def interpolateIndependent(xf, c0, c1, f): """Interpolate by splitting the transformation into a rotation and a translation.""" import chimera vr, a = xf.getRotation() # a is in degrees xt = xf.getTranslation() Tinv = chimera.Xform.translation(-xt) T = chimera.Xform.translation(xt * f) X0 = chimera.Xform(T) X0.multiply(chimera.Xform.rotation(vr, a * f)) X1 = chimera.Xform(T) X1.multiply(chimera.Xform.rotation(vr, -a * (1 - f))) X1.multiply(Tinv) return X0, X1
def create_object(self):
import chimera
xf = chimera.Xform()
trans = apply(chimera.Vector, self.translation)
xf.translate(trans)
axis = apply(chimera.Vector, self.rotation_axis)
xf.rotate(axis, self.rotation_angle)
return xf
def BoxArrowMesh (w, h, l, al, color, xf, mol) :
if mol == None :
import _surface
mol = _surface.SurfaceModel()
chimera.openModels.add ( [mol] ) # , sameAs = alignTo)
mol.name = "Box"
v = numpy.zeros ( [14,3] )
# print "BoxMesh:", div
at = 0
w = w / 2.0
h = h / 2.0
l = l / 2.0
if xf == None :
xf = chimera.Xform()
v[0] = xf.apply ( chimera.Point ( -w,-h,-l ) )
v[1] = xf.apply ( chimera.Point ( w,-h,-l ) )
v[2] = xf.apply ( chimera.Point ( w,h,-l ) )
v[3] = xf.apply ( chimera.Point ( -w,h,-l ) )
v[4] = xf.apply ( chimera.Point ( -w,-h,l-al ) )
v[5] = xf.apply ( chimera.Point ( w,-h,l-al ) )
v[6] = xf.apply ( chimera.Point ( w,h,l-al ) )
v[7] = xf.apply ( chimera.Point ( -w,h,l-al ) )
vi = []
vi.extend( Quad2Tri ( [0,3,2,1] ) )
vi.extend( Quad2Tri ( [1,5,6,2] ) )
vi.extend( Quad2Tri ( [2,6,7,3] ) )
vi.extend( Quad2Tri ( [0,4,5,1] ) )
vi.extend( Quad2Tri ( [0,4,7,3] ) )
vi.extend( Quad2Tri ( [5,4,7,6] ) )
v[8] = xf.apply ( chimera.Point ( -w,-h-al/2.0,l-al ) )
v[9] = xf.apply ( chimera.Point ( w,-h-al/2.0,l-al ) )
v[10] = xf.apply ( chimera.Point ( w,h+al/2.0,l-al ) )
v[11] = xf.apply ( chimera.Point ( -w,h+al/2.0,l-al ) )
v[12] = xf.apply ( chimera.Point ( -w,0,l ) )
v[13] = xf.apply ( chimera.Point ( w,0,l ) )
vi.extend( Quad2Tri ( [8,11,10,9] ) )
vi.extend( Quad2Tri ( [8,9,13,12] ) )
vi.extend( Quad2Tri ( [11,12,13,10] ) )
vi.extend( [(8,12,11)] )
vi.extend( [(9,10,13)] )
sph = mol.addPiece ( v, vi, color )
return sph
def interpolateLinear(xf, c0, c1, f): """Interpolate by translating c1 to c0 linearly along with rotation about translation point.""" import chimera vr, a = xf.getRotation() # a is in degrees c0v = c0.toVector() c1v = c1.toVector() Tinv0 = chimera.Xform.translation(-c0v) Tinv1 = chimera.Xform.translation(-c1v) dt = c1 - c0 R0 = chimera.Xform.rotation(vr, a * f) R1 = chimera.Xform.rotation(vr, -a * (1 - f)) T = chimera.Xform.translation(c0v + dt * f) X0 = chimera.Xform(T) X0.multiply(R0) X0.multiply(Tinv0) X1 = chimera.Xform(T) X1.multiply(R1) X1.multiply(Tinv1) return X0, X1
def handle_model_drag(self):
if self.mode == 'move models':
xf = self.phantom_device.transform()
if self.last_phantom_transform:
delta = chimera.Xform()
delta.multiply(self.last_phantom_transform)
delta.invert()
delta.premultiply(xf)
move_active_models(delta)
self.last_phantom_transform = xf
else:
self.last_phantom_transform = None
def orient_bar(self, horizontal=1):
m = self.model
if m == None:
return
xf = chimera.Xform()
xyz = m.openState.xform.getTranslation()
xf.translate(xyz)
if not horizontal:
xf.zRotate(-90)
m.openState.xform = xf
def topology(self):
if self.gui.ui_input_note.index(self.gui.ui_input_note.select()):
return self.gui.var_path.get()
# else:
model = self.gui.ui_chimera_models.getvalue()
if model:
sanitized_path = '{0[0]}{1}{0[1]}'.format(
os.path.splitext(model.name), '_fixed')
if os.path.isfile(sanitized_path):
return sanitized_path
else:
output = getattr(model, 'openedAs', (model.name + '.pdb', ))[0]
chimera.pdbWrite([model], chimera.Xform(), output)
return output
def matchPositions(fixedPositions, movablePositions):
m = Match(fixedPositions, movablePositions)
mat = m.matrix()
