Merge pull request #78 from aiidalab/release_1.0.0b5

Release 1.0.0b5

Author: yakutovicha

aiidalab_widgets_base/__init__.py

@@ -13,7 +13,8 @@
 from .process import ProcessFollowerWidget, ProgressBarWidget, RunningCalcJobOutputWidget, SubmitButtonWidget  # noqa
 from .structures import StructureManagerWidget  # noqa
 from .structures import StructureBrowserWidget, StructureExamplesWidget, StructureUploadWidget, SmilesWidget  # noqa
+from .structures import BasicStructureEditor  # noqa
 from .structures_multi import MultiStructureUploadWidget  # noqa
 from .viewers import viewer  # noqa
 
-__version__ = "1.0.0b4"
+__version__ = "1.0.0b5"

aiidalab_widgets_base/codes.py

@@ -4,7 +4,7 @@
 
 import ipywidgets as ipw
 from IPython.display import clear_output
-from traitlets import Dict, Instance, Unicode, Union, link, validate
+from traitlets import Bool, Dict, Instance, Unicode, Union, link, validate
 
 from aiida.orm import Code, QueryBuilder, User
 
@@ -30,35 +30,43 @@ class CodeDropdown(ipw.VBox):
         codes(Dict): Trait that contains a dictionary (label => Code instance) for all
             codes found in the AiiDA database for the selected plugin. It is linked
             to the 'options' trait of the `self.dropdown` widget.
+
+        allow_hidden_codes(Bool): Trait that defines whether to show hidden codes or not.
+
+        allow_disabled_computers(Bool): Trait that defines whether to show codes on disabled
+            computers.
     """
     selected_code = Union([Unicode(), Instance(Code)], allow_none=True)
     codes = Dict(allow_none=True)
+    allow_hidden_codes = Bool(False)
+    allow_disabled_computers = Bool(False)
 
-    def __init__(self, input_plugin, text='Select code:', path_to_root='../', **kwargs):
+    def __init__(self, input_plugin, description='Select code:', path_to_root='../', **kwargs):
         """Dropdown for Codes for one input plugin.
 
-        :param input_plugin: Input plugin of codes to show
-        :type input_plugin: str
-        :param text: Text to display before dropdown
-        :type text: str
+        input_plugin (str): Input plugin of codes to show.
+
+        description (str): Description to display before the dropdown.
         """
+        self.output = ipw.Output()
 
         self.input_plugin = input_plugin
-        self.output = ipw.Output()
 
-        self.dropdown = ipw.Dropdown(optionsdescription=text, disabled=True, value=None)
+        self.dropdown = ipw.Dropdown(description=description, disabled=True, value=None)
         link((self, 'codes'), (self.dropdown, 'options'))
         link((self.dropdown, 'value'), (self, 'selected_code'))
 
-        self._btn_refresh = ipw.Button(description="Refresh", layout=ipw.Layout(width="70px"))
-        self._btn_refresh.on_click(self.refresh)
+        btn_refresh = ipw.Button(description="Refresh", layout=ipw.Layout(width="70px"))
+        btn_refresh.on_click(self.refresh)
+
+        self.observe(self.refresh, names=['allow_disabled_computers', 'allow_hidden_codes'])
 
         # FOR LATER: use base_url here, when it will be implemented in the appmode.
         self._setup_another = ipw.HTML(value="""<a href={path_to_root}aiidalab-widgets-base/setup_code.ipynb?
                       label={label}&plugin={plugin} target="_blank">Setup new code</a>""".format(
             path_to_root=path_to_root, label=input_plugin, plugin=input_plugin))
 
-        children = [ipw.HBox([self.dropdown, self._btn_refresh, self._setup_another]), self.output]
+        children = [ipw.HBox([self.dropdown, btn_refresh, self._setup_another]), self.output]
 
         super().__init__(children=children, **kwargs)
 
@@ -67,23 +75,15 @@ def __init__(self, input_plugin, text='Select code:', path_to_root='../', **kwar
     def _get_codes(self):
         """Query the list of available codes."""
 
-        querybuild = QueryBuilder()
-        querybuild.append(Code,
-                          filters={
-                              'attributes.input_plugin': {
-                                  '==': self.input_plugin
-                              },
-                              'extras.hidden': {
-                                  "~==": True
-                              }
-                          },
-                          project=['*'])
-
-        # Only codes on computers configured for the current user.
+        user = User.objects.get_default()
+
         return {
             self._full_code_label(c[0]): c[0]
-            for c in querybuild.all()
-            if c[0].computer.is_user_configured(User.objects.get_default())
+            for c in QueryBuilder().append(Code, filters={
+                'attributes.input_plugin': self.input_plugin
+            }).all()
+            if c[0].computer.is_user_configured(user) and (self.allow_hidden_codes or not c[0].hidden) and
+            (self.allow_disabled_computers or c[0].computer.is_user_enabled(user))
         }
 
