def rotate(molecule, at, alpha):
if len(at) == 3:
try:
a1, a2, a3 = [a.coord() for a in at]
except AttributeError:
a1, a2, a3 = at
axis_a = a1 - a2
axis_b = a3 - a2
delta = chimera.angle(a1, a2, a3) - alpha
axis = chimera.cross(axis_a, axis_b)
if axis.data() == (0.0, 0.0, 0.0):
axis = chimera.cross(axis_a, axis_b + chimera.Vector(1, 0, 0))
logger.warning("Had to choose arbitrary normal vector")
pivot = a2
elif len(at) == 4:
try:
a1, a2, a3, a4 = [a.coord() for a in at]
except AttributeError:
a1, a2, a3, a4 = at
axis = a3 - a2
delta = chimera.dihedral(a1, a2, a3, a4) - alpha
pivot = a3
else:
raise ValueError(
"Atom list must contain 3 (angle) or 4 (dihedral) atoms only")
r = X.translation(pivot - ZERO) # move to origin
r.multiply(X.rotation(axis, -delta)) # rotate
r.multiply(X.translation(ZERO - pivot)) # return to orig pos
for a in molecule.atoms:
a.setCoord(r.apply(a.coord()))
def symmetry_xform(mol_xform, sym_xform, ref_xform):
from chimera import Xform
xf = Xform(mol_xform)
xf.premultiply(ref_xform.inverse())
xf.premultiply(sym_xform)
xf.premultiply(ref_xform)
return xf
def triangle_transformation(t1, t2): tf1 = triangle_frame(t1) tf2 = triangle_frame(t2) xf = frame_transform(tf1, tf2) c1 = center(t1) from chimera import Xform xf.multiply(Xform.translation(-c1[0], -c1[1], -c1[2])) c2 = center(t2) xf.premultiply(Xform.translation(c2[0], c2[1], c2[2])) return xf
def rotate_mouse_drag_cb(self, viewer, event):
# Get rotation about origin.
xf = viewer.vsphere(event.time, event.x, event.y, event.state % 2 == 1)
cx, cy, cz = self.rotation_center
# Change center of rotation to act about center of movable objects.
from chimera import Xform
xf.multiply(Xform.translation(-cx, -cy, -cz))
xf.premultiply(Xform.translation(cx, cy, cz))
self.move_objects(xf)
def rotation_axis_angle(r):
from chimera import Xform
xf = Xform.xform(r[0][0], r[0][1], r[0][2], 0, r[1][0], r[1][1], r[1][2],
0, r[2][0], r[2][1], r[2][2], 0)
axis, angle = xf.getRotation()
return tuple(axis.data()), angle
def rotation_from_axis_angle(axis, angle):
from chimera import Xform, Vector
r = Xform.rotation(Vector(*axis), angle)
m = r.getOpenGLMatrix()
rm = ((m[0], m[4], m[8]), (m[1], m[5], m[9]), (m[2], m[6], m[10]))
return rm
def map_overlap_and_correlation(map1, map2, above_threshold, xform = None):
p, w1 = map_points_and_weights(map1, above_threshold)
if xform is None:
from chimera import Xform
xform = Xform()
w2 = map2.interpolated_values(p, xform, subregion = None, step = None)
return overlap_and_correlation(w1, w2)
def euler_rotation(phi, theta, psi):
from chimera import Xform, Vector
xf1 = Xform.rotation(Vector(0, 0, 1), phi) # Rotate about z-axis
xp = xf1.apply(Vector(1, 0, 0)) # New x-axis
xf2 = Xform.rotation(xp, theta) # Rotate about new x-axis
zp = xf2.apply(Vector(0, 0, 1)) # New z-axis
xf3 = Xform.rotation(zp, psi) # Rotate about new z-axis
xf = Xform()
xf.premultiply(xf1)
xf.premultiply(xf2)
xf.premultiply(xf3)
return xf
def atoms_outside_contour(atoms, volume = None):
if volume is None:
from VolumeViewer import active_volume
volume = active_volume()
points = atom_coordinates(atoms)
from chimera import Xform
poc, clevel = points_outside_contour(points, Xform(), volume)
return poc, clevel
