def restore_state(self):
import SurfaceColor
for surface_id_subid, (color_state,
caps_only) in self.coloring_table.items():
from SimpleSession import modelMap
from _surface import SurfaceModel
slist = [
s for s in modelMap.get(surface_id_subid, [])
if isinstance(s, SurfaceModel)
]
if len(slist) > 0:
surface = slist[0]
color_source = color_state.create_color_source()
SurfaceColor.color_surface(surface,
color_source,
caps_only,
auto_update=True)
else:
from chimera import replyobj
replyobj.info(
'Warning: Could not restore surface color on surface model\n\twith id %d.%d because that surface was not restored.\n'
% surface_id_subid)
# Update gui to show settings from restored session.
if self.version >= 2:
if self.coloring_table:
if self.is_visible:
from gui import surface_color_dialog
d = surface_color_dialog(create=True)
if self.geometry:
from SessionUtil import set_window_position
set_window_position(d.toplevel_widget, self.geometry)
d.surface_menu_cb()
d.enter()
def Apply(self):
selectedResidues = chimera.selection.currentResidues()
if not selectedResidues:
self.enter()
raise UserError("No residues selected")
if len(selectedResidues) > 10:
from chimera.baseDialog import AskYesNoDialog
numSel = len(selectedResidues)
if AskYesNoDialog("You have %d residues selected which"
" could bring up %d rotamer dialogs.\n"
"Continue?" % (numSel, numSel)).run(
chimera.tkgui.app) == "no":
self.enter()
return
resType = self.resType.get()
lib = self.rotLib.get()
from Rotamers import NoResidueRotamersError
try:
for sr in selectedResidues:
RotamerDialog(sr, resType, lib)
except NoResidueRotamersError:
from SwapRes import swap
for sr in selectedResidues:
replyobj.info("Swapping %s to %s\n"
% (sr, resType))
swap(sr, resType, bfactor=None)
replyobj.status("Swapped %d residue(s)\n"
% len(selectedResidues))
def Apply(self):
selectedResidues = chimera.selection.currentResidues()
if not selectedResidues:
self.enter()
raise UserError("No residues selected")
if len(selectedResidues) > 10:
from chimera.baseDialog import AskYesNoDialog
numSel = len(selectedResidues)
if AskYesNoDialog("You have %d residues selected which"
" could bring up %d rotamer dialogs.\n"
"Continue?" % (numSel, numSel)).run(
chimera.tkgui.app) == "no":
self.enter()
return
resType = self.resType.get()
lib = self.rotLib.get()
from Rotamers import NoResidueRotamersError
try:
for sr in selectedResidues:
RotamerDialog(sr, resType, lib)
except NoResidueRotamersError:
from SwapRes import swap
for sr in selectedResidues:
replyobj.info("Swapping %s to %s\n" % (sr, resType))
swap(sr, resType, bfactor=None)
replyobj.status("Swapped %d residue(s)\n" % len(selectedResidues))
def restore_state(self):
from ColorZone import color_zone
from SessionUtil import string_to_array, float32
czt = self.color_zone_table
for surface_id_subid, (points, colors, distance) in czt.items():
from SimpleSession import modelMap
from _surface import SurfaceModel
surfaces = [s for s in modelMap.get(surface_id_subid, [])
if isinstance(s, SurfaceModel)]
if surfaces:
# TODO: If more than one surface may get wrong one.
surface = surfaces[0]
if self.version >= 2:
npoints = string_to_array(points, float32, 3)
ncolors = string_to_array(colors, float32, 4)
else:
from numpy import array, single as floatc
npoints = array(points, floatc)
ncolors = array(colors, floatc)
color_zone(surface, npoints, ncolors, distance, auto_update = True)
else:
from chimera import replyobj
replyobj.info('Warning: Could not restore color zone on surface model\n\twith id %d.%d because that surface was not restored.\n' % surface_id_subid)
def report_atom_fit(self, stats):
mlist = stats['molecules']
mnames = map(lambda m: '%s (%s)' % (m.name, m.oslIdent()), mlist)
mnames = ', '.join(mnames)
if len(mlist) > 1: plural = 's'
else: plural = ''
vname = stats['data region'].name
natom = stats['points']
aoc = stats['atoms outside contour']
clevel = stats['contour level']
ave = stats['average map value']
steps = stats['steps']
shift = stats['shift']
angle = stats['angle']
message = ('Fit molecule%s %s to map %s using %d atoms\n'
% (plural, mnames, vname, natom) +
' average map value = %.4g, steps = %d\n' % (ave, steps) +
' shifted from previous position = %.3g\n' % (shift,) +
' rotated from previous position = %.3g degrees\n' % (angle,))
if (not clevel is None) and (not aoc is None):
message += (' atoms outside contour = %d, contour level = %.5g\n'
% (aoc, clevel))
from chimera import replyobj
replyobj.info(message)
self.report_average(ave)
self.report_correlation(None)
if not aoc is None:
status_message = '%d of %d atoms outside contour' % (aoc, natom)
self.message(status_message)
def select_atoms_outside_map():
from chimera.replyobj import status, info
from VolumeViewer import active_volume
dr = active_volume()
if dr is None:
status('No density map opened.')
return
if dr.surface_model() == None or not dr.surface_model().display:
status('No surface shown for map.')
return
levels = dr.surface_levels
if len(levels) == 0:
status('No surface shown for map.')
return
contour_level = min(levels)
from chimera import selection
atoms = selection.currentAtoms()
aolist = atoms_outside_map(atoms, dr, contour_level)
msg = ('%d of %d selected atoms outside %s at level %.5g' %
(len(aolist), len(atoms), dr.name, contour_level))
status(msg)
info(msg + '\n')
selection.setCurrent(aolist)
def color_and_measure(self, window_x, window_y):
from VolumeViewer import slice
xyz_in, xyz_out = slice.clip_plane_points(window_x, window_y)
import PickBlobs
smlist = PickBlobs.surface_models()
p, vlist, tlist = PickBlobs.picked_surface_component(
smlist, xyz_in, xyz_out)
if p is None:
self.message('No intercept with surface.')
