def __init__(self,
session,
tug_mgr,
atoms,
spring_constant=None,
mode='atom'):
MouseMode.__init__(self, session)
self.tug_mode = mode
self._tugging = False
self._last_xy = None
self.name = 'ISOLDE_mouse_tug'
self._focal_atom = None
self._picked_atoms = None
self._picked_tuggables = None
self._pull_vector = None
self._xyz0 = None
self._xy = None
# Atomic array to pick from
self._atoms = atoms
# Tuggable atoms manager
self._tug_mgr = tug_mgr
if spring_constant is None:
from .constants import defaults
spring_constant = defaults.MOUSE_TUG_SPRING_CONSTANT
self.spring_constant = spring_constant
self.structure = atoms.unique_structures[0]
# Variables to be set by the caller
self.last_tugged_atom = None
self.already_tugging = False
def mouse_up(self, event):
MouseMode.mouse_up(self, event)
if self._markers:
self._log_tape_command()
self._markers = []
else:
self._clear()
def __init__(self, session):
MouseMode.__init__(self, session)
self._moving_marker = None # Atom
self._resizing_marker_or_link = None # Atom or Bond
self._set_initial_sizes = True # First marker on volume sets marker radius
def mouse_up(self, event):
if self._dragged:
self.log_volume_command()
elif self._multiwindow:
self._window_num += 1
self._maps = []
MouseMode.mouse_up(self, event)
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
res = self._mouse_pick(event)
if res:
self._show_zone(res)
elif not self._unlabel():
self._unzone()
def __init__(self, session):
MouseMode.__init__(self, session)
self._zone_range = 3 # Angstroms from chosen residue
self._minimize_steps = 10 # Number of steps per coordinate update
self._tugger = None
self._minimize_handler = None
def __init__(self, session):
MouseMode.__init__(self, session)
self._residue = None
self._align_atom_names = ['N', 'C', 'CA']
self._step_pixels = 20
self._step_meters = 0.05
self._last_y = None
self._label_atom_name = 'CA' # Which atom to show residue label on.
def __init__(self, session):
MouseMode.__init__(self, session)
self._map = None
self._matching_maps = [] # Adjust region for these maps too.
self._xy_last = None
self._center = None # Center of rotation
def __init__(self, session):
MouseMode.__init__(self, session)
self._maps = []
# Allow adjusting multiple windows (non-zero regions of brightness curve).
self._multiwindow = True
self._centers = []
self._window_num = 0
self._vr_window_switch_motion = 0.02 # meters
self._dragged = False
def __init__(self, session):
MouseMode.__init__(self, session)
self._start_point = None
self._marker_set = None
self._markers = []
self._color = (255, 255, 0, 255)
self._radius = .1 # scene units (usually Angstroms)
self._vr_radius = .002 # meters, for use in VR
self._min_move = 5 # minimum pixels to draw tape
self._start_time = 0
self._clear_time = 0.3 # seconds. Fast click/release causes clear.
def __init__(self, session):
MouseMode.__init__(self, session)
self._tugger = None
self._tugging = False
self._tug_handler = None
self._last_frame_number = None
self._puller = None
self._arrow_model = None
self._log = Logger('tug.log' if write_logs else None)
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
x, y = event.position()
from .label2d import label_under_window_position
self._label = label = label_under_window_position(self.session, x, y)
self._arr_part = None
if label is None:
from .arrows import arrow_under_window_position
self._label, self._arr_part = arrow_under_window_position(
self.session, x, y)
if self._label is None:
from .label3d import picked_3d_label
self._label = picked_3d_label(self.session, x, y)
def __init__(self, session):
MouseMode.__init__(self, session)
self.bound_button = None
self._map = None
self._matching_maps = [] # Adjust region for these maps too.
