def _setLightFromParams(self, params, activeName, saveName):
import chimera
active, diff, diffScale, spec, specScale, dir = params
light = self._setActiveLight(active, activeName, saveName)
light.diffuse = chimera.MaterialColor(*diff)
light.diffuseScale = diffScale
light.specular = chimera.MaterialColor(*spec)
light.specularScale = specScale
light.direction = chimera.Vector(*dir)
def Apply(self):
from chimera import UserError
self.clashDef.invoke()
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow.invoke()
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[CLASH_PBS] = self.pbVar.get()
if prefs[CLASH_PBS]:
prefs[CLASH_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[CLASH_COLOR])
self.pbWidthEntry.invoke()
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width")
prefs[CLASH_WIDTH] = float(self.pbWidthEntry.getvalue())
else:
pbColor = None
prefs[CLASH_METHOD] = self.buttonInfo[self.computeType.index(
self.computeType.getvalue())][1]
prefs[CLASH_IGNORE_OTHERS] = self.ignoreOthersVar.get()
self.rotDialog.addClashColumn(prefs[CLASH_THRESHOLD],
prefs[HBOND_ALLOWANCE],
prefs[CLASH_METHOD], prefs[CLASH_PBS],
pbColor, prefs[CLASH_WIDTH],
prefs[CLASH_IGNORE_OTHERS])
def Apply(self):
dhb = self.drawHbondsVar.get()
prefs[DRAW_HBONDS] = dhb
prefs[HBOND_COLOR] = self.hbColorWell.rgba
bc = chimera.MaterialColor(*prefs[HBOND_COLOR])
self.hbWidthEntry.invoke()
if not self.hbWidthEntry.valid():
self.enter()
raise UserError("Invalid H-bond width")
lw = prefs[HBOND_WIDTH] = float(self.hbWidthEntry.getvalue())
distSlop = 0.0
angleSlop = 0.0
twoColors = False
relax = self.relaxParams.relaxConstraints
rc = self.relaxParams.relaxColor
if relax:
distSlop = self.relaxParams.relaxDist
angleSlop = self.relaxParams.relaxAngle
if self.relaxParams.useRelaxColor:
twoColors = True
prefs[RELAX_COLOR] = rc.rgba()
self.groupName = "H-bonds for rotamers of %s" % (
self.rotDialog.residue)
prefs[HBOND_IGNORE_OTHERS] = self.ignoreOthersVar.get()
self.rotDialog.addHbondColumn(dhb, bc, lw, relax, distSlop, angleSlop,
twoColors, rc, self.groupName,
prefs[HBOND_IGNORE_OTHERS])
def _backgroundColorCB(option):
rgba = option.get()
if not rgba:
color = None
else:
color = chimera.MaterialColor(*rgba)
chimera.viewer.background = color
def create_box(self):
m = chimera.Molecule()
m.name = 'Subregion Selection Box'
chimera.openModels.add([m], noprefs=True)
chimera.addModelClosedCallback(m, self.model_closed_cb)
rid = chimera.MolResId(1)
r = m.newResidue('markers', rid)
corners = []
for name in ('a000', 'a001', 'a010', 'a011', 'a100', 'a101', 'a110',
'a111'):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
corners.append(a)
green = chimera.MaterialColor(0, 1, 0, 1)
for a1, a2 in ((0, 1), (2, 3), (4, 5), (6, 7), (0, 2), (1, 3), (4, 6),
(5, 7), (0, 4), (1, 5), (2, 6), (3, 7)):
b = m.newBond(corners[a1], corners[a2])
b.halfbond = 0
b.drawMode = chimera.Bond.Wire
b.color = green
return corners
def _highlightColorCB(option):
rgba = option.get()
if not rgba:
color = None
else:
color = chimera.MaterialColor(*rgba)
chimera.viewer.highlightColor = color
def ColorMol ( mol ) :
if not hasattr ( mol, 'chainColors' ) :
from random import random
mol.chainColors = {}
for r in mol.residues :
if not r.id.chainId in mol.chainColors :
clr = chimera.MaterialColor ( random(), random(), random(), 1.0 )
mol.chainColors[r.id.chainId] = clr
for r in mol.residues :
rt = r.type.upper()
if rt in protein3to1 or rt in nucleic3to1 or rt in nucleic1to3 :
r.ribbonDisplay = True
r.ribbonDrawMode = 2
r.ribbonColor = mol.chainColors[r.id.chainId]
for at in r.atoms :
at.display = False
at.drawMode = at.EndCap
if at.element.name.upper() in atomColors :
at.color = atomColors[at.element.name.upper()]
else :
at.color = mol.chainColors[r.id.chainId]
else :
for at in r.atoms :
at.display = True
at.drawMode = at.EndCap
if at.element.name.upper() in atomColors :
at.color = atomColors[at.element.name.upper()]
else :
at.color = mol.chainColors[r.id.chainId]
for b in mol.bonds :
b.drawMode = b.Stick
b.display = b.Smart
def matchStructureColor(atoms):
# try to use ribbon color if appropriate
displayedRgbas = []
undisplayedRgbas = []
for a in atoms:
if a.hide:
# ribbon showing
r = a.residue
if r.ribbonDisplay:
if r.ribbonColor:
rgba = r.ribbonColor.rgba()
else:
rgba = r.molecule.color.rgba()
else:
rgba = r.molecule.color.rgba()
else:
if a.color:
rgba = a.color.rgba()
else:
rgba = a.molecule.color.rgba()
if (a.hide and r.ribbonDisplay) or a.display:
displayedRgbas.append(rgba)
else:
undisplayedRgbas.append(rgba)
if displayedRgbas:
rgbas = displayedRgbas
else:
rgbas = undisplayedRgbas
import numpy
avgRgba = numpy.mean(numpy.array(rgbas), 0)
import chimera
return chimera.MaterialColor(*tuple(avgRgba))
def pseudobond(atom1, atom2, group, color=None, label=None):
pbg = chimera.misc.getPseudoBondGroup(group)
pb = pbg.newPseudoBond(atom1, atom2)
if color is not None:
pb.color = chimera.MaterialColor(*color)
if label is not None:
pb.label = str(label)
return pb
def __init__(self, f, reply_dialog, prmtop, trajectory):
MovieCallbacks.__init__(self, f, reply_dialog)
self.prmtop = prmtop
self.trajectory = trajectory
self.bondColor = chimera.MaterialColor()
self.bondColor.ambientDiffuse = (0.0, 0.8, 0.9)
self.bondColor.opacity = 1
def getColor(colorID):
if colorID is None:
return None
if globals.colorMap.has_key(colorID):
return globals.colorMap[colorID]
name, rgba = globals.colorInfo[colorID]
if name:
c = chimera.Color.lookup(name)
if not c:
c = chimera.MaterialColor(*rgba)
c.save(name)
else:
c.ambientDiffuse = rgba[:3]
c.opacity = rgba[3]
else:
c = chimera.MaterialColor(*rgba)
globals.colorMap[colorID] = c
return c
def getColorByName(name):
# can raise KeyError
import chimera
color = chimera.Color.lookup(name)
if not color:
r, g, b = colors[name]
color = chimera.MaterialColor(r / 255.0, g / 255.0, b / 255.0)
color.save(name)
return color
def restyleXlinks(xMgrs, threshold=None):
'''Restyle xlinks in provided XlinkDataMgr objects.'''
