the cartoon style from the decoded contents
datstyle = sparser.create_style(fname, 'cartoon', 'residue', **{})
fstyle = files_data_style(datstyle)
with open(fstyle) as sf:
data_style = json.load(sf)
pdb = dbc.Card(
[
html.H4("Potential allosteric site of IP-10 (CXCL10) oligomer (PDB entry = 1O80).", className="card-title"),
#html.H6("a subtitle about pdb file", className="card-subtitle"),
html.P(
"Our initial network analysis revealed that IP-10/CXCL10 might be a beneficial protein target for reducing cytokine storm in COVID-19 patients if inhibited by a small molecule for example. We have identified a potentially druggable allosteric site for follow-up in silico screening against compound databases (e.g. BindingDB - https://www.bindingdb.org/bind/index.jsp). Please feel free to manipulate the structure to gain more insight. ",
className="card-text",
),
html.Div(
[
from selenium.webdriver.common.action_chains import ActionChains
import dash
import dash_bio
import dash_html_components as html
from dash_bio_utils import pdb_parser as parser, styles_parser as sparser
from common_features import simple_app_layout, simple_app_callback
_model_data = None
_styles_data = None
_model_data = json.loads(
parser.create_data('tests/dashbio_demos/sample_data/molecule3d_1bna.pdb'))
_styles_data = json.loads(
sparser.create_style('tests/dashbio_demos/sample_data/molecule3d_1bna.pdb',
'cartoon', 'atom'))
_COMPONENT_ID = 'test-mol3d'
def test_dbm3001_selection_type(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(
dash_bio.Molecule3dViewer(id=_COMPONENT_ID,
modelData=_model_data,
styles=_styles_data)))
simple_app_callback(app,
import json
from dash_bio_utils import pdb_parser, protein_reader, \
styles_parser, xyz_reader
with open('mol3d_model_data.json', 'w+') as f:
f.write(pdb_parser.create_data(
'../dashbio_demos/sample_data/molecule3d_1bna.pdb'
))
with open('mol3d_styles_data.json', 'w+') as f:
f.write(styles_parser.create_style(
'../dashbio_demos/sample_data/molecule3d_1bna.pdb',
'cartoon',
'atom'
))
with open('sequence_viewer_data.json', 'w+') as f:
f.write(json.dumps(protein_reader.read_fasta(
datapath_or_datastring='../dashbio_demos/sample_data/sequence_viewer_P01308.fasta.txt'
)[0]))
with open('speck_data.json', 'w+') as f:
f.write(json.dumps(xyz_reader.read_xyz(
datapath_or_datastring='../dashbio_demos/sample_data/speck_methane.xyz'
)))
