def parse_surface_id(sid, cmdname):
if sid[:1] == '#':
sid = sid[1:]
fields = sid.split('.')
if len(fields) == 1:
fields.append('0')
try:
id, subid = int(fields[0]), int(fields[1])
except ValueError:
from Midas.midas_text import error
error('%s: Bad model specifier %s' % (cmdname, sid))
return None
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(id = id, subid = subid, modelTypes = [SurfaceModel])
if len(mlist) == 0:
from Midas.midas_text import error
error('%s: No surface with id %d.%d' % (cmdname, id, subid))
return None
return mlist[0]
def mesh_to_molecule(cmdname, args):
fields = args.split()
if len(fields) != 2:
from Midas.midas_text import error
error('%s requires 2 argument: %s <surface-model-id> <stick-radius>' %
(cmdname, cmdname))
return
sid, rad = fields
s = parse_surface_id(sid, cmdname)
if s == None:
return
# Parse stick radius
try:
radius = float(rad)
except ValueError:
from Midas.midas_text import error
error('%s: Invalid radius value %s' % (cmdname, rad))
return
molecule_from_mesh(s, radius)
def multiscale_color(cmdname, args):
fields = args.split()
if len(fields) != 3:
from Midas.midas_text import error
error(
'%s requires 3 arguments, got %d: %s <multiscale-surface-id> <atom-spec> <coloring-distance>'
% (cmdname, len(fields), cmdname))
return
surf_spec, atom_spec, dist = fields
ms_models = parse_multiscale_models(surf_spec, cmdname)
if len(ms_models) == 0:
return
atoms = parse_atom_specifier(atom_spec, cmdname)
if len(atoms) == 0:
return
# Parse coloring distance
try:
distance = float(dist)
except ValueError:
from Midas.midas_text import error
error('%s: Invalid distance value %s' % (cmdname, dist))
return
multiscale_color_by_atoms(ms_models, atoms, distance)
def split_molecules(cmdname, args):
fields = args.split()
from chimera import openModels, Molecule
if len(fields) >= 1:
from chimera import specifier
sel = specifier.evalSpec(fields[0])
mlist = sel.molecules()
else:
mlist = openModels.list(modelTypes=[Molecule])
if len(mlist) == 0:
from Midas.midas_text import error
error('%s: No molecules to split.' % cmdname)
return
slist = []
for m in mlist:
clist = split_molecule(m)
if clist:
openModels.add(clist, baseId=m.id, noprefs=True)
for c in clist:
c.openState.xform = m.openState.xform
slist.append(m)
from chimera import makeLongBondsDashed, makePseudoBondsToMetals
makePseudoBondsToMetals(clist)
makeLongBondsDashed(clist)
openModels.close(slist)
def multiscale_color(cmdname, args):
fields = args.split()
if len(fields) != 3:
from Midas.midas_text import error
error('%s requires 3 arguments, got %d: %s <multiscale-surface-id> <atom-spec> <coloring-distance>' % (cmdname, len(fields), cmdname))
return
surf_spec, atom_spec, dist = fields
ms_models = parse_multiscale_models(surf_spec, cmdname)
if len(ms_models) == 0:
return
atoms = parse_atom_specifier(atom_spec, cmdname)
if len(atoms) == 0:
return
# Parse coloring distance
try:
distance = float(dist)
except ValueError:
from Midas.midas_text import error
error('%s: Invalid distance value %s' % (cmdname, dist))
return
multiscale_color_by_atoms(ms_models, atoms, distance)
def no_bondzone_command(cmdname, args):
from Midas.midas_text import error
fields = args.split()
if len(fields) > 1:
error('Syntax error: %s [relative_point_spacing]' % cmdname)
return
use_bond_zone(False)
def no_bondzone_command(cmdname, args):
from Midas.midas_text import error
fields = args.split()
if len(fields) > 1:
error('Syntax error: %s [relative_point_spacing]' % cmdname)
return
use_bond_zone(False)
def bondzone_command(cmdname, args):
from Midas.midas_text import error
fields = args.split()
if len(fields) > 1:
error('Syntax error: %s [relative_point_spacing]' % cmdname)
return
elif len(fields) == 1:
try:
spacing = float(fields[0])
except ValueError:
error('Error: %s illegal point spacing "%s"' % (cmdname, fields[0]))