good_color = chimera.MaterialColor(0, 0, 255)
bad_color = chimera.MaterialColor(255, 0, 0)
for xMgr in xMgrs:
for b in xMgr.iterXlinkPseudoBonds():
if b is not None:
b.drawMode = chimera.Bond.Stick
if threshold is not None:
if is_satisfied(b, threshold):
b.color = good_color
b.radius = 0.6
else:
b.color = bad_color
b.radius = 0.6
else:
b.color = bad_color
b.radius = 0.6
def color(self, coord): place = coord * (len(self.colors) - 1) leftIndex = int(place) if leftIndex == place: return self.colors[leftIndex] c = chimera.MaterialColor() c1, c2 = self.colors[leftIndex:leftIndex+2] f = place - leftIndex c.ambientDiffuse = tuple(map(lambda a,b: a*(1-f) + b*f, c1.ambientDiffuse, c2.ambientDiffuse)) c.opacity = c1.opacity * (1-f) + c2.opacity * f return c
def testAddDomainsSubcomplexes(self):
self.g.configFrame.domainsButton.invoke()
domWind = self.g.configFrame._getDomainsWindow()
self.assertIsNotNone(domWind)
itemList = domWind.winfo_children()[0]
self.assertEqual(1, len(self.g.configFrame.config.domains))
self.assertEqual(1, len(itemList.frames))
activeItemFrame = itemList.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'testdom')
activeItemFrame.fields['subunit'][3].set('A135')
activeItemFrame.fields['ranges'][1].insert(0, '1-200')
activeItemFrame.fields['color'][1].set(chimera.MaterialColor(
0, 255, 0))
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.domains))
self.assertEqual(2, len(itemList.frames))
self.g.configFrame.subCompButton.invoke()
subWind = self.g.configFrame._getSubcomplexesWindow()
self.assertIsNotNone(subWind)
itemList = subWind.winfo_children()[0]
self.assertEqual(1, len(self.g.configFrame.config.subcomplexes))
self.assertEqual(1, len(itemList.frames))
activeItemFrame = itemList.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'new_subcomplex')
activeItemFrame.fields['color'][1].set(chimera.MaterialColor(
0, 255, 0))
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.subcomplexes))
self.assertEqual(2, len(itemList.frames))
newSubcomplex = self.g.configFrame.config.subcomplexes[-1]
self.assertEqual(0, len(newSubcomplex.items))
subFrame = itemList.frames[-1]
def color_element(obj, level, maxLevel):
#print(obj, level, maxLevel)
if(not obj.doneC):
wait_time = speed
col = (float(level)/max(maxLevel, 1) )
#print level, obj, "coloring"
set_color(obj, chimera.MaterialColor(1.0, col, col))
obj.doneC = True
real_eye = ch_get_real_eye()
coords = get_coords(obj)
has_sobj = False
sobjs = list()
amp = (1.0 - (float(level)/(maxLevel + 1)))
#print(grain_maker_fn)
if hasattr(obj, 'sobj') and (obj.sobj != None):
for sid in obj.sobj:
if sid in cg.mapping_objects:
has_sobj = True
sobjs.append(cg.mapping_objects[sid])
if has_sobj:
for sobj in sobjs:
so.modify_sound_object(sobj, "gate", amp, "t_trig", 1)
elif grains:
real_eye = ch_get_real_eye()
coords = get_coords(obj)
dist, az, ele = ch_calculate_position(real_eye, coords)
sobj = grain_maker_fn(obj, dist, az, ele, level, maxLevel+1)
if (sobj != None):
sobjs.append(sobj)
if(level == 0) or not stagger:
time.sleep(wait_time)
else:
time.sleep(wait_time * 2)
if(level < maxLevel):
neighbors = list()
for i,r in enumerate(get_neighbors(obj)):
t = threading.Thread(target=color_element,
args=(r, level +1, maxLevel))
t.start()
if (level == 0) and (i == 0) and stagger:
time.sleep(wait_time)
time.sleep(wait_time*4)
for sobj in sobjs:
so.modify_sound_object(sobj, "gate", 0)
#print level, obj, "restoring"
restore_color(obj)
def draw_interactions(interactions,
startCol='FF0000',
endCol='FFFF00',
key=None,
name="Custom pseudobonds"):
"""
Draw pseudobonds depicting atoms relationships.
Parameters
----------
interactions : list of tuples
Each tuple contains an interaction, defined, at least,
by the two atoms involved.
startCol : str, optional
Hex code for the initial color of the pseudobond
(closer to the first atom of the pair).
endCol : str, optional
Hex code for the final color of the pseudobond.
(closer to the second atom of the pair)
key : int, optional
The index of an interaction tuple that represent the alpha
channel in the color used to depict the interaction.
name : str, optional
Name of the pseudobond group created.