return
PickBlobs.color_blob(p, vlist, self.blob_color.rgba)
# Report enclosed volume and area
from MeasureVolume import enclosed_volume, surface_area
varray, tarray = PickBlobs.blob_geometry(p, vlist, tlist)
v, h = enclosed_volume(varray, tarray)
if v == None:
vstr = 'undefined (non-oriented surface)'
else:
vstr = '%.5g' % v
if h > 0:
vstr += ' (%d holes)' % h
area = surface_area(varray, tarray)
s = p.model
msg = ('Surface %s (%s) piece: volume = %s, area = %.5g' %
(s.name, s.oslIdent(), vstr, area))
self.message(msg)
from chimera.replyobj import info, status
info(msg + '\n')
status(msg)
def report_surface_areas(self, compareas):
mname = self.molecule.name
cname = self.category
ncomp = len(compareas)
lines = \
['',
'Surface %s, category %s, probe radius %.4g, vertex density %.4g'
% (mname, cname, self.probeRadius, self.density),
' %d connected surface components' % ncomp,
' Total solvent excluded surface area = %.6g' % self.areaSES]
if ncomp > 1:
careas = [(sesa, sasa) for sesa, sasa in compareas]
careas.sort()
careas.reverse()
eareas = ', '.join(['%.6g' % sesa for sesa, sasa in careas])
aareas = ', '.join(['%.6g' % sasa for sesa, sasa in careas])
lines.append(' component areas = %s' % eareas)
lines.append(' Total solvent accessible surface area = %.6g' %
self.areaSAS)
if ncomp > 1:
lines.append(' component areas = %s' % aareas)
msg = '\n'.join(lines) + '\n'
from chimera.replyobj import info, status
info(msg)
smsg = ('Surface %s, category %s has %d components' %
(mname, cname, ncomp))
status(smsg)
def restore_state(self):
from ColorZone import color_zone
from SessionUtil import string_to_array, float32
czt = self.color_zone_table
for surface_id_subid, (points, colors, distance) in czt.items():
from SimpleSession import modelMap
from _surface import SurfaceModel
surfaces = [
s for s in modelMap.get(surface_id_subid, [])
if isinstance(s, SurfaceModel)
]
if surfaces:
# TODO: If more than one surface may get wrong one.
surface = surfaces[0]
if self.version >= 2:
npoints = string_to_array(points, float32, 3)
ncolors = string_to_array(colors, float32, 4)
else:
from numpy import array, single as floatc
npoints = array(points, floatc)
ncolors = array(colors, floatc)
color_zone(surface,
npoints,
ncolors,
distance,
auto_update=True)
else:
from chimera import replyobj
replyobj.info(
'Warning: Could not restore color zone on surface model\n\twith id %d.%d because that surface was not restored.\n'
% surface_id_subid)
def createPlane(self, name, atoms, number=None, radius=None,
radiusOffset=0.0, color=None, sourceModel=None,
thickness=defaults[PLANE_THICKNESS]):
if len(atoms) < 3:
raise ValueError("Need at least 3 atoms to define plane")
numbers = dict([(pl.number, pl) for pl in self.planes])
if number == None:
if numbers:
number = max(numbers.keys()) + 1
else:
number = 1
elif number in numbers:
self.removePlanes([numbers[number]])
if color == None:
from StructMeasure import matchStructureColor
color = matchStructureColor(atoms)
if sourceModel == None:
sourceModel = self._getSourceModel(atoms)
import StructMeasure
if radius == None:
plane, proj, radius = StructMeasure.plane(
chimera.numpyArrayFromAtoms(atoms), findBounds=True)
radius += radiusOffset
else:
plane = StructMeasure.plane(
chimera.numpyArrayFromAtoms(atoms), findBounds=False)
replyobj.info("%s has radius %g\n" % (name, radius))
self.planeOrdinal += 1
return self._instantiatePlane(number, name, self.planeOrdinal, color,
radius, thickness, sourceModel, atoms, plane)
def report_correlations_with_rotation(v1, v2, aboveThreshold, axis, center,
angleRange, plot):
from chimera import Vector, Point, replyobj
# Convert axis and center to v1 local coordinates so transformation
# is still valid if user rotates entire scene.
xf = v1.openState.xform.inverse()
axis = xf.apply(Vector(*axis)).data()
center = xf.apply(Point(*center)).data()
import FitMap, Matrix
replyobj.info('Correlation between %s and %s\n' % (v1.name, v2.name) +
'Rotation\tCorrelation\n')
a0, a1, astep = angleRange
angle = a0
clist = []
from Matrix import multiply_matrices, xform_matrix, rotation_transform, chimera_xform
while angle < a1:
tf = multiply_matrices(xform_matrix(v1.openState.xform),
rotation_transform(axis, angle, center),
xform_matrix(v1.openState.xform.inverse()))
xf = chimera_xform(tf)
olap, cor = FitMap.map_overlap_and_correlation(v1, v2, aboveThreshold,
xf)
replyobj.status('angle = %.4g, correlation = %.4g\n' % (angle, cor))
replyobj.info('%.4g\t%.4g\n' % (angle, cor))
clist.append((angle, cor))
angle += astep
if plot:
angles = [a for a, c in clist]
corr = [c for a, c in clist]
plot_correlation(angles, corr, v1, v2, axis, center)
def report_atom_fit(self, stats):
mlist = stats['molecules']
mnames = map(lambda m: '%s (%s)' % (m.name, m.oslIdent()), mlist)
mnames = ', '.join(mnames)
if len(mlist) > 1: plural = 's'
else: plural = ''
vname = stats['data region'].name
natom = stats['points']
aoc = stats['atoms outside contour']
clevel = stats['contour level']
ave = stats['average map value']
steps = stats['steps']
shift = stats['shift']
angle = stats['angle']
message = ('Fit molecule%s %s to map %s using %d atoms\n' %
(plural, mnames, vname, natom) +
' average map value = %.4g, steps = %d\n' % (ave, steps) +
' shifted from previous position = %.3g\n' % (shift, ) +
' rotated from previous position = %.3g degrees\n' %
(angle, ))
if (not clevel is None) and (not aoc is None):
message += (
' atoms outside contour = %d, contour level = %.5g\n' %
(aoc, clevel))
from chimera import replyobj
replyobj.info(message)
self.report_average(ave)
self.report_correlation(None)
if not aoc is None:
status_message = '%d of %d atoms outside contour' % (aoc, natom)
self.message(status_message)
def select_atoms_outside_map():
from chimera.replyobj import status, info
from VolumeViewer import active_volume
dr = active_volume()
if dr is None:
status('No density map opened.')
