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 unselAtoms(): from chimera.selection import currentAtoms selAtoms = currentAtoms(asDict=True) unsel = [] for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): unsel.extend(filter(lambda a: a not in selAtoms, m.atoms)) return unsel
def _finishDockPrep(self):
timestamp("end _getParameters")
from chimera import selection
selectedAtoms = set(selection.currentAtoms())
addSelected = []
numAdded = 0
for m in self.mols:
for a in m.atoms:
if a in self.originalAtoms:
continue
numAdded += 1
# This atom was added. If it was added to
# a selected atom, then we add this atom
# into the current selection as well.
for b in a.bonds:
oa = a.bonds[0].otherAtom(a)
if oa in selectedAtoms:
addSelected.append(a)
break
del self.originalAtoms
if addSelected:
selection.addCurrent(addSelected)
#from chimera import replyobj
#replyobj.info("%d atoms added, %d selected\n"
# % (numAdded, len(addSelected)))
self._finishInit()
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 analysisAtoms(movie, useSel, ignoreBulk, ignoreHyds):
mol = movie.model.Molecule()
if useSel:
selAtoms = selection.currentAtoms()
if selAtoms:
# reduce to just ours
sel1 = selection.ItemizedSelection()
sel1.add(selAtoms)
sel2 = selection.ItemizedSelection()
sel2.add(mol.atoms)
sel1.merge(selection.INTERSECT, sel2)
atoms = sel1.atoms()
if not atoms:
raise UserError("No selected atoms in" " trajectory!")
else:
atoms = mol.atoms
else:
atoms = mol.atoms
if ignoreBulk:
bulkSel = selection.OSLSelection("@/surfaceCategory="
"solvent or surfaceCategory=ions")
atomSel = selection.ItemizedSelection()
atomSel.add(atoms)
atomSel.merge(selection.REMOVE, bulkSel)
atoms = atomSel.atoms()
if not atoms:
raise UserError("No atoms remaining after ignoring"
" solvent/ions")
if ignoreHyds:
atoms = [a for a in atoms if a.element.number != 1]
if not atoms:
raise UserError("No atoms remaining after ignoring" " hydrogens")
return atoms
def ShowEllipsoids(self, *args):
if self.showAxesVar.get():
axisFactor = self.axisFactorOpt.get()
else:
axisFactor = None
if self.showEllipsesVar.get():
ellipseFactor = self.ellipseFactorOpt.get()
else:
ellipseFactor = None
kw = {
'color': self.ellipsoidColorOpt.get(),
'smoothing': int(self.smoothing.getvalue()),
'scale': float(self.scaling.getvalue()),
'showEllipsoid': self.showEllipsoidVar.get(),
'transparency': self.transparencyOpt.get(),
'axisFactor': axisFactor,
'axisColor': self.axisColorOpt.get(),
'axisThickness': self.axisThicknessOpt.get(),
'ellipseFactor': ellipseFactor,
'ellipseColor': self.ellipseColorOpt.get(),
'ellipseThickness': self.ellipseThicknessOpt.get()
}
if self.selRestrictVar.get():
from chimera.selection import currentAtoms
selAtoms = currentAtoms()
if selAtoms:
kw['targets'] = selAtoms
from Aniso import aniso
from Midas import MidasError
try:
aniso(**kw)
except MidasError:
from chimera import UserError
raise UserError("No atoms chosen had anisotropic" " information")
def _atomsDistanceCB(self):
atoms = selection.currentAtoms()
if not atoms:
self.status("No atoms selected", color="red")
return
items = self.table.selected()
if not items:
self.status("No objects chosen", color="red")
return
for item in items:
points = []
dists = item.pointDistances([a.xformCoord()
for a in atoms])
if len(dists) == 1:
self.status("Distance from %s to %s: %.1f\n" %
(atoms[0], item, dists[0]), log=True)
continue
import numpy
dists = numpy.array(dists)
imin = dists.argmin()
imax = dists.argmax()
self.status("Distance from %d atoms to %s: "
"min: %.1f (%s), mean: %.1f, max: %.1f (%s)\n"
% (len(atoms), item, dists[imin], atoms[imin],
dists.mean(), dists[imax], atoms[imax]),
log=True)
def align_backbones_using_selected_atoms():
# Find atom pairs
from chimera import selection
a1, a2 = backbone_atom_pairs(selection.currentAtoms())
if a1 == None:
return
# Compute alignment
from chimera import match
xform, rmsd = match.matchAtoms(a1, a2)
# Apply transformation
m1 = a1[0].molecule
m2 = a2[0].molecule
xf = m1.openState.xform
xf.multiply(xform)
xf2 = m2.openState.xform
m2.openState.xform = xf
# Report atom count, rmsd, and angle
xf2.invert()
xf.multiply(xf2)
axis, angle = xf.getRotation()
from chimera import replyobj
replyobj.status('RMSD between %d atom pairs is %.3f angstroms, rotation angle = %.2f degrees\n'
% (len(a1), rmsd, angle), log = True)
def _finishDockPrep(self):
timestamp("end _getParameters")
from chimera import selection
selectedAtoms = set(selection.currentAtoms())
addSelected = []
numAdded = 0
for m in self.mols:
for a in m.atoms:
if a in self.originalAtoms:
continue
numAdded += 1
# This atom was added. If it was added to
# a selected atom, then we add this atom
# into the current selection as well.
for b in a.bonds:
oa = a.bonds[0].otherAtom(a)
if oa in selectedAtoms:
addSelected.append(a)
break
del self.originalAtoms
if addSelected:
selection.addCurrent(addSelected)
#from chimera import replyobj
#replyobj.info("%d atoms added, %d selected\n"
# % (numAdded, len(addSelected)))
self._finishInit()
def align_molecule():
# TODO: Not ported.
from chimera import selection
atoms = selection.currentAtoms(ordered=True)
mols = set([a.molecule for a in atoms])
if len(mols) != 1:
return
mol = mols.pop()
molxf = mol.openState.xform
from Molecule import atom_positions
axyz = atom_positions(atoms, molxf)
from numpy import roll, float32, float64
from Matrix import xform_matrix, xform_points
from chimera.match import matchPositions
xflist = []
for mset in cage_marker_sets():
for p in polygons(mset):
if p.n == len(atoms):
c = p.center()
vxyz = [p.vertex_xyz(m) for m in p.vertices]
exyz = (0.5 * (vxyz + roll(vxyz, 1, axis=0))).astype(float32)
xform_points(exyz, mset.transform(), molxf)
xf, rms = matchPositions(exyz.astype(float64),
axyz.astype(float64))
xflist.append(xf)
molxf.multiply(xflist[0])
mol.openState.xform = molxf
import MultiScale
mm = MultiScale.multiscale_manager()
tflist = [xform_matrix(xf) for xf in xflist]
mm.molecule_multimer(mol, tflist)
def Apply(self):
from chimera import UserError
if self.replaceExisting.get():
axisManager.removeAxes(axisManager.axes)
kw = {}
kw['color'] = self.colorOpt.get()
if self.fixedRadiusVar.get():
kw['radius'] = prefs[AXIS_RADIUS] = self.radiusOpt.get()
kw['massWeighting'] = self.massWeighting.get() \
and self.modeVar.get() == self.MODE_SELECTION
kw['helicalCorrection'] = self.helixCorrection.get() \
and not kw['massWeighting']
if kw['helicalCorrection']:
replyobj.info("Creating axes with helical correction\n")
elif kw['massWeighting']:
replyobj.info("Creating axes with mass weighting\n")
else:
replyobj.info("Creating axes\n")
if self.modeVar.get() == self.MODE_HELICES:
mols = self.molList.getvalue()
if not mols:
self.enter()
raise UserError("No molecules chosen")
created = 0
for m in mols:
createHelices(m, **kw)
else:
selAtoms = selection.currentAtoms()
if len(selAtoms) < 3:
self.enter()
raise UserError("Need to select at least three"
" atoms to define an axis")
axisManager.createAxis(self.axisNameVar.get().strip(), selAtoms,
**kw)
def align_backbones_using_selected_atoms():
# Find atom pairs
from chimera import selection
a1, a2 = backbone_atom_pairs(selection.currentAtoms())
if a1 == None:
return
# Compute alignment
from chimera import match
xform, rmsd = match.matchAtoms(a1, a2)
# Apply transformation
m1 = a1[0].molecule
m2 = a2[0].molecule
xf = m1.openState.xform
xf.multiply(xform)
xf2 = m2.openState.xform
m2.openState.xform = xf
# Report atom count, rmsd, and angle
xf2.invert()
xf.multiply(xf2)
axis, angle = xf.getRotation()
from chimera import replyobj
replyobj.status(
'RMSD between %d atom pairs is %.3f angstroms, rotation angle = %.2f degrees\n'
% (len(a1), rmsd, angle),
log=True)
def unselAtoms():
from chimera.selection import currentAtoms
selAtoms = currentAtoms(asDict=True)
unsel = []
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
unsel.extend(filter(lambda a: a not in selAtoms, m.atoms))
return unsel
def move_selected_atoms_to_maximum(max_steps=2000,
ijk_step_size_min=0.01,
ijk_step_size_max=0.5,
optimize_translation=True,
optimize_rotation=True,
move_whole_molecules=True,
request_stop_cb=None):
from . import active_volume
volume = active_volume()
if volume == None or volume.model_transform() == None:
if request_stop_cb:
request_stop_cb('No volume data set.')