Returns
-------
chimera.pseudoBondGroup
"""
if not len(interactions):
return
pb = chimera.misc.getPseudoBondGroup(name)
color = _hex_to_rgb(startCol) + [1.0]
if key:
max_ = max(abs(_[3]) for _ in interactions)
for i in interactions:
npb = pb.newPseudoBond(i[0], i[1])
if key is not None:
intensity = (max_ - abs(i[key])) / (max_)
opacity = 1 - 0.7 * intensity
if startCol != endCol:
color = _linear_color(intensity, startCol, endCol) + [opacity]
else:
color = _hex_to_rgb(startCol) + [opacity]
npb.color = chimera.MaterialColor(*color)
return pb
def settings_changed_cb(self, event=None):
if not self.have_phantom():
return
phantom_on = self.phantom_on.get()
if not phantom_on:
if self.cursor_model:
chimera.openModels.close([self.cursor_model])
return
phantom_range_mm = float_variable_value(self.phantom_range)
box_size_mm = (phantom_range_mm, phantom_range_mm, phantom_range_mm)
shape = self.cursor_shape.get()
from _phantomcursor import Cursor_Model
cursor_shape = {
'cross': Cursor_Model.Cross,
'jack': Cursor_Model.Jack,
'sphere': Cursor_Model.Sphere,
'volume crosshair': Cursor_Model.Cross,
}[shape]
cursor_size = float_variable_value(self.cursor_size)
r, g, b = self.cursor_color.rgb
cursor_color = chimera.MaterialColor(r, g, b)
pd = self.phantom_device
cm = self.cursor_model
if pd == None or cm == None:
pd, cm = self.make_phantom_cursor_model(box_size_mm, cursor_shape,
cursor_size, cursor_color)
self.phantom_device = pd
self.cursor_model = cm
chimera.addModelClosedCallback(cm, self.model_closed_cb)
else:
pd.box_size_mm = box_size_mm
cm.cursor_style = cursor_shape
cm.cursor_size = cursor_size
cm.cursor_color = cursor_color
crosshair_on = (self.cursor_shape.get() == 'volume crosshair')
cm.show_crosshair = crosshair_on
self.update_force_field()
def rainbowTexture(colors): key = tuple(colors) if key not in _rainbowColors: actualColors = [] for color in colors: if isinstance(color, basestring): c = getColorByName(color) elif isinstance(color, chimera.MaterialColor): c = color else: c = chimera.MaterialColor() c.ambientDiffuse = color[:3] if len(color) > 3: c.opacity = color[-1] else: c.opacity = 1.0 actualColors.append(c) _rainbowColors[key] = RainbowColors(actualColors) return _rainbowColors[key]
def testDeleteStuff(self):
'''Test deletion of Subunits and Data, adding them back, setting mapping, and mapping copy from.
'''
xFrame = self.g.Xlinks
xFrame.displayDefault()
subUnitFrame = self.g.configFrame.subUnitFrame
self.assertEqual(14, len(subUnitFrame.frames))
self.assertEqual(14, len(self.g.configFrame.config.subunits))
subUnitFrame.frames[0].delete.invoke()
self.assertEqual(13, len(subUnitFrame.frames))
self.assertEqual(13, len(self.g.configFrame.config.subunits))
self.assertEqual(0, len(self.g.configFrame.config.domains))
dataFrame = self.g.configFrame.dataFrame
self.assertEqual(10, len(dataFrame.frames))
self.assertEqual(10, len(self.g.configFrame.config.dataItems))
dataFrame.frames[0].delete.invoke()
self.assertEqual(9, len(dataFrame.frames))
self.assertEqual(9, len(self.g.configFrame.config.dataItems))
xmgr = xFrame.getXlinkDataMgrs()[0]
self.assertEqual(74, len(xmgr.pbg.pseudoBonds))
#Test adding after deleting:
activeItemFrame = subUnitFrame.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'A190')
activeItemFrame.fields['chainIds'][1].insert(0, 'A')
activeItemFrame.fields['color'][1].set(chimera.MaterialColor(
0, 255, 0))
activeItemFrame.add.invoke()
self.assertEqual(14, len(self.g.configFrame.config.subunits))
self.assertEqual(170, len(xmgr.pbg.pseudoBonds))
dataFrame = self.g.configFrame.dataFrame
activeItemFrame = dataFrame.activeItemFrame
activeItemFrame.fields['name'][1].insert(
0, '0.05 mM X-linker, 30min at 37 C')
paths = [
'xlinks/Pol1_1_Inter.xls', 'xlinks/Pol1_1_Intra.xls',
'xlinks/Pol1_1_Loop.xls,', 'xlinks/Pol1_1_Mono.xls'
]
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields['fileGroup'][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields['type'][3].set('xquest')
activeItemFrame.add.invoke()
for frame in dataFrame.frames[1:]:
mapFrame = frame.fields['mapping'][1]
mapFrame.mapButton.invoke()
for seqName, subset in mapFrame.subsetframes.iteritems():
if 'sp|P10964|RPA1_YEAST' in seqName:
subset.menus[0].var.set('A190')
mapFrame.onSave()
lastFrame = dataFrame.frames[-1]
mapFrame = lastFrame.fields['mapping'][1]
mapFrame.mapButton.invoke()
mapFrame.mapVar.set('0.2 mM X-linker, 30min at 37 C')
mapFrame.onSave()
xFrame.displayDefault()
self.assertEqual(171, len(xmgr.pbg.pseudoBonds))
def readPBinfo(fileName,
category=None,
clearCategory=1,
lineWidth=None,
drawMode=None,
leftModel=None,
rightModel=None,
defColor=None):
"""read a file containing pseudobond info and display those bonds
'category' defaults to 'fileName'. 'clearCategory' controls
whether the pseudobond group should be cleared of pre-existing
pseudobonds before reading the file. 'lineWidth' is a floating-
point number and controls the width of lines used to draw the
pseudobonds. This only is relevant if 'drawMode' is Wire.
'drawMode' controls the depiction style of the pseudobonds.
Possible modes are:
Wire (aka chimera.Bond_Wire) -- wireframe
Stick (aka chimera.Bond_Stick) -- sticks
'leftModel' and 'rightModel' control what models the endpoints
of the pseudobond lie in, if none are specified in the input file.
'defColor' is the color assigned to the pseudobond group as a whole,
which can be overridden by specific pseudobonds.
