class RingTable(QWidget): def __init__(self, parent=None): super().__init__(parent) layout = QGridLayout(self) self.table = QTableWidget() self.table.setColumnCount(1) self.table.setHorizontalHeaderLabels(['name']) self.add_rings() for i in range(0, 1): self.table.resizeColumnToContents(i) self.table.horizontalHeader().setSectionResizeMode( 0, QHeaderView.Stretch) self.table.setSortingEnabled(True) self.table.setSelectionBehavior(QTableWidget.SelectRows) self.table.setEditTriggers(QTableWidget.NoEditTriggers) self.filterEdit = QLineEdit() self.filterEdit.textChanged.connect(self.apply_filter) self.filterEdit.setClearButtonEnabled(True) self.filter_columns = QComboBox() self.filter_columns.addItem("name") self.filter_columns.currentTextChanged.connect( self.change_filter_method) self.name_regex_option = QComboBox() self.name_regex_option.addItem("case-insensitive") self.name_regex_option.addItem("case-sensitive") self.name_regex_option.currentTextChanged.connect(self.apply_filter) self.name_regex_option.setVisible( self.filter_columns.currentText() == "name") layout.addWidget(self.table, 0, 0, 1, 4) layout.addWidget(QLabel("filter based on"), 1, 0) layout.addWidget(self.filter_columns, 1, 1) layout.addWidget(self.name_regex_option, 1, 2) layout.addWidget(self.filterEdit, 1, 3) self.change_filter_method("name") def change_filter_method(self, text): if text == "name": self.filterEdit.setToolTip("name regex") self.name_regex_option.setVisible(True) self.apply_filter() def apply_filter(self, *args): text = self.filterEdit.text() if text: if self.filter_columns.currentText() == "name": m = QRegularExpression(text) if m.isValid(): if self.name_regex_option.currentText( ) == "case-insensitive": m.setPatternOptions( QRegularExpression.CaseInsensitiveOption) m.optimize() filter = lambda row_num: m.match( self.table.item(row_num, 0).text()).hasMatch() else: return else: filter = lambda row: True for i in range(0, self.table.rowCount()): self.table.setRowHidden(i, not filter(i)) def add_rings(self): from AaronTools.ring import Ring names = [] for lib in [Ring.AARON_LIBS, Ring.BUILTIN]: if not os.path.exists(lib): continue for ring in os.listdir(lib): name, ext = os.path.splitext(ring) if not any(".%s" % x == ext for x in read_types): continue if name in names: continue names.append(name) row = self.table.rowCount() self.table.insertRow(row) self.table.setItem(row, 0, QTableWidgetItem(name)) self.ring_list = names
class LigandTable(QWidget): def __init__( self, parent=None, singleSelect=False, maxDenticity=None, include_substituents=False, ): super().__init__(parent) self._include_substituents = include_substituents layout = QGridLayout(self) self.table = QTableWidget() self.table.setColumnCount(3) self.table.setHorizontalHeaderLabels( ['name', 'denticity', 'coordinating elements']) self.add_ligands(maxDenticity) for i in range(0, 3): self.table.resizeColumnToContents(i) self.table.horizontalHeader().setStretchLastSection(False) self.table.horizontalHeader().setSectionResizeMode( 0, QHeaderView.Fixed) self.table.horizontalHeader().setSectionResizeMode( 1, QHeaderView.Fixed) self.table.horizontalHeader().setSectionResizeMode( 2, QHeaderView.Stretch) self.table.setSortingEnabled(True) self.table.setSelectionBehavior(QTableWidget.SelectRows) if singleSelect: self.table.setSelectionMode(QTableWidget.SingleSelection) self.table.setEditTriggers(QTableWidget.NoEditTriggers) self.filterEdit = QLineEdit() self.filterEdit.textChanged.connect(self.apply_filter) self.filterEdit.setClearButtonEnabled(True) self.filter_columns = QComboBox() self.filter_columns.addItem("name") self.filter_columns.addItem("denticity") self.filter_columns.addItem("coordinating elements") self.filter_columns.currentTextChanged.connect( self.change_filter_method) self.name_regex_option = QComboBox() self.name_regex_option.addItem("case-insensitive") self.name_regex_option.addItem("case-sensitive") self.name_regex_option.currentTextChanged.connect(self.apply_filter) self.name_regex_option.setVisible( self.filter_columns.currentText() == "name") self.coordinating_elements_method = QComboBox() self.coordinating_elements_method.addItem("exactly") self.coordinating_elements_method.addItem("at least") self.coordinating_elements_method.currentTextChanged.connect( self.apply_filter) self.coordinating_elements_method.setVisible( self.filter_columns.currentText() == "coordinating elements") layout.addWidget(self.table, 0, 0, 1, 4) layout.addWidget(QLabel("filter based on"), 1, 0) layout.addWidget(self.filter_columns, 1, 1) layout.addWidget(self.coordinating_elements_method, 1, 2) layout.addWidget(self.name_regex_option, 1, 2) layout.addWidget(self.filterEdit, 1, 3) self.change_filter_method("name") def add_ligands(self, maxDenticity=None): from AaronTools.component import Component names = [] for lib in [Component.AARON_LIBS, Component.BUILTIN]: if not os.path.exists(lib): continue for lig in os.listdir(lib): name, ext = os.path.splitext(lig) if not any(".%s" % x == ext for x in read_types): continue if name in names: continue names.append(name) geom = Geometry( os.path.join(lib, lig), refresh_connected=False, refresh_ranks=False, ) key_atoms = [geom.atoms[i] for i in geom.other["key_atoms"]] if maxDenticity and len(key_atoms) > maxDenticity: continue row = self.table.rowCount() self.table.insertRow(row) self.table.setItem(row, 0, QTableWidgetItem(name)) #this is an integer, so I need to initialize it then set the data denticity = QTableWidgetItem() denticity.setData(Qt.DisplayRole, len(key_atoms)) self.table.setItem(row, 1, denticity) self.table.setItem( row, 2, QTableWidgetItem(", ".join( sorted([atom.element for atom in key_atoms])))) if self._include_substituents: from AaronTools.substituent import Substituent for lib in [Substituent.AARON_LIBS, Substituent.BUILTIN]: if not os.path.exists(lib): continue for sub in os.listdir(lib): name, ext = os.path.splitext(sub) if not any(".%s" % x == ext for x in read_types): continue if name in names: continue names.append(name) geom = Geometry( os.path.join(lib, sub), refresh_connected=False, refresh_ranks=False, ) key_atoms = [geom.atoms[0]] if maxDenticity and len(key_atoms) > maxDenticity: continue row = self.table.rowCount() self.table.insertRow(row) self.table.setItem(row, 0, QTableWidgetItem(name)) #this is an integer, so I need to initialize it then set the data denticity = QTableWidgetItem() denticity.setData(Qt.DisplayRole, len(key_atoms)) self.table.setItem(row, 1, denticity) self.table.setItem( row, 2, QTableWidgetItem(", ".join( sorted([atom.element for atom in key_atoms])))) self.ligand_list = names def change_filter_method(self, text): if text == "coordinating elements": self.filterEdit.setToolTip("comma and/or space delimited elements") self.coordinating_elements_method.setVisible(True) self.name_regex_option.setVisible(False) elif text == "name": self.filterEdit.setToolTip("name regex") self.coordinating_elements_method.setVisible(False) self.name_regex_option.setVisible(True) elif text == "denticity": self.filterEdit.setToolTip("number of key atoms") self.coordinating_elements_method.setVisible(False) self.name_regex_option.setVisible(False) self.apply_filter() def apply_filter(self, *args): text = self.filterEdit.text() if text: if self.filter_columns.currentText() == "name": m = QRegularExpression(text) if m.isValid(): if self.name_regex_option.currentText( ) == "case-insensitive": m.setPatternOptions( QRegularExpression.CaseInsensitiveOption) m.optimize() filter = lambda row_num: m.match( self.table.item(row_num, 0).text()).hasMatch() else: return elif self.filter_columns.currentText() == "denticity": if text.isdigit(): filter = lambda row_num: