def setup():
import StdTools
preferences.addCategory("Tools", ToolsCategory, aliases=["Extensions"],
manager=manager)
manager.loadDirectory(chimera.pathFinder().dataRoot)
StdTools.registerStandardTools()
if chimera.nogui:
return
manager.createMenu()
manager.showToolbarButtons()
def setup():
import StdTools
preferences.addCategory("Tools",
ToolsCategory,
aliases=["Extensions"],
manager=manager)
manager.loadDirectory(chimera.pathFinder().dataRoot)
StdTools.registerStandardTools()
if chimera.nogui:
return
manager.createMenu()
manager.showToolbarButtons()
def initialize(setCurrent=1):
global pref
if pref is not None:
return
from chimera import preferences
pref = preferences.addCategory("Ribbon Styles",
preferences.HiddenCategory)
try:
# Cannot use "setdefault" here since we need to
# check for old preference name and save to
# new preference name
p = pref[PREF_SCALING]
except KeyError:
try:
p = pref[PREF_OLD_SCALING]
except KeyError:
p = {}
pref[PREF_SCALING] = p
import scaling
scaling.initialize(p)
p = pref.setdefault(PREF_XSECTION, {})
import xsection
xsection.initialize(p)
p = pref.setdefault(PREF_ATOMS, {})
import atoms
atoms.initialize(p)
import chimera
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION, saveSession,
None)
def __init__(self, model):
self.title = 'PDB Headers for %s' % model.name
self.model = model
from chimera import preferences
self.prefs = preferences.addCategory("PDB headers dialog",
preferences.HiddenCategory,
optDict={"ordering": "Alphabetical"})
ModelessDialog.__init__(self)
def __init__(self, model):
self.title = 'PDB Headers for %s' % model.name
self.model = model
from chimera import preferences
self.prefs = preferences.addCategory(
"PDB headers dialog",
preferences.HiddenCategory,
optDict={"ordering": "Alphabetical"})
ModelessDialog.__init__(self)
def volume_menu_preferences():
global vmpref
if vmpref is None:
from chimera import preferences
vmpref = preferences.addCategory('Volume Menu',
preferences.HiddenCategory,
optDict = {'shown': False})
return vmpref
def volume_menu_preferences():
global vmpref
if vmpref is None:
from chimera import preferences
vmpref = preferences.addCategory('Volume Menu',
preferences.HiddenCategory,
optDict={'shown': False})
return vmpref
def initialize():
global pref, userStyles, prefStyles
from chimera import preferences
pref = preferences.addCategory(PREF_CATEGORY,
preferences.HiddenCategory)
prefStyles = pref.setdefault(PREF_SLAB_STYLES, {})
import copy
userStyles = copy.deepcopy(prefStyles)
chimera.triggers.addTrigger(TRIGGER_SLAB_STYLES)
def __init__(self):
self.prefs = preferences.addCategory("write PDB dialog",
preferences.HiddenCategory,
optDict={"multiSavePDB": "multiple"})
self.haveTraj = False
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("PDB", "*.pdb", ".pdb")])
openModels.addAddHandler(self._modelsChange, None),
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def fillInUI(self, parent):
self.plot = None
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight = 1)
row = 0
from chimera.preferences import addCategory, HiddenCategory
prefs = addCategory("SAXS", HiddenCategory,
optDict = {'saxs executable': ''})
self.preferences = prefs
import Tkinter
from CGLtk import Hybrid
from chimera import widgets as w
mm = w.ExtendedMoleculeOptionMenu(parent, label_text = 'Molecule ',
labelpos = 'w',
labels = ['selected atoms','all molecules'])
mm.grid(row = row, column = 0, sticky = 'w')
row += 1
self.molecule_menu = mm
ep = Hybrid.Entry(parent, 'Experimental profile ', 25, browse = True)
ep.frame.grid(row = row, column = 0, sticky = 'ew')
row += 1
self.experimental_profile = ep.variable
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row = row, column = 0, sticky = 'news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row = orow, column = 1, sticky = 'e')