"""
foundErrors = False
colorCache = {}
if not category:
category = fileName
group = chimera.misc.getPseudoBondGroup(category)
if lineWidth:
group.lineWidth = lineWidth
if drawMode:
group.drawMode = drawMode
if clearCategory:
group.deleteAll()
if defColor:
if isinstance(defColor, basestring):
c = chimera.Color.lookup(defColor)
if not c:
replyobj.message("Cannot find color '%s'\n" % defColor)
foundErrors = True
else:
c = defColor
group.color = c
from OpenSave import osOpen
bondFile = osOpen(fileName)
lineNum = 0
for line in bondFile.readlines():
line = line.strip()
lineNum = lineNum + 1
if not line:
# blank line
continue
try:
spec1, spec2, color = line.split(None, 2)
except:
label = color = None
try:
spec1, spec2 = line.split()
except ValueError:
replyobj.message("Line %d does not have at"
" least two atom specifiers.")
foundErrors = True
continue
if color:
# try to distinguish between color name and label
try:
color, label = color.split(None, 1)
except:
label = None
if color[0] != "#":
while (label and not colors.has_key(color)):
try:
c, label = label.split(None, 1)
except:
color = " ".join([color, label])
label = None
else:
color = " ".join([color, c])
atom1 = _processSpec(spec1, leftModel)
if not atom1:
replyobj.message("Left atom spec of line %d of file doesn't"
" select exactly one atom."
" Skipping.\n" % lineNum)
foundErrors = True
continue
atom2 = _processSpec(spec2, leftModel)
if not atom2:
replyobj.message("Right atom spec of line %d of file doesn't"
" select exactly one atom."
" Skipping.\n" % lineNum)
foundErrors = True
continue
if color:
if color[0] == '#':
fieldLen = int((len(color) - 1) / 3)
if 3 * fieldLen + 1 != len(color):
replyobj.message("Bad Tk color '%s'"
" on line %d of file.\n" %
(color, lineNum))
foundErrors = True
elif colorCache.has_key(color):
color = colorCache[color]
else:
r = color[1:1 + fieldLen]
g = color[1 + fieldLen:1 + 2 * fieldLen]
b = color[1 + 2 * fieldLen:]
r = int(r, 16)
g = int(g, 16)
b = int(b, 16)
maxVal = int('f' * fieldLen, 16)
maxVal = float(maxVal)
c = chimera.MaterialColor(r / maxVal, g / maxVal,
b / maxVal)
colorCache[color] = c
color = c
else:
try:
color = getColorByName(color)
except KeyError:
replyobj.message("Unknown color '%s' on line %d"
" of file.\n" % (color, lineNum))
foundErrors = True
color = None
pb = group.newPseudoBond(atom1, atom2)
if color:
pb.color = color
if label:
pb.label = label
bondFile.close()
if foundErrors:
chimera.replyobj.error("Errors encountered while reading file.\n"
"Check reply log for details.\n")
def ReadMol ( fpath, log=False ) :
from random import random
cif, loops = ReadCif ( fpath, log )
# descriptions by chain id:
descrByEntityId = GetEntityDescr ( cif, loops )
try :
atoms = loops['_atom_site']['data']
print " - %d atom records" % len(atoms)
except :
print " - no atoms in cif?"
return None
labels = loops['_atom_site']['labels']
if 0 :
print "Labels:"
for l in labels :
print " : ", l
import time
start = time.time()
rmap = {}
nmol = chimera.Molecule()
from os import path
#nmol.name = path.splitext ( path.split (fpath)[1] )[0]
nmol.name = path.split (fpath) [1]
nmol.openedAs = [ fpath, [] ]
nmol.cif = cif
nmol.cifLoops = loops
nmol.chainColors = {}
nmol.chainDescr = {}
numQ = 0
first = True
for at in atoms :
mp = at['asMap']
if log and first :
#for label, val in mp.iteritems () :
for li, label in enumerate ( labels ) :
print " %d : %s : %s" % (li+1, label, mp[label])
first = False
atType = mp['type_symbol']
atName = mp['label_atom_id']
rtype = mp['label_comp_id']
chainId = mp['label_asym_id']
chainEId = mp['label_entity_id']
px = mp['Cartn_x']
py = mp['Cartn_y']
pz = mp['Cartn_z']
occ = mp['occupancy']
bfactor = mp['B_iso_or_equiv']
altLoc = mp['label_alt_id']
if altLoc == "." : altLoc = ''
if chainEId in descrByEntityId :
nmol.chainDescr [chainId] = descrByEntityId [chainEId]
resId = ResId ( mp )
if resId == None :
continue
ris = "%s%d" % (chainId, resId)
res = None
if not ris in rmap :
res = nmol.newResidue ( rtype, chimera.MolResId(chainId, resId) )
rmap[ris] = res
else :
res = rmap[ris]
clr = None
if not chainId in nmol.chainColors :
clr = chimera.MaterialColor ( random(), random(), random(), 1.0 )
nmol.chainColors[chainId] = clr
if 0 and log :
print " - chain %s" % chainId
else :
clr = nmol.chainColors [chainId]
nat = nmol.newAtom ( atName, chimera.Element(atType) )
drawRib = rtype in protein3to1 or rtype in nucleic3to1
#aMap[at] = nat
res.addAtom( nat )
nat.setCoord ( chimera.Point( float(px), float(py), float(pz) ) )
nat.altLoc = altLoc
nat.occupancy = float(occ)
nat.bfactor = float(bfactor)
if 'Q-score' in mp :
try :
Q = float ( mp['Q-score'] )
nat.Q = Q
numQ += 1
except :
#print " - q score is", mp['Q-score']
pass
end = time.time()
print " - created %d atoms, %.1fs, %d q-scores" % ( len(nmol.atoms), end-start, numQ )
return nmol
def _addAttr(attrFile, models, log, raiseAttrDialog):
setAttrs = {}
colors = {}
from CGLutil.annotatedDataFile import readDataFile
control = { 'match mode': _MATCH_MODE_ANY, 'recipient': "atoms" }
for rawControl, data in readDataFile(attrFile):
control.update(rawControl)
legalNames = ["attribute", "match mode", "recipient"]
for name in control.keys():
if name not in legalNames:
raise SyntaxError("Unknown name part of control"
" line: '%s'\nMust be one of: %s" % (
name, ", ".join(legalNames)))
if "attribute" not in control:
raise SyntaxError("No attribute name specified in file")
attrName = control["attribute"]
if not attrName.replace("_", "").isalnum() \
or attrName[0].isdigit():
raise SyntaxError("Attribute name (%s) is bad.\n"
"It must be strictly alphanumeric characters or"
" underscores with no spaces and must not start"
" with a digit." % control["attribute"])
colorAttr = attrName.lower().endswith("color")
matchMode = control["match mode"]
if matchMode not in _matchModes:
raise SyntaxError("Unknown match mode (%s) specified.\n"
"It must be one of: %s" % (
control["match mode"], ", ".join(_matchModes)))
recipient = control["recipient"]
if not hasattr(selection.ItemizedSelection, recipient):
raise SyntaxError("Unknown attribute recipient (%s)"
" specified.\nSuggest using atoms, residues, or"
" molecules" % control["recipient"])
dataErrors = []
for lineNum, d in enumerate(data):
try:
selector, value = d
except ValueError:
dataErrors.append("Data line %d of file either"
" not selector/value or not"
" tab-delimited" % (lineNum+1))
continue
try:
sel = specifier.evalSpec(selector, models)
except:
import sys
dataErrors.append("Mangled selector (%s) on"
" data line %d: %s" % (selector,
lineNum+1, sys.exc_value))
continue
matches = getattr(sel, recipient)()
# restrict to models; the "models" argument to evalSpec
# only works if the selector is an OSL
if matches and models is not None:
md = set(models)
level = matches[0].oslLevel()
if level == selection.SelGraph:
filterFunc = lambda x, md=md: x in md
elif level == selection.SelEdge:
filterFunc = lambda x, md=md: \
x.atoms[0].molecule in md
else:
filterFunc = lambda x, md=md: \
x.molecule in md
matches = filter(filterFunc, matches)
if not matches:
if matchMode != _MATCH_MODE_ANY:
dataErrors.append("Selector (%s) on"
" data line %d matched nothing"
% (selector, lineNum+1))
continue
elif len(matches) > 1:
if matchMode == _MATCH_MODE_1_TO_1:
dataErrors.append("Selector (%s) on"
" data line %d matched multiple"
" items: %s" % (selector,
lineNum+1, ", ".join(map(lambda
m: m.oslIdent(), matches))))
if log:
replyobj.info("Selector %s matched " % selector
+ ", ".join(map(misc.chimeraLabel,
matches)) + "\n")
if colorAttr:
if value[0].isalpha():
# color name
from chimera.colorTable \
import getColorByName
try:
value = getColorByName(value)
except KeyError:
dataErrors.append("Unknown"
" color name on data"
" line %d: '%s'" %
(lineNum+1, value))
continue
else:
try:
rgba = tuple(map(float,
value.split()))
except ValueError:
dataErrors.append(
"Unrecognizable color"
" value on data line"
" %d: '%s'; Must be"
" either color name or"
" 3 or 4 numbers"
" between 0 and 1"
" (RGBA)" % (lineNum+1))
continue
if max(rgba) > 1.0 or min(rgba) < 0.0:
dataErrors.append("Color"
" component values on"
" data line %d not"
" in the range 0 to 1"
% (lineNum+1))
continue
if rgba in colors:
value = colors[rgba]
elif len(rgba) in [3, 4]:
value = chimera.MaterialColor(
*rgba)
colors[rgba] = value
else:
dataErrors.append("Bad number"
" of color components"
" on data line %d; Must"
" be either 3 or 4 (was"
" %d)" % (lineNum+1,
len(rgba)))
continue
else:
value = convertType(value)
for match in matches:
setattr(match, attrName, value)
if matches and not colorAttr:
setAttrs[(recipient, attrName)] = value
recipMapping = {
"molecules": chimera.Molecule,
"residues": chimera.Residue,
"bonds": chimera.Bond,
"atoms": chimera.Atom
}
from SimpleSession import registerAttribute
for recipient, attrName in setAttrs:
if recipient in recipMapping:
registerAttribute(recipMapping[recipient], attrName)
if setAttrs and not chimera.nogui and raiseAttrDialog:
from ShowAttr import ShowAttrDialog, screenedAttrs
from chimera import dialogs
showableAttr = False
reasons = []
for recipient, attrName in setAttrs.keys():
if recipient == "molecules":
recipient = "models"
validRecipients = ["atoms", "residues", "models"]
if recipient not in validRecipients:
reasons.append("%s not assigned to atoms,"
" residues, or models" % attrName)
continue
key = [chimera.Atom, chimera.Residue, chimera.Model][
validRecipients.index(recipient)]
if attrName in screenedAttrs[key]:
reasons.append("%s automatically screened out"
" by Render By Attribute" % attrName)
continue
if attrName[0] == '_':
reasons.append("%s considered to be a private"
" variable" % attrName)
continue
if attrName[0].isupper():
reasons.append("%s considered to be a symbolic"
" constant due to initial capital"
" letter" % attrName)
continue
showableAttr = True
break
if showableAttr:
if models is None:
ms = chimera.openModels.list()
else:
ms = models
if colorAttr:
an = None
mode = None
else:
an = attrName
from types import StringTypes
if type(setAttrs[(recipient, attrName)]) in (
bool,) + StringTypes:
mode = "Select"
else:
mode = "Render"
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=[m for m in ms
if isinstance(m, chimera.Molecule)],
attrsOf=recipient, attrName=an, mode=mode)
else:
replyobj.warning("No attributes usable by Render dialog"
" were defined:\n" + "\n".join(reasons) + "\n")
if dataErrors:
raise SyntaxError, "\n".join(dataErrors)
return setAttrs
try :
import chimera
import numpy
from chimera.resCode import nucleic3to1
from chimera.resCode import protein3to1, protein1to3
protein3to1['HSD'] = protein3to1['HIS']
protein3to1['HSE'] = protein3to1['HIS']
nucleic1to3 = { 'T':'THY', 'C':'CYT', 'G':'GUA', 'A':'ADE', 'U':'URA'}
nucleic3to1['GDP'] = nucleic3to1['GUA']
atomColors = {'C' : chimera.MaterialColor (0.565,0.565,0.565),
'Cbb' : chimera.MaterialColor (0.2,0.6,0.2),
'S' : chimera.MaterialColor (1.000,1.000,0.188),
'O' : chimera.MaterialColor (1.000,0.051,0.051),
'N' : chimera.MaterialColor (0.188,0.314,0.973),
'P' : chimera.MaterialColor (1.0, 0.502, 0.0),
'H' : chimera.MaterialColor (0.9,.9,.9),
' ' : chimera.MaterialColor (0.2,1,.2),
"MG" : chimera.MaterialColor (0,1,0),
"NA" : chimera.MaterialColor (.6,.3,.6),
"CL" : chimera.MaterialColor (.2,.6,.2),
"CA" : chimera.MaterialColor (.4,.4,.6),
"ZN" : chimera.MaterialColor (.2,.8,.2),
"MN" : chimera.MaterialColor (.4,.4,.6),
"FE" : chimera.MaterialColor (.4,.4,.6),
"CO" : chimera.MaterialColor (.4,.4,.6),
def wellCB(clr, cb=cb, mdl=model):
if clr is not None:
clr = chimera.MaterialColor(*clr)
cb(mdl, clr)
def chimera_color(rgb):
return chimera.MaterialColor(*rgb)
def testTutorial(self):
subUnitFrame = self.g.configFrame.subUnitFrame