def translate(molecule, anchor, target):
if isinstance(anchor, chimera.Atom):
anchor = anchor.coord()
if isinstance(target, chimera.Atom):
target = target.coord()
t = X.translation(target - anchor)
for a in molecule.atoms:
a.setCoord(t.apply(a.coord()))
def atoms_outside_map(atoms, dr, contour_level):
from _multiscale import get_atom_coordinates
xyz = get_atom_coordinates(atoms, transformed=True)
from chimera import Xform
values = dr.interpolated_values(xyz, Xform())
from numpy import compress
aolist = list(compress(values < contour_level, atoms))
return aolist
def same_xform(xf1, xf2, angle_tolerance=0, shift_tolerance=0):
if angle_tolerance == 0 and shift_tolerance == 0:
return xf1.getOpenGLMatrix() == xf2.getOpenGLMatrix()
from chimera import Xform
xf = Xform()
xf.multiply(xf1)
xf.multiply(xf2.inverse())
trans = xf.getTranslation()
axis, angle = xf.getRotation()
if (abs(angle) > angle_tolerance or trans.length > shift_tolerance):
return False
return True
def show_cumulative_transform(self, m):
from chimera import Xform
mxf = getattr(m, 'applied_xform', Xform())
import Matrix
tf = Matrix.xform_matrix(mxf)
angles = Matrix.euler_angles(tf)
shift = mxf.getTranslation().data()
text = ('Cumulative:\n' + ' Euler angles %.5g %.5g %.5g\n' % angles +
' Shift: %.5g %.5g %.5g' % shift)
self.cumulative['text'] = text
def coordinate_transform_xforms(xflist, from_xf, to_xf):
cxf = from_xf.inverse()
cxf.multiply(to_xf)
cxfinv = cxf.inverse()
from chimera import Xform
xftlist = []
for xf in xflist:
xft = Xform()
xft.multiply(cxfinv)
xft.multiply(xf)
xft.multiply(cxf)
xftlist.append(xft)
return xftlist
def addDihedralBond(a1, a2, length, angleInfo, dihedInfo):
"""Make bond between two models.
The models will be combined and the originals closed.
The new model will be opened in the same id/subid as the
non-moving model.
a1/a2 are atoms in different models.
a2 and atoms in its model will be moved to form the bond.
'length' is the bond length.
'angleInfo' is a two-tuple of sequence of three atoms and
an angle that the three atoms should form.
'dihedInfo' is like 'angleInfo', but 4 atoms.
angleInfo/dihedInfo can be None if insufficient atoms
"""
if a1.molecule == a2.molecule:
raise ValueError("Atoms to be bonded must be in different models")
# first, get the distance correct
from chimera import Xform, cross, angle, Point
dvector = a1.xformCoord() - a2.xformCoord()
dvector.length = dvector.length + length
openState = a2.molecule.openState
openState.globalXform(Xform.translation(dvector))
# then angle
if angleInfo:
atoms, angleVal = angleInfo
p1, p2, p3 = [a.xformCoord() for a in atoms]
axis = cross(p1-p2, p2-p3)
curAngle = angle(p1, p2, p3)
delta = angleVal - curAngle
v2 = p2 - Point(0.0, 0.0, 0.0)
trans1 = Xform.translation(v2)
v2.negate()
trans2 = Xform.translation(v2)
trans1.multiply(Xform.rotation(axis, delta))
trans1.multiply(trans2)
openState.globalXform(trans1)
def addDihedralBond(a1, a2, length, angleInfo, dihedInfo):
"""Make bond between two models.
The models will be combined and the originals closed.
The new model will be opened in the same id/subid as the
non-moving model.
a1/a2 are atoms in different models.
a2 and atoms in its model will be moved to form the bond.