np = Hybrid.Checkbutton(opf, 'Use new plot window', False)
np.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.new_plot = np.variable
ex = Hybrid.Entry(opf, 'Executable ', 25,
initial = prefs['saxs executable'], browse = True)
ex.frame.grid(row = orow, column = 0, sticky = 'ew')
orow += 1
ex.entry.xview('end')
self.executable = ex.variable
def __init__(self, groupPanel):
self.groupPanel = groupPanel
options = {
"shownButs": {},
"executionList": ['attributes...'],
"shownColumns": {}
}
self.prefs = preferences.addCategory("Pseudobond Group Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def __init__(self):
self.prefs = preferences.addCategory("write Mol2 dialog",
preferences.HiddenCategory,
optDict={"multiSaveMol2": "multiple",
"hydrogen naming": "sybyl",
"residue numbers": True})
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("Mol2", "*.mol2", ".mol2")])
openModels.addAddHandler(self._modelsChange, None)
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def __init__(self, groupPanel):
self.groupPanel = groupPanel
options = {
"shownButs": {},
"executionList": ['attributes...'],
"shownColumns": {}
}
self.prefs = preferences.addCategory("Pseudobond Group Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def __init__(self, modelPanel):
self.modelPanel = modelPanel
options = {
"freqButs": {},
"executionList": ['attributes...'],
"shownColumns": {},
"showColor": False,
"lastUse": None
}
self.prefs = preferences.addCategory("Model Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def __init__(self, modelPanel):
self.modelPanel = modelPanel
options = {
"freqButs": {},
"executionList": ['attributes...'],
"shownColumns": {},
"showColor": False,
"lastUse": None
}
self.prefs = preferences.addCategory("Model Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def accelerator_preferences_category():
global prefcat
if prefcat is None:
options = {
'path': default_accelerator_file(),
'time out': '2',
'enable at startup': None,
}
from chimera import preferences as preferences
prefcat = preferences.addCategory('Accelerators',
preferences.HiddenCategory,
optDict=options)
return prefcat
def accelerator_preferences_category():
global prefcat
if prefcat is None:
options = {
'path': default_accelerator_file(),
'time out': '2',
'enable at startup': None,
}
from chimera import preferences as preferences
prefcat = preferences.addCategory('Accelerators',
preferences.HiddenCategory,
optDict=options)
return prefcat
def __init__(self, singleton=True):
from chimera import preferences
self.dialog = None
self.master = None
self.trackLights = None
self.trackViewers = None
self.trackMaterials = None
self.saveKey = None
self.saveFill = None
self.restoreShinyBrightness = None
self.prefs = preferences.addCategory("Lighting",
preferences.HiddenCategory)
self.light = None
if singleton:
global _singleton
_singleton = self
def __init__(self):
options = self.factory_defaults()
from chimera import preferences
self.saved_prefs = preferences.addCategory('Volume Viewer',
preferences.HiddenCategory,
optDict=options)
self.current_prefs = options.copy()
self.change_callbacks = []
#
# Fix values from old preferences files (<= 1.2154) which were written
# as strings instead of floats.
#
cp = self.current_prefs
for name in ('box_padding', 'data_cache_size', 'voxel_limit',
'voxel_limit_for_open'):
if name in cp and type(cp[name]) is str:
cp[name] = float(cp[name])
def __init__(self):
options = self.factory_defaults()
from chimera import preferences
self.saved_prefs = preferences.addCategory('Volume Viewer',
preferences.HiddenCategory,
optDict = options)
self.current_prefs = options.copy()
self.change_callbacks = []
