is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| properties_dialog.py (pymol-v2.1.0.tar.bz2) | : | properties_dialog.py (pymol-open-source-2.2.0) |
|---|
| import os | | import os |
| | |
| from pymol.Qt import QtGui, QtCore, QtWidgets | | from pymol.Qt import QtGui, QtCore, QtWidgets |
|
| from pymol.Qt.utils import UpdateLock | | from pymol.Qt.utils import UpdateLock, PopupOnException |
| import pymol | | import pymol |
| | |
| class UneditableDelegate(QtWidgets.QStyledItemDelegate): | | class UneditableDelegate(QtWidgets.QStyledItemDelegate): |
| def createEditor(self, parent, option, index): | | def createEditor(self, parent, option, index): |
| return None | | return None |
| | |
| class FunctionSuspender: | | class FunctionSuspender: |
| def __init__(self, func): | | def __init__(self, func): |
| self.func = func | | self.func = func |
| def __enter__(self): | | def __enter__(self): |
| | |
| skipping to change at line 27 | | skipping to change at line 27 |
|---|
| self.func.suspended = False | | self.func.suspended = False |
| | |
| def suspendable(func): | | def suspendable(func): |
| def wrapper(*args, **kwargs): | | def wrapper(*args, **kwargs): |
| if not func.suspended: | | if not func.suspended: |
| return func(*args, **kwargs) | | return func(*args, **kwargs) |
| func.suspended = False | | func.suspended = False |
| wrapper.suspend = FunctionSuspender(func) | | wrapper.suspend = FunctionSuspender(func) |
| return wrapper | | return wrapper |
| | |
|
| | def get_object_names(_self): |
| | # was _self.get_names('public_objects') in PyMOL 2.1 |
| | # but that throws exceptions for groups/isosurfaces/etc. |
| | names = _self.get_object_list() |
| | return names |
| | |
| def props_dialog(parent): #noqa | | def props_dialog(parent): #noqa |
| from pymol.setting import name_dict | | from pymol.setting import name_dict |
| | |
| cmd = parent.cmd | | cmd = parent.cmd |
| form = parent.load_form('props', 'floating') | | form = parent.load_form('props', 'floating') |
| parent.addDockWidget(QtCore.Qt.RightDockWidgetArea, form._dialog) | | parent.addDockWidget(QtCore.Qt.RightDockWidgetArea, form._dialog) |
| | |
| def make_entry(parent, label): | | def make_entry(parent, label): |
| item = QtWidgets.QTreeWidgetItem(parent) | | item = QtWidgets.QTreeWidgetItem(parent) |
| item.setText(0, str(label)) | | item.setText(0, str(label)) |
| | |
| skipping to change at line 78 | | skipping to change at line 84 |
|---|
| item_atom_properties = Ellipsis # Incentive PyMOL only | | item_atom_properties = Ellipsis # Incentive PyMOL only |
| | |
| item_astate = make_cat(form.treeWidget, "Atom-State-Level") | | item_astate = make_cat(form.treeWidget, "Atom-State-Level") |
| item_astate_builtins = make_cat(item_astate, "Properties (built-in)") | | item_astate_builtins = make_cat(item_astate, "Properties (built-in)") |
| item_astate_settings = Ellipsis # Incentive PyMOL only | | item_astate_settings = Ellipsis # Incentive PyMOL only |
| | |
| keys_atom_identifiers = ['model', 'index', 'segi', 'chain', 'resi', | | keys_atom_identifiers = ['model', 'index', 'segi', 'chain', 'resi', |
| 'resn', 'name', 'alt', 'ID', 'rank'] | | 'resn', 'name', 'alt', 'ID', 'rank'] |
| keys_atom_builtins = ['elem', 'q', 'b', 'type', 'formal_charge', | | keys_atom_builtins = ['elem', 'q', 'b', 'type', 'formal_charge', |
| 'partial_charge', 'numeric_type', 'text_type', | | 'partial_charge', 'numeric_type', 'text_type', |
|
| 'stereo', 'vdw', 'ss', 'color', 'reps', | | # avoid stereo auto-assignment errors |
| | # 'stereo', |
| | 'vdw', 'ss', 'color', 'reps', |
| 'protons', 'geom', 'valence', 'elec_radius'] | | 'protons', 'geom', 'valence', 'elec_radius'] |
