def check_matching_sizes(v1, v2, step, subregion, operation):
if v1.data.size != v2.data.size:
raise CommandError('Cannot %s grids of different size' % operation)
if step or subregion:
if not v1.same_region(v1.region, v2.region):
raise CommandError('Cannot %s grids with different subregions' % operation)
def show_axis(tf, color, os):
import Matrix
axis, axis_point, angle, axis_shift = Matrix.axis_center_angle_shift(tf)
if angle < 0.1:
raise CommandError('Rotation angle is near zero (%g degrees)' % angle)
have_box, box = os.bbox()
if not have_box:
# TODO: Chimera does not provide bounding box of full model.
raise CommandError('First model must be visible to show axis')
axis_center = Matrix.project_to_axis(box.center().data(), axis, axis_point)
axis_length = max((box.urb - box.llf).data())
hl = 0.5 * axis_length
ap1 = map(lambda a, b: a - hl * b, axis_center, axis)
ap2 = map(lambda a, b: a + hl * b, axis_center, axis)
from VolumePath import Marker_Set, Link
from VolumePath.markerset import chimera_color
m = Marker_Set('rotation axis')
mm = m.marker_model()
mm.openState.xform = os.xform
if color:
mm.color = chimera_color(color)
radius = 0.025 * axis_length
m1 = m.place_marker(ap1, None, radius)
m2 = m.place_marker(ap2, None, radius)
Link(m1, m2, None, radius)
def parse_arg(fields, spec, cmd_name, session, akw):
name, parse, pkw, multiple = arg_spec(spec)
n = len(parse) if isinstance(parse, tuple) else 1
if len(fields) < n:
raise CommandError('%s: Missing argument for keyword "%s"'
% (cmd_name, name))
try:
if isinstance(parse, tuple):
value = True if n == 0 else tuple(p(a, session, **pkw)
for p,a in zip(parse,fields[:n]))
else:
value = parse(fields[0], session, **pkw)
except CommandError as e:
args = ' '.join(f for f in fields[:n])
raise CommandError('%s invalid %s argument "%s": %s'
% (cmd_name, name, args, str(e)))
except:
args = ' '.join(f for f in fields[:n])
raise
raise CommandError('%s invalid %s argument "%s"'
% (cmd_name, name, args))
if multiple:
if name in akw:
akw[name].append(value)
else:
akw[name] = [value]
else:
akw[name] = value
return n
def spine(operation,
regions,
spacing=None,
tipLength=None,
color=None,
showDiameter=False):
sel = parse_object_specifier(regions, 'segmentation region')
import Surface
plist = Surface.selected_surface_pieces(sel, include_outline_boxes=False)
from Segger.regions import Segmentation
rlist = [
p.region for p in plist
if (hasattr(p, 'region') and isinstance(p.model, Segmentation))
]
if len(rlist) == 0:
raise CommandError('No segmentation regions specified: "%s"' % regions)
if not (spacing is None or isinstance(spacing,
(int, float)) and spacing > 0):
raise CommandError('spacing must be positive numeric value')
if not (tipLength is None or isinstance(tipLength,
(int, float)) and tipLength > 0):
raise CommandError('tipLength must be positive numeric value')
if not color is None:
from Commands import parse_color
color = parse_color(color)
if showDiameter:
from _surface import SurfaceModel
diam_model = SurfaceModel()
diam_model.name = 'Diameters'
from chimera import openModels
openModels.add([diam_model], sameAs=rlist[0].segmentation)
else:
diam_model = None
import spine
from chimera import replyobj
from PathLength import path_length
for r in rlist:
mset = spine.trace_spine(r, spacing, tipLength, color)
slen = path_length([l.bond for l in mset.links()])
r.set_attribute('spine length', slen)
msg = 'Spine length for region %d is %.4g' % (r.rid, slen)
dmax, dmin = spine.measure_diameter(r, mset, diam_model)
if not dmax is None:
r.set_attribute('diameter1', dmax)
r.set_attribute('diameter2', dmin)
msg += ', diameters %.4g, %.4g' % (dmax, dmin)
kave, kmin, kmax = spine.measure_curvature(mset)
if not kmax is None:
r.set_attribute('curvature average', kave)
r.set_attribute('curvature minimum', kmin)