'length' is the bond length.
'angleInfo' is a two-tuple of sequence of three atoms and
an angle that the three atoms should form.
'dihedInfo' is like 'angleInfo', but 4 atoms.
angleInfo/dihedInfo can be None if insufficient atoms
"""
if a1.molecule == a2.molecule:
raise ValueError("Atoms to be bonded must be in different models")
# first, get the distance correct
from chimera import Xform, cross, angle, Point
dvector = a1.xformCoord() - a2.xformCoord()
dvector.length = dvector.length + length
openState = a2.molecule.openState
openState.globalXform(Xform.translation(dvector))
# then angle
if angleInfo:
atoms, angleVal = angleInfo
p1, p2, p3 = [a.xformCoord() for a in atoms]
axis = cross(p1 - p2, p2 - p3)
curAngle = angle(p1, p2, p3)
delta = angleVal - curAngle
v2 = p2 - Point(0.0, 0.0, 0.0)
trans1 = Xform.translation(v2)
v2.negate()
trans2 = Xform.translation(v2)
trans1.multiply(Xform.rotation(axis, delta))
trans1.multiply(trans2)
openState.globalXform(trans1)
def symmetry_xform(mol_xform, sym_xform, ref_xform):
from chimera import Xform
xf = Xform(mol_xform)
xf.premultiply(ref_xform.inverse())
xf.premultiply(sym_xform)
xf.premultiply(ref_xform)
return xf
def anglePos(atomPos, bondPos, bondLength, degrees, coplanar=None): if coplanar: # may have one or two coplanar positions specified, # if two, compute both resultant positions and average # (the up vector has to be negated for the second one) xforms = [] if len(coplanar) > 2: raise ValueError, \ "More than 2 coplanar positions specified!" for cpos in coplanar: up = cpos - atomPos if xforms: up.negate() xform = Xform.lookAt(atomPos, bondPos, up) # lookAt puts ref point opposite that of zAlign, so # rotate 180 degrees around y axis xform.premultiply(Xform.yRotation(180)) xforms.append(xform) else: xforms = [Xform.zAlign(atomPos, bondPos)] points = [] for xform in xforms: radians = pi * degrees / 180.0 angle = Point(0.0, bondLength * sin(radians), bondLength * cos(radians)) xform.invert() points.append(xform.apply(angle)) if len(points) > 1: midpoint = points[0] + (points[1] - points[0]) / 2.0 v = midpoint - atomPos v.length = bondLength return atomPos + v return points[0]
def anglePos(atomPos, bondPos, bondLength, degrees, coplanar=None):
if coplanar:
# may have one or two coplanar positions specified,
# if two, compute both resultant positions and average
# (the up vector has to be negated for the second one)
xforms = []
if len(coplanar) > 2:
raise ValueError, \
"More than 2 coplanar positions specified!"
