def __init__(self,
part: NucleicAcidPartT,
x: float,
y: float,
z: float,
length: int,
direction: Vec3T = (0, 0, 1.),
id_num: int = None,
properties: Union[tuple, dict] = None,
safe: bool = True,
parity: int = None):
'''``UndoCommand`` to create a virtual helix in a ``NucleicAcidPart``
Args:
part: The parent ``NucleicAcidPart``
x: ``x`` coordinate of the 0 - index base
y: ``y`` coordinate of the 0 - index base
z: ``z`` coordinate of the 0 - index base
length: Length of the virtual helix in bases
direction: the direction of the virtual helix
id_num: the ID number of the helix in the ``part``
properties: the initial or inherited properties of the ``part``
safe: Default is ``True``. safe must be ``True`` to update neighbors.
otherwise, neighbors need to be explicitly updated. Set to
``False`` to speed up creation of many virtual helices
parity: even == 0, odd == 1, None == doesn't matter. Legacy from
scaffold based design
'''
super(CreateVirtualHelixCommand, self).__init__("create virtual helix")
self.part: NucleicAcidPartT = part
if id_num is None:
id_num = part._getNewIdNum(parity=parity)
else:
part._reserveIdNum(id_num)
self.id_num: int = id_num
self.origin_pt: Vec3T = (x, y, z)
self.direction: Vec3T = direction
self.length: int = length
self.color: str = part.getColor()
self.keys: List[str] = None
if properties is not None:
if isinstance(properties, tuple): # usually for unsafe
self.keys, self.values = properties
else:
self.keys = list(properties.keys())
self.values = list(properties.values())
self.neighbors: List[int] = []
if not safe:
self.neighbors = literal_eval(
self.values[self.keys.index('neighbors')])
self.threshold: float = 2.1 * part.radius()
self.safe: bool = safe
self.old_limits: RectT = None
def __init__(self,
part: NucleicAcidPartT,
x: float,
y: float,
z: float,
length: int,
direction: Vec3T = (0, 0, 1.),
id_num: int = None,
properties: Union[tuple, dict] = None,
safe: bool = True,
parity: int = None):
'''``UndoCommand`` to create a virtual helix in a ``NucleicAcidPart``
Args:
part: The parent ``NucleicAcidPart``
x: ``x`` coordinate of the 0 - index base
y: ``y`` coordinate of the 0 - index base
z: ``z`` coordinate of the 0 - index base
length: Length of the virtual helix in bases
direction: the direction of the virtual helix
id_num: the ID number of the helix in the ``part``
properties: the initial or inherited properties of the ``part``
safe: Default is ``True``. safe must be ``True`` to update neighbors.
otherwise, neighbors need to be explicitly updated. Set to
``False`` to speed up creation of many virtual helices
parity: even == 0, odd == 1, None == doesn't matter. Legacy from
scaffold based design
'''
super(CreateVirtualHelixCommand, self).__init__("create virtual helix")
self.part: NucleicAcidPartT = part
if id_num is None:
id_num = part._getNewIdNum(parity=parity)
else:
part._reserveIdNum(id_num)
self.id_num: int = id_num
self.origin_pt: Vec3T = (x, y, z)
self.direction: Vec3T = direction
self.length: int = length
self.color: str = part.getColor()
self.keys: List[str] = None
if properties is not None:
if isinstance(properties, tuple): # usually for unsafe
self.keys, self.values = properties
else:
self.keys = list(properties.keys())
self.values = list(properties.values())
self.neighbors: List[int] = []
if not safe:
self.neighbors = literal_eval(self.values[self.keys.index('neighbors')])
self.threshold: float = 2.1*part.radius()
self.safe: bool = safe
self.old_limits: RectT = None
def __init__(self, is_fwd: bool, id_num: int, part: NucleicAcidPartT,
initial_size: int):
self._document = part.document()
super(StrandSet, self).__init__(part)
self._is_fwd = is_fwd
self._is_scaffold = is_fwd if (id_num % 2 == 0) else not is_fwd
self._strand_type = StrandEnum.FWD if self._is_fwd else StrandEnum.REV
self._id_num = id_num
self._part = part
self._reset(int(initial_size))
self._undo_stack = None
def __init__(self, is_fwd: bool,
id_num: int,
part: NucleicAcidPartT,
initial_size: int):
self._document = part.document()
super(StrandSet, self).__init__(part)
self._is_fwd = is_fwd
self._is_scaffold = is_fwd if (id_num % 2 == 0) else not is_fwd
self._strand_type = StrandEnum.FWD if self._is_fwd else StrandEnum.REV
self._id_num = id_num
self._part = part
self._reset(int(initial_size))
self._undo_stack = None
def __init__(self, part: NucleicAcidPartT, id_num: int):
super(RemoveVirtualHelixCommand, self).__init__("remove virtual helix")
self.part = part
self.id_num = id_num
_, self.length = part.getOffsetAndSize(id_num)
x, y, _ = part.getVirtualHelixOrigin(id_num)
self.origin_pt = (x, y, 0.)
