def Apply(self):
val = self.seqMenu1.get()
if val == self.ALL:
seqs1 = self.mav.seqs
else:
seqs1 = [s for s in self.mav.seqs if s.name == val]
val = self.seqMenu2.get()
if val == self.ALL:
seqs2 = self.mav.seqs
else:
seqs2 = [s for s in self.mav.seqs if s.name == val]
denom = self.denominator.get()
for s1 in seqs1:
for s2 in seqs2:
pi = percentIdentity(s1, s2, denominator=denom)
self.mav.status("%s vs. %s:\n"
" %.2f%% identity\n" %
(s1.name, s2.name, pi))
# since once OK is clicked, the mouse may be
# over a part of the alignment that causes a
# status message, also send to regular status
# line
replyobj.status("%s vs. %s: %.2f%% identity\n" %
(s1.name, s2.name, pi),
log=True)
if len(seqs1) > 1 or len(seqs2) > 1:
self.mav.status("Percent identity info in Reply Log")
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
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 write_grasp_surface_file():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes=[SurfaceModel])
if len(mlist) == 0:
from chimera import replyobj
replyobj.status('No displayed surfaces')
return
varray, tarray, narray = surface_geometry(mlist)
if len(tarray) == 0:
from chimera import replyobj
replyobj.status('No displayed triangles')
return
def save_geometry(okay, d, varray=varray, tarray=tarray, narray=narray):
if not okay:
return # User canceled action.
path = d.getPaths()[0]
f = grasp_surface_file(varray, tarray, narray)
file = open(path, 'wb')
file.write(f)
file.close()
from OpenSave import SaveModeless
SaveModeless(title="Save Surface",
filters=[('GRASP surface', ['*.srf'], '.srf')],
command=save_geometry)
def _deregisteredTask(self, iTask):
# This is called after the user task instance has been
# disposed of.
from chimera import replyobj
if iTask.modal:
self._modalTasks.remove(iTask)
if iTask.canceled:
msg = "canceled"
else:
msg = "finished"
replyobj.status("%s: %s\n" % (iTask.title, msg), blankAfter=10)
import statusline
sl = statusline.status_line(create=False)
if iTask.modal:
# Terminate the input grab
if sl:
sl.grab_task_button(False)
else:
# If there are no more tasks with status updates,
# deregister our "check for changed" handler
if self._cfcHandler and self._statusCount() == 0:
import chimera
chimera.triggers.deleteHandler(CFC, self._cfcHandler)
self._cfcHandler = None
if sl:
sl.update_task_buttons()
from chimera import dialogs
d = dialogs.find(TaskPanel.name, create=False)
if d:
d.updateTaskStatus(iTask)
d.refreshCancelButtons()
def startCommand(molecule,
name="default",
method="corkscrew",
rate="linear",
frames=20,
cartesian=False):
from chimera import UserError
if len(molecule) != 1:
raise UserError("You must specify exactly one molecule")
m = molecule[0]
try:
ms = _find(name)
except UserError:
pass
else:
raise UserError("You already defined \"%s\"" % name)
kw = {
"method": method,
"rate": rate,
"frames": frames,
"cartesian": cartesian,
}
_verifyOpts(kw)
from base import Script
ms = Script(m, closeCB=_close, **kw)
_add(name, ms)
from chimera import replyobj
msg = "Interpolation \"%s\" created\n" % name
replyobj.message(msg)
replyobj.status(msg)
return ms
def move_atom_to_maximum(a,
max_steps=2000,
ijk_step_size_min=0.001,
ijk_step_size_max=0.5):
from chimerax.map import active_volume
dr = active_volume()
if dr == None or dr.model_transform() == None:
from chimera.replyobj import status
status('No data shown by volume viewer dialog')
return
points = atom_coordinates([a])
point_weights = None
move_tf, stats = motion_to_maximum(points,
point_weights,
dr,
max_steps,
ijk_step_size_min,
ijk_step_size_max,
optimize_translation=True,
optimize_rotation=False)