#
# Fix values from old preferences files (<= 1.2154) which were written
# as strings instead of floats.
#
cp = self.current_prefs
for name in ('box_padding', 'data_cache_size', 'voxel_limit',
'voxel_limit_for_open'):
if name in cp and type(cp[name]) is str:
cp[name] = float(cp[name])
from chimera import replyobj
from DelPhiGlobals import *
from DelPhiHelp import *
# preferences
from chimera import preferences
SURF_RGBA_POS = "surf rgba pos"
SURF_RGBA_MID = "surf rgba mid"
SURF_RGBA_NEG = "surf rgba neg"
prefOptions = {
"executable": "",
"radii": "",
"charges": "",
}
prefs = preferences.addCategory("DelphiController",
preferences.HiddenCategory,
optDict=prefOptions)
Executable = prefs["executable"]
if not Executable:
import os, os.path
execNames = ["delphi", "delphi.exe"]
path = os.getenv("PATH", os.defpath)
pathList = path.split(os.pathsep)
for p in pathList:
for e in execNames:
filename = os.path.join(p, e)
if os.access(filename, os.X_OK):
Executable = filename
break
if Executable:
break
from chimera import preferences
BOND_COLOR = 'bondColor'
RELAX_COLOR = 'relaxColor'
LINE_WIDTH = 'line width'
defaults = {
BOND_COLOR: (0.0, 0.8, 0.9, 1.0),
RELAX_COLOR: (0.95, 0.5, 0.0, 1.0),
LINE_WIDTH: 1.0,
}
prefs = preferences.addCategory("FindHBonds", preferences.HiddenCategory,
optDict=defaults.copy())
# --- UCSF Chimera Copyright ---
import os
import math
import Tkinter
import chimera
from chimera import selection
from chimera import chimage
from chimera import tkgui
from chimera import match
from chimera import preferences
from chimera.baseDialog import ModelessDialog
import Midas
prefs = preferences.addCategory("EnsembleCluster", preferences.HiddenCategory)
class EnsembleMatch(ModelessDialog):
"""Display a table for manipulating one ensemble relative to another.
The two ensembles should consist of conformers of the same model.
Table rows correspond to conformers in the reference ensemble.
Table columns correspond to conformers in the alternative ensemble.
A conformer in the alternative ensemble will be matched onto
a conformer in the reference ensemble when a table entry is
clicked. The table entry label is the RMSD between the two
conformers."""
title = "Ensemble Match"
help = "ContributedSoftware/ensemblematch/ensemblematch.html"
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
PRESETS = "user presets"
defaults = {
PRESETS: []
}
prefs = preferences.addCategory("Aniso", preferences.HiddenCategory,
optDict=defaults.copy())
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
CHARGE_METHOD = "charge method"
options = {
CHARGE_METHOD: "AM1-BCC"
}
prefs = preferences.addCategory("AddCharge", preferences.HiddenCategory,
optDict=options)
# --- UCSF Chimera Copyright ---
import os
import math
import Tkinter
import chimera
from chimera import selection
from chimera import chimage
from chimera import tkgui
from chimera import match
from chimera import preferences
from chimera.baseDialog import ModelessDialog
import Midas
prefs = preferences.addCategory("EnsembleCluster", preferences.HiddenCategory)
class EnsembleMatch(ModelessDialog):
"""Display a table for manipulating one ensemble relative to another.
The two ensembles should consist of conformers of the same model.
Table rows correspond to conformers in the reference ensemble.
Table columns correspond to conformers in the alternative ensemble.
A conformer in the alternative ensemble will be matched onto
a conformer in the reference ensemble when a table entry is
clicked. The table entry label is the RMSD between the two
conformers."""
title = "Ensemble Match"
help = "ContributedSoftware/ensemblematch/ensemblematch.html"
buttons = ("Hide", "Quit")
from chimera import preferences
BOND_COLOR = 'bondColor'
RELAX_COLOR = 'relaxColor'
LINE_WIDTH = 'line width'
defaults = {
BOND_COLOR: (0.0, 0.8, 0.9, 1.0),
RELAX_COLOR: (0.95, 0.5, 0.0, 1.0),
LINE_WIDTH: 1.0,
}
prefs = preferences.addCategory("FindHBonds",
preferences.HiddenCategory,
optDict=defaults.copy())
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
COLOR = "color"
options = {
COLOR: (1, 1, 1, 1), # white
}
prefs = preferences.addCategory("ReadMS", preferences.HiddenCategory,
optDict=options)
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 29678 2009-12-23 21:26:15Z pett $
from chimera import preferences
from Rotamers.prefs import defaults as rotamerDefaults
from Rotamers.prefs import LIBRARY as ROTAMER_LIBRARY
INCOMPLETE_SC = "incomplete side chains"
MEMORIZED_SETTINGS = "memorized settings"
defaults = {
INCOMPLETE_SC: rotamerDefaults[ROTAMER_LIBRARY],
MEMORIZED_SETTINGS: {}
}
# so the defaults above can be used elsewhere, send a copy of the dictionary...
prefs = preferences.addCategory("DockPrep",
preferences.HiddenCategory,
optDict=defaults.copy())
dat = ''
if 'NCIPLOT_HOME' in os.environ:
dat = os.path.join(os.environ['NCIPLOT_HOME'], 'dat')
preferences.set('tangram_nciplot', 'nciplot_bin', binary)
preferences.set('tangram_nciplot', 'nciplot_dat', dat)
preferences.save()
return binary, dat
def set_preferences(binary, dat):
assert_preferences()
if os.path.isfile(binary) and os.path.isdir(dat):
preferences.set('tangram_nciplot', 'nciplot_bin', binary)
preferences.set('tangram_nciplot', 'nciplot_dat', dat)
preferences.save()
else:
raise ValueError('One or more of the specified paths do not exist.')