     @staticmethod

aiidalab_widgets_base/computers.py

@@ -7,7 +7,7 @@
 import pexpect
 import ipywidgets as ipw
 from IPython.display import clear_output
-from traitlets import Bool, Dict, Instance, Int, Unicode, Union, link, observe, validate
+from traitlets import Bool, Dict, Instance, Int, Unicode, Union, link, validate
 
 from aiida.common import NotExistent
 from aiida.orm import Computer, QueryBuilder, User
@@ -663,28 +663,27 @@ class ComputerDropdown(ipw.VBox):
         computers(Dict): Trait that contains a dictionary (label => Computer instance) for all
         computers found in the AiiDA database. It is linked to the 'options' trait of
         `self._dropdown` widget.
+
+        allow_select_disabled(Bool):  Trait that defines whether to show disabled computers.
     """
 
     selected_computer = Union([Unicode(), Instance(Computer)], allow_none=True)
     computers = Dict(allow_none=True)
     allow_select_disabled = Bool(False)
 
-    def __init__(self, text='Select computer:', path_to_root='../', **kwargs):
+    def __init__(self, description='Select computer:', path_to_root='../', **kwargs):
         """Dropdown for configured AiiDA Computers.
 
-        text (str): Text to display before dropdown.
+        description (str): Text to display before dropdown.
 
         path_to_root (str): Path to the app's root folder.
         """
 
         self.output = ipw.Output()
 
-        if 'allow_select_disabled' in kwargs:
-            self.allow_select_disabled = kwargs['allow_select_disabled']
-
         self._dropdown = ipw.Dropdown(options={},
                                       value=None,
-                                      description=text,
+                                      description=description,
                                       style={'description_width': 'initial'},
                                       disabled=True)
         link((self, 'computers'), (self._dropdown, 'options'))
@@ -693,6 +692,8 @@ def __init__(self, text='Select computer:', path_to_root='../', **kwargs):
         btn_refresh = ipw.Button(description="Refresh", layout=ipw.Layout(width="70px"))
         btn_refresh.on_click(self.refresh)
 
+        self.observe(self.refresh, names='allow_select_disabled')
+
         self._setup_another = ipw.HTML(
             value="""<a href={path_to_root}aiidalab-widgets-base/setup_computer.ipynb target="_blank">
             Setup new computer</a>""".format(path_to_root=path_to_root))
@@ -713,7 +714,6 @@ def _get_computers(self):
             if c[0].is_user_configured(user) and (self.allow_select_disabled or c[0].is_user_enabled(user))
         }
 
-    @observe('allow_select_disabled')
     def refresh(self, _=None):
         """Refresh the list of configured computers."""
 

aiidalab_widgets_base/data/__init__.py

@@ -0,0 +1,61 @@
+"""Useful functions that provide access to some data. """
+from ase import Atom, Atoms
+import numpy as np
+import ipywidgets as ipw
+
+# The first atom is anchoring, so the new bond will be connecting it
+# The direction of the new bond is (-1, -1, -1).
+LIGANDS = {
+    'Select ligand':
+        0,
+    'Methyl -CH3': [('C', 0, 0, 0), ('H', 0.23962342, -0.47699124, 0.78585262),
+                    ('H', 0.78584986, 0.23962732, -0.47698795), ('H', -0.47699412, 0.78585121, 0.23962671)],
+    'Methylene =CH2': [('C', 0, 0, 0), ('H', -0.39755349, 0.59174911, 0.62728004),
+                       ('H', 0.94520686, -0.04409933, -0.07963039)],
+    'Hydroxy -OH': [('O', 0, 0, 0), ('H', 0.87535922, -0.3881659, 0.06790889)],
+    'Amine -NH2': [('N', 0, 0, 0), ('H', 0.7250916, -0.56270993, 0.42151063),
+                   ('H', -0.56261958, 0.4215284, 0.72515241)],
+}
+
+
+class LigandSelectorWidget(ipw.Dropdown):
+    """Class to select ligands that are returned as `Atoms` object"""
+
+    def __init__(self, value=0, description="Select ligand", **kwargs):
+        self.style = {'description_width': 'initial'}
+        self.layout = {'width': 'initial'}
+        super().__init__(value=value, description=description, options=LIGANDS, **kwargs)
+
+    def rotate(self, align_to=(0, 0, 1), remove_anchor=False):
+        """Rotate group in such a way that vector which was (-1,-1,-1)
+        is alligned with align_to."""
+
+        vect = np.array(align_to)
+        norm = np.linalg.norm(vect)
+
+        if self.value == 0:
+            return None
+
+        mol = Atoms()
+        for atm in self.value:
+            mol.append(Atom(atm[0], atm[1:]))
+
+        # Bad cases.
+        if norm == 0.0:
+            vect = np.array((1, 1, 1)) / np.sqrt(3)
+        else:
+            vect = vect / norm
+
+        mol.rotate((1, 1, 1), vect)
+
+        if remove_anchor:
+            del mol[0]
+
+        return mol
+
+    @property
+    def anchoring_atom(self):
+        """Return anchoring atom chemical symbol."""
+        if self.value == 0:
+            return None
+        return self.value[0][0]