def readParsHelpFile(self):
self.tags = {}
fileLocation = os.path.join(getTopDirectory(), 'data', 'ccp', 'varian',
'parhelp.txt')
fin = open(fileLocation, 'rU')
line = fin.readline()
while line:
if not (self.patt['emptyline'].search(line)
or self.patt['hash'].search(line)):
cols = line.split()
if len(cols) < 3 or cols[1] != '=':
print "Error parsing following line:" + self.newline + line + self.newline
else:
# Sort out tag
tag = cols[0]
# Sort out value (remove ' and rejoin with single spaces)
value = joinUnquote(cols[2:], "'")
self.tags[tag] = value
line = fin.readline()
def determineHelpUrl(clazz=None, name=None):
assert clazz or name
topDir = getTopDirectory()
#dir = splitPath(__file__)[0]
#if (dir):
# dir = dir + '/'
if (not name):
name = clazz.__name__
help_url = 'file:' + topDir + LOCAL_HELP_DOC_DIR + 'popups/' + name + '.html'
return help_url
def readParsHelpFile(self):
self.tags = {}
fileLocation = os.path.join(getTopDirectory(), 'data', 'ccp', 'bruker',
'parhelp.txt')
fin = open(fileLocation, 'rU')
line = fin.readline()
while line:
if not (self.patt['emptyline'].search(line)
or self.patt['hash'].search(line)):
cols = line.split()
if len(cols) < 3 or cols[1] != '=':
print "Error parsing following line:" + self.newline + line + self.newline
else:
# Sort out tag
tag = cols[0]
# Sort out value (remove ' and rejoin with single spaces)
value = joinUnquote(cols[2:], "'")
# Check if multivalue line (eg. SFO1, SFO2, ...)
searchobj = self.patt[self.format +
'BracketMultiValue'].search(tag)
if searchobj:
for i in range(int(searchobj.group(1)),
int(searchobj.group(2)) + 1):
curTag = self.patt[self.format +
'BracketMultiValue'].sub(
str(i), tag)
curValue = self.patt[self.format +
'BracketMultiValue'].sub(
str(i), value)
self.tags[curTag] = curValue
else:
self.tags[tag] = value
line = fin.readline()
def setIconSize(self, iconSize, redraw=True):
size = ICON_SIZE_DICT.get(iconSize, 22)
if size != self.rowHeight:
self.rowHeight = size + 1
self.font = 'Helvetica %d' % (size / 2)
ccpnDir = getTopDirectory()
iconDir = '%dx%d' % (size, size)
imageDir = path.join(ccpnDir, 'python', 'memops', 'gui',
'graphics', iconDir)
files = [f for f in listdir(imageDir) if f.endswith('.gif')]
for file in files:
imageFile = path.join(imageDir, file)
self.icons[file[:-4]] = PhotoImage(file=imageFile)
if redraw:
self._changeSize()
return size
self.atomSerial = returnInt(atomSerial,default=None,verbose=verbose)
self.value = returnFloat(value,default=None,verbose=verbose)
self.valueError = returnFloat(valueError,default=None,verbose=verbose)
self.atomName = atomName
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = parent.defaultMolCode
###################
# Main of program #
###################
if __name__ == "__main__":
files = [['../reference/xeasy/3d.1.chemShifts','local/cs.test1']
]
for (inFile,outFile) in files:
chemShiftFile = XEasyChemShiftFile(os.path.join(getTopDirectory(),inFile))
chemShiftFile.read(verbose = 1)
for chemShift in chemShiftFile.chemShifts:
print chemShift.seqCode, chemShift.atomName, chemShift.value
chemShiftFile.name = outFile
chemShiftFile.write(verbose = 1)
def __init__(self,
parent,
widgetClass,
options=None,
values=None,
callback=None,
minRows=3,
maxRows=None,
useImages=True,
*args,
**kw):
Frame.__init__(self, parent, **kw)
if not values:
values = []
if not options:
options = []
# Widget types currently: Entries, Pulldown, Checkbutton
if useImages:
gfxDir = path.join(getTopDirectory(), 'python', 'memops', 'gui',
'graphics')
