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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Oct 21, 2022
1 parent 745e6cb commit 472cdaf
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Showing 2 changed files with 196 additions and 164 deletions.
61 changes: 31 additions & 30 deletions aiidalab_widgets_base/structures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,11 @@
import pathlib
import tempfile
from collections import OrderedDict
from copy import deepcopy

import ase
import ipywidgets as ipw
import numpy as np
from copy import deepcopy

# spglib for cell converting
import spglib
Expand All @@ -30,7 +30,19 @@
from ase import Atom, Atoms
from ase.data import chemical_symbols, covalent_radii
from sklearn.decomposition import PCA
from traitlets import Bool,Dict, Instance, Int, List, Unicode, Union, default, dlink, link, observe
from traitlets import (
Bool,
Dict,
Instance,
Int,
List,
Unicode,
Union,
default,
dlink,
link,
observe,
)

# Local imports
from .data import LigandSelectorWidget
Expand All @@ -57,7 +69,7 @@ class StructureManagerWidget(ipw.VBox):
structure = Union([Instance(Atoms), Instance(Data)], allow_none=True)
structure_node = Instance(Data, allow_none=True, read_only=True)
node_class = Unicode()
#brand_new_structure = Bool()
# brand_new_structure = Bool()

SUPPORTED_DATA_FORMATS = {"CifData": "cif", "StructureData": "structure"}

Expand Down Expand Up @@ -161,12 +173,11 @@ def _structure_importers(self, importers):
if len(importers) == 1:
# Assigning a function which will be called when importer provides a structure.
dlink((importers[0], "structure"), (self, "input_structure"))
#if importers[0].has_trait("brand_new_structure"):
# if importers[0].has_trait("brand_new_structure"):
# link((importers[0], "brand_new_structure"), (self.viewer, "brand_new_structure"))
# link((importers[0], "brand_new_structure"), (self, "brand_new_structure"))

return importers[0]


# Otherwise making one tab per importer.
importers_tab = ipw.Tab()
Expand All @@ -175,7 +186,7 @@ def _structure_importers(self, importers):
# Labeling tabs.
importers_tab.set_title(i, importer.title)
dlink((importer, "structure"), (self, "input_structure"))
#if importer.has_trait("brand_new_structure"):
# if importer.has_trait("brand_new_structure"):
# link((importer, "brand_new_structure"), (self.viewer, "brand_new_structure"))
# link((importer, "brand_new_structure"), (self, "brand_new_structure"))
return importers_tab
Expand All @@ -201,7 +212,7 @@ def _structure_editors(self, editors):
editors_tab.set_title(i, editor.title)
link((editor, "structure"), (self, "structure"))
if editor.has_trait("selection"):
link((editor, "selection"), (self.viewer, "selection"))
link((editor, "selection"), (self.viewer, "selection"))
if editor.has_trait("camera_orientation"):
dlink(
(self.viewer._viewer, "_camera_orientation"),
Expand Down Expand Up @@ -343,15 +354,14 @@ def _observe_input_structure(self, change):
else:
self.structure = None


@observe("structure")
def _structure_changed(self, change=None):
"""Perform some operations that depend on the value of `structure` trait.
This function enables/disables `btn_store` widget if structure is provided/set to None.
Also, the function sets `structure_node` trait to the selected node type.
"""

if not self.structure_set_by_undo:
self.history.append(change["new"])

Expand Down Expand Up @@ -692,7 +702,7 @@ class SmilesWidget(ipw.VBox):
"""Convert SMILES into 3D structure."""

structure = Instance(Atoms, allow_none=True)
#brand_new_structure = Bool()
# brand_new_structure = Bool()

SPINNER = """<i class="fa fa-spinner fa-pulse" style="color:red;" ></i>"""

Expand Down Expand Up @@ -1195,8 +1205,7 @@ def disable_element(_=None):
]
)


def find_index(self,list_of_lists, element):
def find_index(self, list_of_lists, element):
for i, x in enumerate(list_of_lists):
if element in x:
return i
Expand Down Expand Up @@ -1278,7 +1287,7 @@ def translate_dr(self, _=None, atoms=None, selection=None):
self.action_vector * self.displacement.value
)