int( self.table.item(row_num, 1).text()) == int(text) else: filter = lambda row: True elif self.filter_columns.currentText() == "coordinating elements": method = self.coordinating_elements_method.currentText() def filter(row_num): row_key_atoms = [ item.strip() for item in self.table.item( row_num, 2).text().split(',') ] search_atoms = [] for item in text.split(): for ele in item.split(','): if ele.strip() != "": search_atoms.append(ele) if method == "exactly": if all([row_key_atoms.count(element) == search_atoms.count(element) for element in set(search_atoms)]) and \ all([row_key_atoms.count(element) == search_atoms.count(element) for element in set(row_key_atoms)]): return True else: return False elif method == "at least": if all([ row_key_atoms.count(element) >= search_atoms.count(element) for element in set(search_atoms) ]): return True else: return False else: filter = lambda row: True for i in range(0, self.table.rowCount()): self.table.setRowHidden(i, not filter(i))
class SubstituentTable(QWidget): def __init__(self, parent=None, singleSelect=False): super().__init__(parent) layout = QGridLayout(self) self.table = QTableWidget() self.table.setColumnCount(3) self.table.setHorizontalHeaderLabels( ['name', 'conformers', 'conf. angle']) self.add_subs() for i in range(0, 3): self.table.resizeColumnToContents(i) self.table.horizontalHeader().setStretchLastSection(False) self.table.horizontalHeader().setSectionResizeMode( 0, QHeaderView.Fixed) self.table.horizontalHeader().setSectionResizeMode( 1, QHeaderView.Fixed) self.table.horizontalHeader().setSectionResizeMode( 2, QHeaderView.Stretch) self.table.setSortingEnabled(True) self.table.setSelectionBehavior(QTableWidget.SelectRows) if singleSelect: self.table.setSelectionMode(QTableWidget.SingleSelection) self.table.setEditTriggers(QTableWidget.NoEditTriggers) self.filterEdit = QLineEdit() self.filterEdit.textChanged.connect(self.apply_filter) self.filterEdit.setClearButtonEnabled(True) self.filter_columns = QComboBox() self.filter_columns.addItem("name") self.filter_columns.addItem("conformers") self.filter_columns.addItem("conf. angle") self.filter_columns.currentTextChanged.connect( self.change_filter_method) self.name_regex_option = QComboBox() self.name_regex_option.addItem("case-insensitive") self.name_regex_option.addItem("case-sensitive") self.name_regex_option.currentTextChanged.connect(self.apply_filter) self.name_regex_option.setVisible( self.filter_columns.currentText() == "name") layout.addWidget(self.table, 0, 0, 1, 4) layout.addWidget(QLabel("filter based on"), 1, 0) layout.addWidget(self.filter_columns, 1, 1) layout.addWidget(self.name_regex_option, 1, 2) layout.addWidget(self.filterEdit, 1, 3) self.change_filter_method("name") def change_filter_method(self, text): if text == "name": self.filterEdit.setToolTip("name regex") self.name_regex_option.setVisible(True) elif text == "conformers": self.filterEdit.setToolTip("number of conformers") self.name_regex_option.setVisible(False) elif text == "conf. angle": self.filterEdit.setToolTip("angle between conformers") self.name_regex_option.setVisible(False) self.apply_filter() def apply_filter(self, *args): text = self.filterEdit.text() if text: if self.filter_columns.currentText() == "name": m = QRegularExpression(text) if m.isValid(): if self.name_regex_option.currentText( ) == "case-insensitive": m.setPatternOptions( QRegularExpression.CaseInsensitiveOption) m.optimize() filter = lambda row_num: m.match( self.table.item(row_num, 0).text()).hasMatch() else: return elif self.filter_columns.currentText() == "conformers": if text.isdigit(): filter = lambda row_num: int( self.table.item(row_num, 1).text()) == int(text) else: filter = lambda row: True elif self.filter_columns.currentText() == "conf. angle": if text.isdigit(): filter = lambda row_num: int( self.table.item(row_num, 2).text()) == int(text) else: filter = lambda row: True else: filter = lambda row: True for i in range(0, self.table.rowCount()): self.table.setRowHidden(i, not filter(i)) def add_subs(self): from AaronTools.substituent import Substituent names = [] for lib in [Substituent.AARON_LIBS, Substituent.BUILTIN]: if not os.path.exists(lib): continue for ring in os.listdir(lib): name, ext = os.path.splitext(ring) if not any(".