| keys_astate_builtins = ['state', 'x', 'y', 'z'] | | keys_astate_builtins = ['state', 'x', 'y', 'z'] |
| | |
| items = {} | | items = {} |
| for key in keys_atom_identifiers: | | for key in keys_atom_identifiers: |
| items[key] = make_entry(item_atom_identifiers, key) | | items[key] = make_entry(item_atom_identifiers, key) |
| for key in keys_atom_builtins: | | for key in keys_atom_builtins: |
| items[key] = make_entry(item_atom_builtins, key) | | items[key] = make_entry(item_atom_builtins, key) |
| for key in keys_astate_builtins: | | for key in keys_astate_builtins: |
| items[key] = make_entry(item_astate_builtins, key) | | items[key] = make_entry(item_astate_builtins, key) |
| | |
| skipping to change at line 120 | | skipping to change at line 128 |
|---|
| try: | | try: |
| if new_value: | | if new_value: |
| result = cmd.set_object_ttt(model, new_value) | | result = cmd.set_object_ttt(model, new_value) |
| except (ValueError, IndexError): | | except (ValueError, IndexError): |
| result = False | | result = False |
| elif item == item_ostate_title: | | elif item == item_ostate_title: |
| result = cmd.set_title(model, state, new_value) | | result = cmd.set_title(model, state, new_value) |
| elif item == item_ostate_matrix: | | elif item == item_ostate_matrix: |
| cmd.matrix_reset(model, state) | | cmd.matrix_reset(model, state) |
| try: | | try: |
|
| | new_value = cmd.safe_eval(new_value) |
| result = cmd.transform_object(model, new_value, state) | | result = cmd.transform_object(model, new_value, state) |
| except: # CmdTransformObject-DEBUG: bad matrix | | except: # CmdTransformObject-DEBUG: bad matrix |
| result = False | | result = False |
| elif parent == item_object_settings: | | elif parent == item_object_settings: |
|
| cmd.set(key, new_value, model, quiet=0) | | with PopupOnException(): |
| | cmd.set(key, new_value, model, quiet=0) |
| elif parent == item_ostate_settings: | | elif parent == item_ostate_settings: |
|
| cmd.set(key, new_value, model, state, quiet=0) | | with PopupOnException(): |
| | cmd.set(key, new_value, model, state, quiet=0) |
| elif parent == item_ostate_properties: | | elif parent == item_ostate_properties: |
| cmd.set_property(key, new_value, model, state, quiet=0) | | cmd.set_property(key, new_value, model, state, quiet=0) |
| else: | | else: |
| is_state = False | | is_state = False |
| | |
| if parent == item_atom_properties: | | if parent == item_atom_properties: |
| key = 'p.' + key | | key = 'p.' + key |
| elif parent == item_atom_settings: | | elif parent == item_atom_settings: |
| key = 's.' + key | | key = 's.' + key |
| elif parent == item_astate_settings: | | elif parent == item_astate_settings: |
| | |
| skipping to change at line 169 | | skipping to change at line 180 |
|---|
| else: | | else: |
| result = cmd.alter(*alter_args) | | result = cmd.alter(*alter_args) |
| | |
| if not result: | | if not result: |
| update_treewidget_model() | | update_treewidget_model() |
| | |
| item_changed.skip = False | | item_changed.skip = False |
| | |
| def update_object_settings(parent, model, state): | | def update_object_settings(parent, model, state): |
| parent.takeChildren() | | parent.takeChildren() |
|
| for sitem in ( | | for sitem in (cmd.get_object_settings(model, state) or []): |
| pymol.querying.get_object_settings( | | |
| model, | | |
| state, | | |
| _self=cmd) or []): | | |
| key = name_dict.get(sitem[0], sitem[0]) | | key = name_dict.get(sitem[0], sitem[0]) |
| item = make_entry(parent, key) | | item = make_entry(parent, key) |
| item.setText(1, str(sitem[2])) | | item.setText(1, str(sitem[2])) |
