Package schrodinger :: Package application :: Package desmond :: Module maestro :: Class Workspace

Class Workspace

object --+
         |
        Workspace

A class for representing the Workspace.

Instance Methods

[hide private]

__init__(self)
Does nothing.

_show_entry(self, eid)
Displays the entry or entries as given by 'eid' in the Workspace.

show_entry(self, eid)

_show_only_entry(self, eid)
Displays only the entry or entries as given by 'eid' in the Workspace.

show_only_entry(self, eid)

_grab(self)
Gets the CTs and entry IDs for the entries currently displayed in the Workspace.

grab(self)

_paint_asl(self, asl, color)
Colors the selected atoms as given by 'asl'.

paint_asl(self, asl, color)

paint_mol(self, i_mol, color)
Colors a molecule as given by the index of the molecule ('i_mol').

_ball_atom(self, atom=[], asl='', should_ball=True)
Represents selected atoms in the ball-and-stick mode.

ball_atom(self, atom=[], asl='', should_ball=True)

display_asl(self, asl, should_display=True)
Display the selected atoms (as given by the ASL expression 'asl') in the Workspace.

display_only_asl(self, asl, should_display=True)
Similar to display_asl, but non-selected atoms will be hidden.

_get_ct(self)

_commit(self)
Commits changes on 'self.ct' to the Workspace.

commit(self)

get_atom(self, asl)
Returns a list of indices of atoms as selected by the 'asl'.

_create_atom_tag(self, tag, value=None)
Creates one or more atom properties for all atoms included into the Workspace.

create_atom_tag(self, tag, value=None)

_delete_atom_tag(self, tag)
Deletes one or more atom properties for all atoms included into the Workspace.

delete_atom_tag(self, tag)

_mark_atom(self, tag, value, atom=[], asl='')
Sets value (given by the 'value' argument) to atom property (given by the 'tag' argument) for selected atoms in the Workspace.

mark_atom(self, tag, value, atom=[], asl='')

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

_ct = None
hash(x)

Properties

[hide private]

ct
Readonly property: returns the workspace as a 'Structure' object.

Inherited from object: __class__

Method Details

[hide private]

init(self)
(Constructor)

Does nothing.

Overrides: object.__init__

_show_entry(self, eid)

Displays the entry or entries as given by 'eid' in the Workspace.

Note that 'eid' can be either an integer that is the ID of a single entry or a list of integers that are the IDs of a few entries.

_show_only_entry(self, eid)

Displays only the entry or entries as given by 'eid' in the Workspace. The meaning of 'eid' is similar to that in _show_enty.

_grab(self)

Gets the CTs and entry IDs for the entries currently displayed in the Workspace.

This function returns a tuple of two elements. The 1st element is a list of schrodinger.structure.Structure objects, the 2nd one is a list of entry IDs.

_ball_atom(self, atom=`[]`, asl=`''`, should_ball=True)

Represents selected atoms in the ball-and-stick mode.

The selected atoms are chosen by either 'atom' or 'asl' argument. If both are given, 'asl' will be ignored.

Parameters:

atom - A list of atom indices.
asl - An ASL expression (as a string).
should_ball - If True, then the selected atoms will be drawn in the wire mode.

display_asl(self, asl, should_display=True)

Display the selected atoms (as given by the ASL expression 'asl') in the Workspace.

If 'should_display' is False, then the selected atoms will be undisplayed.

display_only_asl(self, asl, should_display=True)

Similar to display_asl, but non-selected atoms will be hidden.

If 'should_display' is False, then the selected atoms will be undisplayed without any effect on the non-selected atoms.

_create_atom_tag(self, tag, value=None)

Creates one or more atom properties for all atoms included into the Workspace.

The change will be committed to the included entries.

Parameters:

tag - The property name as a string or a list of property names in a list of strings.
value - The value for the corresponding atom property. If 'tag' is a list, then 'value' should also be a list.

_delete_atom_tag(self, tag)

Deletes one or more atom properties for all atoms included into the Workspace.

The change will be committed to the included entries.

Parameters:

tag - The property name as a string or a list of property names in a list of strings.

_mark_atom(self, tag, value, atom=`[]`, asl=`''`)

Sets value (given by the 'value' argument) to atom property (given by the 'tag' argument) for selected atoms in the Workspace.

The 'tag' and 'value' arguments can be lists, but they must be both lists or both not.

The selected atoms are given by the 'atom' argument or by an ASL expression ('asl'). Either 'atom' or 'asl' should be provided; if both are provided, 'asl' will be ignored.

The change will be committed to the included entries.

Property Details

[hide private]

ct

Readonly property: returns the workspace as a 'Structure' object.

Get Method:: _get_ct(self)

Class Workspace

__init__(self) (Constructor)

_show_entry(self, eid)

_show_only_entry(self, eid)

_grab(self)

_ball_atom(self, atom=[], asl='', should_ball=True)

display_asl(self, asl, should_display=True)

display_only_asl(self, asl, should_display=True)

_create_atom_tag(self, tag, value=None)

_delete_atom_tag(self, tag)

_mark_atom(self, tag, value, atom=[], asl='')

ct

init(self)
(Constructor)

_ball_atom(self, atom=`[]`, asl=`''`, should_ball=True)

_mark_atom(self, tag, value, atom=`[]`, asl=`''`)