return {}
from chimera import selection
atoms = selection.currentAtoms()
if len(atoms) == 0:
if request_stop_cb:
request_stop_cb('No atoms selected.')
return {}
stats = move_atoms_to_maximum(atoms, volume, max_steps, ijk_step_size_min,
ijk_step_size_max, optimize_translation,
optimize_rotation, move_whole_molecules,
request_stop_cb)
return stats
def move_selected_atoms_to_maximum(max_steps = 100, ijk_step_size_min = 0.01,
ijk_step_size_max = 0.5,
optimize_translation = True,
optimize_rotation = True,
move_whole_molecules = True,
request_stop_cb = None):
from VolumeViewer import active_volume
volume = active_volume()
if volume == None or volume.model_transform() == None:
if request_stop_cb:
request_stop_cb('No volume data set.')
return {}
from chimera import selection
atoms = selection.currentAtoms()
if len(atoms) == 0:
if request_stop_cb:
request_stop_cb('No atoms selected.')
return {}
stats = move_atoms_to_maximum(atoms, volume, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
move_whole_molecules,
request_stop_cb)
return stats
def record_movable_objects(self, event):
mode = self.mode
if mode == self.MOVE_SELECTION:
from chimera import selection
atoms = selection.currentAtoms()
chains = selected_multiscale_chains()
spieces = selected_surface_pieces()
self.movable_groups = objects_grouped_by_model(
atoms, chains, spieces)
elif mode in (self.MOVE_MOLECULE, self.MOVE_CHAIN,
self.MOVE_SECONDARY_STRUCTURE):
from chimera import viewer, Atom, Residue
# TODO: Appears to be a bug where picking 1a0m ribbon gives
# lists of many erroneous residues. It is caused by LensViewer
# pick(x,y) doing drag pick using previously set x,y! Not clear
# why since there is separate dragPick(x,y) method.
viewer.delta(event.x, event.y) # Sets lastx, lasty
objects = viewer.pick(event.x, event.y)
atoms = [a for a in objects if isinstance(a, Atom)]
residues = [r for r in objects if isinstance(r, Residue)]
if mode == self.MOVE_MOLECULE:
catoms = extend_to_molecules(atoms, residues)
mschains = multiscale_chain_pieces(objects,
full_molecules=True)
elif mode == self.MOVE_CHAIN:
catoms = extend_to_chains(atoms, residues)
mschains = multiscale_chain_pieces(objects)
elif mode == self.MOVE_SECONDARY_STRUCTURE:
catoms = extend_to_secondary_structure(atoms, residues)
mschains = []
self.movable_groups = objects_grouped_by_model(catoms, mschains)
else:
self.movable_groups = []
def selected_markers(self):
atoms = selection.currentAtoms()
markers = []
for a in atoms:
if self.atom_to_marker.has_key(a):
markers.append(self.atom_to_marker[a])
return markers
def _createDistance(self):
"""'Create distance' callback"""
selAtoms = selection.currentAtoms()
if len(selAtoms) != 2:
replyobj.error("Exactly two atoms must be selected "
"in graphics window\n")
return
addDistance(*tuple(selAtoms))
def HideEllipsoids(self):
kw = {}
if self.selRestrictVar.get():
from chimera.selection import currentAtoms
selAtoms = currentAtoms()
if selAtoms:
kw['targets'] = selAtoms
from Aniso import unaniso
unaniso(**kw)
def selected_markers(self):
from chimera.selection import currentAtoms
atoms = currentAtoms()
markers = []
for a in atoms:
if self.atom_to_marker.has_key(a):
markers.append(self.atom_to_marker[a])
return markers
def show_surface():
'Show MSMS molecular surface'
from chimera.selection import currentAtoms
from Surface import selected_surface_pieces, show_surfaces
if len(currentAtoms()) > 0 or len(selected_surface_pieces()) == 0:
# If actions.showSurface() with no atoms selected and a SurfacePiece is
# selected then it shows a warning dialog. Suppress that.
from chimera import actions
actions.showSurface() # MSMSModel surfaces
show_surfaces(selected_surface_pieces()) # SurfaceModel surfaces
def selected_and_unselected_atom_sets(displayed_only):
# Get selected atoms.
from chimera import selection
atoms = selection.currentAtoms()