%s" % x == ext for x in read_types): continue if name in names: continue names.append(name) geom = Geometry( os.path.join(lib, ring), refresh_connected=False, refresh_ranks=False, ) conf_info = re.search(r"CF:(\d+),(\d+)", geom.comment) row = self.table.rowCount() self.table.insertRow(row) self.table.setItem(row, 0, QTableWidgetItem(name)) #the next two items are integers - need to initialize then setData so they sort and display correctly conf_num = QTableWidgetItem() conf_num.setData(Qt.DisplayRole, conf_info.group(1)) self.table.setItem(row, 1, conf_num) conf_angle = QTableWidgetItem() conf_angle.setData(Qt.DisplayRole, conf_info.group(2)) self.table.setItem(row, 2, conf_angle) self.substituent_list = names
class PrecisionRotate(ToolInstance): help = "https://github.com/QChASM/SEQCROW/wiki/Rotate-Tool" SESSION_ENDURING = False SESSION_SAVE = False def __init__(self, session, name): super().__init__(session, name) self.tool_window = MainToolWindow(self) self.settings = _PrecisionRotateSettings(session, name) self.bonds = {} self.bond_centers = {} self.groups = {} self.perpendiculars = {} self.perp_centers = {} self.manual_center = {} self._build_ui() self._show_rot_vec = self.session.triggers.add_handler( SELECTION_CHANGED, self.show_rot_vec) global_triggers = get_triggers() self._changes = global_triggers.add_handler("changes done", self.show_rot_vec) self.show_rot_vec() def _build_ui(self): layout = QGridLayout() layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.cor_button = QComboBox() self.cor_button.addItems( ["automatic", "select atoms", "view's center of rotation"]) layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop) self.set_cor_selection = QPushButton("set selection") self.cor_button.currentTextChanged.connect( lambda t, widget=self.set_cor_selection: widget.setEnabled( t == "select atoms")) self.set_cor_selection.clicked.connect(self.manual_cor) layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop) self.set_cor_selection.setEnabled(False) layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.vector_option = QComboBox() self.vector_option.addItems([ "axis", "view axis", "bond", "perpendicular to plane", "centroid of atoms", "custom" ]) layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter) vector = QWidget() vector.setToolTip("vector will be normalized before rotating") vector_layout = QHBoxLayout(vector) vector_layout.setContentsMargins(0, 0, 0, 0) self.vector_x = QDoubleSpinBox() self.vector_y = QDoubleSpinBox() self.vector_z = QDoubleSpinBox() self.vector_z.setValue(1.0) for c, t in zip([self.vector_x, self.vector_y, self.vector_z], [" x", " y", " z"]): c.setSingleStep(0.01) c.setRange(-100, 100) # c.setSuffix(t) c.valueChanged.connect(self.show_rot_vec) vector_layout.addWidget(c) layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop) vector.setVisible(self.vector_option.currentText() == "custom") self.vector_option.currentTextChanged.connect( lambda text, widget=vector: widget.setVisible(text == "custom")) self.view_axis = QComboBox() self.view_axis.addItems(["z", "y", "x"]) layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop) self.view_axis.setVisible( self.vector_option.currentText() == "view axis") self.vector_option.currentTextChanged.connect( lambda text, widget=self.view_axis: widget.setVisible(text == "view axis")) self.axis = QComboBox() self.axis.addItems(["z", "y", "x"]) layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop) self.axis.setVisible(self.vector_option.currentText() == "axis") self.vector_option.currentTextChanged.connect( lambda text, widget=self.axis: widget.setVisible(text == "axis")) self.bond_button = QPushButton("set selected bond") self.bond_button.clicked.connect(self.set_bonds) layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop) self.bond_button.setVisible(self.vector_option.currentText() == "bond") self.vector_option.currentTextChanged.connect( lambda text, widget=self.bond_button: widget.setVisible(text == "bond")) self.perp_button = QPushButton("set selected atoms") self.perp_button.clicked.connect(self.set_perpendicular) layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop) self.perp_button.setVisible( self.vector_option.currentText() == "perpendicular to plane") self.vector_option.currentTextChanged.connect( lambda text, widget=self.perp_button: widget.setVisible( text == "perpendicular to plane")) self.group_button = QPushButton("set selected atoms") self.group_button.clicked.connect(self.set_group) layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop) self.group_button.setVisible( self.vector_option.currentText() == "centroid of atoms") self.vector_option.currentTextChanged.connect( lambda text, widget=self.group_button: widget.setVisible( text == "centroid of atoms")) layout.addWidget(QLabel("angle:"), 2, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.angle = QDoubleSpinBox() self.angle.setRange(-360, 360) self.angle.setSingleStep(5) self.angle.setSuffix("°") layout.addWidget(self.angle, 2, 1, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) self.display_rot_vec = QCheckBox() self.display_rot_vec.setCheckState(Qt.Checked) self.display_rot_vec.stateChanged.connect(self.show_rot_vec) layout.addWidget(self.display_rot_vec, 3, 1, 1, 1, Qt.AlignLeft | Qt.AlignVCenter) rotate_button = QPushButton("rotate selected atoms") rotate_button.clicked.connect(self.do_rotate) layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop) self.rotate_button = rotate_button self.status_bar = QStatusBar() self.status_bar.setSizeGripEnabled(False) layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop) self.vector_option.currentTextChanged.connect(self.show_auto_status) self.cor_button.currentIndexChanged.connect( lambda *args: self.show_auto_status("select atoms")) self.cor_button.currentIndexChanged.connect(self.show_rot_vec) self.set_cor_selection.clicked.connect(self.show_rot_vec) self.vector_option.currentIndexChanged.connect(self.show_rot_vec) self.axis.currentIndexChanged.connect(self.show_rot_vec) self.view_axis.currentIndexChanged.connect(self.show_rot_vec) self.bond_button.clicked.connect(self.show_rot_vec) self.perp_button.clicked.connect(self.show_rot_vec) self.group_button.clicked.connect(self.show_rot_vec) layout.setRowStretch(0, 0) layout.setRowStretch(1, 0) layout.setRowStretch(2, 0) layout.setRowStretch(3, 0) layout.setRowStretch(4, 0) layout.setRowStretch(5, 1) layout.setColumnStretch(0, 0) layout.setColumnStretch(1, 1) layout.setColumnStretch(2, 1) self.tool_window.ui_area.setLayout(layout) self.tool_window.manage(None) def manual_cor(self, *args): selection = selected_atoms(self.session) models = {} for atom in selection: if atom.structure not in models: models[atom.structure] = [atom] else: models[atom.structure].append(atom) self.manual_center = {} for model in models: atoms = models[model] coords = np.array([atom.coord for atom in atoms]) self.manual_center[model] = np.mean(coords, axis=0) def show_auto_status(self, text): if self.cor_button.currentText() == "automatic": if text == "bond": self.status_bar.showMessage( "center set to one of the bonded atoms") elif text == "perpendicular to plane": self.status_bar.showMessage("center set to centroid of atoms") else: self.status_bar.showMessage( "center