def get_preferences():
return preferences.get('tangram_nciplot', 'nciplot_bin'), \
preferences.get('tangram_nciplot', 'nciplot_dat')
def test_preferences():
binary, dat = get_preferences()
return os.path.isfile(binary) and os.path.isdir(dat)
preferences.addCategory('tangram_nciplot', preferences.HiddenCategory)
assert_preferences()
#
def atom_rgba(atom):
c = atom.color
if c == None:
c = atom.molecule.color
rgba = c.rgba()
return rgba
# -----------------------------------------------------------------------------
#
from chimera.preferences import addCategory, HiddenCategory
bzone_prefs = addCategory('BondZone',
HiddenCategory,
optDict={
'active': False,
'spacing': 1.0
})
# -----------------------------------------------------------------------------
#
def use_bond_zone(use=None, bond_point_spacing=None):
if use == None:
return bzone_prefs['active']
bzone_prefs['active'] = use
if bond_point_spacing != None:
bzone_prefs['spacing'] = bond_point_spacing
__version__ = '1.1.2beta'
def get_gui():
for insta in chimera.extension.manager.instances:
if hasattr(insta, 'name') and insta.name == 'Xlink Analyzer':
return insta
def getConfig():
for insta in chimera.extension.manager.instances:
if hasattr(insta, 'name') and insta.name == 'Xlink Analyzer':
return insta.configFrame.config
prefs = preferences.addCategory("xlinkanalyzer", preferences.HiddenCategory)
def pushRecentToPrefs(path):
otherPaths = [p for p in getRecentPaths() if p != path]
prefs["path1"] = path
for i, p in zip(range(2, 11), otherPaths):
prefs["path{0}".format(i)] = p
def getRecentPaths():
ret = []
for s in ["path" + str(i) for i in range(1, 11)]:
if s in prefs:
ret.append(prefs[s])
return ret
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 29678 2009-12-23 21:26:15Z pett $
from chimera import preferences
from Rotamers.prefs import defaults as rotamerDefaults
from Rotamers.prefs import LIBRARY as ROTAMER_LIBRARY
INCOMPLETE_SC = "incomplete side chains"
MEMORIZED_SETTINGS = "memorized settings"
defaults = {
INCOMPLETE_SC: rotamerDefaults[ROTAMER_LIBRARY],
MEMORIZED_SETTINGS: {}
}
# so the defaults above can be used elsewhere, send a copy of the dictionary...
prefs = preferences.addCategory("DockPrep", preferences.HiddenCategory,
optDict=defaults.copy())
activity = None
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
if activity is None:
activity = m.openState.active
elif activity != m.openState.active:
updateDistance()
return
distanceHandlers['OpenState'] = chimera.triggers.addHandler(
'OpenState', openStateCB, None)
from chimera import preferences
_pref = preferences.addCategory("Distance Monitors",
preferences.HiddenCategory,
optDict={
'precision': 3,
'show units': True
})
def precision():
return _pref['precision']
def setPrecision(p):
if not isinstance(p, int):
raise TypeError, "precision must be integer"
if p < 0:
raise ValueError, "precision must be non-negative"
_pref['precision'] = p
updateDistance()
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26899 2009-02-13 01:19:04Z pett $
from chimera import preferences
DIST_CUTOFF = "distance cutoff"
CIRCULAR = "circular permutation"
ANYALL = "match type"
GAPCHAR = "gap character"
ITERATE = "iterate"