# Group atoms by multiscale chain piece or non-multiscale molecule.
ca_sel, ma_sel = group_atoms(atoms)
# Get multiscale chains with selected surfaces.
cp_sel = selected_multiscale_chains()
# When chain atoms and surface are both selected ignore surface selection.
cp_sel = filter(lambda cp: not cp in ca_sel, cp_sel)
# Separate out unloaded selected chains.
cpul_sel = filter(lambda cp: not cp.lan_chain.is_loaded(), cp_sel)
# Merge loaded selected chains into table of atoms grouped by chain.
cpl_sel = filter(lambda cp: cp.lan_chain.is_loaded(), cp_sel)
for cp in cpl_sel:
catoms = cp.lan_chain.atoms()
ca_sel[cp] = catoms
atoms.extend(catoms)
# Get unselected atoms
unsel_atoms = subtract_lists(all_atoms(), atoms)
ca_unsel, ma_unsel = group_atoms(unsel_atoms)
# Get unselected multiscale chains.
cp_unsel = subtract_lists(all_multiscale_chains(), cp_sel)
# Don't include chains with selected atoms.
cp_unsel = filter(lambda cp: not cp in ca_sel, cp_unsel)
# Separate out unloaded unselected chains.
cpul_unsel = filter(lambda cp: not cp in ca_unsel, cp_unsel)
# Eliminate undisplayed atoms and chains.
if displayed_only:
cpul_sel = filter(lambda cp: cp.surface_shown(), cpul_sel)
cpul_unsel = filter(lambda cp: cp.surface_shown(), cpul_unsel)
for table in (ca_sel, ca_unsel, ma_sel, ma_unsel):
remove_undisplayed_table_atoms(table)
# Make selected and unselected atom sets for non-multiscale models,
# loaded multiscale chains, and unloaded multiscale chains.
asets_sel = (map(molecule_atom_set, ma_sel.items()) +
map(chain_atom_subset, ca_sel.items()) +
chain_atom_sets(cpul_sel))
asets_unsel = (map(molecule_atom_set, ma_unsel.items()) +
map(chain_atom_subset, ca_unsel.items()) +
chain_atom_sets(cpul_unsel))
return asets_sel, asets_unsel
def molecular_weight():
'Report molecular weight of selected atoms'
from chimera import selection, replyobj
w = sum([a.element.mass for a in selection.currentAtoms()])
if w >= 1.0e6:
s = '%.4g MDa' % (w * 1.0e-6)
elif w >= 1.0e3:
s = '%.4g KDa' % (w * 1.0e-3)
else:
s = '%.4g Daltons' % (w * 1.0e-3)
replyobj.status('Molecular weight ' + s)
def _itemsSelectAtoms(self, items, add=False): atoms = set() for item in items: atoms.update(item.atoms) if self.geomSelAtomsVar.get(): if add: selection.addCurrent(atoms) else: selection.setCurrent(atoms) elif set(atoms) == set(selection.currentAtoms()): selection.removeCurrent(atoms)
def move_atoms_to_maxima():
from chimera.selection import currentAtoms
atoms = currentAtoms()
if len(atoms) == 0:
from chimera.replyobj import status
status('No atoms selected.')
return
for a in atoms:
move_atom_to_maximum(a)
def move_atoms_to_maxima():
from chimera.selection import currentAtoms
atoms = currentAtoms()
if len(atoms) == 0:
from chimera.replyobj import status
status('No atoms selected.')
