def morph_op(volumes, frames = 25, start = 0, playStep = 0.04,
playDirection = 1, playRange = None, addMode = False,
constantVolume = False, scaleFactors = None,
hideOriginalMaps = True, subregion = 'all', step = 1,
modelId = None):
volumes = filter_volumes(volumes)
check_number(frames, 'frames', int, nonnegative = True)
check_number(start, 'start')
check_number(playStep, 'playStep', nonnegative = True)
if playRange is None:
if addMode:
prange = (-1.0,1.0)
else:
prange = (0.0,1.0)
else:
prange = parse_floats(playRange, 'playRange', 2)
check_number(playDirection, 'playDirection')
sfactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
vs = [tuple(v.matrix_size(step = step, subregion = subregion))
for v in volumes]
if len(set(vs)) > 1:
sizes = ' and '.join([str(s) for s in vs])
raise CommandError, "Volume grid sizes don't match: %s" % sizes
from MorphMap import morph_maps
morph_maps(volumes, frames, start, playStep, playDirection, prange,
addMode, constantVolume, sfactors,
hideOriginalMaps, subregion, step, modelId)
def parse_box(box, x, y, z, bname, xname, yname, zname):
if box is None and x is None and y is None and z is None:
return None
if box:
b6 = parse_floats(box, bname, 6)
return (b6[:3], b6[3:])
box = ([None,None,None], [None,None,None])
for a,x,name in zip((0,1,2),(x,y,z),(xname,yname,zname)):
if x:
box[0][a], box[1][a] = parse_floats(x, name, 2)
return box
def parse_box(box, x, y, z, bname, xname, yname, zname):
if box is None and x is None and y is None and z is None:
return None
if box:
b6 = parse_floats(box, bname, 6)
return (b6[:3], b6[3:])
box = ([None, None, None], [None, None, None])
for a, x, name in zip((0, 1, 2), (x, y, z), (xname, yname, zname)):
if x:
box[0][a], box[1][a] = parse_floats(x, name, 2)
return box
def parse_rotation(rotation, qrotation):
if rotation:
aa = parse_floats(rotation, 'rotation', 4)
axis, angle = aa[:3], aa[3]
elif qrotation:
q = parse_floats(qrotation, 'qrotation', 4)
from Matrix import norm
from math import atan2, pi
angle = (360/pi)*atan2(norm(q[:3]), q[3])
axis = q[:3]
else:
axis = angle = None
if axis and tuple(axis) == (0,0,0):
axis = angle = None
return axis, angle
def sphere_shape(radius = 10.0, center = None, rotation = None,
qrotation = None, coordinateSystem = None,
divisions = 72,
color = (.745,.745,.745,1), mesh = False, linewidth = 1,
slab = None, modelName = None, modelId = None):
try:
r = parse_floats(radius, 'radius', 3)
except CommandError:
check_number(radius, 'radius', nonnegative = True)
r = (radius, radius, radius)
check_number(divisions, 'divisions', positive = True)
check_number(linewidth, 'linewidth', nonnegative = True)
model_id = parse_model_id(modelId)
varray, tarray = icosahedral_geometry(1.0, divisions, sphere_factor = 1)
for a in range(3):
varray[:,a] *= r[a]
edge_mask = None
if modelName is None:
modelName = 'sphere' if r[1] == r[0] and r[2] == r[0] else 'ellipsoid'
show_surface(varray, tarray, edge_mask, color, mesh, linewidth,
center, rotation, qrotation, coordinateSystem,
slab, model_id, modelName)
def parse_rotation(rotation, qrotation):
if rotation:
aa = parse_floats(rotation, 'rotation', 4)
axis, angle = aa[:3], aa[3]
elif qrotation:
q = parse_floats(qrotation, 'qrotation', 4)
from Matrix import norm
from math import atan2, pi
angle = (360 / pi) * atan2(norm(q[:3]), q[3])
axis = q[:3]
else:
axis = angle = None
if axis and tuple(axis) == (0, 0, 0):
axis = angle = None
return axis, angle
def subtract_op(vol1,
vol2,
onGrid=None,
boundingGrid=False,
subregion='all',
step=1,
gridSubregion='all',
gridStep=1,
inPlace=False,
scaleFactors=None,
minRMS=False,
modelId=None):
vol1 = filter_volumes(vol1)
vol2 = filter_volumes(vol2)
if len(vol1) != 1 or len(vol2) != 1:
raise CommandError, 'vop subtract operation requires exactly two volumes'
if minRMS and scaleFactors:
raise CommandError, 'vop subtract cannot specify both minRMS and scaleFactors options.'