ITER_CONVERGE = "iter until convergence"
ITER_AMOUNT = "iter amount"
ITER_ALL_COLS = "iter all columns"
ITER_CONSECUTIVE_COLS = "iter stretch"
defaults = {
DIST_CUTOFF: 5.0,
CIRCULAR: False,
ANYALL: "any",
GAPCHAR: ".",
ITERATE: False,
ITER_CONVERGE: False,
ITER_AMOUNT: 3,
ITER_ALL_COLS: False,
ITER_CONSECUTIVE_COLS: 3
}
prefs = preferences.addCategory("StructSeqAlign", preferences.HiddenCategory,
optDict=defaults.copy())
SHOW_SEL: 1,
NEW_REGION_BORDER: None,
NEW_REGION_INTERIOR: "white",
SEL_REGION_BORDER: None,
SEL_REGION_INTERIOR: "green",
SEQ_NAME_ELLIPSIS: 30,
REGION_NAME_ELLIPSIS: 25,
MATRIX: mmDefaults[MATRIX],
GAP_OPEN: mmDefaults[GAP_OPEN],
GAP_EXTEND: mmDefaults[GAP_EXTEND],
MATCH_REG_ACTIVE: False,
MATCH_REG_EDGE: "black",
MATCH_REG_FILL: None,
ERROR_REG_ACTIVE: True,
ERROR_REG_EDGE: None,
ERROR_REG_FILL: "red",
GAP_REG_ACTIVE: True,
GAP_REG_EDGE: "red",
GAP_REG_FILL: None,
USE_SS: mmDefaults[USE_SS],
SS_MIXTURE: mmDefaults[SS_MIXTURE],
SS_SCORES: mmDefaults[SS_SCORES],
HELIX_OPEN: mmDefaults[HELIX_OPEN],
STRAND_OPEN: mmDefaults[STRAND_OPEN],
OTHER_OPEN: mmDefaults[OTHER_OPEN],
}
from copy import deepcopy
prefs = preferences.addCategory("MultAlignViewer",
preferences.HiddenCategory, optDict=deepcopy(defaults))
def fillInUI(self, parent):
self.plot = None
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
from chimera.preferences import addCategory, HiddenCategory
prefs = addCategory("SAXS",
HiddenCategory,
optDict={'saxs executable': ''})
self.preferences = prefs
import Tkinter
from CGLtk import Hybrid
from chimera import widgets as w
mm = w.ExtendedMoleculeOptionMenu(
parent,
label_text='Molecule ',
labelpos='w',
labels=['selected atoms', 'all molecules'])
mm.grid(row=row, column=0, sticky='w')
row += 1
self.molecule_menu = mm
ep = Hybrid.Entry(parent, 'Experimental profile ', 25, browse=True)
ep.frame.grid(row=row, column=0, sticky='ew')
row += 1
self.experimental_profile = ep.variable
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=1, sticky='e')
np = Hybrid.Checkbutton(opf, 'Use new plot window', False)
np.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.new_plot = np.variable
ex = Hybrid.Entry(opf,
'Executable ',
25,
initial=prefs['saxs executable'],
browse=True)
ex.frame.grid(row=orow, column=0, sticky='ew')
orow += 1
ex.entry.xview('end')
self.executable = ex.variable
from chimera.preferences import addCategory, HiddenCategory
defaults = {
CHAIN_PAIRING: CP_BEST,
SEQUENCE_ALGORITHM: SA_NEEDLEMAN_WUNSCH,
SHOW_SEQUENCE: False,
MATRIX: "BLOSUM-62",
GAP_OPEN: 12,
GAP_EXTEND: 1,
USE_SS: True,
SS_MIXTURE: 0.3,
SS_SCORES: {
('H', 'H'): 6,
('S', 'S'): 6,
('O', 'O'): 4,
('S', 'H'): -9,
('H', 'S'): -9,
('S', 'O'): -6,
('O', 'S'): -6,
('H', 'O'): -6,
('O', 'H'): -6
},
ITERATE: True,
ITER_CUTOFF: 2.0,
HELIX_OPEN: 18,
STRAND_OPEN: 18,
OTHER_OPEN: 6,
COMPUTE_SS: True,
}
from copy import deepcopy
prefs = addCategory("MatchMaker", HiddenCategory, optDict=deepcopy(defaults))
# delphi/chimera-related modules
from chimera import replyobj
from DelPhiGlobals import *
from DelPhiHelp import *
# preferences
from chimera import preferences
SURF_RGBA_POS = "surf rgba pos"
SURF_RGBA_MID = "surf rgba mid"