return
for a in atoms:
move_atom_to_maximum(a)
def setFixed(self, which):
from chimera import selection
if which == "none" or selection.currentEmpty():
for ma in self.universe.atomList():
ma.fixed = False
elif which == "selected":
import chimera
for ma in self.universe.atomList():
ma.fixed = False
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = True
else:
import chimera
for ma in self.universe.atomList():
ma.fixed = True
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = False
def setFixed(self, which): from chimera import selection if which == "none" or selection.currentEmpty(): for ma in self.universe.atomList(): ma.fixed = False elif which == "selected": import chimera for ma in self.universe.atomList(): ma.fixed = False for a in selection.currentAtoms(): if a.molecule in self.mols: ma = self.atomMap[a] ma.fixed = True else: import chimera for ma in self.universe.atomList(): ma.fixed = True for a in selection.currentAtoms(): if a.molecule in self.mols: ma = self.atomMap[a] ma.fixed = False
def fit_atoms(self):
m = self.object_menu.getvalue()
if m == 'selected atoms':
from chimera import selection
atoms = selection.currentAtoms()
return atoms
from chimera import Molecule
if isinstance(m, Molecule):
return m.atoms
return []
def chosen_atoms(self):
m = self.molecule_menu.getvalue()
from chimera import Molecule, openModels, selection
if isinstance(m, Molecule):
return [m], False
elif m == 'selected atoms':
mlist = list(set([a.molecule for a in selection.currentAtoms()]))
return mlist, True
elif m == 'all molecules':
mlist = openModels.list(modelTypes=[Molecule])
return mlist, False
return [], False
def chosen_atoms(self):
m = self.molecule_menu.getvalue()
from chimera import Molecule, openModels, selection
if isinstance(m, Molecule):
return [m], False
elif m == 'selected atoms':
mlist = list(set([a.molecule for a in selection.currentAtoms()]))
return mlist, True
elif m == 'all molecules':
mlist = openModels.list(modelTypes = [Molecule])
return mlist, False
return [], False
def selection_surface_distance():
from chimera import selection
alist = selection.currentAtoms()
if len(alist) == 0:
from chimera.replyobj import status
status('No atoms or markers selected')
return
from chimera import openModels
from _surface import SurfaceModel
smlist = openModels.list(modelTypes = [SurfaceModel])
write_surface_distances(alist, smlist)
def fit_atoms(self):
m = self.object_menu.getvalue()
if m == 'selected atoms':
from chimera import selection
atoms = selection.currentAtoms()
return atoms
from VolumeViewer import Volume
from chimera import Molecule
if isinstance(m, Molecule):
return m.atoms
return []
def select_connected():
'Select atoms and bonds connected to currently selected atoms and bnods'
from chimera import selection, Atom
atoms_and_bonds = selection.currentAtoms() + selection.currentBonds()
reached = set(atoms_and_bonds)
i = 0
while i < len(atoms_and_bonds):
ab = atoms_and_bonds[i]
if isinstance(ab, Atom):
n = ([b for b in ab.bonds if not b in reached] +
[a for a in ab.neighbors if not a in reached])
else:
n = [a for a in ab.atoms if not a in reached]
atoms_and_bonds.extend(n)
reached.update(set(n))
i += 1
selection.setCurrent(atoms_and_bonds)
def _selChanged(self, trigName, myData, trigData):
ats = selection.currentAtoms()
if len(ats) != 1:
return
entry = self.cmd.component('entry')
text = entry.get()
pre = True
for i in range(len(text)):
c = text[i]
if c == '+' and pre and (i == len(text) - 1
or text[i + 1].isspace()):
break
pre = c.isspace()
else:
return
entry.delete(i)
entry.insert(i, ats[0].oslIdent())
def _getMolecules(self, assignsel, usesel, restrict): if assignsel or usesel: sel = selection.currentMolecules() if usesel: for r in selection.currentResidues(): restrict[r] = True for a in selection.currentAtoms(): restrict[a] = True for m in sel: restrict[m] = True if assignsel: molecules = sel else: molecules = [] if not molecules: molecules = chimera.openModels.list( modelTypes=[chimera.Molecule]) return molecules
def bounding_map(pad = 5.0):
from chimera.selection import currentAtoms
atoms = currentAtoms()
if len(atoms) == 0:
from chimera.replyobj import status
status('No atoms selected')
return
from volumedialog import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('No volume shown in volume dialog')
return
from volume import map_covering_atoms
bv = map_covering_atoms(atoms, pad, v)
bv.show()
v.show(show = False)
def bounding_map(pad=5.0):
from chimera.selection import currentAtoms
atoms = currentAtoms()
if len(atoms) == 0:
from chimera.replyobj import status
status('No atoms selected')
return
from volumedialog import active_volume
v = active_volume()
if v is None:
from chimera.replyobj import status
status('No volume shown in volume dialog')
return
from volume import map_covering_atoms
bv = map_covering_atoms(atoms, pad, v)
bv.show()
v.show(show=False)
def Apply(self):
from chimera import UserError
if self.replaceExistingOpt.get():
planeManager.removePlanes(planeManager.planes)
kw = {
'color': self.colorOpt.get(),
'thickness': self.thicknessOpt.get()
}
prefs[PLANE_THICKNESS] = kw['thickness']
if self.autoRadiusOpt.get():
kw['radiusOffset'] = self.radOffsetOpt.get()
else:
kw['radius'] = self.radiusOpt.get()
replyobj.info("Creating plane\n")
selAtoms = selection.currentAtoms()
if len(selAtoms) < 3:
self.enter()
raise UserError("Need to select at least three"
" atoms to define a plane")
planeManager.createPlane(self.nameOpt.get().strip(), selAtoms, **kw)
def illustrate_backbone_alignment():
# Find atom pairs
from chimera import selection
a1, a2 = backbone_atom_pairs(selection.currentAtoms())
if a1 == None:
return
# Compute alignment
from chimera import match
xform, rmsd = match.matchAtoms(a1, a2)
# Find aligning transformation to apply to molecule 2 object coordinates
m1 = a1[0].molecule
m2 = a2[0].molecule
xf = m1.openState.xform
xf.multiply(xform) # New m2 transform to align.