self.crossImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'cross.gif'))
self.tickImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'tick.gif'))
self.plusImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'plus.gif'))
self.minusImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'minus.gif'))
else:
self.crossImage = None
self.tickImage = None
self.plusImage = None
self.minusImage = None
module = widgetClass.__module__
self.widgetType = module.split('.')[-1]
self.widgetClass = widgetClass
self.callback = callback
self.numRows = 0
self.values = values
self.options = options
self.minRows = minRows
self.maxRows = maxRows
self.widgets = []
self.labels = []
self.grid_columnconfigure(1, weight=1)
self.topFrame = Frame(self)
self.topFrame.grid(row=0, column=0, columnspan=4, sticky=Tkinter.NSEW)
self.topFrame.grid_columnconfigure(1, weight=1)
self.topFrame.grid_rowconfigure(0, weight=1)
self.addButton = None
self.removeButton = None
self.commitButton = None
self.cancelButton = None
self.set(self.values, self.options)
self.updateButtons()
self.bind('<KeyPress-Return>', self.commit)
self.bind('<KeyPress-Escape>', self.cancel)
###################
# Main of program #
###################
if __name__ == "__main__":
files = [
'../../reference/nmrView/Brucd44_new2.str',
#'python/ccpnmr/format/examples/data/withass20010817.str'
]
for inFile in files:
nmrViewStarFile = NmrViewStarFile(
os.path.join(getTopDirectory(), inFile))
nmrViewStarFile.read(verbose=1)
for peakFile in nmrViewStarFile.peakFiles:
print peakFile.specNames
print peakFile.numDims
print peakFile.peaks[0].ppm
print peakFile.peaks[-1].ppm
for sequence in nmrViewStarFile.sequenceFile.sequences:
for seqEl in sequence.elements:
print seqEl.seqCode, seqEl.code3Letter
import os
from memops.universal.Io import getTopDirectory
# TODO: make these local-settable as well?
try:
from localConstants import dataDir
except:
dataDir = os.path.join(getTopDirectory(), 'data')
try:
from localConstants import tmpDataDir
except:
tmpDataDir = os.path.join(dataDir, 'tmp')
try:
from localConstants import archivesDataDir
except:
archivesDataDir = os.path.join(dataDir, 'archives')
generalReferenceDir = os.path.join(archivesDataDir, 'reference')
alignMatrixDir = os.path.join(dataDir, 'alignMatrices')
try:
from localConstants import customArchivesDataDir
except:
customArchivesDataDir = os.path.join(archivesDataDir, 'custom')
# TODO THIS ONE MIGHT GO!
try:
from localConstants import archivesCcpnDataDir
self.assign.append(None)
###################
# Main of program #
###################
if __name__ == "__main__":
files = [
'../reference/autoassign/hncacb.pks',
'../reference/autoassign/hnca.pks',
'../reference/autoassign/hncocacb.pks',
'../reference/autoassign/hncoca.pks',
'../reference/autoassign/hnco.pks',
'../reference/autoassign/hsqc.pks',
]
for inFile in files:
peakFile = AutoAssignPeakFile(os.path.join(getTopDirectory(), inFile))
peakFile.read(verbose=1)
for rawPeak in peakFile.peaks:
print rawPeak.intensity
(path, fileName) = os.path.split(peakFile.name)
peakFile.name = os.path.join('local', fileName)
peakFile.write()
CCPN project: An interim report on a data model for the NMR community
(Progress report). Nature Struct. Biol. 9, 416-418.
Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus
H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John
Ionides and Ernest D. Laue (2005). The CCPN Data Model for NMR Spectroscopy:
Development of a Software Pipeline. Proteins 59, 687 - 696.