return
if dr.surface_model() == None or not dr.surface_model().display:
status('No surface shown for map.')
return
levels = dr.surface_levels
if len(levels) == 0:
status('No surface shown for map.')
return
contour_level = min(levels)
from chimera import selection
atoms = selection.currentAtoms()
aolist = atoms_outside_map(atoms, dr, contour_level)
msg = ('%d of %d selected atoms outside %s at level %.5g' %
(len(aolist), len(atoms), dr.name, contour_level))
status(msg)
info(msg + '\n')
selection.setCurrent(aolist)
def create_object(self):
if self.version >= 3:
source_molecule = find_molecule_by_id(self.source_molecule_id)
else:
source_molecule = find_molecule_by_name(self.name)
if source_molecule is None:
from chimera.replyobj import info
info('Multiscale session restore error, molecule "%s" missing.\n'
% self.name)
return None
import MultiScale
lm = MultiScale.LAN_Molecule(source_molecule)
lm.dont_unload = self.dont_unload
if self.molecule_id:
m = find_molecule_by_id(self.molecule_id)
if m:
lm.associate_molecule(m, allow_close = not self.dont_unload)
if self.chain_states != None:
clist = map(lambda cs: cs.create_object(lm), self.chain_states)
lm.chain_list = clist
return lm
def _readHeader(self):
# version string
replyobj.info("%s\n" % self._readString())
realSize = self.xdr.unpack_uint()
if realSize == 4:
self.unpackFloatFunc = self.xdr.unpack_float
replyobj.info("using floats\n")
elif realSize == 8:
self.unpackFloatFunc = self.xdr.unpack_double
replyobj.info("using doubles\n")
else:
raise ValueError("Floating-point values in .tpr file"
" are not the same as either single-precision"
" or double-precision floating point on this"
" machine")
version = self.xdr.unpack_uint()
if version >= 26:
generation = self.xdr.unpack_uint()
else:
generation = 0
replyobj.info("version %d, generation %d\n" % (version, generation))
natoms = self.xdr.unpack_uint()
replyobj.info("%d atoms\n" % natoms)
if version >= 28:
tempCouplingGroups = self.xdr.unpack_uint()
curStep = self.xdr.unpack_uint()
curTime = self.unpackFloatFunc()
curLambda = self.unpackFloatFunc()
hasInputRec = self.xdr.unpack_uint()
hasTopology = self.xdr.unpack_uint()
if not hasTopology:
raise ValueError(".tpr file does not have topology section")
hasCoord = self.xdr.unpack_uint()
hasVelocities = self.xdr.unpack_uint()
hasForces = self.xdr.unpack_uint()
hasBbox = self.xdr.unpack_uint()
if hasBbox:
for i in range(9):
self.unpackFloatFunc()
if version >= 51:
for i in range(9):
self.unpackFloatFunc()
if version >= 28:
for i in range(9):
self.unpackFloatFunc()
if version < 56:
for i in range(9):
self.unpackFloatFunc()
if version >= 28 and tempCouplingGroups > 0:
for i in range(tempCouplingGroups):
self.unpackFloatFunc()
self.unpackFloatFunc()
if version < 26 and hasInputRec:
raise ValueError("Cannot read version 26 or earlier" " .tpr files")
return version
def report_correlations_with_rotation(v1, v2, aboveThreshold,
axis, center, angleRange, plot):
