def colorBB():
red = getColorByName('red')
yellow = getColorByName('yellow')
# return a list of opened molecules
for mol in openModels.list(modelTypes=[Molecule]):
mol.color = red # change model color to be red
atoms = mol.atoms
for atom in atoms:
if atom.name == 'CA':
atom.color = yellow
def getRGBcolor_byName(sCol): from chimera import colorTable try: c = colorTable.getColorByName(sCol) return c.rgba()[:3] except KeyError: return None
def fillInUI(self, parent):
self.info = [
("Helix", HELIX_COLOR, 'isHelix'),
("Strand", SHEET_COLOR, 'isSheet'),
("Other", OTHER_COLOR, None)
]
header = Tkinter.Frame(parent)
header.grid(row=0, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
for i in range(len(self.info)):
parent.columnconfigure(i, weight=1)
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(header,
selectioncommand=lambda: self.configure(
models=self.molListBox.getvalue()),
listbox_selectmode="extended",
labelpos="nw", label_text="Models")
self.molListBox.grid(row=0, column=0,
rowspan=len(self.info), sticky="nsew")
for i in range(3):
header.rowconfigure(i, weight=1)
header.columnconfigure(0, weight=1)
self.colorRibVar = Tkinter.IntVar(parent)
self.colorRibVar.set(True)
self.colorAtomVar = Tkinter.IntVar(parent)
self.colorAtomVar.set(False)
self.colorSurfVar = Tkinter.IntVar(parent)
self.colorSurfVar.set(False)
varFrame = Tkinter.Frame(parent)
varFrame.grid(row=1, column=0)
for i, info in enumerate([(self.colorRibVar, "Color ribbons"),
(self.colorAtomVar, "Color atoms"),
(self.colorSurfVar, "Color surfaces")]):
var, text = info
but = Tkinter.Checkbutton(varFrame, variable=var,
text=text)
but.grid(row=i, column=0, sticky='w')
self.wells = []
self.actVars = []
from CGLtk.color.ColorWell import ColorWell
from chimera.colorTable import getColorByName
for row, ssInfo in enumerate(self.info):
ssType, prefName, attrName = ssInfo
rgba = prefs[prefName]
if isinstance(rgba, basestring):
rgba = getColorByName(rgba).rgba()
well = ColorWell(header, color=rgba,
noneOkay=True)
self.wells.append(well)
well.grid(row=row, column=2)
actVar = Tkinter.IntVar(parent)
actVar.set(True)
self.actVars.append(actVar)
Tkinter.Checkbutton(header, variable=actVar,
text=ssType).grid(row=row,
column=1, sticky='w')
def _rgba(self, colorInfo):
if colorInfo is None:
colorInfo = self['newcolor']
if isinstance(colorInfo, basestring):
from chimera.colorTable import getColorByName
colorInfo = getColorByName(colorInfo)
if hasattr(colorInfo, 'rgba'):
if callable(colorInfo.rgba):
return colorInfo.rgba()
return colorInfo.rgba
return colorInfo
def _rgba(self, colorInfo): if colorInfo is None: colorInfo = self['newcolor'] if isinstance(colorInfo, basestring): from chimera.colorTable import getColorByName colorInfo = getColorByName(colorInfo) if hasattr(colorInfo, 'rgba'): if callable(colorInfo.rgba): return colorInfo.rgba() return colorInfo.rgba return colorInfo
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 draw_bond_orders(molecule, error_spring=True):
pbg = getPseudoBondGroup('Bond order errors', associateWith=[molecule])
pbg.lineWidth, pbg.lineType, pbg.color = 2, 1, getColorByName('red')
def draw_spring(bond):
pbg = getPseudoBondGroup('Bond order errors')
pb = pbg.newPseudoBond(*bond.atoms)
pb.drawMode = 2
pb.radius = bond.radius + 0.1
for bond in molecule.bonds:
order = getattr(bond, 'order', None)
if not order:
print('! Invalid order for bond', bond)
if error_spring:
draw_spring(bond)
continue
if not hasattr(bond, '_oldradius'):
bond._oldradius = bond.radius
bond.radius = bond._oldradius * order * 0.5
return pbg
def color_path_regions(markers, reg_path, seq_start):
'''
TODO: This Chimera code has not been ported to ChimeraX.