# Update atom position.
p = a.structure.position.inverse() * (move_tf * a.xformCoord())
a.setCoord(p)
def pairAlign(chains, cutoff, gapChar, statusPrefix=""):
chain1, chain2 = chains
# go through chain 1 and put each residue's principal
# atom in a spatial tree
from chimera.misc import principalAtom
from CGLutil.AdaptiveTree import AdaptiveTree
xyzs = []
data = []
for i in range(len(chain1)):
res = chain1.residues[i]
pa = principalAtom(res)
if not pa:
replyobj.warning("Cannot determine principal"
" atom for residue %s\n"
% res.oslIdent())
continue
xyzs.append(pa.xformCoord().data())
data.append((i, pa.xformCoord()))
tree = AdaptiveTree(xyzs, data, cutoff)
# initialize score array
from numpy import zeros
scores = zeros((len(chain1),len(chain2)), float)
scores -= 1.0
# find matches and update score array
for i2 in range(len(chain2)):
res = chain2.residues[i2]
pa = principalAtom(res)
if not pa:
replyobj.warning("Cannot determine principal"
" atom for residue %s\n"
% res.oslIdent())
continue
coord2 = pa.xformCoord()
matches = tree.searchTree(coord2.data(), cutoff)
for i1, coord1 in matches:
dist = coord1.distance(coord2)
if dist > cutoff:
continue
scores[i1][i2] = cutoff - dist
# use NeedlemanWunsch to establish alignment
from NeedlemanWunsch import nw
score, seqs = nw(chain1, chain2, scoreMatrix=scores, gapChar=gapChar,
returnSeqs=True, scoreGap=0, scoreGapOpen=0)
smallest = min(len(chain1), len(chain2))
minDots = max(len(chain1), len(chain2)) - smallest
extraDots = len(seqs[0]) - smallest - minDots
numMatches = smallest - extraDots
replyobj.status("%s%d residue pairs aligned\n"
% (statusPrefix, numMatches), log=True)
if numMatches == 0:
from chimera import UserError
raise UserError("Cannot generate alignment because no"
" residues within cutoff distance")
return score, seqs
def myRunCommand(*args): from Midas import MidasError try: runCommand(*args) except MidasError, v: from chimera import replyobj replyobj.status(str(v), color="red")
def startCommand(molecule, name="default", method="corkscrew",
rate="linear", frames=20, cartesian=False):
from chimera import UserError
if len(molecule) != 1:
raise UserError("You must specify exactly one molecule")
m = molecule[0]
try:
ms = _find(name)
except UserError:
pass
else:
raise UserError("You already defined \"%s\"" % name)
kw = {
"method": method,
"rate": rate,
"frames": frames,
"cartesian": cartesian,
}
_verifyOpts(kw)
from base import Script
ms = Script(m, closeCB=_close, **kw)
_add(name, ms)
from chimera import replyobj
msg = "Interpolation \"%s\" created\n" % name
replyobj.message(msg)
replyobj.status(msg)
return ms
def fetch_file(url, name, minimum_file_size = None, save_dir = '',
save_name = '', uncompress = False, ignore_cache = False):
"""a fetched non-local file that doesn't get cached will be
removed when Chimera exits
if 'ignore_cache' is True, then cached values will be ignored,
though the retrieved values will still be cached if appropriate
"""
from chimera.replyobj import status
status('Fetching %s\n' % (name,))
if save_name and not ignore_cache:
path = fetch_local_file(save_dir, save_name)
if path:
return path, {}
from chimera import tasks
task = tasks.Task("Fetch %s" % name, modal=True)
def report_cb(barrived, bsize, fsize):
if fsize > 0:
percent = min(100.0,(100.0*barrived*bsize)/fsize)
prog = '%.0f%% of %s' % (percent, byte_text(fsize))
else:
prog = '%s received' % (byte_text(barrived*bsize),)
task.updateStatus(prog)
