def show_struc(click_data, stage):
if stage == len(GPARAMS.Esoinn_setting.Model.learn_history_edge):
speckdata = xyz_reader.read_xyz(datapath_or_datastring=representstruc[
click_data['points'][0]['pointIndex']],
is_datafile=False)
else:
speckdata = xyz_reader.read_xyz(
datapath_or_datastring=representstruc[0], is_datafile=False)
return speckdata
def update_molecule(molecule_fname, upload_contents):
data = {}
if upload_contents is not None and molecule_fname is None:
try:
content_type, content_string = upload_contents.split(',')
data = base64.b64decode(content_string).decode('UTF-8')
except AttributeError:
pass
data = read_xyz(data, is_datafile=False)
elif molecule_fname is not None:
data = read_xyz(molecule_fname)
return data
def tab_content(active_tab, memory):
if 'point' not in memory:
raise PreventUpdate
mol_name = DATA.iloc[memory['point']].xyz_file_name
path = structures_dir + '/' + mol_name
if active_tab == 'tab-speck':
mol = xyz_reader.read_xyz(datapath_or_datastring=path,
is_datafile=True)
mol_plot = dashbio.Speck(
id='my-speck',
data=mol,
view={
'zoom': 0.06,
'resolution': 450,
# 'ao': 0.1,
'outline': 0.001,
'atomScale': 0.15,
'relativeAtomScale': 0.33,
'bonds': True
},
presetView='stickball',
)
else:
mol = aio.read(path)
model_data = xyz_to_json(mol)
mol = xyz_reader.read_xyz(datapath_or_datastring=path,
is_datafile=True)
mol_plot = html.Div([
dashbio.Molecule2dViewer(
id='my-dashbio-molecule2d',
modelData=model_data,
width=450,
height=400,
),
# html.Hr(style={'padding-top': '0pt'}),
html.Div(id='molecule2d-output')
])
return mol_plot
def display_click_data(clickData):
input_in = json.dumps(clickData, indent=2)
#print(elements)
curveNumber = json.loads(input_in)['points'][0]['curveNumber']
Index = json.loads(input_in)['points'][0]['pointIndex'] + 1
print(curveNumber)
if curveNumber == 3:
data_in = f'./test_out/{Index}.xyz'
molecule = xyz_reader.read_xyz(datapath_or_datastring=data_in,
is_datafile=True)
return speck_component(Index, molecule)
#print(f'notebooks/test_out/{Index}.xyz')
elif curveNumber == 2:
pass
else:
pass
return json.dumps(clickData, indent=2)
def update_output(n_clicks,value):
smile=str(value)
slist=[]
slist.append(smile)
##mol = [Chem.MolFromSmiles(s) for s in slist]
##img = Draw.MolsToGridImage(mol, molsPerRow=1,subImgSize=(250, 200),)
## plogp = [env.penalized_logp(m) for m in mol]
#run model optimization
property_name='plogp'
debug=True
src,new_smiles=constrain_optimization_smiles_input(smile,model, property_model,device, data_name, property_name,
atomic_num_list, debug, sim_cutoff=0.0)
mol_optm = Molecule.from_file("dash_output/constr_opt_input.sdf")
mol_optm.write_to_file("dash_output/constr_opt_input.xyz")
data=xyz_reader.read_xyz('dash_output/constr_opt_input.xyz')
return data,src,"Optimized SMILES: {}".format(new_smiles)
import dash_html_components as html
import dash_core_components as dcc
from dash_bio_utils import xyz_reader
external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']
app = dash.Dash(__name__, external_stylesheets=external_stylesheets)
data = urlreq.urlopen(
'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/' +
'speck_methane.xyz').read()
if PY3:
data = data.decode('utf-8')
data = xyz_reader.read_xyz(data_string=data)
app.layout = html.Div([
dcc.Dropdown(id='speck-preset-views',
options=[{
'label': 'Default',
'value': 'default'
}, {
'label': 'Ball and stick',