return
use_bond_zone(True, spacing)
else:
use_bond_zone(True)
def multiscale_uncolor(cmdname, args):
fields = args.split()
if len(fields) != 1:
from Midas.midas_text import error
error('%s requires 1 argument, got %d: %s <multiscale-surface-id>' %
(cmdname, len(fields), cmdname))
return
surf_spec = fields[0]
ms_models = parse_multiscale_models(surf_spec, cmdname)
if len(ms_models) == 0:
return
multiscale_uncolor_surfaces(ms_models)
def multiscale_uncolor(cmdname, args):
fields = args.split()
if len(fields) != 1:
from Midas.midas_text import error
error('%s requires 1 argument, got %d: %s <multiscale-surface-id>'
% (cmdname, len(fields), cmdname))
return
surf_spec = fields[0]
ms_models = parse_multiscale_models(surf_spec, cmdname)
if len(ms_models) == 0:
return
multiscale_uncolor_surfaces(ms_models)
def bondzone_command(cmdname, args):
from Midas.midas_text import error
fields = args.split()
if len(fields) > 1:
error('Syntax error: %s [relative_point_spacing]' % cmdname)
return
elif len(fields) == 1:
try:
spacing = float(fields[0])
except ValueError:
error('Error: %s illegal point spacing "%s"' %
(cmdname, fields[0]))
return
use_bond_zone(True, spacing)
else:
use_bond_zone(True)
def parse_atom_specifier(atom_spec, cmdname):
# Parse atoms
from chimera import specifier
try:
asel = specifier.evalSpec(atom_spec)
except:
from Midas.midas_text import error
error('%s: Bad atom specifier %s' % (cmdname, atom_spec))
return []
atoms = asel.atoms()
if len(atoms) == 0:
from Midas.midas_text import error
error('%s: No atoms specified by specifier %s' % (cmdname, atom_spec))
return []
return atoms
def parse_atom_specifier(atom_spec, cmdname):
# Parse atoms
from chimera import specifier
try:
asel = specifier.evalSpec(atom_spec)
except:
from Midas.midas_text import error
error('%s: Bad atom specifier %s' % (cmdname, atom_spec))
return []
atoms = asel.atoms()
if len(atoms) == 0:
from Midas.midas_text import error
error('%s: No atoms specified by specifier %s' % (cmdname, atom_spec))
return []
return atoms
def parse_multiscale_models(surf_spec, cmdname):
# Parse multiscale models
from chimera import specifier
try:
ssel = specifier.evalSpec(surf_spec)
except:
from Midas.midas_text import error
error('%s: Bad model specifier %s' % (cmdname, surf_spec))
return []
ms_models = multiscale_models(ssel.models())
if len(ms_models) == 0:
from Midas.midas_text import error
error('%s: No multiscale models specified by %s' % (cmdname, surf_spec))
return []
return ms_models
def parse_multiscale_models(surf_spec, cmdname):
# Parse multiscale models
from chimera import specifier
try:
ssel = specifier.evalSpec(surf_spec)
except:
from Midas.midas_text import error
error('%s: Bad model specifier %s' % (cmdname, surf_spec))
return []
ms_models = multiscale_models(ssel.models())
if len(ms_models) == 0:
from Midas.midas_text import error
error('%s: No multiscale models specified by %s' %
(cmdname, surf_spec))
return []
return ms_models
def hkcage(h,
k,
radius=100.0,
orientation='222',
color=(1, 1, 1, 1),
linewidth=1.0,
sphere=0.0,
replace=True):
from Midas.midas_text import error
if not type(h) is int or not type(k) is int:
error('h and k must be integers, got %s %s' % (repr(h), repr(k)))
return
if h < 0 or k < 0 or (h == 0 and k == 0):
error('h and k must be non-negative and one > 0, got %d %d' % (h, k))
return
from chimera import MaterialColor
if isinstance(color, MaterialColor):
color = color.rgba()
from Icosahedron import coordinate_system_names
if not orientation in coordinate_system_names:
error('Invalid orientation %s, must be one of: %s' %
(orientation, ', '.join(coordinate_system_names)))
return
from cages import show_hk_lattice
show_hk_lattice(h, k, radius, orientation, color, linewidth, sphere,
replace)