if minRMS:
mult = (1, 'minrms')
elif scaleFactors:
m0, m1 = parse_floats(scaleFactors, 'scaleFactors', 2)
mult = (m0, -m1)
else:
mult = (1, -1)
add_op(vol1 + vol2, onGrid, boundingGrid, subregion, step, gridSubregion,
gridStep, inPlace, mult, modelId)
def add_op(volumes, onGrid = None, boundingGrid = None,
subregion = 'all', step = 1,
gridSubregion = 'all', gridStep = 1,
inPlace = False, scaleFactors = None, modelId = None):
volumes = filter_volumes(volumes)
if boundingGrid is None and not inPlace:
boundingGrid = (onGrid is None)
if onGrid is None:
onGrid = volumes[:1]
onGrid = filter_volumes(onGrid, 'onGrid')
subregion = parse_subregion(subregion)
step = parse_step(step)
gridSubregion = parse_subregion(gridSubregion, 'gridSubregion')
gridStep = parse_step(gridStep, 'gridStep')
if inPlace:
if boundingGrid or gridStep != 1 or gridSubregion != 'all':
raise CommandError, "Can't use inPlace option with boundingGrid or gridStep or gridSubregion options"
for gv in onGrid:
if not gv.data.writable:
raise CommandError, "Can't modify volume in place: %s" % gv.name
if not gv in volumes:
raise CommandError, "Can't change grid in place"
if isinstance(scaleFactors, basestring):
scaleFactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
modelId = parse_model_id(modelId)
for gv in onGrid:
add_operation(volumes, subregion, step,
gv, gridSubregion, gridStep,
boundingGrid, inPlace, scaleFactors, modelId)
def sphere_shape(radius=10.0,
center=None,
rotation=None,
qrotation=None,
coordinateSystem=None,
divisions=72,
color=(.745, .745, .745, 1),
mesh=False,
linewidth=1,
slab=None,
modelName=None,
modelId=None):
try:
r = parse_floats(radius, 'radius', 3)
except CommandError:
check_number(radius, 'radius', nonnegative=True)
r = (radius, radius, radius)
check_number(divisions, 'divisions', positive=True)
check_number(linewidth, 'linewidth', nonnegative=True)
model_id = parse_model_id(modelId)
varray, tarray = icosahedral_geometry(1.0, divisions, sphere_factor=1)
for a in range(3):
varray[:, a] *= r[a]
edge_mask = None
if modelName is None:
modelName = 'sphere' if r[1] == r[0] and r[2] == r[0] else 'ellipsoid'
show_surface(varray, tarray, edge_mask, color, mesh, linewidth, center,
rotation, qrotation, coordinateSystem, slab, model_id,
modelName)
def octant_complement_op(volumes, center = None, iCenter = None,
subregion = 'all', step = 1, inPlace = False,
fillValue = 0, modelId = None):
volumes = filter_volumes(volumes)
center = parse_floats(center, 'center', 3)
iCenter = parse_floats(iCenter, 'iCenter', 3)
subregion = parse_subregion(subregion)
step = parse_step(step)
check_in_place(inPlace, volumes)
check_number(fillValue, 'fillValue')
modelId = parse_model_id(modelId)
outside = False
for v in volumes:
octant_operation(v, outside, center, iCenter, subregion, step,
inPlace, fillValue, modelId)
def add_op(volumes,
onGrid=None,
boundingGrid=None,
subregion='all',
step=1,
gridSubregion='all',
gridStep=1,
inPlace=False,
scaleFactors=None,
modelId=None):
volumes = filter_volumes(volumes)
if boundingGrid is None and not inPlace:
boundingGrid = (onGrid is None)
if onGrid is None:
onGrid = volumes[:1]
onGrid = filter_volumes(onGrid, 'onGrid')
subregion = parse_subregion(subregion)
step = parse_step(step)
gridSubregion = parse_subregion(gridSubregion, 'gridSubregion')
gridStep = parse_step(gridStep, 'gridStep')
if inPlace:
if boundingGrid or gridStep != 1 or gridSubregion != 'all':
raise CommandError, "Can't use inPlace option with boundingGrid or gridStep or gridSubregion options"
for gv in onGrid:
if not gv.data.writable:
raise CommandError, "Can't modify volume in place: %s" % gv.name
if not gv in volumes:
raise CommandError, "Can't change grid in place"
if isinstance(scaleFactors, basestring):
scaleFactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
modelId = parse_model_id(modelId)
for gv in onGrid:
add_operation(volumes, subregion, step, gv, gridSubregion, gridStep,
boundingGrid, inPlace, scaleFactors, modelId)
def show_surface(varray, tarray, edge_mask, color, mesh, linewidth,
center, rotation, qrotation, coordinate_system,
slab, model_id, shape_name):
from Commands import parse_rgba
rgba = parse_rgba(color)
if coordinate_system:
from Commands import openStateFromSpec
os = openStateFromSpec(coordinate_system, 'coordinateSystem')
cxf = os.xform
else:
cxf = None
s = surface_model(model_id, shape_name, cxf)
sxf = s.openState.xform
sxfinv = sxf.inverse()
if cxf is None:
cxf = sxf
axis, angle = parse_rotation(rotation, qrotation)
if axis:
from chimera import Vector
csaxis = cxf.apply(Vector(*axis)).data()
from Matrix import rotation_transform
saxis = sxfinv.apply(Vector(*csaxis)).data()
rtf = rotation_transform(saxis, angle)
from _contour import affine_transform_vertices
affine_transform_vertices(varray, rtf)
if center:
from Commands import parseCenterArg
center, csys = parseCenterArg(center, 'shape')
if csys:
center = csys.xform.apply(center)
else:
center = cxf.apply(center)
scenter = sxfinv.apply(center)
varray += scenter.data()
if not slab is None:
if isinstance(slab, (float,int)):
pad = (-0.5*slab, 0.5*slab)
else:
pad = parse_floats(slab, 'slab', 2)
import _surface
narray = _surface.calculate_vertex_normals(varray, tarray)
from Mask import depthmask
varray, tarray = depthmask.slab_surface(varray, tarray, narray, pad)
p = s.addPiece(varray, tarray, rgba)
if mesh:
p.displayStyle = p.Mesh
if not edge_mask is None:
p.setEdgeMask(edge_mask) # Hide spokes of hexagons.