for cpos in coplanar:
up = cpos - atomPos
if xforms:
up.negate()
xform = Xform.lookAt(atomPos, bondPos, up)
# lookAt puts ref point opposite that of zAlign, so
# rotate 180 degrees around y axis
xform.premultiply(Xform.yRotation(180))
xforms.append(xform)
else:
xforms = [Xform.zAlign(atomPos, bondPos)]
points = []
for xform in xforms:
radians = pi * degrees / 180.0
angle = Point(0.0, bondLength * sin(radians),
bondLength * cos(radians))
xform.invert()
points.append(xform.apply(angle))
if len(points) > 1:
midpoint = points[0] + (points[1] - points[0]) / 2.0
v = midpoint - atomPos
v.length = bondLength
return atomPos + v
return points[0]
def update(self, trigName, myData, changes):
# print >> __stdout__, "update", trigName, myData, dir(changes), changes.modified
# coordSet = list(changes.modified)[0]
# print >> __stdout__, len(coordSet.coords())
# print >> __stdout__, dir(coordSet)
# print >> __stdout__, "update"
# atoms = []
# for selection in xla.get_gui().Subunits.getMovableAtomSpecs():
# atoms.extend(evalSpec(selection).atoms())
for serie in self.series:
serie['new'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['new'].append(numpyArrayFromAtoms(atoms))
# if self.was_changed():
i = 0
changed_c = None
for old_c, new_c in zip(serie['old'], serie['new']):
if not (old_c == new_c).all():
changed_c = i
i = i + 1
if changed_c is not None:
other = set(range(len(serie['chainIds'])))
other.remove(changed_c)
t3d, rmsd = matchPositions(serie['new'][changed_c],
serie['old'][changed_c])
for o in other:
newT = Xform.identity()
newT.premultiply(serie['t3ds'][o][changed_c])
newT.premultiply(t3d)
newT.premultiply(serie['t3ds'][changed_c][o])
atoms = evalSpec(':.{0}'.format(
serie['chainIds'][o])).atoms()
for a in atoms:
a.setCoord(newT.apply(a.coord()))
serie['old'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def update(self, trigName, myData, changes):
# print >> __stdout__, "update", trigName, myData, dir(changes), changes.modified
# coordSet = list(changes.modified)[0]
# print >> __stdout__, len(coordSet.coords())
# print >> __stdout__, dir(coordSet)
# print >> __stdout__, "update"
# atoms = []
# for selection in xla.get_gui().Subunits.getMovableAtomSpecs():
# atoms.extend(evalSpec(selection).atoms())
for serie in self.series:
serie['new'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['new'].append(numpyArrayFromAtoms(atoms))
# if self.was_changed():
i = 0
changed_c = None
for old_c, new_c in zip(serie['old'], serie['new']):
if not (old_c == new_c).all():
changed_c = i
i = i + 1
if changed_c is not None:
other = set(range(len(serie['chainIds'])))
other.remove(changed_c)
t3d, rmsd = matchPositions(serie['new'][changed_c], serie['old'][changed_c])
for o in other:
newT = Xform.identity()
newT.premultiply(serie['t3ds'][o][changed_c])
newT.premultiply(t3d)
newT.premultiply(serie['t3ds'][changed_c][o])
atoms = evalSpec(':.{0}'.format(serie['chainIds'][o])).atoms()
for a in atoms:
a.setCoord(newT.apply(a.coord()))
serie['old'] = []
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def orthogonalize(r):
from chimera import Xform
xf = Xform.xform(r[0][0],
r[0][1],
r[0][2],
0,
r[1][0],
r[1][1],
r[1][2],
0,
r[2][0],
r[2][1],
r[2][2],
0,
orthogonalize=True)
ro = xform_matrix(xf)
ro33 = tuple([row[:3] for row in ro])
return ro33
def position_orthoviews(tv):
# Put all 3 planes in xy plane.
vx, vy, vz = tv
from chimera import Xform
vx.openState.localXform(Xform.xRotation(-90))
vx.openState.localXform(Xform.zRotation(-90))
vy.openState.localXform(Xform.xRotation(-90))
vy.openState.localXform(Xform.zRotation(180))
# Horz/vert axes vx:(y,z), vy:(x,z), vz:(x,y)
sizes = []
for v in tv:
(x0, y0, z0), (x1, y1, z1) = v.xyz_bounds(step=1, subregion='all')
sizes.append((x1 - x0, y1 - y0, z1 - z0))
# Align lower left corners
vy.openState.localXform(Xform.translation(-sizes[1][0]))
# Center vertically and spread out horizontally.
vx.openState.localXform(Xform.translation(0, 0, -0.5 * sizes[0][2]))
offset = 1.05 * sizes[0][1]
vy.openState.localXform(Xform.translation(offset, 0, -0.5 * sizes[1][2]))
offset += .05 * sizes[0][1] + sizes[1][0]
vz.openState.localXform(Xform.translation(offset, -0.5 * sizes[2][1], 0))
# Hide all other models.
from chimera import openModels
mset = set(tv + [v.solid_model() for v in tv])
for m in openModels.list():
if not m in mset:
m.display = False
# Standard orientation, fit in window.
from Midas import reset
reset()
from chimera import viewer
viewer.viewAll()
viewer.scaleFactor *= 0.95
viewer.depthCue = False
def translate_xy_mouse_drag_cb(self, viewer, event):
px, py = self.previous_xy
dx = event.x - px
dy = event.y - py
self.previous_xy = (event.x, event.y)
psize = pixel_size_at_rotation_center(self.rotation_center)
if event.state & 0x1:
psize *= 0.1 # Slow motion when shift key held
from chimera import Xform
xf = Xform.translation(psize * dx, -psize * dy, 0)
self.move_objects(xf)
# Translate fixed rotation center.
from chimera import openModels
if openModels.cofrMethod == openModels.Fixed:
openModels.cofr = xf.apply(openModels.cofr)
def accSynAnti(donor, donorHyds, acceptor, synAtom, planeAtom, synR2, synPhi, synTheta, antiR2, antiPhi, antiTheta): """'planeAtom' (in conjunction with acceptor, and with 'synAtom' defining the 'up' direction) defines a plane. If donor is on the same side as 'synAtom', use syn params, otherwise anti params. """ if base.verbose: print "accSynAnti" dc = donor.xformCoord() dp = dc ac = acceptor.xformCoord() ap = ac pp = planeAtom.xformCoord() sp = synAtom.xformCoord() synXform = Xform.lookAt(ap, pp, sp - pp) xdp = synXform.apply(dp) phiBasePos = pp phiPlane = [ap, pp, sp] if xdp.y > 0.0: if base.verbose: print "Syn" if donor.element.name == "S": # increase distance cutoff to allow for larger # vdw radius of sulphur (which isn't considered # considered as a donor in original paper) synR2 = sulphurCompensate(synR2) return testPhiPsi(dp, donorHyds, ap, phiBasePos, phiPlane, synR2, synPhi, synTheta) if base.verbose: print "Anti" if donor.element.name == "S": # increase distance to compensate for sulphur radius antiR2 = sulphurCompensate(antiR2) return testPhiPsi(dp, donorHyds, ap, phiBasePos, phiPlane, antiR2, antiPhi, antiTheta)
def map_points_and_weights(v, above_threshold, metric = 'sum product'):
from chimera import Xform
m, tf_inv = v.matrix_and_transform(Xform(), subregion = None, step = None)
from Matrix import invert_matrix
tf = invert_matrix(tf_inv)
size = list(m.shape)
size.reverse()
from VolumeData import grid_indices
from numpy import single as floatc, ravel, nonzero, take
points = grid_indices(size, floatc) # i,j,k indices
import _contour
_contour.affine_transform_vertices(points, tf)
weights = ravel(m).astype(floatc)
if above_threshold:
# Keep only points where density is above lowest displayed threshold
threshold = min(v.surface_levels)
from numpy import greater_equal, compress
ge = greater_equal(weights, threshold)
points = compress(ge, points, 0)
weights = compress(ge, weights)
if metric == 'correlation about mean':
wm = weights.sum() / len(weights)
weights -= wm
else:
# Eliminate points with zero weight.
nz = nonzero(weights)[0]
if len(nz) < len(weights):
points = take(points, nz, axis=0)
weights = take(weights, nz, axis=0)
return points, weights
def findPt(n1, n2, n3, dist, angle, dihed):
# cribbed from Midas addgrp command
v12 = n2 - n1
v13 = n3 - n1
v12.normalize()
x = cross(v13, v12)
x.normalize()
y = cross(v12, x)
y.normalize()
mat = [0.0] * 12
for i in range(3):
mat[i * 4] = x[i]
mat[1 + i * 4] = y[i]
mat[2 + i * 4] = v12[i]
mat[3 + i * 4] = n1[i]
xform = Xform.xform(*mat)
radAngle = pi * angle / 180.0
tmp = dist * sin(radAngle)
radDihed = pi * dihed / 180.0
pt = Point(tmp * sin(radDihed), tmp * cos(radDihed), dist * cos(radAngle))
return xform.apply(pt)
def findPt(n1, n2, n3, dist, angle, dihed): # cribbed from Midas addgrp command v12 = n2 - n1 v13 = n3 - n1 v12.normalize() x = cross(v13, v12) x.normalize() y = cross(v12, x) y.normalize() mat = [0.0] * 12 for i in range(3): mat[i*4] = x[i] mat[1 + i*4] = y[i] mat[2 + i*4] = v12[i] mat[3 + i*4] = n1[i] xform = Xform.xform(*mat) radAngle = pi * angle / 180.0 tmp = dist * sin(radAngle) radDihed = pi * dihed / 180.0 pt = Point(tmp*sin(radDihed), tmp*cos(radDihed), dist*cos(radAngle)) return xform.apply(pt)
def __init__(self):
self.m = chimera.openModels.list()[0]
# Matchmaker yRvb12.hexamer.pdb, chain C (#1) with yRvb12.hexamer.pdb, chain A (#0), sequence alignment score = 1986.2
# with these parameters:
# chain pairing: bb
# Needleman-Wunsch using BLOSUM-62
# ss fraction: 0.3
# gap open (HH/SS/other) 18/18/6, extend 1
# ss matrix:
# (H, O): -6
# (S, S): 6
# (H, H): 6
# (O, S): -6
# (O, O): 4
# (H, S): -9
# iteration cutoff: 2
# RMSD between 393 atom pairs is 0.001 angstroms
# Position of yRvb12.hexamer.pdb (#0) relative to yRvb12.hexamer.pdb (#1) coordinates:
# Matrix rotation and translation
# -0.50000042 0.86602516 0.00000116 -103.53997515
# -0.86602516 -0.50000042 0.00000058 179.33655802
# 0.00000108 -0.00000072 1.00000000 0.00005125
# Axis -0.00000075 0.00000005 -1.00000000
# Axis point -0.00001174 119.55767842 0.00000000
# Rotation angle (degrees) 120.00002798
# Shift along axis 0.00003425
self.series = [
{
'tr3d': Xform.xform(-0.50000042, 0.86602516, 0.00000116, -103.53997515,
-0.86602516, -0.50000042, 0.00000058, 179.33655802,
0.00000108, -0.00000072, 1.00000000, 0.00005125, orthogonalize=True),
'chainIds': ['A', 'C', 'E'],
'old': [],
'new': []
}
]
# for a in evalSpec(':.A').atoms():
# a.setCoord(self.symTr3d.apply(a.coord()))
for serie in self.series:
serie['t3ds'] = [[None for i in range(len(serie['chainIds']))] for j in range(len(serie['chainIds']))]
for i in range(len(serie['chainIds'])):
# self.t3ds.append([])
for j in range(len(serie['chainIds'])):
count = abs(j-i)
symTr3d = Xform.identity()
for c in range(count):
symTr3d.multiply(serie['tr3d'])
newT = Xform.identity()
if i < j:
newT = symTr3d
elif i > j:
newT = symTr3d.inverse()
serie['t3ds'][i][j] = newT
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
def check_space_navigator(self, trigger_name, d1, d2):
e = self.device.last_event()
if e is None:
return
rot, trans, buttons = e
from math import sqrt, pow
from chimera import Vector, Xform, viewer