SURF_RGBA_NEG = "surf rgba neg"
prefOptions = {
"executable": "",
"radii": "",
"charges": "",
}
prefs = preferences.addCategory("DelphiController",
preferences.HiddenCategory, optDict=prefOptions)
Executable = prefs["executable"]
if not Executable:
import os, os.path
execNames = [ "delphi", "delphi.exe" ]
path = os.getenv("PATH", os.defpath)
pathList = path.split(os.pathsep)
for p in pathList:
for e in execNames:
filename = os.path.join(p, e)
if os.access(filename, os.X_OK):
Executable = filename
break
if Executable:
break
import sys
from base import readPBinfo
import Pmw
ui = None
def showUI():
global ui
if not ui:
ui = PBreaderDialog()
ui.enter()
from chimera import preferences
options = { "line width": 1.0 }
prefs = preferences.addCategory("pseudobond reader", preferences.HiddenCategory,
optDict=options)
class PBreaderDialog(OpenModeless):
title = "Pseudobond Reader"
help = "ContributedSoftware/pbreader/pbreader.html"
def __init__(self):
OpenModeless.__init__(self, title="Pseudobond File to Read",
historyID="PBReader open", clientPos='s')
def fillInUI(self, parent):
OpenModeless.fillInUI(self, parent)
group = Pmw.Group(self.clientArea, tag_text='Further info')
group.grid(row=0, column=0, sticky='nsew')
self.catName = StringOption(group.interior(), 0,
ROT_LABEL = "rot label"
ROT_DIAL_SIZE = "dial size"
ANGLE_PRECISION = "angle precision"
TORSION_PRECISION = "torsion precision"
SHOW_DEGREE_SYMBOL = "show degree symbol"
AXIS_RADIUS = "axis radius"
AXIS_SEL_OBJ = "axis sel obj"
AXIS_SEL_ATOMS = "axis sel atoms"
OBJ_SEL_AXIS = "obj sel axis"
ATOMS_SEL_AXIS = "atoms sel axis"
PLANE_THICKNESS = "plane thickness"
defaults = {
ROT_LABEL: 'None',
ROT_DIAL_SIZE: 1,
ANGLE_PRECISION: 3,
TORSION_PRECISION: 3,
SHOW_DEGREE_SYMBOL: True,
AXIS_RADIUS: 1,
AXIS_SEL_OBJ: True,
AXIS_SEL_ATOMS: False,
OBJ_SEL_AXIS: True,
ATOMS_SEL_AXIS: False,
PLANE_THICKNESS: 0.1
}
# so the defaults above can be used elsewhere, send a copy of the dictionary...
prefs = preferences.addCategory("Struct Measure", preferences.HiddenCategory,
optDict=defaults.copy())
if 'transformation change' not in changes.reasons:
return
activity = None
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
if activity is None:
activity = m.openState.active
elif activity != m.openState.active:
updateDistance()
return
distanceHandlers['OpenState'] = chimera.triggers.addHandler(
'OpenState', openStateCB, None)
from chimera import preferences
_pref = preferences.addCategory("Distance Monitors",
preferences.HiddenCategory,
optDict={
'precision': 3,
'show units': True
})
def precision():
return _pref['precision']
def setPrecision(p):
if not isinstance(p, int):
raise TypeError, "precision must be integer"
if p < 0:
raise ValueError, "precision must be non-negative"
_pref['precision'] = p
updateDistance()
def showUnits(val=None):
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26899 2009-02-13 01:19:04Z pett $
from chimera import preferences
DIST_CUTOFF = "distance cutoff"
CIRCULAR = "circular permutation"
ANYALL = "match type"
GAPCHAR = "gap character"
ITERATE = "iterate"
ITER_CONVERGE = "iter until convergence"
ITER_AMOUNT = "iter amount"
ITER_ALL_COLS = "iter all columns"