from chimera import Vector, Point, replyobj
# Convert axis and center to v1 local coordinates so transformation
# is still valid if user rotates entire scene.
xf = v1.openState.xform.inverse()
axis = xf.apply(Vector(*axis)).data()
center = xf.apply(Point(*center)).data()
import FitMap, Matrix
replyobj.info('Correlation between %s and %s\n' % (v1.name, v2.name) +
'Rotation\tCorrelation\n')
a0, a1, astep = angleRange
angle = a0
clist = []
from Matrix import multiply_matrices, xform_matrix, rotation_transform, chimera_xform
while angle < a1:
tf = multiply_matrices(xform_matrix(v1.openState.xform),
rotation_transform(axis, angle, center),
xform_matrix(v1.openState.xform.inverse()))
xf = chimera_xform(tf)
olap, cor = FitMap.map_overlap_and_correlation(v1, v2,
aboveThreshold, xf)
replyobj.status('angle = %.4g, correlation = %.4g\n' % (angle, cor))
replyobj.info('%.4g\t%.4g\n' % (angle, cor))
clist.append((angle,cor))
angle += astep
if plot:
angles = [a for a,c in clist]
corr = [c for a,c in clist]
plot_correlation(angles, corr, v1, v2, axis, center)
def report_surface_areas(self, compareas):
mname = self.molecule.name
cname = self.category
ncomp = len(compareas)
lines = \
['',
'Surface %s, category %s, probe radius %.4g, vertex density %.4g'
% (mname, cname, self.probeRadius, self.density),
' %d connected surface components' % ncomp,
' Total solvent excluded surface area = %.6g' % self.areaSES]
if ncomp > 1:
careas = [(sesa, sasa) for sesa, sasa in compareas]
careas.sort()
careas.reverse()
eareas = ', '.join(['%.6g' % sesa for sesa, sasa in careas])
aareas = ', '.join(['%.6g' % sasa for sesa, sasa in careas])
lines.append(' component areas = %s' % eareas)
lines.append(' Total solvent accessible surface area = %.6g'
% self.areaSAS)
if ncomp > 1:
lines.append(' component areas = %s' % aareas)
msg = '\n'.join(lines) + '\n'
from chimera.replyobj import info, status
info(msg)
smsg = ('Surface %s, category %s has %d components'
% (mname, cname, ncomp))
status(smsg)
def create_object(self):
if self.version >= 3:
source_molecule = find_molecule_by_id(self.source_molecule_id)
else:
source_molecule = find_molecule_by_name(self.name)
if source_molecule is None:
from chimera.replyobj import info
info('Multiscale session restore error, molecule "%s" missing.\n' %
self.name)
return None
import MultiScale
lm = MultiScale.LAN_Molecule(source_molecule)
lm.dont_unload = self.dont_unload
if self.molecule_id:
m = find_molecule_by_id(self.molecule_id)
if m:
lm.associate_molecule(m, allow_close=not self.dont_unload)
if self.chain_states != None:
clist = map(lambda cs: cs.create_object(lm), self.chain_states)
lm.chain_list = clist
return lm
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 show_saxs_profile(molecules, selected_only, epath, expath, dialog=None):
if len(molecules) <= 2:
name = ', '.join([m.name for m in molecules])
else:
name = '%d models' % len(molecules)
import tempfile, os
fd, pdbpath = tempfile.mkstemp(suffix='.pdb')
os.close(fd)
import Midas
Midas.write(molecules, molecules[0], pdbpath, selOnly=selected_only)
if not epath:
# Use web services if no executable is given
if dialog is None:
dialog = PlotDialog()
ProfileOpalService(pdbpath, expath, name, dialog.figure)
else:
cmd = '%s %s %s' % (epath, pdbpath, expath)
from chimera.replyobj import info, warning
info('Executing command: %s\n' % cmd)
status = os.system(cmd)
if status != 0:
warning('Error %d executing command "%s"' % (status, cmd))
return dialog
if expath:
from os.path import basename
ppath = pdbpath[:-4] + '_' + basename(expath)
p = read_profile(ppath, 3)
else:
ppath = pdbpath + '.dat'
p = read_profile(ppath, 2)
plot_profile(p, name, dialog.figure)
return dialog
def _phosphorylate(mols, status, deletes):
replyobj.info("Deleting 5' phosphates from: %s\n" %
", ".join([str(r) for r in deletes]))
from chimera.molEdit import addAtom
for r in deletes:
r.amberName += "5"
for p in r.atomsMap['P']:
o = None
for nb in p.neighbors:
for nnb in nb.neighbors:
if nnb == p:
continue
if nnb.element.number > 1:
o = nb
continue
r.molecule.deleteAtom(nnb)
if nb != o:
r.molecule.deleteAtom(nb)
v = p.coord() - o.coord()
sn = getattr(p, "serialNumber", None)
r.molecule.deleteAtom(p)
v.length = 0.96
addAtom("H5T",
chimera.Element('H'),
r,
o.coord() + v,
serialNumber=sn,
bondedTo=o)
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 normalize5BU(r):
for a in r.atoms:
if a.element.name == "Br":
r.molecule.deleteAtom(a)
break
r.type = "U"
replyobj.info("5BU residue %s changed to U\n" % str(r))
def restore_state(self):
import SurfaceColor
for surface_id_subid, (color_state, caps_only) in self.coloring_table.items():
from SimpleSession import modelMap
from _surface import SurfaceModel
slist = [s for s in modelMap.get(surface_id_subid, [])
if isinstance(s, SurfaceModel)]
if len(slist) > 0:
surface = slist[0]
color_source = color_state.create_color_source()
SurfaceColor.color_surface(surface, color_source, caps_only,
auto_update = True)
else:
from chimera import replyobj
replyobj.info('Warning: Could not restore surface color on surface model\n\twith id %d.%d because that surface was not restored.\n' % surface_id_subid)
# Update gui to show settings from restored session.
if self.version >= 2:
if self.coloring_table:
if self.is_visible:
from gui import surface_color_dialog
d = surface_color_dialog(create = True)
if self.geometry:
from SessionUtil import set_window_position
set_window_position(d.toplevel_widget, self.geometry)
d.surface_menu_cb()
d.enter()
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 normalize5BU(r):
for a in r.atoms:
if a.element.name == "Br":
r.molecule.deleteAtom(a)
break
r.type = "U"
replyobj.info("5BU residue %s changed to U\n" % str(r))
def show_saxs_profile(molecules, selected_only, epath, expath, dialog = None):
if len(molecules) <= 2:
name = ', '.join([m.name for m in molecules])
else:
name = '%d models' % len(molecules)
import tempfile, os
fd, pdbpath = tempfile.mkstemp(suffix = '.pdb')
os.close(fd)
import Midas
Midas.write(molecules, molecules[0], pdbpath, selOnly = selected_only)