inv_xf2 = m2.openState.xform
inv_xf2.invert()
xf.premultiply(inv_xf2) # xform in m2 object coordinates
# Make schematic illustrating rotation
# alpha = .5
from_rgba = list(m2.color.rgba())
# from_rgba[3] = alpha
to_rgba = list(m1.color.rgba())
# to_rgba[3] = alpha
sm = transform_schematic(xf, center_of_atoms(a2), from_rgba, to_rgba)
if sm:
sm.name = 'Transform from %s to %s' % (m2.name, m1.name)
from chimera import openModels
openModels.add([sm], sameAs=m2)
# Report atom count, rmsd, and angle
axis, angle = xf.getRotation()
from chimera import replyobj
replyobj.status(
'RMSD between %d atom pairs is %.3f angstroms, rotation angle = %.2f degrees\n'
% (len(a1), rmsd, angle),
log=True)
def illustrate_backbone_alignment():
# Find atom pairs
from chimera import selection
a1, a2 = backbone_atom_pairs(selection.currentAtoms())
if a1 == None:
return
# Compute alignment
from chimera import match
xform, rmsd = match.matchAtoms(a1, a2)
# Find aligning transformation to apply to molecule 2 object coordinates
m1 = a1[0].molecule
m2 = a2[0].molecule
xf = m1.openState.xform
xf.multiply(xform) # New m2 transform to align.
inv_xf2 = m2.openState.xform
inv_xf2.invert()
xf.premultiply(inv_xf2) # xform in m2 object coordinates
# Make schematic illustrating rotation
# alpha = .5
from_rgba = list(m2.color.rgba())
# from_rgba[3] = alpha
to_rgba = list(m1.color.rgba())
# to_rgba[3] = alpha
sm = transform_schematic(xf, center_of_atoms(a2), from_rgba, to_rgba)
if sm:
sm.name = 'Transform from %s to %s' % (m2.name, m1.name)
from chimera import openModels
openModels.add([sm], sameAs = m2)
# Report atom count, rmsd, and angle
axis, angle = xf.getRotation()
from chimera import replyobj
replyobj.status('RMSD between %d atom pairs is %.3f angstroms, rotation angle = %.2f degrees\n'
% (len(a1), rmsd, angle), log = True)
def zone_cb(self, event = None):
self.message('')
surface = self.chosen_surface()
if surface == None:
self.message('Select a surface')
return
radius = self.radius_from_gui()
if radius == None:
return
from chimera import selection
atoms = selection.currentAtoms()
bonds = selection.currentBonds()
from SurfaceZone import path_points, surface_zone
points = path_points(atoms, bonds, surface.openState.xform.inverse())
if len(points) > 0:
surface_zone(surface, points, radius, auto_update = True)
else:
self.message('No atoms are selected')
def zone_cb(self, event=None):
self.message('')
surface = self.chosen_surface()
if surface == None:
self.message('Select a surface')
return
radius = self.radius_from_gui()
if radius == None:
return
from chimera import selection
atoms = selection.currentAtoms()
bonds = selection.currentBonds()
from SurfaceZone import path_points, surface_zone
points = path_points(atoms, bonds, surface.openState.xform.inverse())
if len(points) > 0:
surface_zone(surface, points, radius, auto_update=True)
else:
self.message('No atoms are selected')
def analysisAtoms(movie, useSel, ignoreBulk, ignoreHyds):
mol = movie.model.Molecule()
if useSel:
selAtoms = selection.currentAtoms()
if selAtoms:
# reduce to just ours
sel1 = selection.ItemizedSelection()
sel1.add(selAtoms)
sel2 = selection.ItemizedSelection()
sel2.add(mol.atoms)
sel1.merge(selection.INTERSECT, sel2)
atoms = sel1.atoms()
if not atoms:
raise UserError("No selected atoms in"
" trajectory!")