===========================REFERENCE END===============================
"""
from os import path, mkdir, system, environ
from memops.universal.Io import getTopDirectory
rootDir = path.split(getTopDirectory())[0]
defaultDir = path.join(rootDir,'other','shiftx')
SHIFTX_DIR = environ.get('SHIFTX_DIR', defaultDir)
def testShiftxMacro(argServer):
structure = argServer.getStructure()
shiftList = shiftx(structure)
def shiftx(structure, atomType=None):
self.ppm = []
for i in range(0, len(ppm)):
self.ppm.append(returnFloat(ppm[i]))
###################
# Main of program #
###################
if __name__ == "__main__":
files = [
'../../reference/ccpNmr/michaelNewYork/050309/fhsqc_stapp.PCK',
'../../reference/pipp/3d.1.peaks',
'../../reference/pipp/3d.2.peaks',
'../../reference/ccpNmr/michaelNewYork/050323/n15noehsqc.PCK',
'../../reference/ccpNmr/michaelNewYork/050425/motafl6dipsisecryo.PCK',
'../../reference/ccpNmr/michaelNewYork/050425/motafl6hbhaconhsecryophos.PCK',
]
for inFile in files:
peakFile = PippPeakFile(os.path.join(getTopDirectory(), inFile))
peakFile.read(verbose=1)
for rawPeak in peakFile.peaks:
print rawPeak.num, rawPeak.assign, rawPeak.intensity
testChemCompDir = os.path.join(workChemCompDir,'test') testChemCompDataDir = os.path.join(testChemCompDir,'ChemComp') testChemCompCoordDataDir = os.path.join(testChemCompDir,'ChemCompCoord') obsoleteChemCompDir = os.path.join(workChemCompDir,'obsolete') obsoleteChemCompDataDir = os.path.join(obsoleteChemCompDir,'ChemComp') obsoleteChemCompCoordDataDir = os.path.join(obsoleteChemCompDir,'ChemCompCoord') # # ChemComp directory for editing, in ccpn-chemcomp repository directly # try: from localConstants import editChemCompDir except: editChemCompDir = joinPath(getTopDirectory(),'..','ccpn-chemcomp','data','pdbe','chemComp','archive') editChemCompDataDir = joinPath(editChemCompDir,'ChemComp') editChemCompCoordDataDir = joinPath(editChemCompDir,'ChemCompCoord') editLinkedChemCompDir = os.path.join(workChemCompDir,'archive') editLinkedChemCompDataDir = os.path.join(editLinkedChemCompDir,'ChemComp') editLinkedChemCompCoordDataDir = os.path.join(editLinkedChemCompDir,'ChemCompCoord') # # Repository for standard residues, in ccpn sourceforge repository directly # try: from localConstants import standardRepChemCompDataDir
self.atomSerial2 = parent.atoms.index(atom2) + 1
self.bondType = 'single' # TODO: can we do better here?
###################
# Main of program #
###################
if __name__ == "__main__":
files = ['../../reference/pdb/cyclic.pdb', '../../reference/pdb/mcys.pdb']
for inFile in files:
pdbFile = PdbChemCompFile(os.path.join(getTopDirectory(), inFile))
pdbFile.read(verbose=1)
for chemComp in pdbFile.chemComps:
for atom in chemComp.atoms:
print atom.atomType,
print
for bond in chemComp.bonds:
print bond.bondType
#(path,baseName) = os.path.split(inFile)
#pdbFile.name = ("local/%s" % baseName)
#pdbFile.write(verbose = 1)
"""
###################
# Main of program #
###################
if __name__ == "__main__":
files = [
'../../reference/mol/example.mol', '../../reference/mol/cyclic.mol',
'../../reference/mol/mcys.mol'
]
for inFile in files:
molFile = MolChemCompFile(os.path.join(getTopDirectory(), inFile))
molFile.read(verbose=1)
for chemComp in molFile.chemComps:
for atom in chemComp.atoms:
print atom.atomType,
print
for bond in chemComp.bonds:
print bond.bondType
#(path,baseName) = os.path.split(inFile)
#molFile.name = ("local/%s" % baseName)
#molFile.write(verbose = 1)
################################################################################
if __name__ == '__main__':
if 1:
# 0 is only errors, 1 is warnings as well, 2 is normal and 9 is debug
STAR.verbosity = 2
strf = File(verbosity=STAR.verbosity)
if os.name == 'posix':
pathname = '.'