if not epath:
# Use web services if no executable is given
if dialog is None:
dialog = PlotDialog()
ProfileOpalService(pdbpath, expath, name, dialog.figure)
else:
cmd = '%s %s %s' % (epath, pdbpath, expath)
from chimera.replyobj import info, warning
info('Executing command: %s\n' % cmd)
status = os.system(cmd)
if status != 0:
warning('Error %d executing command "%s"' % (status, cmd))
return dialog
if expath:
from os.path import basename
ppath = pdbpath[:-4] + '_' + basename(expath)
p = read_profile(ppath, 3)
else:
ppath = pdbpath + '.dat'
p = read_profile(ppath, 2)
plot_profile(p, name, dialog.figure)
return dialog
def rotation_axis(operation, model1, model2,
showAxis = True, showSlabs = False, color = None):
os1 = set([m.openState for m in model1])
os2 = set([m.openState for m in model2])
if len(os1) != 1:
raise CommandError, 'First model spec names %d models, require 1' % len(os1)
if len(os2) != 1:
raise CommandError, 'Second model spec names %d models, require 1' % len(os2)
os1 = os1.pop()
os2 = os2.pop()
xf = os1.xform.inverse()
xf.multiply(os2.xform)
import Matrix
tf = Matrix.xform_matrix(xf)
message = ('Position of %s (%s) relative to %s (%s) coordinates:\n'
% (model2[0].name, model2[0].oslIdent(),
model1[0].name, model1[0].oslIdent()))
message += Matrix.transformation_description(tf)
from chimera import replyobj
replyobj.info(message)
from chimera import MaterialColor
if isinstance(color, MaterialColor):
color = color.rgba()
elif not color is None:
raise CommandError, 'Unknown color "%s"' % str(color)
if showAxis:
show_axis(tf, color, os1)
if showSlabs:
show_slabs(xf, color, os1)
def report_correlation(v1, v2, aboveThreshold):
from chimera import replyobj
import FitMap
olap, cor = FitMap.map_overlap_and_correlation(v1, v2, aboveThreshold)
replyobj.status('correlation = %.4g\n' % cor)
replyobj.info('Correlation between %s and %s = %.4g\n'
% (v1.name, v2.name, cor))
def report_correlation(v1, v2, aboveThreshold):
from chimera import replyobj
import FitMap
olap, cor = FitMap.map_overlap_and_correlation(v1, v2, aboveThreshold)
replyobj.status('correlation = %.4g\n' % cor)
replyobj.info('Correlation between %s and %s = %.4g\n' %
(v1.name, v2.name, cor))
def no_feature(self, name=None):
if name == None:
name = ''
msg = 'Feature %s not available!\n' % (name)
self.status(msg, color='blue', blankAfter=3)
replyobj.info(msg)
return
def morph_apply(self):
"""morph_apply() - applies appropriate morphing
Applies appropriate morphing after Apply button
is specified. Checks values and passes a message if
incorrect parameters.
"""
# check input data exists
if self.data_item == None:
name = '%s' % (self.data_panel.data_menu.variable.get())
msg = 'Input data %s not found!\n' % name
self.status(msg, color='red', blankAfter=15)
replyobj.error(msg)
return
# get input file path, name, and size in pixels
infile_path = str(self.data_item.path)
infile = str(self.data_item.name)
infile_size = self.data_item.size
# get morph models
morph0, morph1 = self.get_morph_models()
if (morph0 == None or morph1 == None):
return
# get morph parameters
morph_type = self.morph_type.variable.get()
if morph_type == self.morph_choices[0]:
frac, thr, filt = self.get_simple_morph_param()
# check and set output name
self.output_item = None
outfile = str(self.data_output.variable.get())
if (outfile == '') or (outfile == infile):
first_part, last_part = self.name_and_dot_suffix(infile)
outfile = '%s-m%s' % (first_part, last_part)
msg = 'Using default output file %s\n'% outfile
replyobj.info(msg)
self.data_output.variable.set(outfile)
# output
out_dir = os.getcwd()
out_files = [outfile]
# run morph command
seg_sucess = 0
if morph_type == self.morph_choices[0]:
seg_success = self.morph_apply_simple(self.data_item,
morph0, morph1, outfile, frac, thr, filt)
# open output
if seg_success:
self.open_output_data_items(out_dir, out_files)
self.enter()
return
def doneCB(ur, ua, cb=cb, status=status, models=models):
if status:
status("Done adding charges\n")
if models is None:
models = chimera.openModels.list(
modelTypes=[chimera.Molecule])
warnMsg = ""
if ur:
warnMsg += "Correct charges are unknown for %d"\
" non-standard residue types\n\n" % len(ur)
replyobj.info("Non-standard residue types:\n")
for t, rs in ur.items():
info = ", ".join([str(r)
for r in rs[:3]])
if len(rs) > 3:
info += " + %d others" % (
len(rs) - 3)
replyobj.info("\t%s (%s)\n" % (t, info))
warnMsg = unchargedAtomsWarning(ua, warning=warnMsg)
if warnMsg:
warnMsg += "Charges of 0.0 were assigned to the" \
" unknown atoms\n\n"
nonIntegral = []
from math import floor
numNImodels = 0
def isNonIntegral(val):
return abs(floor(val+0.5) - val) > 0.0005
for m in models:
totCharge = 0.0
for r in m.residues:
resCharge = 0.0
for a in r.atoms:
resCharge += getattr(a, 'charge', 0.0)
totCharge += resCharge
if isNonIntegral(resCharge):
nonIntegral.append((r, resCharge))
tChargeMsg = "Total charge for %s: %.4f\n" % (str(m),
totCharge)
replyobj.info(tChargeMsg)
if status:
status(tChargeMsg)
if isNonIntegral(totCharge):
numNImodels += 1
if nonIntegral:
if numNImodels:
warnMsg += "%d model(s) had non-integral total"\
" charge\n" % numNImodels
replyobj.info("The following residues had non-integral"
" charges:\n")
for r, charge in nonIntegral:
replyobj.info("\t%s %g\n" % (str(r), charge))
if warnMsg:
warnMsg += "Details in reply log\n"
replyobj.warning(warnMsg, help="ContributedSoftware/addcharge/addcharge.html#warnings")
if cb:
cb(ur, ua)
def status(self, msg, blankAfter=None, echoToMain=False, log=False,
followWith="", followTime=20, color='black'):
"""Display a status message
'blankAfter' controls how long (in seconds) before the
status area is automatically cleared. Use zero to disable
auto-clearing this message. 'None' uses the user preference.
'echoToMain' and 'log' control sending an identical message
to the main window status line and the reply log,
respectively.
'followWith' is a message to follow the first one with.
'followTime' is how long until the followup message is
cleared (ala blankAfter).
Show the text in 'color' color.