p.lineThickness = linewidth
p.save_in_session = True
def show_surface(varray, tarray, edge_mask, color, mesh, linewidth, center,
rotation, qrotation, coordinate_system, slab, model_id,
shape_name):
from Commands import parse_rgba
rgba = parse_rgba(color)
if coordinate_system:
from Commands import openStateFromSpec
os = openStateFromSpec(coordinate_system, 'coordinateSystem')
cxf = os.xform
else:
cxf = None
s = surface_model(model_id, shape_name, cxf)
sxf = s.openState.xform
sxfinv = sxf.inverse()
if cxf is None:
cxf = sxf
axis, angle = parse_rotation(rotation, qrotation)
if axis:
from chimera import Vector
csaxis = cxf.apply(Vector(*axis)).data()
from Matrix import rotation_transform
saxis = sxfinv.apply(Vector(*csaxis)).data()
rtf = rotation_transform(saxis, angle)
from _contour import affine_transform_vertices
affine_transform_vertices(varray, rtf)
if center:
from Commands import parseCenterArg
center, csys = parseCenterArg(center, 'shape')
if csys:
center = csys.xform.apply(center)
else:
center = cxf.apply(center)
scenter = sxfinv.apply(center)
varray += scenter.data()
if not slab is None:
if isinstance(slab, (float, int)):
pad = (-0.5 * slab, 0.5 * slab)
else:
pad = parse_floats(slab, 'slab', 2)
import _surface
narray = _surface.calculate_vertex_normals(varray, tarray)
from Mask import depthmask
varray, tarray = depthmask.slab_surface(varray, tarray, narray, pad)
p = s.addPiece(varray, tarray, rgba)
if mesh:
p.displayStyle = p.Mesh
if not edge_mask is None:
p.setEdgeMask(edge_mask) # Hide spokes of hexagons.
p.lineThickness = linewidth
p.save_in_session = True
def parse_offset(offset):
from Commands import check_number, parse_floats
if isinstance(offset, (basestring, tuple, list)):
o1, o2, n = parse_floats(offset, 'offset', 3)
if n <= 1:
raise CommandError, 'Offset count must be greater than 1'
offset = [o1 + (o2 - o1) * float(i) / (n - 1) for i in range(n)]
else:
check_number(offset, 'offset')
return offset
def parse_offset(offset):
from Commands import check_number, parse_floats
if isinstance(offset, (basestring,tuple,list)):
o1, o2, n = parse_floats(offset, 'offset', 3)
if n <= 1:
raise CommandError, 'Offset count must be greater than 1'
offset = [o1 + (o2-o1)*float(i)/(n-1) for i in range(n)]
else:
check_number(offset, 'offset')
return offset
def octant_complement_op(volumes,
center=None,
iCenter=None,
subregion='all',
step=1,
inPlace=False,
fillValue=0,
modelId=None):
volumes = filter_volumes(volumes)
center = parse_floats(center, 'center', 3)
iCenter = parse_floats(iCenter, 'iCenter', 3)
subregion = parse_subregion(subregion)
step = parse_step(step)
check_in_place(inPlace, volumes)
check_number(fillValue, 'fillValue')
modelId = parse_model_id(modelId)
outside = False
for v in volumes:
octant_operation(v, outside, center, iCenter, subregion, step, inPlace,
fillValue, modelId)
def morph_op(volumes,
frames=25,
start=0,
playStep=0.04,
playDirection=1,
playRange=None,
addMode=False,
constantVolume=False,
scaleFactors=None,
hideOriginalMaps=True,
subregion='all',
step=1,
modelId=None):
volumes = filter_volumes(volumes)
check_number(frames, 'frames', int, nonnegative=True)
check_number(start, 'start')
check_number(playStep, 'playStep', nonnegative=True)
if playRange is None:
if addMode:
prange = (-1.0, 1.0)
else:
prange = (0.0, 1.0)
else:
prange = parse_floats(playRange, 'playRange', 2)
check_number(playDirection, 'playDirection')
sfactors = parse_floats(scaleFactors, 'scaleFactors', len(volumes))
subregion = parse_subregion(subregion)
step = parse_step(step)