'''
f = open(reg_path)
lines = f.readlines()
f.close()
c3 = [line.split('\t')[:3] for line in lines]
from chimera.colorTable import getColorByName
regions = [(int(i1), int(i2), getColorByName(cname).rgba())
for i1, i2, cname in c3]
color = {}
for i1, i2, rgba in regions:
for i in range(i1, i2 + 1):
color[i] = rgba
for m in markers:
i = seq_start + m.residue.number - 1
if i in color:
m.set_rgba(color[i])
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Show a residue with different color
Tasks
=====
1. Obtain selected residues from interface as Python objects
2. Force display of such residues
3. Color those atoms in red
"""
import chimera
# 1
from chimera import runCommand as rc
rc("sel ligand zr < 5")
selected_residues = chimera.selection.currentResidues()
# 2
for residue in selected_residues:
for atom in residue.atoms:
atom.display = 1
# 3
from chimera.colorTable import getColorByName
red = getColorByName('red')
for residue in selected_residues:
for atom in residue.atoms:
atom.color = red
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 __init__(self):
### Volume name
self.volumepath = os.environ.get('CHIMVOL')
print self.volumepath
if self.volumepath is None:
sys.exit(1)
self.rundir = os.path.dirname(self.volumepath)
self.chimlog = os.path.join(self.rundir, "apChimSnapshot.log")
self.writeMessageToLog("\n\n")
self.writeMessageToLog("======================")
self.writeMessageToLog("Running apChimSnapshot")
self.writeMessageToLog("======================")
self.writeMessageToLog("\n")
### Temporary volume, low pass filtered
self.tmpfilepath = os.environ.get('CHIMTEMPVOL')
if self.tmpfilepath is None:
self.tmpfilepath = self.volumepath
### PDB structure
self.pdbfilepath = os.environ.get('CHIMPDBFILE')
### High resolution rendering
voxellimit = os.environ.get('CHIMVOXELLIMIT')
if voxellimit is not None and bool(voxellimit) is True:
self.voxellimit = True
else:
self.voxellimit = False
### Symmetry
self.symmetry = os.environ.get('CHIMSYM')
if self.symmetry is None:
self.symmetry = 'c1'
else:
self.symmetry = self.symmetry.lower()
### Zoom factor
self.zoom = os.environ.get('CHIMZOOM')
if self.zoom is None:
self.zoom = 1.0
else:
self.zoom = float(self.zoom)
### Contour factor
self.contour = os.environ.get('CHIMCONTOUR')
if self.contour is not None:
self.contour = float(self.contour)
### Image type
self.type = os.environ.get('CHIMTYPE')
if self.type is None or self.type not in ('snapshot', 'animate'):
self.type = 'snapshot'
### Color array
colors = os.environ.get('CHIMCOLORS')
if colors is not None and "," in colors:
self.colors = colors.split(",")
else:
self.colors = None
### Silhouette
silhouette = os.environ.get('CHIMSILHOUETTE')
if silhouette is not None and bool(silhouette) is True:
chimera.viewer.showSilhouette = True
chimera.viewer.silhouetteWidth = 3.0
self.writeMessageToLog("using chimera silhouette")
else:
chimera.viewer.showSilhouette = False
self.writeMessageToLog("skipping chimera silhouette")
### Background
if os.environ.get('CHIMBACK') is None:
white = getColorByName('white')
chimera.viewer.background = white
else:
backcolor = os.environ.get('CHIMBACK').strip()
color = getColorByName(backcolor)
chimera.viewer.background = color
### image format
self.imgformat = os.environ.get('CHIMIMGFORMAT')
if self.imgformat is None:
self.imgformat = "PNG"
### image size
imgsize = os.environ.get('CHIMIMGSIZE')
if imgsize is not None:
imgsize = int(imgsize)
self.imgsize = (imgsize, imgsize)
elif self.type == 'animate':
self.imgsize = (512,512)
else:
self.imgsize = (1024,1024)
### file format
self.fileformat = os.environ.get('CHIMFILEFORMAT')
if self.fileformat is None:
self.fileformat = "mrc"
### write to log
self.writeMessageToLog("Chimera version: %s"%(chimera.version.version))
self.writeMessageToLog("Environmental data: ")
for var in os.environ.keys():
if var[:4] == "CHIM":
if os.environ.get(var) is not None:
self.writeMessageToLog("export %s=%s"%(var, os.environ.get(var)))
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 _setColor(color=color, g=g):
from chimera.colorTable import getColorByName
g.color = getColorByName(color)
g.lineType = chimera.Dash
try:
info = typeInfo[a.idatmType]
except KeyError:
return False
return info.substituents < info.geometry