r.set_attribute('curvature maximum', kmax)
msg += ', curvature %.4g (ave), %.4g (max), %.4g (min)' % (
kave, kmax, kmin)
replyobj.info(msg + '\n')
def color_arg(color, session):
if isinstance(color, (tuple, list)):
if len(color) == 4:
return tuple(color)
elif len(color) == 3:
return tuple(color) + (1,)
elif isinstance(color, str):
fields = color.split(',')
if len(fields) == 1:
from webcolors import name_to_rgb
try:
rgb = name_to_rgb(color)
except ValueError:
raise CommandError('Unknown color: "%s"' % repr(color))
return (rgb[0]/255.0,rgb[1]/255.0,rgb[2]/255.0,1)
else:
try:
rgba = tuple(float(c) for c in fields)
except:
raise CommandError('Unrecognized color: "%s"' % repr(color))
if len(rgba) == 3:
rgba = rgba + (1.0,)
if len(rgba) == 4:
return rgba
raise CommandError('Unrecognized color: "%s"' % repr(color))
def float_arg(s, session, min = None, max = None):
x = float(s)
if not min is None and x < min:
raise CommandError('Value must be >= %g, got %g' % (min, x))
if not max is None and x > max:
raise CommandError('Value must be <= %g, got %g' % (max, x))
return x
def chain_arg(s, session):
sel = parse_specifier(s, session)
clist = sel.chains()
if len(clist) == 0:
raise CommandError('No chains specified')
elif len(clist) > 1:
raise CommandError('Multiple chains specified')
return clist[0]
def model_arg(s, session):
sel = parse_specifier(s, session)
mlist = sel.models()
if len(mlist) == 0:
raise CommandError('No models specified')
elif len(mlist) > 1:
raise CommandError('Multiple models specified')
return mlist[0]
def model_id_arg(s, session):
if len(s) == 0 or s[0] != '#':
raise CommandError('model id argument must start with "#", got "%s"' % s)
try:
mid = tuple(int(i) for i in s[1:].split('.'))
except ValueError:
raise CommandError('model id argument be integers separated by ".", got "%s"' % s)
return mid
def openstate_arg(s, session):
sel = parse_specifier(s, session)
oslist = set([m.openState for m in sel.models()])
if len(oslist) == 0:
raise CommandError('No models specified')
elif len(oslist) > 1:
raise CommandError('Multiple coordinate systems specified')
return oslist.pop()
def molecules_arg(s, session, min = 0):
sel = parse_specifier(s, session)
mlist = sel.molecules()
if len(mlist) < min:
if len(mlist) == 0:
raise CommandError('No molecule specified, require %d' % min)
else:
raise CommandError('%d molecules specified, require at least %d' % (len(mlist), min))
return mlist
def check_number(value, name, type = (float,int), allow_none = False,
positive = False, nonnegative = False):
if allow_none and value is None:
return
if not isinstance(value, type):
raise CommandError('%s must be number, got "%s"' % (name, str(value)))
if positive and value <= 0:
raise CommandError('%s must be > 0' % name)
if nonnegative and value < 0:
raise CommandError('%s must be >= 0' % name)
def parse_arguments(cmd_name, arg_string, session,
required_args = (), optional_args = (), keyword_args = ()):
fields = split_fields(arg_string)
n = len(fields)
akw = {}
a = 0
spec = None
args = []
# Make keyword abbreviation table.
kw_args = tuple(optional_args) + tuple(keyword_args)
kwnames = [arg_specifier_name(s) for s in kw_args]
kwt = abbreviation_table(kwnames)
# Parse keyword arguments.
keyword_spec = dict([(arg_specifier_name(s),s) for s in kw_args])
while a < n:
f = fields[a]
fl = f.lower()
if not fl in kwt:
args.append(f)
a += 1
continue
spec = keyword_spec[kwt[fl]]
a += 1 + parse_arg(fields[a+1:], spec, cmd_name, session, akw)
# Parse required arguments.
a = 0
na = len(args)
for spec in required_args:
if a >= na:
raise CommandError('%s: Missing required argument "%s"'
% (cmd_name, arg_specifier_name(spec)))
a += parse_arg(args[a:], spec, cmd_name, session, akw)
# Parse optional arguments.
for spec in optional_args:
if a >= na:
break
a += parse_arg(args[a:], spec, cmd_name, session, akw)