else:
pathname = r'C:\Temp'
## filename = 'local/test_nopound.txt'
## filename = 'local/block_21921.txt'
topDir = getTopDirectory()
#filename = os.path.join(topDir, '../rawdata/8/1/1/info.general/bmr5106.str')
filename = os.path.join(topDir, '../reference/nmrStar/1b4c.restraints')
#filename = os.path.join(topDir, '../rawdata/2/2/1/info.general/bmr5307.str')
strf.filename = filename
## def myfunc():
if strf.read():
print "ERROR: In read. Exiting program"
# strf.filename
# strf.formatNMRSTAR: REFORMATS FILE! Don't use!!
# strf.attrnames: bulk output of everything in file
# strf.flavor: mmCIF, ... (in principle only nmrStar works?)
# strf.title: pdb code?
def body(self, guiParent):
self.geometry('700x600')
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
# this is going to set up the options on the tabs. Really we need
# stronger bookeeping between the options and the frames. it
# might make sense to define a master dictionary with option_name
# => index. We can use this dictionary to build up the software
# options and can also use it to define any refreshes etc (although
# these would be better done through notifiers)
softwareOpts = [
'Repository', 'Project', 'Process', 'Client Tasks', 'Server Tasks',
'Data Exchange', 'Workflow', 'Protocols', 'User'
]
# FIXME JMCI
# we should have a tidier tabbed frame. ned to discuss rules with
# tjs but it would seem to make sense to have the tabs stretch
# across the entire top of the frame. Check the existing options
# first, though
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0)
self.tabbedFrame.grid(row=0, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
# jmci we are going to have to change these drastically
self.mainMenu = Menu(self)
self.userMenu = self.makeUserMenu()
self.repositoryMenu = self.makeRepositoryMenu()
self.otherMenu = self.makeOtherMenu()
# Put the top level menu
self.config(menu=self.mainMenu)
self.initRepository(frames[0])
self.initProjectFrame(frames[1])
self.initWms(frames[2])
self.initTasks(frames[3])
self.initDataExch(frames[5])
self.initWorkflow(frames[6])
self.initProtocol(frames[7])
self.initUserFrame(frames[8])
self.initProject()
if not self.project:
for button in self.projButtons:
button.disable()
# the main client side daemon. This is going to run in the background
# and control the task processing
self.taskDaemon = TaskManager(self)
self.taskDaemon.active = False
self.taskDaemon.start()
self.x = returnFloat(x,default=None,verbose=verbose)
self.y = returnFloat(y,default=None,verbose=verbose)
self.z = returnFloat(z,default=None,verbose=verbose)
self.insertionCode = insertionCode
self.chainId = self.segId = string.strip(segId)
if not self.chainId:
self.chainId = defaultMolCode
###################
# Main of program #
###################
if __name__ == "__main__":
file = os.path.join(getTopDirectory(),'../../reference/charmm/ref03_min.crd')
charmmFile = CharmmCoordinateFile(file)
charmmFile.read(maxNum = 1)
for mc in charmmFile.modelCoordinates:
for coo in charmmFile.modelCoordinates[mc]:
print coo.serial, coo.resName, coo.chainId
for chain in charmmFile.chains:
print chain, chain.chainId
charmmFile.name = 'local/test.coord'
charmmFile.write()
def __init__(self, num, assign, ppm, intensity, status):
self.num = returnInt(num)
self.intensity = returnFloat(intensity)
self.status = status
self.assign = []
self.ppm = []
for i in range(0, len(assign)):
self.ppm.append(returnFloat(ppm[i]))
self.assign.append(assign[i])
###################
# Main of program #
###################
if __name__ == "__main__":
files = ['../reference/pronto/cp40', '../reference/pronto/cp150']
for inFile in files:
peakFile = ProntoPeakFile(os.path.join(getTopDirectory(), inFile))
peakFile.read(verbose=1)
for rawPeak in peakFile.peaks:
print rawPeak.intensity
def getInstallRoot(self):
self.installRoot = getTopDirectory()
===========================REFERENCE END===============================
