def scolor_command(cmdname, args):
from Commands import doExtensionFunc, parse_enumeration
if cmdname.startswith('un'):
if len(args) == 0:
args = '#'
doExtensionFunc(unscolor,
args,
specInfo=[
('surfaceSpec', 'surfaces', 'models'),
])
else:
sa = args.split(None, 2)
if len(sa) < 2:
raise CommandError, 'scolor requires at least 2 arguments: scolor <surf> <method>'
sspec = ('surfaceSpec', 'surfaces', 'models')
vspec = ('volumeSpec', 'volume', 'models')
gspec = ('gradientSpec', 'gradient', 'models')
cspec = ('coordinateSystemSpec', 'coordinateSystem', 'models')
methods = {
'color': (color_op, [sspec]),
'geometry': (geometry_op, [sspec, cspec]),
'gradient': (gradient_op, [sspec, gspec]),
'volume': (volume_op, [sspec, vspec]),
}
method = parse_enumeration(sa[1], methods.keys())
if method is None:
raise CommandError, 'Unknown scolor method: %s' % sa[1]
func, spec = methods[method]
doExtensionFunc(func, args, specInfo=spec)
def measure_command(cmdname, args):
operations = {
'rotation': (rotation_axis, [('model1Spec', 'model1', 'models'),
('model2Spec', 'model2', 'models')]),
'volume': (volume_area, [('surfaceSpec', 'surface', 'models')]),
'area': (volume_area, [('surfaceSpec', 'surface', 'models')]),
'correlation': (correlation, [('map1Spec', 'map1', 'models'),
('map2Spec', 'map2', 'models')]),
'buriedArea': (buried_area, [('a1Spec', 'atoms1', 'atoms'),
('a2Spec', 'atoms2', 'atoms')]),
'inertia': (inertia, []),
}
from Commands import abbreviation_table
aop = abbreviation_table(operations.keys())
fields = args.split(' ', 1)
if len(fields) == 0:
ops = ', '.join(operations.keys())
raise CommandError, 'Missing required argument: "operation" (%s)' % ops
op = aop.get(fields[0].lower())
if op is None:
ops = ', '.join(operations)
raise CommandError, 'Unknown operation "%s" (use %s)' % (fields[0],
ops)
from Commands import doExtensionFunc
f, specInfo = operations[op]
doExtensionFunc(f, args, specInfo=specInfo)
def scolor_command(cmdname, args):
from Commands import doExtensionFunc, parse_enumeration
if cmdname.startswith('un'):
if len(args) == 0:
args = '#'
doExtensionFunc(unscolor, args,
specInfo = [('surfaceSpec','surfaces','models'),])
else:
sa = args.split(None, 2)
if len(sa) < 2:
raise CommandError, 'scolor requires at least 2 arguments: scolor <surf> <method>'
sspec = ('surfaceSpec','surfaces','models')
vspec = ('volumeSpec','volume','models')
gspec = ('gradientSpec', 'gradient', 'models')
cspec = ('coordinateSystemSpec','coordinateSystem','models')
methods = {
'color': (color_op, [sspec]),
'geometry': (geometry_op, [sspec, cspec]),
'gradient': (gradient_op, [sspec, gspec]),
'volume': (volume_op, [sspec, vspec]),
}
method = parse_enumeration(sa[1], methods.keys())
if method is None:
raise CommandError, 'Unknown scolor method: %s' % sa[1]
func, spec = methods[method]
doExtensionFunc(func, args, specInfo = spec)
def measure_command(cmdname, args):
operations = {'rotation': (rotation_axis, [('model1Spec','model1','models'),
('model2Spec','model2','models')]),
'volume': (volume_area, [('surfaceSpec','surface','models')]),
'area': (volume_area, [('surfaceSpec','surface','models')]),
'correlation': (correlation, [('map1Spec','map1','models'),
('map2Spec','map2','models')]),
'buriedArea': (buried_area, [('a1Spec','atoms1','atoms'),
('a2Spec','atoms2','atoms')]),
'inertia': (inertia, []),
}
from Commands import abbreviation_table
aop = abbreviation_table(operations.keys())
fields = args.split(' ', 1)
if len(fields) == 0:
ops = ', '.join(operations.keys())
raise CommandError, 'Missing required argument: "operation" (%s)' % ops
op = aop.get(fields[0].lower())
if op is None:
ops = ', '.join(operations)
