def correlation(operation, map1, map2, aboveThreshold = True,
rotationAxis = None, angleRange = (0,360,2),
plot = True):
from VolumeViewer import Volume
map1 = [m for m in map1 if isinstance(m, Volume)]
map2 = [m for m in map2 if isinstance(m, Volume)]
if len(map1) == 0 or len(map2) == 0:
raise CommandError, 'Must specify 2 maps'
if rotationAxis:
# Rotate map1 in steps and report correlations.
from Commands import parse_axis
axis, center, csys = parse_axis(rotationAxis, 'measure')
if center is None:
raise CommandError, 'Rotation axis must be atom/bond spec'
axis = csys.xform.apply(axis).data()
center = csys.xform.apply(center).data()
if isinstance(angleRange, str):
try:
angleRange = [float(x) for x in angleRange.split(',')]
except:
angleRange = []
if len(angleRange) != 3:
raise CommandError, 'Angle range must be 3 comma-separated values, got "%s"' % angleRange
for v1 in map1:
for v2 in map2:
report_correlations_with_rotation(v1, v2, aboveThreshold,
axis, center, angleRange,
plot)
else:
for v1 in map1:
for v2 in map2:
report_correlation(v1, v2, aboveThreshold)
def parse_vector(varg, cmdname):
from Commands import parse_axis
v, axis_point, csys = parse_axis(varg, cmdname)
if csys:
v = csys.xform.apply(v)
vc = v.data()
return vc
def parse_center_axis(center, axis, csys, cmdname):
from Commands import parseCenterArg, parse_axis
if isinstance(center, (tuple, list)):
from chimera import Point
center = Point(*center)
ccs = csys
elif center:
center, ccs = parseCenterArg(center, cmdname)
else:
ccs = None
if isinstance(axis, (tuple, list)):
from chimera import Vector
axis = Vector(*axis)
axis_point = None
acs = csys
elif axis:
axis, axis_point, acs = parse_axis(axis, cmdname)
else:
axis_point = None
acs = None
if not center and axis_point:
# Use axis point if no center specified.
center = axis_point
ccs = acs
# If no coordinate system specified use axis or center coord system.
cs = (ccs or acs)
if csys is None and cs:
csys = cs
xf = cs.xform.inverse()
if center and not ccs:
center = xf.apply(center)
if axis and not acs:
axis = xf.apply(axis)
# Convert axis and center to requested coordinate system.
if csys:
xf = csys.xform.inverse()
if center and ccs:
center = xf.apply(ccs.xform.apply(center))
if axis and acs:
axis = xf.apply(acs.xform.apply(axis))
return center, axis, csys
def parse_center_axis(center, axis, csys, cmdname):
from Commands import parseCenterArg, parse_axis
if isinstance(center, (tuple, list)):
from chimera import Point
center = Point(*center)
ccs = csys
elif center:
center, ccs = parseCenterArg(center, cmdname)
else:
ccs = None
if isinstance(axis, (tuple, list)):
from chimera import Vector
axis = Vector(*axis)
acs = csys
elif axis:
axis, axis_point, acs = parse_axis(axis, cmdname)
else:
axis_point = None
acs = None
if not center and axis_point:
# Use axis point if no center specified.
center = axis_point
ccs = acs
# If no coordinate system specified use axis or center coord system.
cs = (ccs or acs)
if csys is None and cs:
csys = cs
xf = cs.xform.inverse()
if center and not ccs:
center = xf.apply(center)
if axis and not acs:
axis = xf.apply(axis)
# Convert axis and center to requested coordinate system.
if csys:
xf = csys.xform.inverse()
if center and ccs:
center = xf.apply(ccs.xform.apply(center))
if axis and acs:
axis = xf.apply(acs.xform.apply(axis))
return center, axis, csys
def correlation(operation,
map1,
map2,
aboveThreshold=True,
rotationAxis=None,
angleRange=(0, 360, 2),
plot=True):
from VolumeViewer import Volume
map1 = [m for m in map1 if isinstance(m, Volume)]
map2 = [m for m in map2 if isinstance(m, Volume)]
if len(map1) == 0 or len(map2) == 0:
raise CommandError('Must specify 2 maps')
if rotationAxis:
# Rotate map1 in steps and report correlations.
from Commands import parse_axis
axis, center, csys = parse_axis(rotationAxis, 'measure')
if center is None:
raise CommandError('Rotation axis must be atom/bond spec')
axis = csys.xform.apply(axis).data()
center = csys.xform.apply(center).data()
if isinstance(angleRange, str):
try:
angleRange = [float(x) for x in angleRange.split(',')]
except:
angleRange = []
if len(angleRange) != 3:
raise CommandError(
'Angle range must be 3 comma-separated values, got "%s"' %
angleRange)
for v1 in map1:
for v2 in map2:
report_correlations_with_rotation(v1, v2, aboveThreshold, axis,
center, angleRange, plot)
else:
for v1 in map1:
for v2 in map2:
report_correlation(v1, v2, aboveThreshold)