| | |
| def update_atom_settings(wrapper, parent): | | def update_atom_settings(wrapper, parent): |
| parent.takeChildren() | | parent.takeChildren() |
| for key in wrapper: | | for key in wrapper: |
| item = make_entry(parent, name_dict.get(key, key)) | | item = make_entry(parent, name_dict.get(key, key)) |
| value = wrapper[key] | | value = wrapper[key] |
| item.setText(1, str(value)) | | item.setText(1, str(value)) |
| | |
| def update_atom_properties(wrapper, parent): | | def update_atom_properties(wrapper, parent): |
| parent.takeChildren() | | parent.takeChildren() |
| for key in wrapper: | | for key in wrapper: |
| item = make_entry(parent, key) | | item = make_entry(parent, key) |
| value = wrapper[key] | | value = wrapper[key] |
| item.setText(1, str(value)) | | item.setText(1, str(value)) |
| | |
| def update_atom_fields(ns): | | def update_atom_fields(ns): |
| for key in keys_atom_identifiers + keys_atom_builtins: | | for key in keys_atom_identifiers + keys_atom_builtins: |
|
| value = ns[key] | | try: |
| | value = ns[key] |
| | except Exception as e: |
| | value = 'ERROR: ' + str(e) |
| items[key].setText(1, str(value)) | | items[key].setText(1, str(value)) |
| update_atom_settings(ns['s'], item_atom_settings) | | update_atom_settings(ns['s'], item_atom_settings) |
| | |
| def update_astate_fields(ns): | | def update_astate_fields(ns): |
| for key in keys_astate_builtins: | | for key in keys_astate_builtins: |
| value = ns[key] | | value = ns[key] |
| items[key].setText(1, str(value)) | | items[key].setText(1, str(value)) |
| | |
| space = { | | space = { |
| 'update_atom_fields': update_atom_fields, | | 'update_atom_fields': update_atom_fields, |
| | |
| skipping to change at line 296 | | skipping to change at line 306 |
|---|
| | |
| update_treewidget_state() | | update_treewidget_state() |
| item_changed.skip = False | | item_changed.skip = False |
| | |
| def update_model_list(*args): | | def update_model_list(*args): |
| if 'pk1' not in cmd.get_names('selections'): | | if 'pk1' not in cmd.get_names('selections'): |
| update_pk1() | | update_pk1() |
| | |
| with update_treewidget_model.suspend: | | with update_treewidget_model.suspend: |
| form.input_model.clear() | | form.input_model.clear() |
|
| form.input_model.addItems(cmd.get_names('public_objects')) | | form.input_model.addItems(get_object_names(cmd)) |
| update_from_pk1() | | update_from_pk1() |
| | |
| update_treewidget_model() | | update_treewidget_model() |
| | |
| # init input fields | | # init input fields |
|
| form.input_model.addItems(cmd.get_names('public_objects')) | | form.input_model.addItems(get_object_names(cmd)) |
| form.input_state.setValue(cmd.get_state()) | | form.input_state.setValue(cmd.get_state()) |
| | |
| # select pk1 atom if available | | # select pk1 atom if available |
| update_from_pk1() | | update_from_pk1() |
| | |
| # hook up events | | # hook up events |
| form.input_model.currentIndexChanged.connect(update_treewidget_model) | | form.input_model.currentIndexChanged.connect(update_treewidget_model) |
| form.input_state.valueChanged.connect(update_treewidget_state) | | form.input_state.valueChanged.connect(update_treewidget_state) |
| form.input_index.valueChanged.connect(update_treewidget) | | form.input_index.valueChanged.connect(update_treewidget) |
| form.button_refresh.clicked.connect(update_model_list) | | form.button_refresh.clicked.connect(update_model_list) |
| | | |
| End of changes. 10 change blocks. |
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| 12 lines changed or deleted | | 22 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 