raise CommandError, 'Unknown operation "%s" (use %s)' % (fields[0], ops)
from Commands import doExtensionFunc
f, specInfo = operations[op]
doExtensionFunc(f, args, specInfo = specInfo)
def shape_command(cmdname, args):
vspec = ('atomSpec','atoms','atoms')
shapes = {
'cylinder': (cylinder_shape, []),
'ellipsoid': (sphere_shape, []),
'icosahedron': (icosahedron_shape, []),
'sphere': (sphere_shape, []),
'tube': (tube_shape, [vspec]),
}
snames = shapes.keys()
sa = args.split(None, 1)
if len(sa) < 1:
raise CommandError, 'shape requires at least 1 argument: shape <name>'
from Commands import parse_enumeration
shape = parse_enumeration(sa[0], snames)
if shape is None:
raise CommandError, 'Unknown shape: %s' % sa[0]
func, specs = shapes[shape]
from Commands import doExtensionFunc
fargs = ' '.join(sa[1:])
doExtensionFunc(func, fargs, specInfo = specs)
def shape_command(cmdname, args):
vspec = ('atomSpec', 'atoms', 'atoms')
shapes = {
'cylinder': (cylinder_shape, []),
'ellipsoid': (sphere_shape, []),
'icosahedron': (icosahedron_shape, []),
'sphere': (sphere_shape, []),
'tube': (tube_shape, [vspec]),
}
snames = shapes.keys()
sa = args.split(None, 1)
if len(sa) < 1:
raise CommandError, 'shape requires at least 1 argument: shape <name>'
from Commands import parse_enumeration
shape = parse_enumeration(sa[0], snames)
if shape is None:
raise CommandError, 'Unknown shape: %s' % sa[0]
func, specs = shapes[shape]
from Commands import doExtensionFunc
fargs = ' '.join(sa[1:])
doExtensionFunc(func, fargs, specInfo=specs)
def tile_command(cmdname, args):
if len(args) == 0:
args = '#'
from Commands import doExtensionFunc
if cmdname.startswith('un'):
f = untile
else:
f = tile
doExtensionFunc(f, args, specInfo = [('modelSpec','models','models'),])
def tile_command(cmdname, args):
if len(args) == 0:
args = '#'
from Commands import doExtensionFunc
if cmdname.startswith('un'):
f = untile
else:
f = tile
doExtensionFunc(f, args, specInfo=[
('modelSpec', 'models', 'models'),
])
def vop_command(cmdname, args):
vspec = ('volumeSpec','volumes','models')
gspec = ('onGridSpec', 'onGrid', 'models')
operations = {
'add': (add_op, [vspec, gspec]),
'bin': (bin_op, [vspec]),
'boxes': (boxes_op, [vspec, ('markersSpec', 'markers', 'atoms')]),
'cover': (cover_op, [vspec, ('atomBoxSpec', 'atomBox', 'atoms')]),
'fourier': (fourier_op, [vspec]),
'gaussian': (gaussian_op, [vspec]),
'laplacian': (laplacian_op, [vspec]),
'median': (median_op, [vspec]),
'morph': (morph_op, [vspec]),
'octant': (octant_op, [vspec]),
'~octant': (octant_complement_op, [vspec]),
'permuteAxes': (permute_axes_op, [vspec]),
'resample': (resample_op, [vspec, gspec]),
'scale': (scale_op, [vspec]),
'subtract': (subtract_op, [('volume1Spec','vol1','models'),
('volume2Spec','vol2','models')]),
'zFlip': (z_flip_op, [vspec]),
}
ops = operations.keys()
sa = args.split(None, 2)
if len(sa) < 2:
raise CommandError, 'vop requires at least 2 arguments: vop <operation> <args...>'
from Commands import parse_enumeration
op = parse_enumeration(sa[0], ops)
if op is None:
# Handle old syntax where operation argument followed volume spec
op = parse_enumeration(sa[1], ops)
if op:
sa = [sa[1], sa[0]] + sa[2:]
else:
raise CommandError, 'Unknown vop operation: %s' % sa[0]
func, spec = operations[op]
from Commands import doExtensionFunc
fargs = ' '.join(sa[1:])
doExtensionFunc(func, fargs, specInfo = spec)
def vop_command(cmdname, args):
vspec = ('volumeSpec', 'volumes', 'models')
gspec = ('onGridSpec', 'onGrid', 'models')
operations = {
'add': (add_op, [vspec, gspec]),
'bin': (bin_op, [vspec]),
'boxes': (boxes_op, [vspec, ('markersSpec', 'markers', 'atoms')]),
'cover': (cover_op, [vspec, ('atomBoxSpec', 'atomBox', 'atoms')]),
'fourier': (fourier_op, [vspec]),