set to centroid of rotating atoms") elif self.cor_button.currentText() == "select atoms": self.status_bar.showMessage( "center set to centroid of specified atoms") else: self.status_bar.showMessage( "center set to view's center of rotation") def set_bonds(self, *args): bonds = selected_bonds(self.session) if len(bonds) == 0: self.session.logger.error("no bonds selected") return models = [bond.structure for bond in bonds] if any(models.count(m) > 1 for m in models): self.session.logger.error( "multiple bonds selected on the same structure") return self.bonds = { model: (bond.atoms[0].coord - bond.atoms[1].coord) for model, bond in zip(models, bonds) } self.bond_centers = { model: bond.atoms[1].coord for model, bond in zip(models, bonds) } def set_perpendicular(self, *args): atoms = selected_atoms(self.session) if len(atoms) == 0: self.session.logger.error("no atoms selected") return self.perpendiculars = {} self.perp_centers = {} models = set(atom.structure for atom in atoms) for model in models: atom_coords = [] for atom in atoms: if atom.structure is model: atom_coords.append(atom.coord) if len(atom_coords) < 3: self.session.logger.error("fewer than 3 atoms selected on %s" % model.atomspec) continue xyz = np.array(atom_coords) xyz -= np.mean(atom_coords, axis=0) R = np.dot(xyz.T, xyz) u, s, vh = np.linalg.svd(R, compute_uv=True) vector = u[:, -1] self.perpendiculars[model] = vector self.perp_centers[model] = np.mean(atom_coords, axis=0) def set_group(self, *args): atoms = selected_atoms(self.session) if len(atoms) == 0: self.session.logger.error("no atoms selected") return self.groups = {} models = set(atom.structure for atom in atoms) for model in models: atom_coords = [] for atom in atoms: if atom.structure is model: atom_coords.append(atom.coord) self.groups[model] = np.mean(atom_coords, axis=0) def do_rotate(self, *args): selection = selected_atoms(self.session) models = {} for atom in selection: if atom.structure not in models: models[atom.structure] = [atom] else: models[atom.structure].append(atom) if len(models.keys()) == 0: return if self.vector_option.currentText() == "axis": if self.axis.currentText() == "z": vector = np.array([0., 0., 1.]) elif self.axis.currentText() == "y": vector = np.array([0., 1., 0.]) elif self.axis.currentText() == "x": vector = np.array([1., 0., 0.]) elif self.vector_option.currentText() == "view axis": if self.view_axis.currentText() == "z": vector = self.session.view.camera.get_position().axes()[2] elif self.view_axis.currentText() == "y": vector = self.session.view.camera.get_position().axes()[1] elif self.view_axis.currentText() == "x": vector = self.session.view.camera.get_position().axes()[0] elif self.vector_option.currentText() == "bond": vector = self.bonds elif self.vector_option.currentText() == "perpendicular to plane": vector = self.perpendiculars elif self.vector_option.currentText() == "centroid of atoms": vector = self.groups elif self.vector_option.currentText() == "custom": x = self.vector_x.value() y = self.vector_y.value() z = self.vector_z.value() vector = np.array([x, y, z]) angle = np.deg2rad(self.angle.value()) center = {} for model in models: atoms = models[model] coords = np.array([atom.coord for atom in atoms]) center[model] = np.mean(coords, axis=0) if self.cor_button.currentText() == "automatic": if self.vector_option.currentText() == "perpendicular to plane": center = self.perp_centers elif self.vector_option.currentText() == "bond": center = self.bond_centers elif self.cor_button.currentText() == "select atoms": center = self.manual_center else: center = self.session.main_view.center_of_rotation for model in models: if isinstance(vector, dict): if model not in vector.keys(): continue else: v = vector[model] else: v = vector if isinstance(center, dict): if model not in center.keys(): continue else: c = center[model] else: c = center if self.vector_option.currentText( ) == "centroid of atoms" and self.cor_button.currentText( ) != "automatic": v = v - c v = v / np.linalg.norm(v) q = np.hstack(([np.cos(angle / 2)], v * np.sin(angle / 2))) q /= np.linalg.norm(q) qs = q[0] qv = q[1:] xyz = np.array([a.coord for a in models[model]]) xyz -= c xprod = np.cross(qv, xyz) qs_xprod = 2 * qs * xprod qv_xprod = 2 * np.cross(qv, xprod) xyz += qs_xprod + qv_xprod + c for t, coord in zip(models[model], xyz): t.coord = coord def show_rot_vec(self, *args): for model in self.session.models.list(type=Generic3DModel): if model.name == "rotation vector": model.delete() if self.display_rot_vec.checkState() == Qt.Unchecked: return selection = selected_atoms(self.session) if len(selection) == 0: return models = {} for atom in selection: if atom.structure not in models: models[atom.structure] = [atom] else: models[atom.structure].append(atom) if len(models.keys()) == 0: return if self.vector_option.currentText() == "axis": if self.axis.currentText() == "z": vector = np.array([0., 0., 1.]) elif self.axis.currentText() == "y": vector = np.array([0., 1., 0.]) elif self.axis.currentText() == "x": vector = np.array([1., 0., 0.]) elif self.vector_option.currentText() == "view axis": if self.view_axis.currentText() == "z": vector = self.session.view.camera.get_position().axes()[2] elif self.view_axis.currentText() == "y": vector = self.session.view.camera.get_position().axes()[1] elif self.view_axis.currentText() == "x": vector = self.session.view.camera.get_position().axes()[0] elif self.vector_option.currentText() == "bond": vector = self.bonds elif self.vector_option.currentText() == "perpendicular to plane": vector = self.perpendiculars elif self.vector_option.currentText() == "centroid of atoms": vector = self.groups elif self.vector_option.currentText() == "custom": x = self.vector_x.value() y = self.vector_y.value() z = self.vector_z.value() vector = np.array([x, y, z]) center = {} for model in models: atoms = models[model] coords = np.array([atom.coord for atom in atoms]) center[model] = np.mean(coords, axis=0) if self.cor_button.currentText() == "automatic": if self.vector_option.currentText() == "perpendicular to plane": center = self.perp_centers elif self.vector_option.currentText() == "bond": center = self.bond_centers elif self.cor_button.currentText() == "select atoms": center = self.manual_center else: center = self.session.main_view.center_of_rotation for model in models: if isinstance(vector, dict): if model not in vector.keys(): continue else: v = vector[model] else: v = vector if isinstance(center, dict): if model not in center.keys(): continue else: c = center[model] else: c = center if self.vector_option.currentText( ) == "centroid of atoms" and self.cor_button.currentText( ) != "automatic": v = v - c if np.linalg.norm(v) == 0: continue residues = [] for atom in models[model]: if atom.residue not in residues: residues.append(atom.residue) v_c = c + v s = ".color red\n" s += ".arrow %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f 0.2 0.4 0.7\n" % ( *c, *v_c) stream = BytesIO(bytes(s, 'utf-8')) bild_obj, status = read_bild(self.session, stream, "rotation vector") self.session.models.add(bild_obj, parent=model) def delete(self): self.session.triggers.remove_handler(self._show_rot_vec) global_triggers = get_triggers() global_triggers.remove_handler(self._changes) for model in self.session.models.list(type=Generic3DModel): if model.name == "rotation vector": model.delete() return super().delete() def close(self): self.session.triggers.remove_handler(self._show_rot_vec) global_triggers = get_triggers() global_triggers.remove_handler(self._changes) for model in self.session.models.list(type=Generic3DModel): if model.name == "rotation vector": model.delete() return super().close()