'value': 'stickball'
}],
value='default'),
dashbio.Speck(id='my-speck', data=data),
])
Refset.Load()
try:
representid = GPARAMS.Esoinn_setting.Model.represent_strucid
except:
signallist = np.array([i.EGCM for i in Refset.mols])
signallist = (signallist - GPARAMS.Esoinn_setting.scalemin) / (
GPARAMS.Esoinn_setting.scalemax - GPARAMS.Esoinn_setting.scalemin)
signallist[~np.isfinite(signallist)] = 0
representid = GPARAMS.Esoinn_setting.Model.select_represent_struc(
signallist)
GPARAMS.Esoinn_setting.Model.Save()
representstruc = []
for i in range(len(representid)):
xyzstr = Refset.mols[representid[i]].transstr()
representstruc.append(xyzstr)
speckdata = xyz_reader.read_xyz(datapath_or_datastring=representstruc[0],
is_datafile=False)
moddevlist = [[[] for j in range(GPARAMS.Train_setting.Trainstage)]
for i in range(len(GPARAMS.MD_setting))]
templist = [[[] for j in range(GPARAMS.Train_setting.Trainstage)]
for i in range(len(GPARAMS.MD_setting))]
timelist = [[[] for j in range(GPARAMS.Train_setting.Trainstage)]
for i in range(len(GPARAMS.MD_setting))]
graphlist = []
modeldev = [[] for j in range(GPARAMS.Train_setting.Trainstage)]
for i in range(len(GPARAMS.MD_setting)):
timemask = 0
moddevdatlist = []
tempdatlist = []
for j in range(GPARAMS.Train_setting.Trainstage):
MDout = '%s/%s_%d' % (GPARAMS.MD_setting[i].Name,
GPARAMS.MD_setting[i].Name, j)
import json
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.keys import Keys
import dash
import dash_bio
import dash_html_components as html
from dash_bio_utils import xyz_reader
from common_features import simple_app_layout, simple_app_callback
_data = None
with open('tests/dashbio_demos/sample_data/speck_methane.xyz', 'r') as f:
_data = xyz_reader.read_xyz(datapath_or_datastring=f.read(),
is_datafile=False)
_COMPONENT_ID = 'test-speck'
def test_dbsp001_rotate(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(dash_bio.Speck(id=_COMPONENT_ID, data=_data))
dash_duo.start_server(app)
dash_duo.wait_for_element('#' + _COMPONENT_ID)
speck = dash_duo.find_element('#' + _COMPONENT_ID + ' canvas')
ac = ActionChains(dash_duo.driver)
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/dash-molecule-3d-viewer/data/1bna.pdb'))
with open('mol3d_styles_data.json', 'w+') as f:
f.write(
styles_parser.create_style(
'../dashbio_demos/dash-molecule-3d-viewer/data/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/dash-sequence-viewer/data/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/dash-speck/data/methane.xyz')))
from dash.dependencies import Input, Output
import dash_html_components as html
import dash_bio as dashbio
import urllib.request as urlreq
import base64
import dash_bio_utils.xyz_reader as xyz_reader
data = urlreq.urlopen("https://raw.githubusercontent.com/plotly/dash-bio/master/tests/dashbio_demos/dash-speck/data/methane.xyz").read().decode("utf-8")
data = xyz_reader.read_xyz(data, is_datafile=False)
component = html.Div(dashbio.Speck(
data=data,
id='speck',
presetView='default',
scrollZoom=True
), style={'transform': 'scale(0.5)',
'margin-top': '-190px'})
component_image = html.Div(html.Img(
src='data:image/png;base64,{}'.format(
base64.b64encode(
open(
'./images/pic_speck.png', 'rb'
).read()
).decode()
),
style={'width': '768px',
'margin-left': '0px',
'float': 'left'}
), style={'transform': 'scale(0.5)'})
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'
)))