def __init__(self, parent, *args, **kw):
helpUrl = kw.get('help_url')
if not helpUrl:
helpUrl = determineHelpUrl(self.__class__)
self.help_url = helpUrl
project = kw.get('project')
parentPopup = getPopup(parent)
if not project and hasattr(parentPopup, 'project'):
project = parentPopup.project
self.project = project
if project:
self.nmrProject = project.currentNmrProject
self.analysisProject = project.currentAnalysisProject
self.analysisProfile = project.currentAnalysisProfile
else:
self.nmrProject = None
self.analysisProject = None
self.analysisProfile = None
application = kw.get('application')
if not application:
if hasattr(self, 'application'):
application = self.application
elif hasattr(parent, 'application'):
application = parent.application
self.project = project
self.application = application
memops.editor.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
def showMainInstructions(self):
popup = getPopup(self)
message = """Use this tab to import the chemical shifts and the coordinate and/or sequence information for your molecular chains.
The imported chemical shift file should contain information for only *one* molecular chain to make it easier to connect the molecule information to the chemical shift information. You therefore have to select a single chain for each shift list from the dropdown menu that will appear after you imported a coordinate or sequence file.
For example, when using sequence files for a dimer, import the information for the chemical shifts for each chain separately:
1. Import the sequence for the first molecular chain.
2. Import a chemical shift file with shifts only for this molecular chain.
3. Reset using the 'Import new sequence' button
4. Import the sequence for the second molecular chain
5. Import a chemical shift file with shifts only for this second chain
Alternatively, it is possible to read in the molecule information from a full coordinate file:
1. Import a coordinate file with all molecular information, including coordinates.
2. Select a molecular chain.
3. Import a chemical shift file with shifts only for the selected molecular chain.
4. Go back to step 2. if necessary.
You can also import multiple sets of chemical shifts (e.g. for the sample in different conditions). In this case, you have to import all chemical shift information that belongs together for all molecular chains, then press the 'Import new set of shifts' button.
Notes:
1. This application always creates a new CCPN project. It is not possible to import files into existing projects.
2. If your chemical shift file contains information for multiple chains, you have to edit it manually to split up the information per chain.
"""
showHelpText(self, message, popup=popup)
def createDismissHelpButtonList(parent, texts = None, commands = None,
direction=Tkinter.HORIZONTAL,
dismiss_text = '', help_text = '',
help_msg = '', help_url = '',
buttonBorderwidth=True, expands=True,
dismiss_cmd = None,
webBrowser = None,
*args, **kw):
if (texts is None):
texts = []
if (commands is None):
commands = []
if (not dismiss_text):
dismiss_text = ''
if (not help_text):
help_text = ''
texts = list(texts) + [dismiss_text, help_text]
popup = getPopup(parent)
if not webBrowser:
webBrowser = WebBrowser(popup.top, popup=popup)
if (not dismiss_cmd):
dismiss_cmd = popup.close
if (help_url):
help_cmd = lambda url=help_url: webBrowser.open(url)
else:
help_cmd = lambda top=popup.top, message=help_msg: memops.gui.HelpPopup.showHelpText(top, message, popup=popup)
if (type(commands) is types.DictType):
commands = commands.copy()
commands[dismiss_text] = dismiss_cmd
commands[help_text] = help_cmd
else:
commands = list(commands) + [dismiss_cmd, help_cmd]
button_list = ButtonList(parent, texts=texts, commands=commands, buttonBorderwidth=buttonBorderwidth,
expands=expands, direction=direction, *args, **kw)
if not dismiss_text:
button_list.cancelIcon = Tkinter.PhotoImage(file=os.path.join(gfxDir,'cancel.gif'))
button_list.buttons[-2].config(image=button_list.cancelIcon, activebackground=button_list.cget('bg'))
if not help_text:
button_list.helpIcon = Tkinter.PhotoImage(file=os.path.join(gfxDir,'help.gif'))