# TODO: In Python 2.5 socket.error is not an IOError, but in Python 2.6
# it is. Remove socket error when Chimera uses Python 2.6.
import urllib, socket
try:
path, headers = urllib.urlretrieve(url, reporthook = report_cb)
except (IOError, socket.error), v:
from chimera import NonChimeraError
raise NonChimeraError('Error fetching %s: %s' % (name, str(v)))
def __init__(self, topology, trajFileName):
# since we need to be able to do seeks, can't use osOpen
# which might return an unseekable stream
self.topology = topology
from OpenSave import osUncompressedPath
path = osUncompressedPath(trajFileName)
import os
self.trajFileSize = os.stat(path).st_size
self.traj = open(path, "rb")
from xdrlib import Unpacker
self.fileString = FileString(self.traj, 0, self.trajFileSize)
self.xdr = Unpacker(self.fileString)
self.crdStarts = []
while True:
replyobj.status("Reading frame %d header\n" %
(len(self.crdStarts) + 1))
try:
crdStart, endFrame = self._readHeader()
except ValueError, e:
raise ValueError("Frame %d: %s" %
(len(self.crdStarts) + 1, str(e)))
if endFrame > self.trajFileSize:
if not self.crdStarts:
raise ValueError("Computed size of"
" first frame (%d) greater than"
" trajectory file size (%s)" %
(endFrame, self.trajFileSize))
replyobj.warning("Truncated trajectory file;"
" skipping last partial frame.\n")
else:
self.crdStarts.append(crdStart)
if endFrame == self.trajFileSize:
break
self.xdr.set_position(endFrame)
def toggle_fly_mode(self):
self.fly_mode = not self.fly_mode
from chimera import viewer
viewer.clipping = False
from chimera.replyobj import status
status('fly through mode: %s' % self.fly_mode)
def toggle_fly_mode(self):
self.fly_mode = not self.fly_mode
from chimera import viewer
viewer.clipping = False
from chimera.replyobj import status
status('fly through mode: %s' % self.fly_mode)
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 write_grasp_surface_file():
from chimera import openModels
from _surface import SurfaceModel
mlist = openModels.list(modelTypes = [SurfaceModel])
if len(mlist) == 0:
from chimera import replyobj
replyobj.status('No displayed surfaces')
return
varray, tarray, narray = surface_geometry(mlist)
if len(tarray) == 0:
from chimera import replyobj
replyobj.status('No displayed triangles')
return
def save_geometry(okay, d, varray=varray, tarray=tarray, narray=narray):
if not okay:
return # User canceled action.
path = d.getPaths()[0]
f = grasp_surface_file(varray, tarray, narray)
file = open(path, 'wb')
file.write(f)
file.close()
from OpenSave import SaveModeless
SaveModeless(title = "Save Surface",
filters = [('GRASP surface', ['*.srf'], '.srf')],
command = save_geometry)
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 backbone_atom_pairs(atoms):
nmol = len(atom_molecules(atoms))
if nmol != 2:
from chimera import replyobj
replyobj.status('alignment: Must select atoms from 2 molecules (%d selected).\n' % nmol, log = True)
return None, None
bb_atoms = filter(lambda a: a.name == 'CA' or a.name == 'P', atoms)
atom_pairs = paired_alignment_atoms(bb_atoms)
if len(atom_pairs) < 3:
from chimera import replyobj
replyobj.status('alignment: Too few backbone atom pairs (%d).\n' %
len(atom_pairs), log = True)
return None, None
a1 = map(lambda p: p[0], atom_pairs)
a2 = map(lambda p: p[1], atom_pairs)
m1 = a1[0].molecule
m2 = a2[0].molecule
if (m1.id, m1.subid) > (m2.id, m2.subid):
return a2, a1
return a1, a2
def show_field_lines(v,
num_lines=1000,
min_potential=10,
step=0.5,
color=(.7, .7, .7, 1),
line_width=1,
tube_radius=None,
circle_subdivisions=12,
markers=False,
model_id=None):
if min_potential is None:
min_potential = v.surface_levels[-1] if v.surface_levels else 10
start_points, cutoff = find_starting_points(v, num_lines, min_potential)
n = len(start_points)
lines = []
for i, xyz in enumerate(start_points):
if i % 100 == 0:
from chimera.replyobj import status
status('Computing field line %d of %d' % (i, n))
line = trace_field_line(v, xyz, cutoff, min_potential, step)
lines.append(line)
if markers:
draw_marker_lines(lines, v, color, tube_radius, model_id)
elif tube_radius is None:
draw_mesh_lines(lines, v, color, line_width, model_id)
else:
draw_tube_lines(lines, v, color, tube_radius, circle_subdivisions,
model_id)
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 _deregisteredTask(self, iTask):