"""
from chimera import replyobj
if not self.provideStatus:
raise ValueError("no status support in dialog")
if self._statusBlankHandle:
self.statusLine.after_cancel(self._statusBlankHandle)
self._statusBlankHandle = None
if echoToMain:
replyobj.status(msg, blankAfter=blankAfter, color=color)
if log:
replyobj.info(msg)
if followWith:
if not msg.endswith("\n"):
msg += "\n"
msg += "[above message copied to Reply Log]"
self.statusLine.configure(text=msg.strip(), fg=color)
self.statusLine.update_idletasks()
blankTime = blankAfter
if blankAfter is None:
import preferences
from replyobj import REPLY_PREFERENCES, STATUS_CLEARING
blankTime = preferences.get(REPLY_PREFERENCES,
STATUS_CLEARING)
if blankTime != 0:
if followWith:
nextMsg = followWith
nextTime = followTime
elif log:
nextMsg = "Previous message also written" \
" to reply log"
nextTime = 20
else:
nextMsg = ""
nextTime = 0
self._statusBlankHandle = self.statusLine.after(
1000 * blankTime, lambda:
self.status(nextMsg, blankAfter=nextTime))
def doneCB(ur, ua, cb=cb, status=status, models=models):
if status:
status("Done adding charges\n")
if models is None:
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
warnMsg = ""
if ur:
warnMsg += "Correct charges are unknown for %d"\
" non-standard residue types\n\n" % len(ur)
replyobj.info("Non-standard residue types:\n")
for t, rs in ur.items():
info = ", ".join([str(r) for r in rs[:3]])
if len(rs) > 3:
info += " + %d others" % (len(rs) - 3)
replyobj.info("\t%s (%s)\n" % (t, info))
warnMsg = unchargedAtomsWarning(ua, warning=warnMsg)
if warnMsg:
warnMsg += "Charges of 0.0 were assigned to the" \
" unknown atoms\n\n"
nonIntegral = []
from math import floor
numNImodels = 0
def isNonIntegral(val):
return abs(floor(val + 0.5) - val) > 0.0005
for m in models:
totCharge = 0.0
for r in m.residues:
resCharge = 0.0
for a in r.atoms:
resCharge += getattr(a, 'charge', 0.0)
totCharge += resCharge
if isNonIntegral(resCharge):
nonIntegral.append((r, resCharge))
tChargeMsg = "Total charge for %s: %.4f\n" % (str(m), totCharge)
replyobj.info(tChargeMsg)
if status:
status(tChargeMsg)
if isNonIntegral(totCharge):
numNImodels += 1
if nonIntegral:
if numNImodels:
warnMsg += "%d model(s) had non-integral total"\
" charge\n" % numNImodels
replyobj.info("The following residues had non-integral"
" charges:\n")
for r, charge in nonIntegral:
replyobj.info("\t%s %g\n" % (str(r), charge))
if warnMsg:
warnMsg += "Details in reply log\n"
replyobj.warning(
warnMsg,
help="ContributedSoftware/addcharge/addcharge.html#warnings")
if cb:
cb(ur, ua)
def show_correlation(self, mmap, fmap):
about_mean = self.corr_about_mean.get()
from FitMap import map_overlap_and_correlation as oc
olap, cor, corm = oc(mmap, fmap, self.above_threshold.get())
self.report_correlation(cor, corm)
msg = 'Correlation = %.4g, Correlation about mean = %.4g, Overlap = %.4g\n' % (cor, corm, olap)
from chimera import replyobj
replyobj.info(msg)
def _reportResidues(residues, attribute): from chimera import replyobj for r in residues: try: attrValue = attrString(r, attribute) except AttributeError: continue info = "residue id %s" % r.oslIdent() info += " %s %s" % (attribute, attrValue) info += '\n' replyobj.info(info)
def _reportAtoms(atoms, attribute): from chimera import replyobj for a in atoms: try: attrValue = attrString(a, attribute) except AttributeError: continue info = "atom id %s" % a.oslIdent() info += " %s %s" % (attribute, attrValue) info += '\n' replyobj.info(info)
def _reportChains(chains, attribute): from chimera import replyobj for seq in chains: try: attrValue = attrString(seq, attribute) except AttributeError: continue info = "chain id %s:.%s" % (seq.molecule.oslIdent(), seq.chain) info += " %s %s" % (attribute, attrValue) info += '\n' replyobj.info(info)
def show_correlation(self, mmap, fmap):
about_mean = self.corr_about_mean.get()
from FitMap import map_overlap_and_correlation as oc
olap, cor, corm = oc(mmap, fmap, self.above_threshold.get())
self.report_correlation(cor, corm)
msg = 'Correlation = %.4g, Correlation about mean = %.4g, Overlap = %.4g\n' % (
cor, corm, olap)
from chimera import replyobj
replyobj.info(msg)
def simpleAddHydrogens(models, unknownsInfo={}, hisScheme=None):
"""Add hydrogens to given models using simple geometric criteria
Geometric info for atoms whose IDATM types don't themselves provide
sufficient information can be passed via the 'unknownsInfo' dictionary.
The keys are atoms and the values are dictionaries specifying the
geometry and number of substituents (not only hydrogens) for the atom.
The 'hisScheme' keyword determines how histidines are handled. If
it is None then the residue name is expected to be HIE, HID, HIP, or
HIS indicating the protonation state is epsilon, delta, both, or
unspecified respectively. Otherwise the value is a dictionary: the
keys are histidine residues and the values are HIE/HID/HIP/HIS
indication of the protonation state. Histindines not in the
dictionary will be protonated based on the nitrogens' atom types.
the protonation is determined by the nitrogen atom type.
This routine adds hydrogens immediately even if some atoms have
unknown geometries. To allow the user to intervene to specify
geometries, use the 'initiateAddHyd' function of the unknownsGUI
module of this package.