'gaussian': (gaussian_op, [vspec]),
'laplacian': (laplacian_op, [vspec]),
'median': (median_op, [vspec]),
'morph': (morph_op, [vspec]),
'octant': (octant_op, [vspec]),
'~octant': (octant_complement_op, [vspec]),
'permuteAxes': (permute_axes_op, [vspec]),
'resample': (resample_op, [vspec, gspec]),
'scale': (scale_op, [vspec]),
'subtract': (subtract_op, [('volume1Spec', 'vol1', 'models'),
('volume2Spec', 'vol2', 'models')]),
'zFlip': (z_flip_op, [vspec]),
}
ops = operations.keys()
sa = args.split(None, 2)
if len(sa) < 2:
raise CommandError, 'vop requires at least 2 arguments: vop <operation> <args...>'
from Commands import parse_enumeration
op = parse_enumeration(sa[0], ops)
if op is None:
# Handle old syntax where operation argument followed volume spec
op = parse_enumeration(sa[1], ops)
if op:
sa = [sa[1], sa[0]] + sa[2:]
else:
raise CommandError, 'Unknown vop operation: %s' % sa[0]
func, spec = operations[op]
from Commands import doExtensionFunc
fargs = ' '.join(sa[1:])
doExtensionFunc(func, fargs, specInfo=spec)
def old_measure_command(cmdname, args):
from Commands import CommandError
operations = {
'rotation': (rotation_axis, [('model1Spec', 'model1', 'models'),
('model2Spec', 'model2', 'models')]),
'volume': (volume_area, [('surfaceSpec', 'surface', 'vertices')]),
'area': (volume_area, [('surfaceSpec', 'surface', 'vertices')]),
'correlation': (correlation, [('map1Spec', 'map1', 'models'),
('map2Spec', 'map2', 'models')]),
'buriedArea': (buried_area, [('a1Spec', 'atoms1', 'atoms'),
('a2Spec', 'atoms2', 'atoms')]),
'contactArea': (contact_area, []),
'inertia': (inertia, []),
'spine': (spine, []),
'distance': (distance, [('object1Spec', 'object1', None),
('object2Spec', 'object2', None)]),
'mapValues': (map_values, [('mapSpec', 'volume', 'models'),
('atomSpec', 'atoms', 'atoms')]),
'pathLength': (path_length, [('pathSpec', 'path', None)]),
'symmetry': (symmetry, [('volumeSpec', 'volume', 'models')]),
'center': (center, [('objectSpec', 'objects', None)]),
'fieldLines': (field_lines, [('volumeSpec', 'volume', 'models')]),
'mapStats': (map_statistics, [('volumeSpec', 'volume', 'models')]),
'mapSum': (map_sum, [('volumeSpec', 'volume', 'models')]),
}
from Commands import abbreviation_table
aop = abbreviation_table(operations.keys())
fields = args.split(' ', 1)
if len(fields) == 0:
ops = ', '.join(operations.keys())
raise CommandError('Missing required argument: "operation" (%s)' % ops)
op = aop.get(fields[0].lower())
if op is None:
ops = ', '.join(operations)
raise CommandError('Unknown operation "%s" (use %s)' %
(fields[0], ops))
from Commands import doExtensionFunc
f, specInfo = operations[op]
doExtensionFunc(f, args, specInfo=specInfo)
def sop_command(cmdname, args):
operations = {
'finerMesh': (subdivide_op, []),
}
ops = operations.keys()
sa = args.split(None, 2)
if len(sa) < 2:
raise CommandError, 'sop requires at least 2 arguments: sop <operation> <args...>'
from Commands import parse_enumeration
op = parse_enumeration(sa[0], ops)
if op is None:
raise CommandError, 'Unknown sop operation: %s' % sa[0]
func, spec = operations[op]
from Commands import doExtensionFunc
fargs = ' '.join(sa[1:])
doExtensionFunc(func, fargs, specInfo = spec)
def molmap_command(cmdname, args):
from Commands import doExtensionFunc
doExtensionFunc(molecule_map, args,
specInfo = [('atomSpec','atoms','atoms')])
def mask_command(cmdname, args):
from Commands import doExtensionFunc
doExtensionFunc(mask, args,
specInfo = [('volumeSpec','volumes','models'),
('surfaceSpec','surfaces',None)])
def molmap_command(cmdname, args):
from Commands import doExtensionFunc
doExtensionFunc(molecule_map,
args,
specInfo=[('atomSpec', 'atoms', 'atoms')])