# This is called after the user task instance has been
# disposed of.
from chimera import replyobj
if iTask.modal:
self._modalTasks.remove(iTask)
if iTask.canceled:
msg = "canceled"
else:
msg = "finished"
replyobj.status("%s: %s\n" % (iTask.title, msg), blankAfter=10)
import statusline
sl = statusline.status_line(create=False)
if iTask.modal:
# Terminate the input grab
if sl:
sl.grab_task_button(False)
else:
# If there are no more tasks with status updates,
# deregister our "check for changed" handler
if self._cfcHandler and self._statusCount() == 0:
import chimera
chimera.triggers.deleteHandler(CFC,
self._cfcHandler)
self._cfcHandler = None
if sl:
sl.update_task_buttons()
from chimera import dialogs
d = dialogs.find(TaskPanel.name, create=False)
if d:
d.updateTaskStatus(iTask)
d.refreshCancelButtons()
def mouse_drag_cb(self, v, e):
if self.last_xy is None:
self.last_xy = (e.x, e.y)
return
import Surface
plist = Surface.selected_surface_pieces()
if len(plist) == 0:
from chimera.replyobj import status
status('No surfaces selected for resizing')
return
dx, dy = (e.x - self.last_xy[0], self.last_xy[1] - e.y)
delta = dx + dy
self.last_xy = (e.x, e.y)
shift_mask = 1
shift = (e.state & shift_mask)
if shift:
factor_per_pixel = 1.001 # shift key held so scale by smaller amount
else:
factor_per_pixel = 1.01
factor = factor_per_pixel ** delta
for p in plist:
scale_surface_piece(p, factor)
def names_of_last_opened():
'Show the names of the last 3 opened files on the status line'
paths = recent_opened_files()
import os.path
last3 = ', '.join(map(os.path.basename, paths[:3]))
from chimera.replyobj import status
status(last3)
def backbone_atom_pairs(atoms):
nmol = len(atom_molecules(atoms))
if nmol != 2:
from chimera import replyobj
replyobj.status(
'alignment: Must select atoms from 2 molecules (%d selected).\n' %
nmol,
log=True)
return None, None
bb_atoms = filter(lambda a: a.name == 'CA' or a.name == 'P', atoms)
atom_pairs = paired_alignment_atoms(bb_atoms)
if len(atom_pairs) < 3:
from chimera import replyobj
replyobj.status('alignment: Too few backbone atom pairs (%d).\n' %
len(atom_pairs),
log=True)
return None, None
a1 = map(lambda p: p[0], atom_pairs)
a2 = map(lambda p: p[1], atom_pairs)
m1 = a1[0].molecule
m2 = a2[0].molecule
if (m1.id, m1.subid) > (m2.id, m2.subid):
return a2, a1
return a1, a2
def __init__(self, topology, trajFileName):
# since we need to be able to do seeks, can't use osOpen
# which might return an unseekable stream
self.topology = topology
from OpenSave import osUncompressedPath
path = osUncompressedPath(trajFileName)
import os
self.trajFileSize = os.stat(path).st_size
self.traj = open(path, "rb")
from xdrlib import Unpacker
self.fileString = FileString(self.traj, 0, self.trajFileSize)
self.xdr = Unpacker(self.fileString)
self.crdStarts = []
while True:
replyobj.status("Reading frame %d header\n" % (
len(self.crdStarts) + 1))
try:
crdStart, endFrame = self._readHeader()
except ValueError, e:
raise ValueError("Frame %d: %s" %
(len(self.crdStarts) + 1, str(e)))
if endFrame > self.trajFileSize:
if not self.crdStarts:
raise ValueError("Computed size of"
" first frame (%d) greater than"
" trajectory file size (%s)" %
(endFrame, self.trajFileSize))
replyobj.warning("Truncated trajectory file;"
" skipping last partial frame.\n")
else:
self.crdStarts.append(crdStart)
if endFrame == self.trajFileSize:
break
self.xdr.set_position(endFrame)
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 split_selected_surfaces():
plist = selected_surface_pieces()
if plist:
pplist = split_surfaces(plist)
from chimera.replyobj import status
status('%d surface pieces' % len(pplist))
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 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 Apply(self):
val = self.seqMenu1.get()
if val == self.ALL:
seqs1 = self.mav.seqs
else:
seqs1 = [s for s in self.mav.seqs if s.name == val]
val = self.seqMenu2.get()
if val == self.ALL:
seqs2 = self.mav.seqs
else:
seqs2 = [s for s in self.mav.seqs if s.name == val]
denom = self.denominator.get()
for s1 in seqs1:
for s2 in seqs2:
pi = percentIdentity(s1, s2, denominator=denom)
self.mav.status("%s vs. %s:\n"
" %.2f%% identity\n" % (s1.name,