"""
from simple import addHydrogens
atomList, typeInfo4Atom, namingSchemas, idatmType, hydrogenTotals, \
hisNs, coordinations, fakeN, fakeC = \
_prepAdd(models, unknownsInfo, hisScheme)
_makeSharedData()
invertXforms = {}
for atom in atomList:
if not typeInfo4Atom.has_key(atom):
continue
bondingInfo = typeInfo4Atom[atom]
try:
invert = invertXforms[atom.molecule]
except KeyError:
try:
invert = atom.molecule.openState.xform
except ValueError:
invert = chimera.Xform.identity()
invert.invert()
invertXforms[atom.molecule] = invert
addHydrogens(
atom, bondingInfo,
(namingSchemas[atom.residue], namingSchemas[atom.molecule]),
hydrogenTotals[atom], idatmType, invert,
coordinations.get(atom, []))
postAdd(fakeN, fakeC)
_deleteSharedData()
replyobj.info("Hydrogens added\n")
def _reportModels(models, attribute): from chimera import replyobj for m in models: try: attrValue = attrString(m, attribute) except AttributeError: continue molType = m.__class__.__name__ info = "model id %s type %s" % (m.oslIdent(), molType) info += " %s %s" % (attribute, attrValue) info += '\n' replyobj.info(info)
def no_feature(self, name=None):
"""no_feature(name=None) - message for missing feature.
Displays a message saying that feature='name' is not
avaialable.
"""
if name == None:
name = ''
msg = 'Feature %s not available!\n' % (name)
self.status(msg, color='blue', blankAfter=3)
replyobj.info(msg)
return
def restore_state(self):
from numpy import array, single as floatc
import dust
for surface_id_subid, (method, limit) in self.dust_table.items():
from SimpleSession import modelMap
if surface_id_subid in modelMap:
surface = modelMap[surface_id_subid][0]
dust.hide_dust(surface, method, limit, auto_update = True)
else:
from chimera import replyobj
replyobj.info('Warning: Could not restore hide dust for surface model\n\twith id %d.%d because that surface was not restored.\n' % surface_id_subid)
def unchargedAtomsWarning(ua, warning=""):
if ua:
warning += "Correct charges are unknown for %d"\
" non-standard atom names in otherwise"\
" standard residues\n\n" % len(ua)
replyobj.info("Non-standard atom names:\n")
for k, atoms in ua.items():
t, n = k
info = ", ".join([str(a) for a in atoms[:3]])
if len(atoms) > 3:
info += " + %d others" % (len(atoms) - 3)
replyobj.info("\t%s %s (%s)\n" % (t, n, info))
return warning
def run_mscalc(xyzr,
probe_radius=1.4,
vertex_density=2.0,
all_components=True,
fallback_to_single_component=True):
from CGLutil.findExecutable import findExecutable
mscalc_path = findExecutable('mscalc')
if mscalc_path is None:
raise Surface_Calculation_Error, 'No mscalc executable found'
if all_components: allc = '1'
else: allc = '0'
args = (mscalc_path, '%f' % probe_radius, '%f' % vertex_density, allc)
from numpy import array, intc
xyzrs = array(len(xyzr), intc).tostring() + xyzr.tostring()
cmd = ' '.join(args)
from chimera.replyobj import info
info(cmd + '\n')
msout, mserr, status = run_shell_command(args, xyzrs)
if status is None:
raise Surface_Calculation_Error, 'Starting mscalc failed.'
if mserr:
info(mserr)
try:
if status != 0:
raise Surface_Calculation_Error, 'Surface calculation failed, mscalc returned code %d' % status
vfloat, vint, tri, atomareas, compareas = parse_mscalc_output(msout)
if atomareas is None and len(xyzr) > 0:
raise Surface_Calculation_Error, 'Surface calculation failed, produced empty surface.\n'
except Surface_Calculation_Error:
if fallback_to_single_component and all_components:
from chimera.replyobj import warning
warning(
'Calculation of some surface components failed.\nFalling back to single-component calculation.\n'
)
return run_mscalc(xyzr,
probe_radius,
vertex_density,
all_components=False)
raise
return vfloat, vint, tri, atomareas, compareas, all_components
def print_axes(axes, d2, m, center):
from math import sqrt
paxes = [
'\tv%d = %7.4f %7.4f %7.4f d%d = %7.3f' %
(a + 1, axes[a][0], axes[a][1], axes[a][2], a + 1, sqrt(d2[a]))
for a in range(3)
]
from chimera.replyobj import info
info('Inertia axes for %s\n%s\n' % (m.name, '\n'.join(paxes)))
info('Centre of mass %7.4f %7.4f %7.4f\n ' %
(center[0], center[1], center[2]))
from Accelerators.standard_accelerators import show_reply_log
show_reply_log()
def addDistance(atom1, atom2):
b = _findDistance(atom1, atom2)
if b is not None:
from chimera import UserError
raise UserError('Distance monitor already exists')
b = distanceMonitor.newPseudoBond(atom1, atom2)
from chimera import replyobj
replyobj.info("Distance between %s and %s: %.*f\n" % (atom1, atom2,
_pref['precision'], b.length()))
b.drawMode = chimera.Bond.Wire
updateDistance()
if not distanceHandlers:
_startHandlers()
return b
def addDistance(atom1, atom2):
b = _findDistance(atom1, atom2)
if b is not None:
from chimera import UserError
raise UserError('Distance monitor already exists')
b = distanceMonitor.newPseudoBond(atom1, atom2)
from chimera import replyobj
replyobj.info("Distance between %s and %s: %.*f\n" %
(atom1, atom2, _pref['precision'], b.length()))
b.drawMode = chimera.Bond.Wire
updateDistance()
if not distanceHandlers:
_startHandlers()
return b
def print_axes(axes, d2, elen, name, xform = None):
if xform:
import Matrix as m
axes = m.apply_matrix_without_translation(m.xform_matrix(xform), axes)
from math import sqrt