rot = chimera.Xform.xform(mat[0, 0], mat[0, 1], mat[0, 2], 0, mat[1, 0],
mat[1, 1], mat[1, 2], 0, mat[2, 0], mat[2, 1],
mat[2, 2], 0, True)
fC = m.center(fixedPositions)
fT = chimera.Xform.translation(chimera.Vector(fC[0], fC[1], fC[2]))
mC = m.center(movablePositions)
mT = chimera.Xform.translation(chimera.Vector(-mC[0], -mC[1], -mC[2]))
xform = chimera.Xform()
xform.multiply(fT)
xform.multiply(rot)
xform.multiply(mT)
return xform, m.rms
def sanitize_model(self):
# Each model in a single model
#Getting molecule attributes
model = self.ui_chimera_models.getvalue()
modelfile_path = getattr(model, 'openedAs', (model.name, ))[0]
basename, ext = os.path.splitext(modelfile_path)
output_file = '{0}{1}{2}'.format(basename, '_fixed', ext or '.pdb')
chimera.pdbWrite([model], chimera.Xform(), output_file)
self.fix_pdb(output_file, out=output_file)
m = chimera.openModels.open(output_file, sameAs=model)[0]
m.name = model.name + ' - Fixed'
self.ui_chimera_models.selection_clear()
self.ui_chimera_models.selection_set(
chimera.openModels.list().index(m))
model.display = False
def same_positions(self, mp1, mp2):
import chimera
angle_tolerance = 1e-5
translation_tolerance = 1e-5
for os, xf1 in mp1.items():
if mp2.has_key(os):
xf2 = mp2[os]
xf = chimera.Xform()
xf.multiply(xf1)
xf.invert()
xf.multiply(xf2)
trans = xf.getTranslation()
axis, angle = xf.getRotation()
if (abs(angle) > angle_tolerance
or trans.length > translation_tolerance):
return False
return True
def _apply_pdbfix(molecule, pH=7.0, add_hydrogens=False):
"""
Run PDBFixer to ammend potential issues in PDB format.
Parameters
----------
molecule : chimera.Molecule
Chimera Molecule object to fix.
pH : float, optional
Target pH for adding missing hydrogens.
add_hydrogens : bool, optional
Whether to add missing hydrogens or not.
Returns
-------
memfile : StringIO
An in-memory file with the modified PDB contents
"""
memfile = StringIO()
chimera.pdbWrite([molecule], chimera.Xform(), memfile)
chimera.openModels.close([molecule])
memfile.seek(0)
fixer = PDBFixer(pdbfile=memfile)
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.removeHeterogens(True)
if add_hydrogens:
fixer.addMissingHydrogens(pH)
memfile.close()
memfile = StringIO()
PDBFile.writeFile(fixer.topology, fixer.positions, memfile)
memfile.seek(0)
molecule = chimera.openModels.open(memfile,
type="PDB",
identifyAs=molecule.name)
chimera.openModels.remove(molecule)
memfile.close()
return molecule[0]
def flatten_icosahedron(multiscale_models, radius):
clist = chains(multiscale_models)
it = icosahedron_triangles(radius)
itc = map(center, it)
centers = map(chain_center, clist)
ci = map(lambda c: closest_point_index(c, itc), centers)
fit = flattened_icosahedron_triangles(radius)
xforms = map(triangle_transformation, it, fit)
for k in range(len(clist)):
c = clist[k]
c.unflatten_xform = c.xform
import chimera
xf = chimera.Xform()
xf.multiply(c.xform)
xf.premultiply(xforms[ci[k]])
c.set_xform(xf)
def PlaneMesh ( w, h, d, color, xf, mol ) :
if mol == None :
import _surface
mol = _surface.SurfaceModel()
chimera.openModels.add ( [mol] ) # , sameAs = alignTo)
mol.name = "Box"
atX = -w/2
atY = -h/2
if xf == None :
xf = chimera.Xform()
numx = int ( max ( numpy.ceil ( w / d ), 2 ) )
numy = int ( max ( numpy.ceil ( h / d ), 2 ) )
dx = w / float(numx-1)
dy = h / float(numx-1)
print " - plane - w %.2f, h %.2f, %d/%d" % (w, h, numx, numy)
v = numpy.zeros ( [numx*numy,3] )
vi = []
for j in range ( numy ) :
for i in range ( numx ) :
v[j*numx+i] = xf.apply ( chimera.Point ( atX + dx*i, atY + dy*j, 0 ) )
#vs.append ( p.data() )
if i > 0 and j > 0 :
p1 = j*numx+i
p2 = j*numx+i-1
p3 = (j-1)*numx+i-1
p4 = (j-1)*numx+i
vi.extend( Quad2Tri ( [p1,p2,p3,p4] ) )
sph = mol.addPiece ( v, vi, color )
return sph
def rotate_around_axis(axis, origin, screen_xy, last_screen_xy):