"""
import sys, os
import types
import Tkinter
from memops.gui.Base import getPopup
from memops.gui.Button import Button
from memops.gui.ButtonList import ButtonList
from memops.gui.WebBrowser import WebBrowser
import memops.gui.HelpPopup
from memops.universal.Io import getTopDirectory
gfxDir = os.path.join(getTopDirectory(),'python','memops','gui','graphics')
# creates quit button
def createQuitButton(parent, text=''):
if not text:
text = ''
b = Button(parent, text=text, command=sys.exit)
if not text:
b.cancelIcon = Tkinter.PhotoImage(file=os.path.join(gfxDir,'cancel.gif'))
b.config(image=b.cancelIcon, activebackground=b.cget('bg'))
return b
def __init__(self, guiParent, basePopup, project=None):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
# FIXME JMCI
# need to work through this far more carefully
self.project = project
# shortcuts to this layer
self.basePopup.frameShortcuts['Task'] = self
# shortcuts to layer below. We should set these in the
# initMethod methods
self.frameShortcuts = {}
# TODO understand what these are doing
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
self.grid_rowconfigure(1, weight=1)
self.grid_columnconfigure(0, weight=1)
# Logos. Code nicked from ExtendNMR GUI
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
# basically nicked from Extend-NMR
softwareOpts = [
'Test1Task', 'ARIA 2', 'Auremol', 'CING', ' ECI ', 'HADDOCK',
' ISD ', 'PRODECOMP'
]
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0)
self.tabbedFrame.grid(row=1, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'Fp6Logo.gif')
self.fp6Logo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'CingLogo.gif')
self.cingLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'AriaLogo.gif')
self.ariaLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'IsdLogo.gif')
self.isdLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'HaddockLogo.gif')
self.haddockLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'AuremolLogo.gif')
self.auremolLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'ProdecompLogo.gif')
self.prodecompLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'MddLogo.gif')
self.mddLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'BrukerLogo.gif')
self.brukerLogo = Tkinter.PhotoImage(file=imageFile)
imageFile = os.path.join(imageDir, 'MsdLogo.gif')
self.msdLogo = Tkinter.PhotoImage(file=imageFile)
# don't know what this does
self.updateFuncs = []
self.projButtons = []
# basically nicked from Extend-NMR
self.initTest1(frames[0])
self.initAria(frames[1])
self.initAuremol(frames[2])
self.initCing(frames[3])
#self.initEci(frames[4])
#self.initHaddock(frames[5])
self.initIsd(frames[6])
self.initProdecomp(frames[7])
def getDataDirectory():
directory = joinPath(getTopDirectory(), 'data')
return directory
###################
# Main of program #
###################
if __name__ == "__main__":
files = [ #['../../reference/nmrView/2d.1.peaks','local/xpk1.test'],
#['../../reference/nmrView/3d.1.peaks','local/xpk2.test'],
#['../../reference/nmrView/2d.2.peaks','local/xpk3.test']
[
'../../reference/ccpNmr/moniqueUtrecht/noeN15hsqc_test.xpk',
'local/monique.test'
]
]
for (inFile, outFile) in files:
peakFile = NmrViewPeakFile(os.path.join(getTopDirectory(), inFile),
assignTagSep=' ')
peakFile.read(verbose=1)
print peakFile.specNames
print peakFile.numDims
print peakFile.hasAssignItems
for rawPeak in peakFile.peaks:
print rawPeak.intensity, rawPeak.assign
# Tested writing v3 18/11/2002: seems OK!
#
projectName = 'test'
projectDir = os.path.join(os.getcwd(),'local',projectName)
ccpnProject = loadProject(projectDir,projectName)
#
# Because the original project was saved in a different directory structure,
# the paths have to be reset first... here I am resetting everything 'hardcoded'
# based on the examples and/or data directory.
#
localDataPaths = {}
localDataPaths['examples'] = os.path.abspath('.')