def hkcage(h, k, radius = 100.0, orientation = '222', color = (1,1,1,1),
linewidth = 1.0, sphere = 0.0, replace = True):
from Midas.midas_text import error
if not type(h) is int or not type(k) is int:
error('h and k must be integers, got %s %s' % (repr(h), repr(k)))
return
if h < 0 or k < 0 or (h == 0 and k == 0):
error('h and k must be non-negative and one > 0, got %d %d' % (h,k))
return
from chimera import MaterialColor
if isinstance(color, MaterialColor):
color = color.rgba()
from Icosahedron import coordinate_system_names
if not orientation in coordinate_system_names:
error('Invalid orientation %s, must be one of: %s' %
(orientation, ', '.join(coordinate_system_names)))
return
from cages import show_hk_lattice
show_hk_lattice(h, k, radius, orientation, color, linewidth, sphere,
replace)
def make_surface(volumes, height = None, interpolation = 'none',
meshType = 'isotropic', colorMap = 'rainbow',
smoothingFactor = 0.3, smoothingIterations = 0,
replace = True):
from Midas.midas_text import error
if not height is None and not isinstance(height, (float,int)):
error('Invalid non-numeric height "%s"' % str(height))
return
if not interpolation in ('cubic', 'none'):
error('Invalid interpolation "%s" (cubic, none)' % str(interpolation))
return
if not meshType in ('isotropic', 'slash', 'backslash'):
error('Invalid meshType "%s" (isotropic, slash, backslash)'
% str(meshType))
return
if not colorMap in ('rainbow', 'none'):
error('Invalid colorMap "%s" (rainbow, none)' % str(colorMap))
return
if not isinstance(smoothingIterations, int):
error('Smoothing iterations must be integer, got "%s"'
% str(smoothingIterations))
return
if not isinstance(smoothingFactor, (float,int)):
error('Smoothing factor must be number, got "%s"'
% str(smoothingFactor))
return
volumes = replace_solid_models_by_volume(volumes)
from VolumeViewer import Volume
for v in volumes:
if not isinstance(v, Volume):
error('Model %s is not a volume' % v.name)
return
for v in volumes:
if len([s for s in v.matrix_size() if s == 1]) != 1:
error('Volume %s is not a plane, size (%d,%d,%d)' %
((v.name,) + tuple(v.matrix_size())))
return
from toposurf import create_volume_plane_surface
for v in volumes:
create_volume_plane_surface(v, height, interpolation, meshType, colorMap,
smoothingFactor, smoothingIterations,
replace = replace)
def make_surface(volumes,
height=None,
interpolation='none',
meshType='isotropic',
colorMap='rainbow',
smoothingFactor=0.3,
smoothingIterations=0,
replace=True):
from Midas.midas_text import error
if not height is None and not isinstance(height, (float, int)):
error('Invalid non-numeric height "%s"' % str(height))
return
if not interpolation in ('cubic', 'none'):
error('Invalid interpolation "%s" (cubic, none)' % str(interpolation))
return
if not meshType in ('isotropic', 'slash', 'backslash'):
error('Invalid meshType "%s" (isotropic, slash, backslash)' %
str(meshType))
return
if not colorMap in ('rainbow', 'none'):
error('Invalid colorMap "%s" (rainbow, none)' % str(colorMap))
return
if not isinstance(smoothingIterations, int):
error('Smoothing iterations must be integer, got "%s"' %
str(smoothingIterations))
return
if not isinstance(smoothingFactor, (float, int)):
error('Smoothing factor must be number, got "%s"' %
str(smoothingFactor))
return
volumes = replace_solid_models_by_volume(volumes)
from VolumeViewer import Volume
for v in volumes:
if not isinstance(v, Volume):
error('Model %s is not a volume' % v.name)
return
for v in volumes:
if len([s for s in v.matrix_size() if s == 1]) != 1:
error('Volume %s is not a plane, size (%d,%d,%d)' %
((v.name, ) + tuple(v.matrix_size())))
return
from toposurf import create_volume_plane_surface
for v in volumes:
create_volume_plane_surface(v,
height,
interpolation,
meshType,
colorMap,
smoothingFactor,
smoothingIterations,
replace=replace)