self.assertEqual(0, len(subUnitFrame.frames))
self.assertEqual(0, len(self.g.configFrame.config.subunits))
activeItemFrame = subUnitFrame.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'Rvb1')
activeItemFrame.fields['chainIds'][1].insert(0, 'A,C,E')
activeItemFrame.fields['color'][1].set(chimera.MaterialColor(
0, 255, 0))
activeItemFrame.add.invoke()
self.assertEqual(1, len(self.g.configFrame.config.subunits))
self.assertEqual(1, len(subUnitFrame.frames))
activeItemFrame.fields['name'][1].insert(0, 'Rvb2')
activeItemFrame.fields['chainIds'][1].insert(0, 'B,D,F')
activeItemFrame.fields['color'][1].set(
chimera.MaterialColor(0.392, 0.584, 0.929))
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.subunits))
self.assertEqual(2, len(subUnitFrame.frames))
configfilename = tempfile.mkstemp()[1]
self.g.configFrame.resMngr._saveAssembly(configfilename)
self.assertEqual(configfilename, xla.getRecentPaths()[0])
self.g.Subunits.table.colorAll.invoke()
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0, 255, 0))
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0.392, 0.584, 0.929))
ctable = self.g.Subunits.table
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.hide.invoke()
for chain in ['A', 'C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(1)
ctable.hide.invoke()
for chain in ['A', 'C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
ctable.show.invoke()
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.showOnly.invoke()
for chain in ['A', 'C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
for chain in ['B', 'D', 'F']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
chimera.selection.clearCurrent()
ctable.select.invoke()
self.assertListEqual(
['A', 'C', 'E'],
[s.chain for s in chimera.selection.currentChains()])
chimera.selection.clearCurrent()
self.assertEqual(2, len(ctable.table._sortedData()))
ctable.chainVar.set(1)
self.assertEqual(6, len(ctable.table._sortedData()))
ctable.showAll.invoke()
ctable.table.tixTable.hlist.selection_clear()
ctable.table.tixTable.hlist.selection_set(0)
ctable.hide.invoke()
for chain in ['A']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, False)
for chain in ['C', 'E']:
ribbonDisplay = evalSpec('#{0}:.{1}'.format(
self.model.id, chain)).residues()[0].ribbonDisplay
self.assertEqual(ribbonDisplay, True)
ctable.table.tixTable.hlist.selection_set(1)
ctable.hide.invoke()
ctable.table.tixTable.hlist.selection_set(2)
ctable.hide.invoke()
ctable.chainVar.set(0)
self.assertEqual(False, self.g.configFrame.config.subunits[0].show)
self.assertEqual(2, len(ctable.table._sortedData()))
ctable.showAll.invoke()
self.assertEqual(True, self.g.configFrame.config.subunits[0].show)
dataFrame = self.g.configFrame.dataFrame
activeItemFrame = dataFrame.activeItemFrame
activeItemFrame.fields['name'][1].insert(0, 'xlinks')
paths = [
'xlinks/inter.csv', 'xlinks/intra.csv', 'xlinks/monolinks.csv'
]
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields['fileGroup'][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields['type'][3].set('xquest')
activeItemFrame.add.invoke()
self.assertEqual(1, len(self.g.configFrame.config.dataItems))
self.assertEqual(1, len(dataFrame.frames))
dataMgrTab = self.g.__dict__['Data manager']
self.assertEqual(3, len(dataMgrTab.winfo_children()))
xFrame = self.g.Xlinks
xFrame.displayDefaultBtn.invoke()
self.assertEqual(1, len(xFrame.getXlinkDataMgrs()))
xmgr = xFrame.getXlinkDataMgrs()[0]
self.assertEqual(216, len(xmgr.pbg.pseudoBonds))
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(75, displayed)
xFrame.ld_score_var.set(30.0)
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.hideAllXlinksBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(0, displayed)
xFrame.displayDefaultBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.hideIntraXlinksBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(24, displayed)
xFrame.displayDefaultBtn.invoke()
xFrame.hideInterXlinksBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(33, displayed)
xFrame.showAllXlinksBtn.invoke()
xFrame.smartModeBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(162, displayed)
xFrame.smartModeBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.confOligBtn.invoke()
xFrame.confOligWindow.winfo_children()[0].winfo_children()[0].invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(18, displayed)
xFrame.confOligWindow.winfo_children()[0].winfo_children()[0].invoke()
activeItemFrame.fields['name'][1].insert(0, 'sequences')
paths = ['sequences.yeast.fasta']
dirname = os.path.dirname(self.xlaTestCPath)
paths = [os.path.join(dirname, p) for p in paths]
fileFrame = activeItemFrame.fields['fileGroup'][1]
map(fileFrame.fileGroup.addFile, paths)
fileFrame.resetFileMenu(paths, 0)
activeItemFrame.fields['type'][3].set('sequences')
activeItemFrame.add.invoke()
self.assertEqual(2, len(self.g.configFrame.config.dataItems))
self.assertEqual(2, len(dataFrame.frames))
sequenceFrame = dataFrame.frames[-1]
mapFrame = sequenceFrame.fields['mapping'][1]
mapFrame.mapButton.invoke()
for seqName, subset in mapFrame.subsetframes.iteritems():
if 'RUVB1' in seqName:
subset.menus[0].var.set('Rvb1')
if 'RUVB2' in seqName:
subset.menus[0].var.set('Rvb2')
mapFrame.onSave()
self.g.configFrame.resMngr._saveAssembly(
self.g.configFrame.config.file)
self.assertEqual(5, len(dataMgrTab.winfo_children()))
dataMgrTab.winfo_children()[2].invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(0, displayed)
dataMgrTab.winfo_children()[2].invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(57, displayed)
xFrame.showModifiedFrame.showModifiedMap()
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('light gray'))
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:.{1}'.format(self.model.id,
chain)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('light gray'))