# Rotation
rx, ry, rz = rot # 10 bits, signed, +/-512
rmag = sqrt(rx * rx + ry * ry + rz * rz)
# Translation
tx, ty, tz = trans # 10 bits, signed, +/-512
if self.zoom and not self.fly_mode:
zm = tz
tz = 0
else:
zm = 0
tmag = sqrt(tx * tx + ty * ty + tz * tz)
zmag = abs(zm)
if self.dominant:
if tmag < rmag or tmag < zmag:
tmag = 0
if rmag < tmag or rmag < zmag:
rmag = 0
if zmag < tmag or zmag < rmag:
zmag = 0
if self.fly_mode:
rt = 50
if abs(ry) > abs(rx) + rt and abs(ry) > abs(rz) + rt:
rx = rz = 0
else:
ry = 0
rmag = sqrt(rx * rx + ry * ry + rz * rz)
if rmag > 0:
axis = Vector(rx / rmag, ry / rmag, rz / rmag)
if self.fly_mode: f = 3
else: f = 30
angle = self.speed * (f * rmag / 512)
xf = Xform.rotation(axis, angle)
self.apply_transform(xf)
if tmag > 0:
axis = Vector(tx / tmag, ty / tmag, tz / tmag)
shift = axis * 0.15 * self.speed * viewer.viewSize * tmag / 512
xf = Xform.translation(shift)
self.apply_transform(xf)
if zmag != 0:
f = pow(1.1, self.speed * float(zm) / 512)
import Midas
Midas.updateZoomDepth(viewer)
try:
viewer.scaleFactor *= f
except ValueError:
import chimera
raise chimera.LimitationError("refocus to continue scaling")
if 'N1' in buttons or 31 in buttons:
self.view_all()
if 'N2' in buttons:
self.toggle_dominant_mode()
def check_space_navigator(self, trigger_name, d1, d2):
e = self.device.last_event()
if e is None:
return
rot, trans, buttons = e
from math import sqrt, pow
from chimera import Vector, Xform, viewer
# Rotation
rx, ry, rz = rot # 10 bits, signed, +/-512
rmag = sqrt(rx*rx + ry*ry + rz*rz)
# Translation
tx, ty, tz = trans # 10 bits, signed, +/-512
if self.zoom and not self.fly_mode:
zm = tz
tz = 0
else:
zm = 0
tmag = sqrt(tx*tx + ty*ty + tz*tz)
zmag = abs(zm)
if self.dominant:
if tmag < rmag or tmag < zmag:
tmag = 0
if rmag < tmag or rmag < zmag:
rmag = 0
if zmag < tmag or zmag < rmag:
zmag = 0
if self.fly_mode:
rt = 50
if abs(ry) > abs(rx)+rt and abs(ry) > abs(rz)+rt: rx = rz = 0
else: ry = 0
rmag = sqrt(rx*rx + ry*ry + rz*rz)
if rmag > 0:
axis = Vector(rx/rmag, ry/rmag, rz/rmag)
if self.fly_mode: f = 3
else: f = 30
angle = self.speed*(f*rmag/512)
xf = Xform.rotation(axis, angle)
self.apply_transform(xf)
if tmag > 0:
axis = Vector(tx/tmag, ty/tmag, tz/tmag)
shift = axis * 0.15 * self.speed * viewer.viewSize * tmag/512
xf = Xform.translation(shift)
self.apply_transform(xf)
if zmag != 0:
f = pow(1.1, self.speed*float(zm)/512)
import Midas
Midas.updateZoomDepth(viewer)
try:
viewer.scaleFactor *= f
except ValueError:
import chimera
raise chimera.LimitationError("refocus to continue scaling")
if 'N1' in buttons or 31 in buttons:
self.view_all()
if 'N2' in buttons:
self.toggle_dominant_mode()
def euler_xform(euler_angles, translation):
xf = euler_rotation(*euler_angles)
from chimera import Xform
xf.premultiply(Xform.translation(*translation))
return xf
def __init__(self):
self.m = chimera.openModels.list()[0]