ITER_CONSECUTIVE_COLS = "iter stretch"
defaults = {
DIST_CUTOFF: 5.0,
CIRCULAR: False,
ANYALL: "any",
GAPCHAR: ".",
ITERATE: False,
ITER_CONVERGE: False,
ITER_AMOUNT: 3,
ITER_ALL_COLS: False,
ITER_CONSECUTIVE_COLS: 3
}
prefs = preferences.addCategory("StructSeqAlign",
preferences.HiddenCategory,
optDict=defaults.copy())
VOLUME_RESOLUTION = "volume resolution"
RECORDER_FORMAT = "animation format"
RECORDER_RECORD_ARGS = "record args"
RECORDER_ENCODE_ARGS = "encode args"
RECORDER_SUPERSAMPLE = "supersample"
RECORDER_SAMPLES = "samples"
RECORDER_ROUNDTRIP = "roundtrip"
RECORDER_RAYTRACE = "raytrace"
options = {
SCRIPT_TYPE: SCRIPT_PYTHON,
DICT_NAME: "mdInfo",
FRAME_TEXT: "<FRAME>",
ZERO_PAD: True,
RMSD_MIN: 0.5,
RMSD_MAX: 3.0,
RMSD_AUTOCOLOR: True,
VOLUME_CUTOFF: 10.0,
VOLUME_RESOLUTION: 1.0,
RECORDER_FORMAT: -1,
RECORDER_RECORD_ARGS: "",
RECORDER_ENCODE_ARGS: "",
RECORDER_SUPERSAMPLE: True,
RECORDER_SAMPLES: 3,
RECORDER_ROUNDTRIP: False,
RECORDER_RAYTRACE: False
}
prefs = preferences.addCategory("MD Movie", preferences.HiddenCategory,
optDict=options)
DEBUG_MODE = False
__version__ = '1.1.2beta'
def get_gui():
for insta in chimera.extension.manager.instances:
if hasattr(insta, 'name') and insta.name == 'Xlink Analyzer':
return insta
def getConfig():
for insta in chimera.extension.manager.instances:
if hasattr(insta, 'name') and insta.name == 'Xlink Analyzer':
return insta.configFrame.config
prefs = preferences.addCategory("xlinkanalyzer", preferences.HiddenCategory)
def pushRecentToPrefs(path):
otherPaths = [p for p in getRecentPaths() if p != path]
prefs["path1"]=path
for i, p in zip(range(2,11), otherPaths):
prefs["path{0}".format(i)] = p
def getRecentPaths():
ret = []
for s in ["path"+str(i) for i in range(1,11)]:
if s in prefs:
ret.append(prefs[s])
return ret
def activateByName(name, chainIds=None): # this is for testing only
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
HELIX_COLOR = "helix color"
SHEET_COLOR = "sheet color"
OTHER_COLOR = "other color"
defaultColors = {
HELIX_COLOR: 'orange red',
SHEET_COLOR: 'purple',
OTHER_COLOR: 'gray'
}
options = {}
options.update(defaultColors)
prefs = preferences.addCategory("ColorSS",
preferences.HiddenCategory,
optDict=options)
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
FORMAT = "format"
INPUT_FILES = "input files"
GROMOS_SCALING = "Gromos coord scaling"
PDB_STYLE = "PDB input scheme"
options = {
FORMAT: 'Amber',
INPUT_FILES: {},
GROMOS_SCALING: 10.0,
PDB_STYLE: "multiple files"
}
prefs = preferences.addCategory("Trajectory",
preferences.HiddenCategory,
optDict=options)
MIDAS_CATEGORY = "Command Line"
preferences.register(MIDAS_CATEGORY, {
STARTUP_FILES:
(tkoptions.OrderedFileListOption, ["~/.chimera/midasrc", ".chmidasrc"
], None, {
'height': 4
}),
SES_MEMORY: (tkoptions.IntOption, 60, None, {
'min': 0
})
},
aliases=["Midas"])
PREV_COMMANDS = "remembered commands"
prefs = preferences.addCategory("command line gui",
preferences.HiddenCategory,
optDict={PREV_COMMANDS: []})
triggerName = "typed Midas command"
chimera.triggers.addTrigger(triggerName)
class MidasUI:
"Class for presenting a Midas command line"
recordLabel = "Command History..."