#self.brand_new_structure = False
# self.brand_new_structure = False
self.structure, self.selection = atoms, selection

@_register_structure
Expand All @@ -1289,7 +1298,7 @@ def translate_dxdydz(self, _=None, atoms=None, selection=None):
# The action.
atoms.positions[self.selection] += np.array(self.str2vec(self.dxyz.value))

#self.brand_new_structure = False
# self.brand_new_structure = False

self.structure, self.selection = atoms, selection

Expand All @@ -1301,7 +1310,7 @@ def translate_to_xyz(self, _=None, atoms=None, selection=None):
geo_center = np.average(self.structure[self.selection].get_positions(), axis=0)
atoms.positions[self.selection] += self.str2vec(self.dxyz.value) - geo_center

#self.brand_new_structure = False
# self.brand_new_structure = False
self.structure, self.selection = atoms, selection

@_register_structure
Expand All @@ -1316,7 +1325,7 @@ def rotate(self, _=None, atoms=None, selection=None):
rotated_subset.rotate(self.phi.value, v=vec, center=center, rotate_cell=False)
atoms.positions[list(self.selection)] = rotated_subset.positions

#self.brand_new_structure = False
# self.brand_new_structure = False
self.structure, self.selection = atoms, selection

@_register_structure
Expand Down Expand Up @@ -1350,7 +1359,7 @@ def mirror(self, _=None, norm=None, point=None, atoms=None, selection=None):
# Mirror atoms.
atoms.positions[selection] -= 2 * projections

#self.brand_new_structure = False
# self.brand_new_structure = False
self.structure, self.selection = atoms, selection

def mirror_3p(self, _=None):
Expand All @@ -1375,7 +1384,7 @@ def align(self, _=None, atoms=None, selection=None):
subset.rotate(self.action_vector, self.str2vec(self.dxyz.value), center=center)
atoms.positions[selection] = subset.positions

#self.brand_new_structure = False
# self.brand_new_structure = False
self.structure, self.selection = atoms, selection

@_register_structure
Expand All @@ -1384,7 +1393,6 @@ def mod_element(self, _=None, atoms=None, selection=None):
"""Modify selected atoms into the given element."""
last_atom = atoms.get_global_number_of_atoms()


if self.ligand.value == 0:
for idx in self.selection:
new = Atom(self.element.value)
Expand All @@ -1399,17 +1407,15 @@ def mod_element(self, _=None, atoms=None, selection=None):
initial_ligand = self.ligand.rotate(
align_to=self.action_vector, remove_anchor=True
)

for idx in self.selection:
position = self.structure.positions[idx].copy()
lgnd = initial_ligand.copy()
lgnd.translate(position)
atoms += lgnd
atoms += lgnd
new_selection = [
i for i in range(last_atom, last_atom + len(selection) * len(lgnd))
]



# the order of the traitlets below is important
self.selection = []
Expand All @@ -1428,12 +1434,8 @@ def copy_sel(self, _=None, atoms=None, selection=None):
add_atoms.translate([1.0, 0, 0])
atoms += add_atoms



new_selection = [i for i in range(last_atom, last_atom + len(selection))]



# the order of the traitlets below is important
self.selection = []
self.structure = atoms
Expand Down Expand Up @@ -1471,7 +1473,7 @@ def add(self, _=None, atoms=None, selection=None):
i for i in range(last_atom, last_atom + len(selection) * len(lgnd))
]

#self.brand_new_structure = False
# self.brand_new_structure = False

# the order of the traitlets below is important
self.selection = []
Expand All @@ -1484,6 +1486,5 @@ def remove(self, _, atoms=None, selection=None):
"""Remove selected atoms."""
del [atoms[selection]]


self.selection = []
self.structure = atoms
self.structure = atoms
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