# Matchmaker yRvb12.hexamer.pdb, chain C (#1) with yRvb12.hexamer.pdb, chain A (#0), sequence alignment score = 1986.2
# with these parameters:
# chain pairing: bb
# Needleman-Wunsch using BLOSUM-62
# ss fraction: 0.3
# gap open (HH/SS/other) 18/18/6, extend 1
# ss matrix:
# (H, O): -6
# (S, S): 6
# (H, H): 6
# (O, S): -6
# (O, O): 4
# (H, S): -9
# iteration cutoff: 2
# RMSD between 393 atom pairs is 0.001 angstroms
# Position of yRvb12.hexamer.pdb (#0) relative to yRvb12.hexamer.pdb (#1) coordinates:
# Matrix rotation and translation
# -0.50000042 0.86602516 0.00000116 -103.53997515
# -0.86602516 -0.50000042 0.00000058 179.33655802
# 0.00000108 -0.00000072 1.00000000 0.00005125
# Axis -0.00000075 0.00000005 -1.00000000
# Axis point -0.00001174 119.55767842 0.00000000
# Rotation angle (degrees) 120.00002798
# Shift along axis 0.00003425
self.series = [{
'tr3d':
Xform.xform(-0.50000042,
0.86602516,
0.00000116,
-103.53997515,
-0.86602516,
-0.50000042,
0.00000058,
179.33655802,
0.00000108,
-0.00000072,
1.00000000,
0.00005125,
orthogonalize=True),
'chainIds': ['A', 'C', 'E'],
'old': [],
'new': []
}]
# for a in evalSpec(':.A').atoms():
# a.setCoord(self.symTr3d.apply(a.coord()))
for serie in self.series:
serie['t3ds'] = [[None for i in range(len(serie['chainIds']))]
for j in range(len(serie['chainIds']))]
for i in range(len(serie['chainIds'])):
# self.t3ds.append([])
for j in range(len(serie['chainIds'])):
count = abs(j - i)
symTr3d = Xform.identity()
for c in range(count):
symTr3d.multiply(serie['tr3d'])
newT = Xform.identity()
if i < j:
newT = symTr3d
elif i > j:
newT = symTr3d.inverse()
serie['t3ds'][i][j] = newT
for chainId in serie['chainIds']:
atoms = evalSpec(':.{0}'.format(chainId)).atoms()
serie['old'].append(numpyArrayFromAtoms(atoms))
import chimera
from chimera import Plane, Xform, cross, Vector, Point
m = chimera.openModels.list()[0]
b = chimera.selection.currentBonds()[0]
bondVec = b.atoms[0].coord() - b.atoms[1].coord()
bondVec.normalize()
axis = Vector(1.0, 0.0, 0.0)
crossProd = cross(axis, bondVec)
if crossProd.sqlength() > 0:
from math import acos, degrees
xform = Xform.rotation(crossProd, degrees(acos(axis * bondVec)))
xform.invert()
else:
xform = Xform.identity()
m.openState.xform = xform
# okay, that puts the bond parallel to the X axis, now swing the plane of
# the rest of the molecule into the xy plane...
molPlane = Plane([a.xformCoord() for a in m.atoms[:3]])
angle = chimera.angle(molPlane.normal, Vector(0, 0, -1))
xform2 = Xform.rotation(b.atoms[0].xformCoord() - b.atoms[1].xformCoord(),
angle)
xform2.multiply(xform)
m.openState.xform = xform2
import chimera from chimera import Plane, Xform, cross, Vector, Point m = chimera.openModels.list()[0] b = chimera.selection.currentBonds()[0] bondVec = b.atoms[0].coord() - b.atoms[1].coord() bondVec.normalize() axis = Vector(1.0, 0.0, 0.0) crossProd = cross(axis, bondVec) if crossProd.sqlength() > 0: from math import acos, degrees xform = Xform.rotation(crossProd, degrees(acos(axis * bondVec))) xform.invert() else: xform = Xform.identity() m.openState.xform = xform # okay, that puts the bond parallel to the X axis, now swing the plane of # the rest of the molecule into the xy plane... molPlane = Plane([a.xformCoord() for a in m.atoms[:3]]) angle = chimera.angle(molPlane.normal, Vector(0, 0, -1)) xform2 = Xform.rotation(b.atoms[0].xformCoord()-b.atoms[1].xformCoord(), angle) xform2.multiply(xform) m.openState.xform = xform2