# Measure drag around axis with mouse on front clip plane.
sx, sy = screen_xy
from VolumeViewer import slice
xyz, back_xyz = slice.clip_plane_points(sx, sy)
lsx, lsy = last_screen_xy
last_xyz, back_last_xyz = slice.clip_plane_points(lsx, lsy)
a = apply(chimera.Vector, axis)
a.normalize()
o = apply(chimera.Vector, origin)
v = apply(chimera.Vector, xyz)
lv = apply(chimera.Vector, last_xyz)
t = chimera.cross(a, v - o)
t2 = t.sqlength()
if t2 > 0:
angle = (t * (v - lv)) / t2
else:
angle = 0
import math
angle_deg = 180 * angle / math.pi
vo = apply(chimera.Vector, origin)
va = apply(chimera.Vector, axis)
xf = chimera.Xform()
xf.translate(vo)
xf.rotate(va, angle_deg)
xf.translate(-vo)
# Applying xf performs the two translations and rotations in the
# opposite order of the function calls. First it translates by -vo,
# then rotates, then translates by +vo.
move_active_models(xf)
def original_positions():
'Move all models to original positions on open. Like reset command.'
identity = chimera.Xform()
for m in chimera.openModels.list():
m.openState.xform = identity
def interpolate(self, m, xform, **kw):
"""Interpolate to new conformation 'm'."""
#
# Get all the options
#
if kw.has_key("method"):
self.method = kw["method"]
if kw.has_key("rate"):
self.rate = kw["rate"]
if kw.has_key("frames"):
self.frames = kw["frames"]
if kw.has_key("cartesian"):
self.cartesian = kw["cartesian"]
if kw.has_key("minimize"):
self.minimize = kw["minimize"]
if kw.has_key("steps"):
self.steps = kw["steps"]
if self.minimize:
self.callback = self.minimizeCallback
else:
self.callback = self.interpolateCallback
#
# Find matching set of residues. First try for
# one-to-one residue match, and, if that fails,
# then finding a common set of residues.
#
import Segment
sm = self.mol
try:
results = Segment.segmentHingeExact(sm, m)
except ValueError:
results = Segment.segmentHingeApproximate(sm, m)
segments, atomMap, unusedResidues, unusedAtoms = results
for r in unusedResidues:
sm.deleteResidue(r)
for a in unusedAtoms:
sm.deleteAtom(a)
if unusedResidues or unusedAtoms:
from chimera import Sequence
Sequence.invalidate(sm)
if self.minimize:
from chimera.baseDialog import AskYesNoDialog
from chimera.tkgui import app
d = AskYesNoDialog(
"Cannot minimize with non-identical models.\n"
"Continue without minimization?",
default="Yes")
if d.run(app) != "yes":
raise ValueError("terminated at user request")
self.minimize = False
self.callback = self.interpolateCallback
#
# Interpolate between last conformation in trajectory
# and new conformations
#
sm.activeCoordSet = sm.coordSets[max(sm.coordSets.keys())]
from Interpolate import interpolate
import chimera
combinedXform = chimera.Xform(self.inverseXform)
combinedXform.multiply(xform)
interpolate(sm, combinedXform, segments, atomMap, self.method,
self.rate, self.frames, self.cartesian, self.callback)