paxes = ['\tv%d = %6.3f %6.3f %6.3f %s = %6.3f r%d = %6.3f' %
(a+1, axes[a][0], axes[a][1], axes[a][2],
('a','b','c')[a], elen[a], a+1, sqrt(d2[a]))
for a in range(3)]
from chimera.replyobj import info
info('Inertia axes for %s\n%s\n' % (name, '\n'.join(paxes)))
from Accelerators.standard_accelerators import show_reply_log
show_reply_log()
def center(operation,
objects,
level=None,
mark=False,
color=(.7, .7, .7, 1),
radius=None,
name=None,
modelId=None):
mlist = objects.models()
from VolumeViewer import Volume
vlist = [m for m in mlist if isinstance(m, Volume)]
atoms = objects.atoms()
if len(vlist) == 0 and len(atoms) == 0:
raise CommandError('No volume or atoms specified')
import Commands as CD
rgba = CD.parse_color(color)
model_id = None if modelId is None else CD.parse_model_id(modelId)
import center as C
from chimera import replyobj
for v in vlist:
ijk = C.volume_center_of_mass(v, level)
xyz = v.data.ijk_to_xyz(ijk)
msg = ('Center of mass grid index for %s = (%.2f, %.2f, %.2f)' %
(v.name, ijk[0], ijk[1], ijk[2]))
replyobj.info(msg + '\n')
replyobj.status(msg)
if mark:
r = max(v.data.step) if radius is None else radius
mname = v.name + ' center' if name is None else name
C.place_marker(xyz, v, rgba, r, mname, model_id)
if len(atoms) > 0:
m0 = atoms[0].molecule
cxf = m0.openState.xform
xyz = C.atoms_center_of_mass(atoms, cxf)
msg = ('Center of mass of %d atoms in %s (%s) coordinate system'
' = (%.2f, %.2f, %.2f)' %
(len(atoms), m0.name, m0.oslIdent(), xyz[0], xyz[1], xyz[2]))
replyobj.info(msg + '\n')
smsg = ('Center for %d atoms = (%.2f, %.2f, %.2f)' %
(len(atoms), xyz[0], xyz[1], xyz[2]))
replyobj.status(smsg)
if mark:
r = atoms[0].radius if radius is None else radius
mname = C.atoms_center_model_name(atoms) if name is None else name
C.place_marker(xyz, m0, rgba, r, mname, model_id)
def unchargedAtomsWarning(ua, warning=""):
if ua:
warning += "Correct charges are unknown for %d"\
" non-standard atom names in otherwise"\
" standard residues\n\n" % len(ua)
replyobj.info("Non-standard atom names:\n")
for k, atoms in ua.items():
t, n = k
info = ", ".join([str(a)
for a in atoms[:3]])
if len(atoms) > 3:
info += " + %d others" % (
len(atoms) - 3)
replyobj.info("\t%s %s (%s)\n"
% (t, n, info))
return warning
def normalizeMSE(r):
S = chimera.Element("S")
from BuildStructure import setBondLength
for a in r.atoms:
if a.element.name != "Se":
continue
a.element = S
a.name = "SD"
a.idatmType = "S3"
for n, b in a.bondsMap.items():
if n.name == "CE":
setBondLength(b, 1.78)
elif n.name == "CG":
setBondLength(b, 1.81)
r.type = "MET"
replyobj.info("MSE residue %s changed to MET\n" % str(r))
def listen(mode, what, prefix=None): from chimera import replyobj mode = findBestMatch(mode, ["start", "stop"]) what = findBestMatch(what, ["models", "selection"]) if what == "models": from chimera import openModels global modelHandler if mode == "start": if modelHandler is not None: msg = "already listening for models\n" else: if prefix is None: prefix = "ModelChanged" modelHandler = openModels.addAddHandler( _alertModel, prefix) msg = "listening for models\n" else: if modelHandler is None: msg = "not listening for models\n" else: openModels.deleteAddHandler(modelHandler) modelHandler = None msg = "stopped listening for models\n" replyobj.info(msg) elif what == "selection": import chimera global selectionHandler if mode == "start": if selectionHandler is not None: msg = "already listening for selection\n" else: if prefix is None: prefix = "SelectionChanged" selectionHandler = chimera.triggers.addHandler( "selection changed", _alertSelection, prefix) msg = "listening for selection\n" else: if selectionHandler is None: msg = "not listening for selection\n" else: chimera.triggers.deleteHandler( "selection changed", selectionHandler) selectionHandler = None msg = "stopped listening for selection\n" replyobj.info(msg)
def fetch_emdb_map(id, open_fit_pdbs = False, open_models = True):
site = 'ftp.ebi.ac.uk'
url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/map/%s'
xml_url_pattern = 'ftp://%s/pub/databases/emdb/structures/EMD-%s/header/%s'
from chimera.replyobj import status, info
status('Fetching %s from %s...\n' % (id,site), blankAfter = False)
# Fetch map.
map_name = 'emd_%s.map' % id
map_gz_name = map_name + '.gz'
map_url = url_pattern % (site, id, map_gz_name)
name = 'EMDB %s' % id
minimum_map_size = 8192 # bytes
from chimera import fetch
map_path, headers = fetch.fetch_file(map_url, name, minimum_map_size,
'EMDB', map_name, uncompress = True)
# Display map.
status('Opening map %s...\n' % map_name, blankAfter = False)
from VolumeViewer import open_volume_file
models = open_volume_file(map_path, 'ccp4', map_name, 'surface',
open_models = open_models)
if open_fit_pdbs:
# Find fit pdb ids.
status('EMDB %s: looking for fits PDBs\n' % id)
pdb_ids = fit_pdb_ids_from_web_service(id)
msg = ('EMDB %s has %d fit PDB models: %s\n'
% (id, len(pdb_ids), ','.join(pdb_ids)))
status(msg)
info(msg)
if pdb_ids:
mlist = []
from chimera import _openPDBIDModel, openModels
for pdb_id in pdb_ids:
status('Opening %s\n' % pdb_id)
if open_models:
m = openModels.open(pdb_id, 'PDBID')
else:
m = _openPDBIDModel(pdb_id)
mlist.extend(m)
models.extend(mlist)
return models