else:
atoms = mol.atoms
else:
atoms = mol.atoms
if ignoreBulk:
bulkSel = selection.OSLSelection("@/surfaceCategory="
"solvent or surfaceCategory=ions")
atomSel = selection.ItemizedSelection()
atomSel.add(atoms)
atomSel.merge(selection.REMOVE, bulkSel)
atoms = atomSel.atoms()
if not atoms:
raise UserError("No atoms remaining after ignoring"
" solvent/ions")
if ignoreHyds:
atoms = [a for a in atoms if a.element.number != 1]
if not atoms:
raise UserError("No atoms remaining after ignoring"
" hydrogens")
return atoms
def color_zone_cb(self, event = None):
self.message('')
surface = self.chosen_surface()
if surface == None:
self.message('Select a surface')
return
radius = self.radius_from_gui()
if radius == None:
return
xform_to_surface = surface.openState.xform.inverse()
from chimera import selection
atoms = selection.currentAtoms()
bonds = selection.currentBonds()
from ColorZone import points_and_colors, color_zone
points, colors = points_and_colors(atoms, bonds, xform_to_surface)
if len(points) > 0:
color_zone(surface, points, colors, radius, auto_update = True)
else:
self.message('No atoms are selected')
def selAtoms(noneReturnsAll=True, implied=False, create=False): atoms = selection.currentAtoms() extendSelection(atoms, 'atoms', noneReturnsAll, implied, create) return atoms
def _any_selected(self):
from chimera import selection, Molecule, MSMSModel, PseudoBondGroup
text = ""
numAtoms = len(selection.currentAtoms())
if numAtoms:
text = "%d atom" % numAtoms
if numAtoms > 1:
text += "s"
numBonds = len(selection.currentBonds())
if numBonds:
if text:
text += ", "
text += "%d bond" % numBonds
if numBonds > 1:
text += "s"
numEdges = len(selection.currentEdges())
if numEdges != numBonds:
if text:
text += ", "
numPBonds = numEdges - numBonds
text += "%d pbond" % numPBonds
if numPBonds > 1:
text += "s"
graphs = selection.currentGraphs()
numSurfs = numObjs = 0
for g in graphs:
if isinstance(g, (Molecule, PseudoBondGroup)):
continue
if isinstance(g, MSMSModel) or "surf" in g.__class__.__name__.lower():
numSurfs += 1
else:
numObjs += 1
if numSurfs:
if text:
text += ", "
text += "%d surf" % numSurfs
if numSurfs > 1:
text += "s"
if numObjs:
if text:
text += ", "
text += "%d obj" % numObjs
if numObjs > 1:
text += "s"
import help
if not text:
help.register(self.selections_button, balloon="no selection")
show_message("selection cleared", blankAfter=5)
return False
else:
help.register(self.selections_button, balloon=text)
if self.first_selection:
self.first_selection = False
show_message(text, followWith="up-arrow to increase selection "
"(atoms->residues->chains etc.)")
else:
show_message(text)
return True
rc("color NIH_blue")
export_scene("surf")
rc("color white")
# output Coulombic coloring surface 3D print if <25000 atoms
if numAtoms < 25000:
description = "coulombicsurf"
rc("addcharge std")
rc("coulombic atoms #0 -10 red 0 white 10 blue #1")
export_scene("surf-coulombic")
# output Kyte-Doolittle coloring surface 3D print (only works on amino acids)
# check for protein (only works on amino acids)
rc("select protein")
if len(selection.currentAtoms()) > 0:
rc("~select")
rc("color magenta #0")
rc("rangecolor kdHydrophobicity min 0.16,0.67,0.87 max 1.00,0.45,0.00 mid white novalue magenta #0")
#Need to loop from 1 to numSubmodels and put into scolor #1
for surfs in range(1, numSubmodelsP):
try:
rc("scolor #" + str(surfs) + " zone #0 range 6.0")
except:
try:
rc("scolor #0." + str(surfs) + " zone #0 range 6.0")
except:
pass
export_scene("surf-hydropathy")
# output colored by chain surface 3D print
def lists(level="atom", mode="any", attribute=None):
import chimera
from chimera import replyobj, selection
mode = findBestMatch(mode, ["any", "all"])
level = findBestMatch(level, ["atom", "residue", "chain", "molecule"])
if level == "atom":
if attribute is None:
attribute = "idatmType"
_reportAtoms(selection.currentAtoms(), attribute)
elif level == "residue":
if mode == "any":
residues = selection.currentResidues()
else:
rMap = {}
for a in selection.currentAtoms():
l = rMap.setdefault(a.residue, [])
l.append(a)
residues = []
for r, aList in rMap.iteritems():
if len(r.atoms) == len(aList):
residues.append(r)
if attribute is None:
attribute = "type"
_reportResidues(residues, attribute)
elif level == "chain":
if mode == "any":