s2.name, pi))
# since once OK is clicked, the mouse may be
# over a part of the alignment that causes a
# status message, also send to regular status
# line
replyobj.status("%s vs. %s: %.2f%% identity\n"
% (s1.name, s2.name, pi), log=True)
if len(seqs1) > 1 or len(seqs2) > 1:
self.mav.status("Percent identity info in Reply Log")
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
def _align(self, ref, match, matrix, alg, gapOpen, gapExtend, ksdsspCache,
**alignKw):
replyobj.status(
"test match %s %s to %s %s" %
(ref.molecule.name, ref.name, match.molecule.name, match.name))
return align(ref, match, matrix, alg, gapOpen, gapExtend, ksdsspCache,
**alignKw)
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 interpolateCommand(molecule,
name="default",
method=None,
rate=None,
frames=None,
cartesian=False):
if len(molecule) != 1:
from chimera import UserError
raise UserError("You must specify exactly one molecule")
m = molecule[0]
ms = _find(name)
kw = {}
if method is not None:
kw["method"] = method
if rate is not None:
kw["rate"] = rate
if frames is not None:
kw["frames"] = frames
_verifyOpts(kw)
ms.addAction(m, **kw)
from chimera import replyobj
msg = "Interpolation \"%s\" updated\n" % name
replyobj.message(msg)
replyobj.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 symmetry(operation,
volume,
minimumCorrelation=0.99,
nMax=8,
helix=None,
points=10000,
set=True):
from VolumeViewer import Volume
vlist = [m for m in volume if isinstance(m, Volume)]
if len(vlist) == 0:
raise CommandError('No volume specified')
if not helix is None:
rise, angle, n, optimize = parse_helix_option(helix)
import symmetry as S
for v in vlist:
if helix:
syms, msg = S.find_helix_symmetry(v, rise, angle, n, optimize,
nMax, minimumCorrelation, points)
else:
syms, msg = S.find_point_symmetry(v, nMax, minimumCorrelation,
points)
if set and syms:
v.data.symmetries = syms
from chimera.replyobj import info, status
status(msg)
info(msg + '\n')
def map_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 processModBaseID(IDcode):
"""Locate a database ID code via ModBase, read it, and add it to the list of open models.
_openModBaseIDModel(IDcode) => [model(s)]
'explodeNMR' controls whether multi-MODEL files are split into
multiple Molecules (if False, use coord sets instead)
"""
identifyAs = IDcode
from chimera import replyobj
statusName = identifyAs or IDcode
path = fetchModBase(IDcode)
# Open PDB file as models
from chimera import PDBio
import os
pdbio = PDBio()
pdbio.explodeNMR = False
molList = pdbio.readPDBfile(path)
if not pdbio.ok():
replyobj.status("\n")
raise UserError("Error reading PDB file: %s" % pdbio.error())
for m in molList:
m.name = identifyAs
# Post-process models to convert remark records
# into molecule dictionary attribute
#from baseDialog import buttonFuncName as makeIdentifier
for m in molList:
attr = {}
remarks = m.pdbHeaders.get("REMARK", [])
for remark in remarks:
parts = remark.split(None, 2)
try:
info = parts[2]
except IndexError:
continue
try:
key, value = [ v.strip()
for v in info.split(':', 1) ]
except ValueError:
continue
try:
value = int(value)
except ValueError:
try:
value = float(value)
except ValueError:
pass
attr[key] = value
#setattr(m, "modbase_%s" % makeIdentifier(key), value)
assignModbaseInfo(m, attr)
# Register open message
chimera._openedInfo = "Opened %s\n" % statusName
ModBaseDialog(IDcode, molList)
return molList
def addTraj(self, trajFileName):
replyobj.status("Reading %s file %s" % (self.TrajName, trajFileName),
blankAfter=0)
try:
self.trajectory.addFile(trajFileName)
finally:
replyobj.status("Done reading %s file %s\n"
% (self.TrajName, trajFileName))
def split_selected_surfaces(session, in_place=True):
import Surface
plist = Surface.selected_surface_pieces()
if plist:
pplist = split_surfaces(plist, session, in_place)
from chimera.replyobj import status
status('%d surface pieces' % len(pplist))
def addTraj(self, trajFileName):
replyobj.status("Reading %s file %s" % (self.TrajName, trajFileName),
blankAfter=0)
try:
self.trajectory.addFile(trajFileName)
finally:
replyobj.status("Done reading %s file %s\n" %
(self.TrajName, trajFileName))
def Execute(self, options):
#print self, "Executing DelPhi..."