hideLabel = "Hide Command Line"
def __init__(self):
from chimera import tkgui
self.frame = Tkinter.Frame(tkgui.app)
LIBRARY = "rotamer library"
CLASH_METHOD = "clash type"
CLASH_PBS = "show clash pseudobonds"
CLASH_COLOR = "clash pb color"
CLASH_WIDTH = "clash pb width"
HBOND_COLOR = "hbond pb color"
RELAX_COLOR = "hbond pb relaxation color"
HBOND_WIDTH = "hbond pb width"
DRAW_HBONDS = "draw hbonds"
CLASH_IGNORE_OTHERS = "Ignore clashes with other models"
HBOND_IGNORE_OTHERS = "Ignore hbonds with other models"
defaults = {
LIBRARY: "Dunbrack",
CLASH_THRESHOLD: clashDefaults[CLASH_THRESHOLD],
HBOND_ALLOWANCE: clashDefaults[HBOND_ALLOWANCE],
CLASH_METHOD: "num",
CLASH_PBS: False,
CLASH_COLOR: clashDefaults[PB_COLOR],
CLASH_WIDTH: clashDefaults[PB_WIDTH],
HBOND_COLOR: hbondDefaults[BOND_COLOR],
RELAX_COLOR: hbondDefaults[FHB_RELAX_COLOR],
HBOND_WIDTH: hbondDefaults[LINE_WIDTH],
DRAW_HBONDS: True,
CLASH_IGNORE_OTHERS: False,
HBOND_IGNORE_OTHERS: False
}
# so the defaults above can be used elsewhere, send a copy of the dictionary...
prefs = preferences.addCategory("Rotamers", preferences.HiddenCategory,
optDict=defaults.copy())
# encoding: utf-8
"""
This is the preferences file for the extension. All default values
should be listed here for reference and easy reuse.
"""
from __future__ import print_function, division
from distutils.spawn import find_executable
import os
# Chimera
from chimera.preferences import preferences, addCategory, HiddenCategory
from core import SNFG
def _defaults():
return dict(
zip(SNFG.__init__.im_func.func_code.co_varnames[1:],
SNFG.__init__.im_func.func_defaults))
DEFAULTS = _defaults()
DEFAULTS['icon_size'] = DEFAULTS['size'] / 2.5
DEFAULTS['full_size'] = DEFAULTS['size']
prefs = addCategory("tangram_snfg", HiddenCategory, optDict=DEFAULTS.copy())
try:
with open(preferences._filename) as f:
d = eval(f.read())
prefs.update(d.get('tangram_snfg', {}))
except Exception as e:
print('Problem loading saved preferences:', e)
NONCLASH_COLOR = "non-clash color"
HBOND_ALLOWANCE = "h-bond allowance"
ACTION_PSEUDOBONDS = "make pseudobonds"
PB_COLOR = "pseudobond color"
PB_WIDTH = "pseudobond width"
BOND_SEPARATION = "bond separation"
ACTION_WRITEINFO = "write info"
IGNORE_INTRA_RES = "ignore intra-residue clashes"
ACTION_REPLYLOG = "log info"
defaults = {
CLASH_THRESHOLD: 0.6,
ACTION_ATTR: False,
ACTION_SELECT: False,
ACTION_COLOR: False,
CLASH_COLOR: "red",
NONCLASH_COLOR: None,
HBOND_ALLOWANCE: 0.4,
ACTION_PSEUDOBONDS: True,
PB_COLOR: "yellow",
PB_WIDTH: 2.0,
BOND_SEPARATION: 4,
ACTION_WRITEINFO: False,
IGNORE_INTRA_RES: True,
ACTION_REPLYLOG: False
}
# so that defaults dict stays unmodified, send a copy...
prefs = preferences.addCategory("DetectClash",
preferences.HiddenCategory,
optDict=defaults.copy())
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
HELIX_COLOR = "helix color"
SHEET_COLOR = "sheet color"
OTHER_COLOR = "other color"
defaultColors = {
HELIX_COLOR: 'orange red',
SHEET_COLOR: 'purple',
OTHER_COLOR: 'gray'
}
options = {}
options.update(defaultColors)
prefs = preferences.addCategory("ColorSS", preferences.HiddenCategory,
optDict=options)
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
SOLVENT_MODEL = "solvent model"
options = {SOLVENT_MODEL: "TIP3PBOX"}
prefs = preferences.addCategory("Solvate",
preferences.HiddenCategory,
optDict=options)
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: prefs.py 26655 2009-01-07 22:02:30Z gregc $
from chimera import preferences
PRESETS = "user presets"
defaults = {PRESETS: []}
prefs = preferences.addCategory("Aniso",
preferences.HiddenCategory,
optDict=defaults.copy())