some_red_resi = map(str, [81, 128, 161, 174, 276])
for resi in some_red_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('red'))
some_red_resi = map(str, [85, 116, 193, 210, 239, 377])
for resi in some_red_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('red'))
some_yellow_resi = map(str, [15, 130, 201, 285, 438])
for resi in some_yellow_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('yellow'))
some_blue_resi = map(str, [198, 331, 338, 357])
for resi in some_blue_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('blue'))
xFrame.ld_score_var.set(0.0)
xFrame.showModifiedFrame.showModifiedMap()
some_blue_resi = map(str, [377])
for resi in some_blue_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('blue'))
xFrame.ld_score_var.set(30.0)
xFrame.showModifiedFrame.showModifiedMap()
modelStatsTable = self.g.Xlinks.modelStatsTable
modelStatsTable.xlinkToolbar.resetView()
self.g.Subunits.table.colorAll.invoke()
self.assertEqual(6, len(modelStatsTable.winfo_children()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
modelStatsTable._exportTable(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertListEqual([
'All xlinks', 'Satisfied', 'Violated', 'Satisfied [%]',
'Violated [%]', 'model'
], reader.fieldnames)
rows = list(reader)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(2, int(row['Violated']))
self.assertEqual(18, int(row['All xlinks']))
self.assertEqual(16, int(row['Satisfied']))
self.assertEqual('88.9', row['Satisfied [%]'])
self.assertEqual('11.1', row['Violated [%]'])
self.assertEqual('yRvb12.hexamer.pdb', row['model'])
modelStatsTable.modelListFrame.winfo_children()[8].invoke()
detailsFrame = modelStatsTable.detailsFrame
self.assertEqual(2, len(detailsFrame.winfo_children()))
detailsFrame.showHistogram()
xlinksSet = detailsFrame.xlinkDataMgr.getXlinksWithDistances(
detailsFrame.xlinkStats)
self.assertEqual(18, len(xlinksSet.data))
#TODO: test exportSelectedXlinkList
detailsFrame.byCompViolatedListFrame.highlightSelBtn.invoke()
self.assertEqual(6, len(chimera.selection.currentPseudobonds()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
detailsFrame.byCompViolatedListFrame._exportSelectedXlinkList(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertEqual(6, len(list(reader)))
chimera.selection.clearCurrent()
detailsFrame.byPairViolatedListFrame.highlightSelBtn.invoke()
self.assertEqual(6, len(chimera.selection.currentPseudobonds()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
detailsFrame.byCompViolatedListFrame._exportSelectedXlinkList(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertEqual(6, len(list(reader)))
chimera.selection.clearCurrent()
modelStatsTable.xlinkToolbar.lengthThreshVar.set(40.0)
modelStatsTable.xlinkToolbar.lengthThresholdFrameApplyBtn.invoke()
modelStatsTable.updateBtn.invoke()
self.assertEqual(6, len(modelStatsTable.winfo_children()))
csvfilename = tempfile.mkstemp()[1]
with open(csvfilename, 'w') as f:
modelStatsTable._exportTable(f)
with open(csvfilename, 'rU') as csvfile:
dialect = csv.Sniffer().sniff(csvfile.readline(), ['\t', ','])
csvfile.seek(0)
reader = csv.DictReader(csvfile, dialect=dialect)
self.assertListEqual([
'All xlinks', 'Satisfied', 'Violated', 'Satisfied [%]',
'Violated [%]', 'model'
], reader.fieldnames)
rows = list(reader)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(1, int(row['Violated']))
self.assertEqual(18, int(row['All xlinks']))
self.assertEqual(17, int(row['Satisfied']))
self.assertEqual('94.4', row['Satisfied [%]'])
self.assertEqual('5.6', row['Violated [%]'])
self.assertEqual('yRvb12.hexamer.pdb', row['model'])
modelStatsTable.xlinkToolbar.lengthThreshVar.set(30.0)
modelStatsTable.xlinkToolbar.lengthThresholdFrameApplyBtn.invoke()
modelStatsTable.updateBtn.invoke()
xFrame.showXlinksFromTabNameCompOptMenuFrom.var.set('Rvb1')
xFrame.showXlinksFromTabNameCompOptMenuTo.var.set('Rvb2')
xFrame.showXlinksFromBtn.invoke()
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(24, displayed)
xFrame.ld_score_var.set(0.0)
displayed = len(
[pb for pb in xmgr.pbg.pseudoBonds if pb.display == True])
self.assertEqual(27, displayed)
xFrame.ld_score_var.set(30.0)
colorXlinkedFrame = xFrame.colorXlinkedFrame
colorXlinkedFrame.compOptMenuFrom.var.set('Rvb1')
colorXlinkedFrame.compOptMenuTo.var.set('Rvb2')
colorXlinkedFrame.colorOptionVar.set(1)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.colorTable.getColorByName('red'))
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
colorXlinkedFrame.colorOptionVar.set(2)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ['A', 'C', 'E']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color,
chimera.MaterialColor(0.392, 0.584, 0.929))
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
colorXlinkedFrame.compOptMenuFrom.var.set('Rvb2')
colorXlinkedFrame.compOptMenuTo.var.set('Rvb1')
colorXlinkedFrame.uncolorOthersBtn.var.set(True)
colorXlinkedFrame.colorOptionVar.set(2)
colorXlinkedFrame.colorBtn.invoke()
some_test_resi = map(str, [31, 171, 174, 432, 450, 454])
for resi in some_test_resi:
for chain in ['A', 'C', 'E']:
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, False)
some_test_resi = map(str, [123, 157, 198, 357, 414])
for resi in some_test_resi:
for chain in ['B', 'D', 'F']:
color = evalSpec('#{0}:{2}.{1}'.format(self.model.id, chain,
resi)).atoms()[0].color
self.assertEqual(color, chimera.MaterialColor(0, 255, 0))
display = evalSpec('#{0}:{2}.{1}'.format(
self.model.id, chain, resi)).atoms()[0].display
self.assertEqual(display, True)
def Apply(self):
colors = {}
for i, ssInfo in enumerate(self.info):
ssType, prefName, attrName = ssInfo
rgba = self.wells[i].rgba
prefs[prefName] = rgba
if not self.actVars[i].get():
continue
if rgba is None:
color = None
else:
color = chimera.MaterialColor(*rgba)
colors[attrName] = color
mols = self.molListBox.getvalue()