localDataPaths['data'] = joinPath(getTopDirectory(),'data')
for repository in ccpnProject.repositories:
for findName in ('examples','data'):
findNameIndex = repository.url.path.find(findName)
if findNameIndex>= 0:
repository.url = Implementation.Url(path = uniIo.joinPath(localDataPaths[findName],repository.url.path[findNameIndex + len(findName) + 1:]))
break
#
# Print out some objects from this project
#
print "Project object:", ccpnProject
print "Project name:", ccpnProject.name
def __init__(self,
parent,
callback=None,
rightCallback=None,
width=420,
height=440,
bgColor='#FFFFFF',
showCoords=True,
xTicks=True,
yTicks=True,
xLabel=u'\u03A6',
yLabel=u'\u03A8',
titleText='',
nullColor='#FFFFFF',
enterCallback=None,
leaveCallback=None,
defaultPlot=True,
*args,
**kw):
self.parent = parent
ScrolledCanvas.__init__(self,
parent,
resizeCallback=self.drawCanvas,
width=width,
height=height)
self.bitmapDir = joinPath(getTopDirectory(), 'data', 'ccpnmr',
'ramachandranPlot')
self.canvas.config(bg=bgColor)
self.rightCallback = rightCallback # handle for change of chosen quadrant
self.callback = callback # handle for estimation selection
self.enterCallback = enterCallback # handle for mouse enter an estimation
self.leaveCallback = leaveCallback # handle for mouse leave an estimation
self.defaultPlot = defaultPlot
self.showCoords = showCoords
self.xTicks = xTicks
self.yTicks = yTicks
self.xLabel = xLabel
self.yLabel = yLabel
self.matrix = [] # bin matrix forming the plot
self.canvasDict = {} # aaType : a list of color distribution
self.intensityDict = {} # aaType : a list of color distribution
self.currentObjDict = {} # object : estimation circle on plot
self.currentCirDict = {} # circle on plot : object
self.residueLabels = {}
self.currentObjects = []
self.selectedObjects = [] # a list of selected objects
self.binSize = 10 # 10 degree for each bin
self.cirTag = "est" # arbitrary tag of estimation circles
self.maxInt = 255 # max number of color used
self.selectColor = "#00C000" # color of a selected estimation
self.unselectColor = "#000000" # color of a unselected estimation
self.nullColor = nullColor
self.objectColors = []
self.titleText = titleText
self.title = None
self.phi = None
self.psi = None
self.sd1 = None
self.sd2 = None
self.phiPsiList = []
self.labels = []
self.crosshair = []
self.plotCoords = []
self.aminoAcid = None
self.binWidth = 10 # Arbitrary deafult - reset dynamically
self.binHeight = 10 # Arbitrary deafult - reset dynamically
self.cirRadius = 4
self.axisObjects = []
self.zoom = 1.0
# add handle function to mouse events on estimation objects
self.canvas.bind("<Button-1>", self.circleClick)
#if self.enterCallback:
# self.canvas.tag_bind(self.cirTag, "<Enter>", self.circleEnter, "+")
#if self.leaveCallback:
# self.canvas.tag_bind(self.cirTag, "<Leave>", self.circleLeave, "+")
self.canvas.bind('<B2-Motion>', self.mouseMotion)
self.canvas.bind('<Button-4>', self.zoomIn)
self.canvas.bind('<Button-5>', self.zoomOut)
self.canvas.bind('<Motion>', self.mouseEnter)
self.canvas.bind('<Enter>', self.mouseEnter)
self.canvas.bind('<Leave>', self.mouseLeave)
# add handle function to double mouse click on Rama plot
#self.canvas.bind("<Button-3>", self.rightClick)
self.drawCanvas()
def __init__(self,seqCode,seqInsertCode,atomName):
self.chainCode = defaultMolCode
self.seqCode = seqCode
self.seqInsertCode = seqInsertCode
self.atomName = atomName
###################
# Main of program #
###################
if __name__ == "__main__":
files = ['../reference/talos/marlies.talosout.tab',
'../reference/talos/list.table']
for inFile in files:
constraintFile = TalosDihedralConstraintFile(os.path.join(getTopDirectory(),inFile))
constraintFile.read(verbose = 1)
for constraint in constraintFile.constraints:
print constraint.Id, constraint.seqCode, constraint.name
print constraint.upperAngle, constraint.lowerAngle
for constraintItem in constraint.items:
for constraintMember in constraintItem.members:
print constraintMember.atomName,
print
pass
###################
# Main of program #
###################
if __name__ == "__main__":