self.direction = tuple(part.directions[id_num]) # (0, 0, 1.)
neighbors = part.getVirtualHelixProperties(id_num, 'neighbors')
self.neighbors = literal_eval(neighbors)
self.color = part.getVirtualHelixProperties(id_num, 'color')
self.props = part.getAllVirtualHelixProperties(id_num, inject_extras=False)
self.old_active_base_info = part.active_base_info
self._vh_order = part.getVirtualHelixOrder().copy() # just copy the whole list
def __init__(self, model_part: NucleicAcidPartT,
part_item: PathNucleicAcidPartItemT):
"""
Args:
model_part:
part_item:
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, part_item.proxy())
self.setAcceptHoverEvents(True)
self.setBrush(getBrushObj(styles.BLUE_FILL, alpha=12))
self.setPen(getNoPen())
self.setZValue(styles.ZWORKPLANE)
self._model_part = model_part
self._part_item = part_item
self._low_drag_bound = 0 # idx, not pos
self._high_drag_bound = model_part.getProperty(
'max_vhelix_length') # idx, not pos
self._moving_via_handle = False
self.outline = PathWorkplaneOutline(self)
self.resize_handle_group = ResizeHandleGroup(self.rect(),
self._HANDLE_SIZE,
styles.BLUE_STROKE,
True,
HandleEnum.LEFT
| HandleEnum.RIGHT,
self,
translates_in=AxisEnum.X)
# Minimum size hint (darker internal rect, visible during resizing)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=64))
m_b_h.setPen(getNoPen())
m_b_h.hide()
# Low and high idx labels
self.resize_handle_group.updateText(HandleEnum.LEFT, self._idx_low)
self.resize_handle_group.updateText(HandleEnum.RIGHT, self._idx_high)
def __init__(self, model_part: NucleicAcidPartT,
part_item: PathNucleicAcidPartItemT):
"""
Args:
model_part:
part_item:
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, part_item.proxy())
self.setAcceptHoverEvents(True)
self.setBrush(getBrushObj(styles.BLUE_FILL, alpha=12))
self.setPen(getNoPen())
self.setZValue(styles.ZWORKPLANE)
self._model_part = model_part
self._part_item = part_item
self._low_drag_bound = 0 # idx, not pos
self._high_drag_bound = model_part.getProperty('max_vhelix_length') # idx, not pos
self._moving_via_handle = False
self.outline = PathWorkplaneOutline(self)
self.resize_handle_group = ResizeHandleGroup(self.rect(),
self._HANDLE_SIZE,
styles.BLUE_STROKE,
True,
HandleEnum.LEFT | HandleEnum.RIGHT,
self,
translates_in=AxisEnum.X)
# Minimum size hint (darker internal rect, visible during resizing)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=64))
m_b_h.setPen(getNoPen())
m_b_h.hide()
# Low and high idx labels
self.resize_handle_group.updateText(HandleEnum.LEFT, self._idx_low)
self.resize_handle_group.updateText(HandleEnum.RIGHT, self._idx_high)
def addToPart(self, part: NucleicAcidPartT, emit_signals: bool = False):
self._part = part
self.setParent(part)
part._addOligoToSet(self, emit_signals)
def addToPart(self, part: NucleicAcidPartT, emit_signals: bool = False):
self._part = part
self.setParent(part)
part._addOligoToSet(self, emit_signals)