# only the protein residues are relevant...
protein = {}
for m in mols:
for r in m.residues:
ratoms = r.atomsMap
if 'CA' not in ratoms:
continue
if len(ratoms) == 1:
# possible CA-only model
if ratoms['CA'][0].element.number == 6:
protein[r] = True
continue
if 'O' in ratoms \
and 'N' in ratoms \
and 'C' in ratoms:
protein[r] = True
atomAttrs = []
resAttrs = []
if self.colorRibVar.get():
resAttrs = ["ribbonColor"]
if self.colorAtomVar.get():
atomAttrs.append("color")
if self.colorSurfVar.get():
atomAttrs.append("surfaceColor")
from chimera.actions import changeSurfsFromCustom
changeSurfsFromCustom(mols)
if atomAttrs:
def colorAttrs(item, res, attrs):
for attrName, color in colors.items():
if attrName is None:
if not (res.isHelix
or res.isSheet):
break
elif getattr(res, attrName):
break
else:
return
for attr in attrs:
setattr(item, attr, color)
for m in mols:
for a in m.atoms:
res = a.residue
if res not in protein:
continue
colorAttrs(a, res, atomAttrs)
if resAttrs:
for m in mols:
for res in m.residues:
if res not in protein:
continue
for attrName, color in colors.items():
if attrName is None:
if not (res.isHelix
or res.isSheet):
break
elif getattr(res, attrName):
break
else:
continue
for attr in resAttrs:
setattr(res, attr, color)
cur_color = None
cur_style = None
cur_typeface = None
if (len(label.lines) > 0) and \
(len(label.lines[0]) > 0):
c = label.lines[0][0]
cur_color = c.rgba
cur_size = c.size
cur_style = c.style
cur_typeface = c.fontName
label.set(text)
if cur_color:
cur_color = chimera.MaterialColor(*cur_color)
changeLabelAttrs(label, cur_size, cur_color, cur_style,
cur_typeface)
if color or size or style or typeface:
if style:
style = styleLookup(style)
if typeface:
typeface = typefaceLookup(typeface)
changeLabelAttrs(label, size, color, style, typeface)
if (xpos != None) or (ypos != None):
cur_xpos, cur_ypos = label.pos
if xpos == None: xpos = cur_xpos
if ypos == None: ypos = cur_ypos
def _selCavityCB(self, tableSel):
prefs[EXCLUDE_MOUTH] = self.excludeMouth.variable.get()
from chimera.selection import ItemizedSelection, mergeCurrent, \
EXTEND, REMOVE
cavitySel = ItemizedSelection()
for cavity in tableSel:
cavitySel.merge(EXTEND, cavity.pocketInfo["atoms"])
if prefs[EXCLUDE_MOUTH]:
cavitySel.merge(REMOVE,
cavity.mouthInfo["atoms"])
cavitySel.addImplied()
# might be no cavities selected...
cav1 = self.cavities[0]
someA = (cav1.mouthInfo["atoms"].atoms()
or cav1.pocketInfo["atoms"].atoms())[0]
if someA.__destroyed__:
return
mol = someA.molecule
cavitySet = set(cavitySel.atoms())
from chimera import selectionOperation
doSelect = self.doSelect.variable.get()
if doSelect != prefs[DO_SELECT]:
#if not doSelect:
# mergeCurrent(REMOVE, cavitySel)
prefs[DO_SELECT] = doSelect
doColor = self.doColor.variable.get()
if doColor != prefs[DO_COLOR]:
if not doColor and hasattr(self, '_prevColors'):
for a, c, sc in self._prevColors:
if a.__destroyed__:
continue
a.color = c
a.surfaceColor = sc
delattr(self, '_prevColors')
prefs[DO_COLOR] = doColor
if doColor:
prefs[POCKET_COLOR] = self.pocketColor.rgba
prefs[NONPOCKET_COLOR] = self.nonpocketColor.rgba
doSurface = self.doSurface.variable.get()
if doSurface != prefs[DO_SURFACE]:
if not doSurface:
for a in cavitySet:
a.surfaceDisplay = False
prefs[DO_SURFACE] = doSurface
doZoom = self.doZoom.variable.get()
if doZoom != prefs[DO_ZOOM]:
if not doZoom:
from Midas import focus, uncofr
focus([mol])
uncofr()
prefs[DO_ZOOM] = doZoom
if doSelect:
selectionOperation(cavitySel)
if doColor:
if prefs[POCKET_COLOR] == None:
pocketColor = None
else:
pocketColor = chimera.MaterialColor(
*prefs[POCKET_COLOR])
if prefs[NONPOCKET_COLOR] == None:
nonpocketColor = None
else:
nonpocketColor = chimera.MaterialColor(
*prefs[NONPOCKET_COLOR])
if not hasattr(self, '_prevColors'):
self._prevColors = [(a, a.color, a.surfaceColor)
for a in mol.atoms]
for a in mol.atoms:
if a in cavitySet:
a.surfaceColor = a.color = pocketColor
else:
a.surfaceColor = a.color = nonpocketColor
if doSurface:
for a in mol.atoms:
a.surfaceDisplay = a in cavitySet
surfs = chimera.openModels.list(mol.id, mol.subid,
modelTypes=[chimera.MSMSModel])
catsurfs = [s for s in surfs if s.category == "main"]
if not catsurfs:
from Midas import surfaceNew
surfaceNew("main", models=[mol])
if doZoom and tableSel:
from Midas import align, focus
align(cavitySel, mol.atoms)
focus(cavitySel)