# Allow last positional argument to have multiple values.
if spec:
multiple = arg_spec(spec)[3]
if multiple:
while a < na:
a += parse_arg(args[a:], spec, cmd_name, session, akw)
if a < na:
raise CommandError('%s: Extra argument "%s"' % (cmd_name, args[a]))
return akw
def distance(operation,
object1,
object2,
multiple=False,
show=False,
color=(0, 1, 1, 1)):
a1 = object1.atoms()
import Surface as s
s1 = s.selected_surface_pieces(object1, include_outline_boxes=False)
if len(a1) == 0 and len(s1) == 0:
raise CommandError('No atoms or surfaces specified')
a2 = object2.atoms()
s2 = s.selected_surface_pieces(object2, include_outline_boxes=False)
if len(a2) == 0 and len(s2) == 0:
raise CommandError('No target atoms or surfaces')
# Remove near stuff.
if a1:
a2 = list(set(a2).difference(a1))
if s1:
s2 = list(set(s2).difference(s1))
name2 = object_name(a2, s2)
xyz2 = point_array(a2, s2)
if show:
from Commands import parse_color
color = parse_color(color)
from _surface import SurfaceModel
surf = SurfaceModel()
surf.name = 'Distance measurement'
from chimera import openModels
openModels.add([surf])
else:
surf = None
if multiple:
pairs = [([a], []) for a in a1] + [([], [s]) for s in s1]
else:
pairs = [(a1, s1)]
for a, s in pairs:
name = object_name(a, s)
xyz = point_array(a, s)
report_distance(xyz, xyz2, name, name2, surf, color)
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 field_lines(operation,
volume,
lines=1000,
startAbove=None,
step=0.5,
color=(.7, .7, .7, 1),
lineWidth=1,
tubeRadius=None,
circleSubdivisions=12,
markers=False,
modelId=None):
from VolumeViewer import Volume
vlist = [m for m in volume if isinstance(m, Volume)]
if len(vlist) == 0:
raise CommandError('No volume specified')
import Commands as CD
rgba = CD.parse_color(color)
model_id = None if modelId is None else CD.parse_model_id(modelId)
import fieldlines
for v in vlist:
fieldlines.show_field_lines(v, lines, startAbove, step, rgba,
lineWidth, tubeRadius, circleSubdivisions,
markers, model_id)
def parse_value_color(vc):
err = 'Colormap entry must be value,color: got "%s"' % vc
svc = vc.split(',',1)
if len(svc) != 2:
raise CommandError(err)
try:
v = float(svc[0])
except ValueError:
raise CommandError(err)
from Commands import convertColor
try:
c = convertColor(svc[1]).rgba()
except:
raise CommandError(err)
return v, c
def symmetry(operation,
volume,
minimumCorrelation=0.99,
nMax=8,
helix=None,
points=10000,
set=True):
from VolumeViewer import Volume
vlist = [m for m in volume if isinstance(m, Volume)]
if len(vlist) == 0:
raise CommandError('No volume specified')
if not helix is None:
rise, angle, n, optimize = parse_helix_option(helix)
import symmetry as S
for v in vlist:
if helix:
syms, msg = S.find_helix_symmetry(v, rise, angle, n, optimize,
nMax, minimumCorrelation, points)
else:
syms, msg = S.find_point_symmetry(v, nMax, minimumCorrelation,
points)
if set and syms:
v.data.symmetries = syms
from chimera.replyobj import info, status
status(msg)
info(msg + '\n')
def map_sum(operation, volume, aboveThreshold=None, step=1, subregion='all'):
from VolumeViewer import Volume
vlist = [m for m in volume if isinstance(m, Volume)]
if len(vlist) == 0:
raise CommandError('No volume specified')
from Commands import parse_step, parse_subregion
subregion_arg = subregion
subregion = parse_subregion(subregion)
step_arg = step
step = parse_step(step)
import numpy
import VolumeStatistics as VS
for v in vlist:
m = v.matrix(step=step, subregion=subregion)
if aboveThreshold is None:
s = m.sum(dtype=numpy.float64)
else:
ma = (m >= aboveThreshold)
na = ma.sum(dtype=numpy.int64)
mt = ma.astype(m.dtype)
mt *= m
s = mt.sum(dtype=numpy.float64)
descrip = v.name
if step_arg != 1:
descrip += ', step %s' % step_arg
if subregion_arg != 'all':
descrip += ', subregion %s' % subregion_arg
if not aboveThreshold is None:
descrip += ', level >= %.5g, npoints %d' % (aboveThreshold, na)
msg = '%s: sum = %.5g' % (descrip, s)
VS.message(msg, show_reply_log=True)
def filter_surfaces(surfaces):
from ..molecule import Molecule
surfs = set([s for s in surfaces if not isinstance(s, Molecule)])
if len(surfs) == 0:
raise CommandError('No surfaces specified')
return surfs
def enum_arg(s, session, values, multiple = False, abbrev = False):
val = abbreviation_table(values) if abbrev else dict((v,v) for v in values)
if multiple:
vlist = s.split(',')
for v in vlist:
if not v in val:
raise CommandError('Values must be in %s, got "%s"'
% (', '.join(values), s))
e = [val[v] for v in vlist]
elif s in val:
e = val[s]
else:
raise CommandError('Value must be one of %s, got "%s"'
% (', '.join(values), s))
return e
def volumes_arg(v, session):
sel = parse_specifier(v, session)
vlist = sel.maps()
if len(vlist) == 0:
raise CommandError('No volumes specified')
return vlist
def map_values(operation, volume, atoms, name=None, report=10):
from VolumeViewer import Volume
vlist = [v for v in volume if isinstance(v, Volume)]
if len(vlist) != 1:
raise CommandError('No volume model specified')
v = vlist[0]
import AtomDensity
if name is None:
name = 'value_' + v.name
name = AtomDensity.replace_special_characters(name, '_')
AtomDensity.set_atom_volume_values(atoms, v, name)
if report:
arep = atoms[:report] if isinstance(report, int) else atoms
values = '\n'.join(
['%s %.5g' % (a.oslIdent(), getattr(a, name)) for a in arep])
n = len(atoms)
t = '%s map values at %d atom positions\n%s\n' % (v.name, n, values)
if n > len(arep):
t += '...\n'
if n == 1:
s = '%s map value at atom %s = %.5g' % (
v.name, atoms[0].oslIdent(), getattr(a, name))
else:
maxa = 3
values = ', '.join(
['%.5g' % getattr(a, name) for a in atoms[:maxa]])
if n > maxa:
values += ', ...'
s = '%s map values at %d atoms: %s' % (v.name, n, values)
from chimera import replyobj
replyobj.info(t)
replyobj.status(s)
def map_statistics(operation, volume, step=1, subregion='all'):
from VolumeViewer import Volume
vlist = [m for m in volume if isinstance(m, Volume)]
if len(vlist) == 0:
raise CommandError('No volume specified')
from Commands import parse_step, parse_subregion
subregion_arg = subregion
subregion = parse_subregion(subregion)
step_arg = step
step = parse_step(step)
import VolumeStatistics as VS
for v in vlist:
m = v.matrix(step=step, subregion=subregion)
mean, sd, rms = VS.mean_sd_rms(m)
descrip = v.name
if step_arg != 1:
descrip += ', step %s' % step_arg
if subregion_arg != 'all':
descrip += ', subregion %s' % subregion_arg
msg = '%s: mean = %.5g, SD = %.5g, RMS = %.5g' % (descrip, mean, sd,
rms)
VS.message(msg, show_reply_log=True)
def single_volume(mlist):
if mlist is None:
return mlist
vlist = filter_volumes(mlist)
if len(vlist) != 1:
raise CommandError('Must specify only one volume')
return vlist[0]
def check_in_place(inPlace, volumes):
if not inPlace:
return
nwv = [v for v in volumes if not v.data.writable]
if nwv:
names = ', '.join([v.name for v in nwv])
raise CommandError("Can't modify volume in place: %s" % names)
def parse_object_specifier(spec, name='object'):
from chimera import specifier
try:
sel = specifier.evalSpec(spec)
except:
raise CommandError('Bad %s specifier "%s"' % (name, spec))
return sel
def float3_arg(s, session):
fl = [float(x) for x in s.split(',')]
if len(fl) != 3:
raise CommandError('Require 3 comma-separated values, got %d' % len(fl))
from numpy import array, float32
a = array(fl, float32)
return a
def ints_arg(s, session, allowed_counts = None):
il = [int(x) for x in s.split(',')]
if not allowed_counts is None and not len(il) in allowed_counts:
allowed = ','.join('%d' % c for c in allowed_counts)
raise CommandError('Wrong number of values, require %s, got %d'
% (allowed, len(il)))
return il
def filter_volumes(models, keyword = ''):
if keyword:
keyword += ' '
if isinstance(models, str):
raise CommandError('No %svolumes specified by "%s"' % (keyword, models))
from ..map import Volume
from _volume import Volume_Model
vids = set([v.id for v in models if isinstance(v, (Volume, Volume_Model))])
for v in models:
if not isinstance(v, (Volume, Volume_Model)) and not v.id in vids:
raise CommandError('Model %s is not a volume' % v.name)
volumes = [v for v in models if isinstance(v, Volume)]
if len(volumes) == 0:
raise CommandError('No %svolumes specified' % keyword)
return volumes