from chimera.colorTable import getColorByName
from prefs import defaults, CLASH_THRESHOLD, HBOND_ALLOWANCE, BOND_SEPARATION, \
IGNORE_INTRA_RES, ACTION_SELECT, ACTION_COLOR, CLASH_COLOR, \
NONCLASH_COLOR, ACTION_PSEUDOBONDS, PB_COLOR, PB_WIDTH, ACTION_ATTR, \
ACTION_REPLYLOG
defColors = {}
for color in [CLASH_COLOR, NONCLASH_COLOR, PB_COLOR]:
val = defaults[color]
if val is not None:
val = getColorByName(val)
defColors[color] = val
_continuousID = None
def cmdDetectClash(testAtoms, overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE], test="others",
setAttrs=defaults[ACTION_ATTR], selectClashes=
defaults[ACTION_SELECT], colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR], nonclashColor=
defColors[NONCLASH_COLOR], makePseudobonds=
defaults[ACTION_PSEUDOBONDS], pbColor=defColors[PB_COLOR],
lineWidth=defaults[PB_WIDTH], bondSeparation=
defaults[BOND_SEPARATION], saveFile=None, namingStyle=None,
ignoreIntraRes=defaults[IGNORE_INTRA_RES], interSubmodel=False,
log=defaults[ACTION_REPLYLOG], summary=True,
continuous=False):
global _continuousID
import chimera
opened = chimera.openModels.open('3fx2', type="PDB")
mol = opened[0]
mol.display = True
from chimera.colorTable import getColorByName
red = getColorByName('red')
mol.color = red
blue = getColorByName('blue')
yellow = getColorByName('yellow')
ATOMS = mol.atoms
for at in ATOMS:
at.drawMode = chimera.Atom.Ball
if at.name == 'CA':
at.color = yellow
else:
at.color = blue
BONDS = mol.bonds
for b in BONDS:
b.display = chimera.Bond.Smart
b.drawMode = chimera.Bond.Stick
b.halfbond = True
RESIDUES = mol.residues
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
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# the 'color' attribute represents the model-level color.
# This color can be controlled by the midas command 'modelcolor'.
# The 'color' assigned to a newly opened model is determined by a configurable preference (see discussion above).
# Programmatically, the model
# color can be changed by simply assigning a 'MaterialColor' to 'molecule.color'. Molecules also have a
# 'display' attribute, where a value of 'True' corresponds to being displayed, and a value of 'False'
# means the molecule is not displayed.
# So to make sure the molecule is shown (it is by default when first opened):
mol.display = True
# To color the molecule red,
# get a reference to Chimera's notion of the color red (returns a 'MaterialColor' object)
from chimera.colorTable import getColorByName
red = getColorByName('red')
# and assign it to 'mol.color'.
mol.color = red
# Note that the model will appear red at this point because all the atoms/bonds/residues
# 'color' attributes are set to 'None'
# Atom Display Properties
# ~~~~~~~~~~~~~~~~~~~~~~~
#
# Each atom in a molecule has its own individual color,
# accessible by the 'color' attribute. Upon opening a molecule, each atom's 'color' is set to 'None';
# it can be changed by assigning a new 'MaterialColor' to 'atom.color'.
# So, if we wanted to color all the alpha-carbon atoms blue, and all the rest yellow,
# get references to the colors:
blue = getColorByName('blue')
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
def _setColor(color=color, g=g): from chimera.colorTable import getColorByName g.color = getColorByName(color) g.lineType = chimera.Dash
info = typeInfo[a.idatmType]
except KeyError:
return False
return info.substituents < info.geometry
from chimera.colorTable import getColorByName
from prefs import defaults, CLASH_THRESHOLD, HBOND_ALLOWANCE, BOND_SEPARATION, \
IGNORE_INTRA_RES, ACTION_SELECT, ACTION_COLOR, CLASH_COLOR, \
NONCLASH_COLOR, ACTION_PSEUDOBONDS, PB_COLOR, PB_WIDTH, ACTION_ATTR, \
ACTION_REPLYLOG
defColors = {}
for color in [CLASH_COLOR, NONCLASH_COLOR, PB_COLOR]:
val = defaults[color]
if val is not None:
val = getColorByName(val)
defColors[color] = val
_continuousID = None
def cmdDetectClash(testAtoms,
overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE],
test="others",
setAttrs=defaults[ACTION_ATTR],
selectClashes=defaults[ACTION_SELECT],
colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR],
nonclashColor=defColors[NONCLASH_COLOR],
makePseudobonds=defaults[ACTION_PSEUDOBONDS],
pbColor=defColors[PB_COLOR],