def getAquaAtomInfo(chemCompCodes = {}):
aquaRefDir = getDataPath('ccp', 'aqua')
files = os.listdir(aquaRefDir)
for file in files:
if file[0:8] == 'AtomLIB-':
format = file[8:]
readAquaFormats(joinPath(aquaRefDir,file),format,chemCompCodes)
for file in files:
if file[-8:] == 'LIB-aqua':
info = file[0:-8]
readAquaDefs(joinPath(aquaRefDir,file),info,chemCompCodes)
return chemCompCodes
def __init__(self, version = None):
self.patt = getRegularExpressions()
self.readComponents = ['STARTGRP','HEADRES','RESIDUE','TAILRES']
self.refInfo = {}
if version in ['2.1']:
fileName = 'cyana2.1.lib'
else:
fileName = 'cyana.lib'
self.read(getDataPath('ccp', 'cyana', fileName))
self.setAtomPosition()
self.setAngleAtoms()
def __init__(self, parent, project, path = None,
molTypeEntries = None, chemCompEntries = None,
selectedChemComps = None, selectLinking = None,
*args, **kw):
Frame.__init__(self, parent, *args, **kw)
self.project = project
self.molTypeEntries = molTypeEntries
self.chemCompEntries = chemCompEntries
self.selectLinking = selectLinking
if (not path):
path = getDataPath()
self.path = path
# Check if all chemComps available locally
self.path_allChemComps = getChemCompArchiveDataDir()
if not os.path.exists(self.path_allChemComps):
self.path_allChemComps = None
self.chemCompInfoDict = {}
self.chemCompInfoList = []
self.chemCompDownload = False
self.chem_comps_shown = {}
for entry in chemCompList:
self.chemCompClasses[entry] = getattr(ccp.api.molecule.ChemComp, entry)
self.grid_columnconfigure(0, weight=1)
row = 0
if (molTypeEntries is None):
headerText = "Show residues (select molecular type(s)):"
else:
headerText = "Show %s residues:" % (str(molTypeEntries))
#
#
# TODO TODO: HERE need to do some niftier stuff for displaying!
#
#
headerTextWidget = Label(self, text = headerText)
headerTextWidget.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
if (molTypeEntries is None):
self.mol_type_buttons = CheckButtons(self, entries=molTypeList,
select_callback=self.updateTables)
self.mol_type_buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
else:
self.mol_type_buttons = None
#
# The chemComps to display...
#
self.showLocalText = 'Show local'
self.showWebText = 'Show available via web'
self.display_buttons = CheckButtons(self, entries=[self.showLocalText,self.showWebText],
select_callback=self.updateTables,
selected = [self.showLocalText])
self.display_buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
self.grid_rowconfigure(row, weight=2)
headings = ('number', 'show details', 'molType', 'ccpCode', 'code1Letter', 'cifCode', 'name')
editWidgets = 7 * [ None ]
editGetCallbacks = [ None, self.toggleShow, None, None, None, None, None ]
editSetCallbacks = 7 * [ None ]
self.chem_comp_table = ScrolledMatrix(self, headingList=headings,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.chem_comp_table.grid(row=row, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = [ 'Show all in details window', 'Clear details window' ]
commands = [ self.showAll, self.showNone ]
buttons = ButtonList(self, texts=texts, commands=commands)
buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
separator = Separator(self,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
headerTextWidget = Label(self, text = "Select the residue variant:")
headerTextWidget.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
if (chemCompEntries is None):
self.chem_comp_buttons = CheckButtons(self, entries=chemCompList,
selected=('ChemComp',),
select_callback=self.updateChemCompVarTable)
self.chem_comp_buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
else:
self.chem_comp_buttons = None
self.grid_rowconfigure(row, weight=1)
headings = ('number', 'molType', 'ccpCode', 'linking', 'descriptor', 'molecularMass', 'formula', 'nonStereoSmiles', 'stereoSmiles')
self.chem_comp_var_table = ScrolledMatrix(self, headingList=headings)
self.chem_comp_var_table.grid(row=row, column=0, sticky=Tkinter.NSEW)
self.chem_comp_var_headings = headings[1:]
if selectedChemComps:
for chemComp in selectedChemComps:
key = (chemComp.molType, chemComp.ccpCode)
self.chem_comps_shown[key] = 1
self.updateTables()
from ccp.general.Io import getDataPath
from pdbe.general.Io import pdbeDataDir
#
# Tag for newly created chemComp(Coord)s - will be removed if modified afterwards!!!
#
freshTag = 'objectGeneratedFromScratch'
#
# Directory containing reference information for substituents
#
origMol2DataDir = getDataPath('ccp','mol2')
#
# Work chemComp directory, in all/
#
try:
from localConstants import workChemCompDir
except:
# Have to work on the actual repository directory for editing!
workChemCompDir = joinPath(pdbeDataDir,'chemComp')
refDataDir = os.path.join(workChemCompDir,'refData')
tempChemCompDir = os.path.join(workChemCompDir,'tmp')
from ccp.general.Io import getDataPath
# This maybe not so good? Or only relevant for large scale testing, not for people to work on own
# workflow
try:
from localConstants import importDataDir
except:
importDataDir = getDataPath('ccpnmr', 'workflow')
try:
from localConstants import cnsExec
except:
cnsExec = 'cns_solve'
programList = ['Aria', 'Cing', 'Cns', 'Fc', 'Haddock', 'Isd']
from memops.api.Implementation import MemopsRoot
from memops.gui.Button import Button
from memops.gui.MessageReporter import showInfo
from ccp.general.Io import getDataPath
project = MemopsRoot(name='p')
root = Tkinter.Tk()
root.top = root
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
path = getDataPath()
frame = ChemCompFrame(root, project, path = path)
frame.grid(sticky=Tkinter.NSEW)
def getSelected():
chemComp = frame.getSelectedChemComp()
if (chemComp):
if hasattr(chemComp,'chemComp'):
ccType = 'chemCompVar'
chemComp = chemComp.chemComp
else:
ccType = 'chemComp'
showInfo('ChemComp', 'Selected %s = (%s, %s)' % (ccType,chemComp.molType, chemComp.ccpCode), parent=root)
try:
from pdbe.general.localConstants import pdbeDataDir
except:
from ccp.general.Io import getDataPath
pdbeDataDir = getDataPath('pdbe')
import os
from ccp.general.Io import getDataPath
pulProgFile = getDataPath('ccp', 'bruker', 'Pulprog.info')
#
# THIS HAS TO BECOME TEXT FILE!!
#
# THIS NOT USED YET!
mappingToCcpn = {
'hnco':
'H[N[CO]]', # Experiment name - can find pathway by looping over all pathways and looking for this name.
# Then need dimension information... WARNING what about reversed dimension stuff?
# In case of hnco, would this generally be F1:1,F3:2,F2:3 (but AQSEQ? Can change?)
#
# For automatic mapping, almost have to read in experiment itself, then compare to possible pathway info
# in Bruker pulse sequence to match up... then also need mapping between atom names (CO->C=O) though.
#
}
stdExpNameDict = {
'adeq': 'ADEQUATE',
'apt': 'APT (attached proton test)',
'aring': 'Anti-ring',
'atocsy': 'Adiabatic TOCSY',
'^b_': 'Best sequence (Brutscher)',
'^c_': 'Carbon detected experiment',
'c6': 'Nucleic acid atom',