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 __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
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