modelId = parse_model_id(modelId)
vs = [
tuple(v.matrix_size(step=step, subregion=subregion)) for v in volumes
]
if len(set(vs)) > 1:
sizes = ' and '.join([str(s) for s in vs])
raise CommandError, "Volume grid sizes don't match: %s" % sizes
from MorphMap import morph_maps
morph_maps(volumes, frames, start, playStep, playDirection, prange,
addMode, constantVolume, sfactors, hideOriginalMaps, subregion,
step, modelId)
def mask(volumes, surfaces, axis = None, fullMap = False,
pad = 0., slab = None, sandwich = True, invertMask = False):
from Commands import CommandError, filter_volumes, parse_floats
vlist = filter_volumes(volumes)
from Surface import selected_surface_pieces
glist = selected_surface_pieces(surfaces, include_outline_boxes = False)
if len(glist) == 0:
raise CommandError, 'No surfaces specified'
axis = parse_floats(axis, 'axis', 3, (0,1,0))
if not isinstance(fullMap, (bool,int)):
raise CommandError, 'fullMap option value must be true or false'
if not isinstance(invertMask, (bool,int)):
raise CommandError, 'invertMask option value must be true or false'
if not isinstance(pad, (float,int)):
raise CommandError, 'pad option value must be a number'
if isinstance(slab, (float,int)):
pad = (-0.5*slab, 0.5*slab)
elif not slab is None:
pad = parse_floats(slab, 'slab', 2)
if not isinstance(sandwich, bool):
raise CommandError, 'sandwich option value must be true or false'
from depthmask import surface_geometry, masked_volume
from Matrix import xform_matrix, invert_matrix
for v in vlist:
tf = invert_matrix(xform_matrix(v.model_transform()))
surfs = surface_geometry(glist, tf, pad)
masked_volume(v, surfs, axis, fullMap, sandwich, invertMask)
def contact_area(operation,
surf1,
surf2,
distance,
show=True,
color=(1, 0, 0, 1),
offset=1,
slab=None,
smooth=False,
optimize=True):
plist = []
import Surface
for spec in (surf1, surf2):
s = parse_object_specifier(spec, 'surface')
p = Surface.selected_surface_pieces(s, include_outline_boxes=False)
if len(p) == 0:
raise CommandError('%s has no surface pieces' % spec)
elif len(p) > 1:
raise CommandError('%s has %d surface pieces, require 1' %
(spec, len(p)))
plist.append(p[0])
p1, p2 = plist
from Commands import parse_color
color = parse_color(color)
if not show:
color = None
from Commands import check_number
check_number(offset, 'offset')
if not slab is None:
if isinstance(slab, (float, int)):
slab = (-0.5 * slab, 0.5 * slab)
else:
from Commands import parse_floats
slab = parse_floats(slab, 'slab', 2)
offset = None
import contactarea as c
area = c.contact_area(p1, p2, distance, color, offset, slab, smooth,
optimize)
from chimera import replyobj
replyobj.info('Contact area on %s within distance %.4g\nof %s = %.4g\n' %
(p1.model.name, distance, p2.model.name, area))
replyobj.status('Contact area = %.4g' % area)
def subtract_op(vol1, vol2, onGrid = None, boundingGrid = False,
subregion = 'all', step = 1,
gridSubregion = 'all', gridStep = 1,
inPlace = False, scaleFactors = None, minRMS = False,
modelId = None):
vol1 = filter_volumes(vol1)
vol2 = filter_volumes(vol2)
if len(vol1) != 1 or len(vol2) != 1:
raise CommandError, 'vop subtract operation requires exactly two volumes'
if minRMS and scaleFactors:
raise CommandError, 'vop subtract cannot specify both minRMS and scaleFactors options.'
if minRMS:
mult = (1,'minrms')
elif scaleFactors:
m0,m1 = parse_floats(scaleFactors, 'scaleFactors', 2)
mult = (m0,-m1)
else:
mult = (1,-1)
add_op(vol1+vol2, onGrid, boundingGrid, subregion, step,
gridSubregion, gridStep, inPlace, mult, modelId)