button_list.buttons[-1].config(image=button_list.helpIcon, activebackground=button_list.cget('bg'))
return button_list
def __init__(self,
parent,
webBrowser=None,
helpUrl=None,
helpMsg=None,
doClone=True,
doHelp=True,
doClose=True,
cloneText=None,
helpText=None,
closeText=None,
cloneCmd=None,
helpCmd=None,
closeCmd=None,
*args,
**kw):
self.helpUrl = helpUrl
self.helpMsg = helpMsg
self.popup = getPopup(parent)
if not isinstance(self.popup, BasePopup):
self.popup = None
if self.popup and not webBrowser:
webBrowser = WebBrowser(self.popup.parent, popup=self.popup)
self.webBrowser = webBrowser
_commands = []
_texts = []
_images = []
_doActions = [
(doClone, cloneCmd, self.clonePopup, cloneText, 'twoWindows.gif'),
(doHelp, helpCmd, self.launchHelp, helpText, 'help.gif'),
(doClose, closeCmd, self.closePopup, closeText, 'cancel.gif')
]
for doAction, userCmd, defaultCmd, text, imageFile in _doActions:
if doAction:
_commands.append(userCmd or defaultCmd)
if text:
_texts.append(text)
_images.append(None)
else:
icon = Tkinter.PhotoImage(
file=os.path.join(GFX_DIR, imageFile))
_texts.append('')
_images.append(icon)
# Needed for photoimage reference count/persistence
self.icons = [img for img in _images if img]
images = kw.get('images')
if images:
kw['images'] = images + _images
else:
kw['images'] = [None] * len(kw.get('texts', [])) + _images
kw['commands'] = kw.get('commands', []) + _commands
kw['texts'] = kw.get('texts', []) + _texts
ButtonList.__init__(self, parent, *args, **kw)
def __init__(self,
parent,
webBrowser=None,
helpUrl=None,
helpMsg=None,
doClone=True,
doHelp=True,
doClose=True,
cloneText=None,
helpText=None,
closeText=None,
cloneCmd=None,
helpCmd=None,
closeCmd=None,
cloneTip=None,
helpTip=None,
closeTip=None,
*args,
**kw):
self.helpUrl = helpUrl
self.helpMsg = helpMsg
self.popup = getPopup(parent)
cloneTip = cloneTip or Doc.cloneDoc.documentation
helpTip = helpTip or Doc.helpDoc.documentation
if not closeTip: # a bit of a hack, this
if closeText == 'Cancel':
closeTip = Doc.cancelDoc.documentation
else:
closeTip = Doc.closeDoc.documentation
cloneKey = cloneText or Doc.cloneDoc.name
helpKey = helpText or Doc.helpDoc.name
closeKey = closeText or Doc.closeDoc.name
if not isinstance(self.popup, BasePopup):
self.popup = None
if self.popup and not webBrowser:
webBrowser = WebBrowser(self.popup.parent, popup=self.popup)
self.webBrowser = webBrowser
_commands = []
_texts = []
_images = []
_docKeys = []
_tipTexts = []
_doActions = [
(doClone, cloneCmd, self.clonePopup, cloneText, 'twoWindows.gif',
cloneTip, cloneKey),
(doHelp, helpCmd, self.launchHelp, helpText, 'help.gif', helpTip,
helpKey),
(doClose, closeCmd, self.closePopup, closeText, 'cancel.gif',
closeTip, closeKey),
]
for doAction, userCmd, defaultCmd, text, imageFile, tipText, docKey in _doActions:
if doAction:
_commands.append(userCmd or defaultCmd)
_docKeys.append(docKey)
_tipTexts.append(tipText)
if text:
_texts.append(text)
_images.append(None)
else:
icon = Tkinter.PhotoImage(
file=os.path.join(GFX_DIR, imageFile))
_texts.append('')
_images.append(icon)
# Needed for photoimage reference count/persistence
self.icons = [img for img in _images if img]
images = kw.get('images')
if images:
kw['images'] = images + _images
else:
kw['images'] = [None] * len(kw.get('texts', [])) + _images
texts = kw.get('texts', [])
commands = kw.get('commands', [])
docKeys = kw.get('docKeys') or [None] * max(
[len(texts), len(commands)])
tipTexts = kw.get('tipTexts') or [None] * max(
[len(texts), len(commands)])
kw['docKeys'] = docKeys + _docKeys
kw['tipTexts'] = tipTexts + _tipTexts
kw['commands'] = commands + _commands
kw['texts'] = texts + _texts
ButtonList.__init__(self, parent, *args, **kw)
def __init__(self, parent, project, utilityButtons=False, *args, **kw):
self.project = project
self.waiting = False
self.dataStore = None
Frame.__init__(self, parent, *args, **kw)
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
tipTexts = [
'Row number',
'Location of the absolute path directory, that may contain multiple spectrum files',
'Location of spectrum file relative to its absolute path directory',
'Identity of the spectrum as experiment:spectrum'
]
headingList = [
'#', 'Absolute Path', 'Relative Path\nand File',