self._axis = None # Clicked face normal axis = 0, 1 or 2
self._side = None # 0 or 1 for min/max box face along axis
self._xy_last = None
self._frac_istep = 0
self._pixel_size = 1 # Screen pixel size in scene units at click point
self._slab_side = 0 # 0 for first slice of tilted slab, 1 for last slice
self._slab_dir = (0, 1)
def mouse_up(self, event):
MouseMode.mouse_up(self, event)
x, y = event.position()
pick = self.view.picked_object(x, y)
if isinstance(pick, PickedPseudobond) and not self._markerset:
bond = pick.pbond
if bond.group.name == "TS bonds":
atom1, atom2 = bond.atoms
run(self.session,
"~tsbond %s %s" % (atom1.atomspec, atom2.atomspec))
self.reset()
return
if isinstance(pick, PickedBond) and not self._markerset:
bond = pick.bond
run(self.session, "tsbond %s" % bond.atomspec)
self.reset()
return
if not self._atom1:
return
if isinstance(
pick,
PickedAtom) and pick.atom.structure is self._atom1.structure:
atom = pick.atom
else:
atom = self._atom2
if not atom:
self.reset()
return
if atom.structure is self._atom1.structure and atom is not self._atom1:
avg_radius = self.avg_bond_radius(self._atom1, atom)
run(
self.session, "tsbond %s %s radius %.3f" % (
self._atom1.atomspec,
atom.atomspec,
avg_radius,
))
self.reset()
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
x, y = event.position()
self._xy = (x, y)
v = self.session.main_view
if self.tug_mode == 'selection':
pa = self._atoms[self._atoms.selecteds]
self._reference_point = v.clip_plane_points(x, y)[0]
else:
# from . import picking
# pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5, hydrogens=True)
pick = v.picked_object(x, y, self._pick_exclude)
pa = self._pick_atoms(pick)
if pa is not None and len(pa):
if self._start_tugging_atoms(pa):
try:
self._set_pull_direction(x, y)
except:
self.tugging = False
def __init__(self, session):
MouseMode.__init__(self, session)
self._zone_center_residue = None
self._residue_distance = 5
self._label_distance = 4
self._label_size = 64 # Pixels
self._label_height = 0.7 # Scene units (Angstroms)
from chimerax.core.colors import BuiltinColors
self._label_color = BuiltinColors['yellow']
self._label_background = BuiltinColors['black']
self._surface_distance = 8
self._coil_width_scale = (0.2, 0.2)
self._helix_width_scale = (0.6, 0.2)
self._helix_arrow_scale = (1.2, 0.2, 0.2, 0.2)
self._sheet_width_scale = (0.6, 0.2)
self._sheet_arrow_scale = (1.2, 0.2, 0.2, 0.2)
self._ribbon_transparency = 100 # 0 = completely transparent, 255 = opaque
self._labeled_residues = None
self._scale_accum = 1
self._scale_step = 1.3 # Minimum scaling step factor
self._original_atom_display = None # Boolean mask of which atoms originally shown
self._original_residue_display = None # Boolean mask of which residues originally shown
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
def __init__(self, session):
MouseMode.__init__(self, session)
self._first_atom = None
def mouse_up(self, event):
self._drawing.display=False
MouseMode.mouse_up(self, event)
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
self._set_drawing_position()
self._set_drawing_color()
self._drawing.display=True
def mouse_down(self, event):
MouseMode.mouse_down(self, event)
pick = self._picked_bond(event)
self._bond_rot = self._bond_rotation(pick)
def move_marker_begin(self, event):
self._moving_marker = self.picked_marker(event)
if not isinstance(event, LaserEvent):
MouseMode.mouse_down(self, event)
def __init__(self, session): MouseMode.__init__(self, session) self._series = None self._player = None self.last_mouse_x = None
def mouse_up(self, event):
MouseMode.mouse_up(self, event)
self.tugging = False
def mouse_up(self, event):
MouseMode.mouse_up(self, event)
x,y = event.position()
pick = self.session.main_view.picked_object(x, y)
self._picked_object(pick)
def resize_begin(self, event):
m, l = self.picked_marker_or_link(event)
self._resizing_marker_or_link = m or l
if not isinstance(event, LaserEvent):
MouseMode.mouse_down(self, event)
def __init__(self, session):
MouseMode.__init__(self, session)
self._bond_rot = None
self._speed_factor = 2
self._minimum_angle_step = 2 # Degrees. Only applies to drag with 3d pointer.
def __init__(self, session):
MouseMode.__init__(self, session)
self._wrap = False
self._vr_full_range = 0.5 # Meters. Motion to play full coordset.
def mouse_up(self, event):
MouseMode.mouse_up(self, event)
self._log_command()
self._delete_bond_rotation()
def mouse_up(self, event):
self._unlabel()
MouseMode.mouse_up(self, event)
_log_swapaa_command(self._residue)
self._residue = None
self._last_y = None