self.options = options
self.executor = DelPhiExecutor.DelPhiExecutor(self.options)
self.process = self.executor()
self.checkHandler = chimera.triggers.addHandler(
"check for changes", self.CheckProcess, None)
replyobj.status("Running DelPhi in background")
def displayDialog(wait=False):
if dialogs.find(BugReportGUI.name):
replyobj.status("Bug report already in progress!",
color="red", blankAfter=15)
return None
else:
br_gui = dialogs.display(BugReportGUI.name, wait)
return br_gui
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 findPruneCrosslinks(allLinks,
pairings,
seq1,
seq2,
linkList,
links1,
links2,
tag="",
statusPrefix=""):
replyobj.status("%sFinding crosslinks %s\n" % (statusPrefix, tag),
blankAfter=0)
# find crossings
ends = []
seq2links = []
for links in links2:
ends.append(len(seq2links))
seq2links.extend(links)
l2lists = []
for end in ends:
l2lists.append(seq2links[:end])
for link1 in linkList:
i1 = link1.info[0].pos
i2 = link1.info[1].pos
for link2 in l2lists[i2]:
if link2.info[0].pos <= i1:
continue
link1.crosslinks.append(link2)
link2.crosslinks.append(link1)
link1.penalty += link2.val
link2.penalty += link1.val
replyobj.status("%sPruning crosslinks %s\n" % (statusPrefix, tag),
blankAfter=0)
while linkList:
pen = pos = None
for i, x in enumerate(linkList):
if pen is None or x.penalty > pen:
pos = i
pen = x.penalty
if pen <= 0.0001:
break
link = linkList.pop(pos)
links1[link.info[0].pos].remove(link)
links2[link.info[1].pos].remove(link)
for clink in link.crosslinks:
clink.penalty -= link.val
for link in linkList:
delattr(link, "crosslinks")
delattr(link, "penalty")
p1 = pairings[seq1]
for i, l in enumerate(links1):
p1[i].extend(l)
allLinks.extend(l)
p2 = pairings[seq2]
for i, l in enumerate(links2):
p2[i].extend(l)
def message(text, show_reply_log=False):
from chimera.replyobj import message, status
message(text + '\n')
status(text, blankAfter=0)
if show_reply_log:
from Accelerators.standard_accelerators import show_reply_log as srl
srl()
def Execute(self, options):
#print self, "Executing DelPhi..."
