def load(self):
# Add button to ribbon for settings
flare.main_window().ribbon["FlareNet"]["Settings"].add_button(
'Settings', self.settings)
self.checker_thread = threading.Thread(
target=self.viewer_changed_checker)
self.checker_thread.start()
def settings(self):
# Get flare main window
window = flare.main_window().widget()
# Open settings dialog
form = Form(flare=self, parent=window)
form.show()
def check_camera(self):
view = flare.main_window().camera.save_view()
if self.last_view != view:
self.last_view = view
if self.websocket:
self.websocket.send_json(command='view_change',
data=dict(key=self.key, view=view))
print('View changed')
def set_camera(self, matrix):
self.last_view = matrix
flare.main_window().camera.restore_view(view=matrix)
from cresset import flare
project = flare.main_window().project
for l in project.ligands:
f_name = l.title.split(':1')[0]
l.minimize()
l.write_file(f_name + '.mol2')
'/Users/toni_brain/Projects/git/BioSimSpace_examples/Flare/bioactivity-18_16_53_02.txt'
) as hnd:
rows = csv.reader(hnd, delimiter='\t')
for i, row in enumerate(rows):
if (i == 0):
headers = list(row)
else:
table.append(list(row))
headers_dict = {h: i for i, h in enumerate(headers)}
smiles_idx = headers_dict['CANONICAL_SMILES']
pchembl_idx = headers_dict['PCHEMBL_VALUE']
chemblid_idx = headers_dict['CMPD_CHEMBLID']
p = flare.Project()
if (flare.main_window()):
flare.main_window().project = p
smiles_set = set()
props = Properties()
n_vec = props.GetPropertyNames()
rdk_mols = []
for row in table:
mol = filter_extract_mol(row, headers_dict)
if (mol is None):
continue
row[smiles_idx] = Chem.MolToSmiles(mol)
if (row[smiles_idx] in smiles_set):
continue
smiles_set.add(row[smiles_idx])
addCoords=(mol.GetNumConformers() > 0),
explicitOnly=True)
Chem.SanitizeMol(mol_copy)
mol_copy.ClearComputedProps()
mol_copy.UpdatePropertyCache()
res.append(mol_copy)
return res
# load molecules:
lig02_pdb = open("17.pdb", "r").read()
lig12_pdb = open("18.pdb", "r").read()
if flare:
ligands = flare.main_window().project.ligands
lig02 = ligands.extend(flare.read_string(lig02_pdb, "pdb"))[-1]
lig12 = ligands.extend(flare.read_string(lig12_pdb, "pdb"))[-1]
lig02_mol = lig02.to_rdmol()
lig12_mol = lig12.to_rdmol()
else:
lig02_mol = rdmolfiles.MolFromPDBBlock(lig02_pdb)
lig12_mol = rdmolfiles.MolFromPDBBlock(lig12_pdb)
# make list of molecules to map the MCS to:
perturbation_pair = []
perturbation_pair.append(lig02_mol)
perturbation_pair.append(lig12_mol)
MCS_object = rdFMCS.FindMCS(perturbation_pair, completeRingsOnly=True)