chains = selection.currentChains()
else:
rcMap = {}
cached = set([])
cMap = {}
for r in selection.currentResidues():
if r.molecule not in cached:
cached.add(r.molecule)
for seq in r.molecule.sequences():
for res in seq.residues:
rcMap[res] = seq
try:
seq = rcMap[r]
except KeyError:
pass
else:
l = cMap.setdefault(seq, [])
l.append(r)
chains = []
for seq, rList in cMap.iteritems():
if len(seq) == len(rList):
chains.append(seq)
if attribute is None:
attribute = "chain"
_reportChains(chains, attribute)
elif level == "molecule":
if mode == "any":
molecules = selection.currentMolecules()
else:
mMap = {}
for a in selection.currentAtoms():
l = mMap.setdefault(a.molecule, [])
l.append(a)
molecules = []
for m, aList in mMap.iteritems():
if len(m.atoms) == len(aList):
molecules.append(m)
if attribute is None:
attribute = "name"
_reportModels(molecules, attribute)
else:
raise chimera.UserError("\"%s\": unknown listselection level"
% level)
def createHBonds(models=None, intramodel=True, intermodel=True, relax=True,
distSlop=recDistSlop, angleSlop=recAngleSlop, twoColors=False,
selRestrict=None, lineWidth=1.0, saveFile=None, batch=False,
interSubmodel=False, makePseudobonds=True, retainCurrent=False,
reveal=False, namingStyle=None, log=False, cacheDA=None,
color=(0.0, 0.8, 0.9, 1.0), slopColor=(0.95, 0.5, 0.0, 1.0)):
"""Wrapper to be called by gui and command line.
Use findHBonds for other programming applications.
"""
inColors = (color, slopColor)
outColors = []
for c in inColors:
if isinstance(c, basestring):
from chimera.colorTable import getColorByName
try:
outColors.append(getColorByName(c))
except KeyError:
raise "No known color named '%s'" % c
elif isinstance(c, tuple):
oc = chimera.MaterialColor()
oc.ambientDiffuse = c[:3]
if len(c) > 3:
oc.opacity = c[-1]
outColors.append(oc)
else:
outColors.append(c)
bondColor, slopColor = outColors
donors = acceptors = None
if selRestrict is not None:
selAtoms = currentAtoms(asDict=True)
if not selAtoms:
if batch:
return
raise UserError("No atoms in selection.")
if (not intermodel or selRestrict == "both") and models is None:
# intramodel only or both ends in selection
models = currentMolecules()
if selRestrict == "both":
# both ends in selection
donors = acceptors = selAtoms
if models is None:
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
if not relax:
distSlop = angleSlop = 0.0
if cacheDA == None:
# cache trajectories by default
cacheDA = len(models) == 1 and len(models[0].coordSets) > 1
hbonds = findHBonds(models, intermodel=intermodel,
intramodel=intramodel, distSlop=distSlop,
angleSlop=angleSlop, donors=donors, acceptors=acceptors,
interSubmodel=interSubmodel, cacheDA=cacheDA)
if selRestrict and donors == None:
hbonds = _filterBySel(hbonds, selAtoms, selRestrict)
outputInfo = (intermodel, intramodel, relax, distSlop, angleSlop,
models, hbonds)
if log:
import sys
# provide a separator from other output
print>>sys.stdout, ""
_fileOutput(sys.stdout, outputInfo, namingStyle)
if saveFile == '-':
from MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(outputInfo, _fileOutput,
initialfile="hbond.info",
title="Choose H-Bond Save File",
historyID="H-bond info")
elif saveFile is not None:
_fileOutput(saveFile, outputInfo, namingStyle)
replyobj.status("%d hydrogen bonds found\n"
% len(hbonds), log=1, blankAfter=120)
if not makePseudobonds:
return
if twoColors:
# color relaxed constraints differently
precise = findHBonds(models,
intermodel=intermodel, intramodel=intramodel,
donors=donors, acceptors=acceptors,
interSubmodel=interSubmodel, cacheDA=cacheDA)
if selRestrict and donors == None:
precise = _filterBySel(precise, selAtoms, selRestrict)
# give another opportunity to read the result...
replyobj.status("%d hydrogen bonds found\n" % len(hbonds),
blankAfter=120)
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup("hydrogen bonds", issueHint=True)
if not retainCurrent:
pbg.deleteAll()
pbg.lineWidth = lineWidth
for don, acc in hbonds:
if don.associated(acc, "hydrogen bonds"):
continue
pb = pbg.newPseudoBond(don, acc)
if twoColors:
if (don, acc) in precise:
color = bondColor
else:
color = slopColor
else:
color = bondColor
pb.color = color
if reveal:
for end in [don, acc]:
if end.display:
continue
for ea in end.residue.oslChildren():
ea.display = True