self.options = options
self.executor = DelPhiExecutor.DelPhiExecutor(self.options)
self.process = self.executor()
self.checkHandler = chimera.triggers.addHandler(
"check for changes",
self.CheckProcess, None)
replyobj.status("Running DelPhi in background")
def print_path_length(): from chimera import selection bonds = selection.currentBonds() msg = '%d bonds with total length %g\n' % (len(bonds), path_length(bonds)) from chimera import replyobj replyobj.status(msg) # Show on status line replyobj.message(msg) # Record in reply log
def print_path_length():
from chimera import selection
bonds = selection.currentBonds()
msg = '%d bonds with total length %g\n' % (len(bonds), path_length(bonds))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def displayDialog(wait=False):
if dialogs.find(BugReportGUI.name):
replyobj.status("Bug report already in progress!",
color="red",
blankAfter=15)
return None
else:
br_gui = dialogs.display(BugReportGUI.name, wait)
return br_gui
def message(text, show_reply_log = False):
from chimera.replyobj import message, status
message(text + '\n')
status(text, blankAfter = 0)
if show_reply_log:
from Accelerators.standard_accelerators import show_reply_log as srl
srl()
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 _postAddCharge(mols, runSaveMol2Dialog=False, doneCB=None):
if runSaveMol2Dialog:
from WriteMol2.gui import WriteMol2Dialog
wmDlg = chimera.dialogs.display(WriteMol2Dialog.name)
wmDlg.saveRelativeVar.set(True)
wmDlg.rigidVar.set(True)
wmDlg.multiSaveMenu.invoke(wmDlg.labelMap["combined"])
replyobj.status("Dock prep finished")
if doneCB:
doneCB()
def _postAddCharge(mols, runSaveMol2Dialog=False, doneCB=None):
if runSaveMol2Dialog:
from WriteMol2.gui import WriteMol2Dialog
wmDlg = chimera.dialogs.display(WriteMol2Dialog.name)
wmDlg.saveRelativeVar.set(True)
wmDlg.rigidVar.set(True)
wmDlg.multiSaveMenu.invoke(wmDlg.labelMap["combined"])
replyobj.status("Dock prep finished")
if doneCB:
doneCB()
def showAlignment(seqs, title):
from MultAlignViewer.MAViewer import MAViewer
replyobj.status("Showing alignment\n")
mav = MAViewer(seqs, autoAssociate=False, title=title)
mav.associate(None)
mav.autoAssociate = True
if len(seqs) < 3:
mav.hideHeaders(mav.headers(shownOnly=True))
mav.showHeaders([h for h in mav.headers() if h.name == "RMSD"])
return mav
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 Apply(self):
path = self.getPaths()[0]
surf = self.surfList.getvalue()
if not surf:
replyobj.error("No surface chosen to save.\n")
return
from WriteDMS import writeDMS
replyobj.status("Writing DMS surface to %s\n" % path)
writeDMS(surf, path, writeNormals=self.saveNormalsVar.get(),
displayedOnly=self.displayedOnlyVar.get())
replyobj.status("Wrote DMS surface to %s\n" % path)
def CheckProcess(self, triggerName, data, data2):
if not self.process.isRunning():
chimera.triggers.deleteHandler("check for changes",
self.checkHandler)
self.checkHandler = None
if self.executor.success():
#print self, "Done executing DelPhi."
self.OutputGUI()
self.gui.savePrefs()
replyobj.status("DelPhi finished")
else:
replyobj.status("DelPhi failed")
def zone_volume(outside = False):
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
mv = v.copy_zone(outside)
if mv is None:
from chimera.replyobj import status
status('No zone for volume %s' % v.name)
def findPruneCrosslinks(allLinks, pairings, seq1, seq2,
linkList, links1, links2, tag="", statusPrefix=""):
replyobj.status("%sFinding crosslinks %s\n" % (statusPrefix, tag),
blankAfter=0)
# find crossings
ends = []
seq2links = []
for links in links2:
ends.append(len(seq2links))
seq2links.extend(links)
l2lists = []
for end in ends:
l2lists.append(seq2links[:end])
for link1 in linkList:
i1 = link1.info[0].pos
i2 = link1.info[1].pos
for link2 in l2lists[i2]:
if link2.info[0].pos <= i1:
continue
link1.crosslinks.append(link2)
link2.crosslinks.append(link1)
link1.penalty += link2.val
link2.penalty += link1.val
replyobj.status("%sPruning crosslinks %s\n" % (statusPrefix, tag),
blankAfter=0)
while linkList:
pen = pos = None
for i, x in enumerate(linkList):
if pen is None or x.penalty > pen:
pos = i
pen = x.penalty
if pen <= 0.0001:
break
link = linkList.pop(pos)
links1[link.info[0].pos].remove(link)
links2[link.info[1].pos].remove(link)
for clink in link.crosslinks:
clink.penalty -= link.val
for link in linkList:
delattr(link, "crosslinks")
delattr(link, "penalty")
p1 = pairings[seq1]
for i, l in enumerate(links1):
p1[i].extend(l)
allLinks.extend(l)
p2 = pairings[seq2]
for i, l in enumerate(links2):
p2[i].extend(l)