# NO REAL EXAMPLE FILE AVAILABLE!
files = ['../reference/aria/ambig.restraints']
for file in files:
file = os.path.join(getTopDirectory(), file)
constraintFile = CnsHBondConstraintFile(file)
constraintFile.read(verbose=1)
for constraint in constraintFile.constraints:
print constraint.Id, constraint.origId,
print constraint.targetDist, constraint.minusDist, constraint.plusDist,
for item in constraint.items:
for member in item.members:
print member.seqCode, member.atomName,
print "|",
if not self.chainId:
self.chainId = defaultMolCode
else:
self.chainId = chainId
###################
# Main of program #
###################
if __name__ == "__main__":
#file = os.path.join(getTopDirectory(),'../../reference/xplor/neuhaus.pdb')
#file = os.path.join(getTopDirectory(),'../../reference/ccpNmr/davidLMB/041029/complex_01.pdb')
file = os.path.join(
getTopDirectory(),
'../../reference/ccpNmr/aartUtrecht/041118/1a7f/coord_reprotonated/1a7f_1.pdb'
)
cnsFile = CnsCoordinateFile(file)
cnsFile.read(maxNum=1)
for mc in cnsFile.modelCoordinates:
for coo in cnsFile.modelCoordinates[mc]:
print coo.serial, coo.resName, coo.chainId
for chain in cnsFile.chains:
print chain, chain.chainId
cnsFile.name = 'local/test.coord'
===========================REFERENCE END===============================
"""
import types, os
import Tkinter
from memops.gui.BasePopup import BasePopup
from memops.gui.Button import Button
from memops.gui.Frame import Frame
from memops.gui.MessageReporter import showInfo
from memops.gui.Spacer import Spacer
from memops.gui.Base import getPopup
from memops.gui.WebBrowser import WebBrowser
from memops.universal.Io import getTopDirectory
GFX_DIR = os.path.join(getTopDirectory(), 'python', 'memops', 'gui',
'graphics')
STRING_TYPE = type('')
UNICODE_TYPE = type(u'')
HORIZONTAL = Tkinter.HORIZONTAL
VERTICAL = Tkinter.VERTICAL
def notYetImplemented(text=''):
if (text):
text = '"' + text + '" '
showInfo('Not Yet Implemented', text + 'not yet implemented')
def setFormat(self):
self.format = getFormat()
class CyanaChain(DyanaChain):
pass
class CyanaCoordinate(DyanaCoordinate):
pass
if __name__ == "__main__":
file = os.path.join(getTopDirectory(),'../reference/diana/example.cor')
cyanaFile = CyanaCoordinateFile(file)
cyanaFile.read(maxNum = 1)
for mc in cyanaFile.modelCoordinates:
for coo in cyanaFile.modelCoordinates[mc]:
print coo.serial, coo.resName, coo.x, coo.y, coo.z
for chain in cyanaFile.chains:
print chain.chainId
cyanaFile.name = 'local/test.coord'
cyanaFile.write()