'Spectrum / FID / Image'
]
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.getDataUrl, self.getDataPath, None]
editSetCallbacks = [None, None, None, None]
self.dataStoreTable = ScrolledMatrix(
self,
headingList=headingList,
tipTexts=tipTexts,
callback=self.selectDataStore,
editWidgets=editWidgets,
multiSelect=True,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
###deleteFunc=self.deleteDataStores,
grid=(0, 0))
texts = [
'Propagate\nAbsolute Path', 'Shift Directory\nTo Absolute Path',
'Shift Directory\nTo Relative Path'
]
tipTexts = [
'Copy absolute path from last row selected to other selected spectra',
'Shift the top directory from the relative path to the absolute path',
'Shift the bottom directory from the absolute path to the relative path'
]
commands = [
self.propagatePath, self.moveDirToAbsolute, self.moveDirToRelative
]
isModal = False
popup = getPopup(parent)
if popup:
isModal = popup.modal
if utilityButtons:
if isModal:
texts = [
'All Done!',
] + texts
tipTexts = ['Close the popup, satisfied that paths are OK'
] + tipTexts
commands = [
popup.close,
] + commands
self.buttonList = UtilityButtonList(self,
texts=texts,
commands=commands,
tipTexts=tipTexts,
doClone=False,
grid=(1, 0))
if isModal:
self.buttonList.buttons[0].config(bg='#B0FFB0')
else:
self.buttonList = ButtonList(self,
texts=texts,
commands=commands,
grid=(1, 0),
tipTexts=tipTexts)
self.updateAfter()
def showFormats(self):
popup = getPopup(self)
message = """For chemical shifts, the following formats are recognised:
*** Auremol ***
section_sequenzdefinition
_Residue_seq_code
_Atom_num_code
_Residue_label
_Atom_name
_Atom_type
_Atom_alias
_Atom_equivalent
_Atom_CSA
1 1 MET HN H - - 8.95
1 2 MET N N - - 157.00
1 3 MET CA C - - 40.00
*** Autoassign ***
AA HN N15 CO-1 CA-1 CB-1 HA-1 CO CA CB HA
A31 8.14 121.4 51.3 19.6 (GS178 115.HSQC)
D32 8.88 122.9 51.3 19.5 55.4 39.6 (GS271 22.HSQC)
*** CNS ***
do ( store1 = 53.13218 ) ( resid 78 and name CA )
do ( store1 = 0.7356673 ) ( resid 15 and name HD1# )
do ( store1 = 120.5381 ) ( resid 8 and name N )
do ( store1 = 121.1414 ) ( resid 78 and name N )
*** Cosmos ***
CS_VALUES 3
C_ALA 176.6
CA_ALA 51.66
CB_ALA 17.26
END
*** CSI ***
# A HA CA CO CB Consensus
#
1 MET 0 C 0 C NA 0 C 0 C
2 GLY 0 C 0 C NA 0 C 0 C
*** MARS ***
H N CO-1 CA CA-1
PR_2 8.900 123.220 170.540 55.080 54.450
PR_4 8.320 115.340 175.920 - 55.080
*** MONTE ***
1 102.544 8.211 45.853 54.925 0.000 18.069 180.112
2 103.276 8.580 45.334 54.154 0.000 35.650 175.087
3 103.997 7.407 45.165 0.000 0.000 0.000 0.000
*** NMR-STAR ***
data_test
save_shifts1
_Saveframe_category assigned_chemical_shifts
loop_
_Atom_shift_assign_ID
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 1 ASP CA C 52.000 0.02 1
2 1 ASP HA H 4.220 0.02 1
stop_
save_
*** NMRVIEW ***
2.CG1 18.549 0
2.CG2 18.844 0
2.HG1# 0.800 0
2.HG2# 0.723 0
3.HG2 2.298 0
3.HG1 2.298 0
*** PIPP ***
RES_ID 1
RES_TYPE MET
SPIN_SYSTEM_ID 1
CA 55.9920
CB 33.1470
HA 4.1141
HB# 2.0492
HG# 2.4250
END_RES_DEF
*** PISTACHIO ***
1 1 GLY C C 172.621 1.000 0
2 1 GLY CA C 44.308 1.000 0
3 2 SER N N 122.241 1.000 0
*** PRONTO ***
Spin system HN HA Other:
1: Val-1 3.76 HB: 1.945, HG1: 0.770, HG2: 0.608
2: Ile-2 8.80 4.26 HB: 1.526, HG1: 1.278, HG2: 0.728, HD: 0.918
*** SHIFTX ***
NUM RES HA H N CA CB C
--- --- ------ ------ -------- ------- ------- --------
2 T 4.4161 8.1749 111.0443 61.8324 70.3867 172.5362
3 Y 4.9022 9.0239 120.2106 56.0493 41.4218 173.0761
NUM RES H HA HB HB2 HB3 HD1 HD2 HD21 HD22 HD3 HE HE1 HE2 HE21 HE22 HE3 HG HG1 HG12 HG13 HG2 HG3 HZ
2 T 8.17 4.42 4.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.21 0.00 0.00
3 Y 9.02 4.90 0.00 2.22 2.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
*** SPARKY ***
Group Atom Nuc Shift SDev Assignments
R2 CA 13C 56.539 0.003 3
R2 CB 13C 30.808 0.009 3
*** TALOS ***
VARS RESID RESNAME PHI PSI DPHI DPSI DIST COUNT CLASS
FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %2d %s
1 Q 9999.000 9999.000 0.000 0.000 0.000 0 None
2 N -85.000 124.000 23.000 28.000 85.920 10 Good
***XEASY/CYANA:
1 117.803 0.000 N 1
2 8.208 0.002 HN 1
3 56.508 0.055 CA 1
4 999.000 0.000 HA 1
5 29.451 0.004 CB 1
"""
showHelpText(self, message, popup=popup)
