""" tasks/phaser_mr/CTaskPhaser_mr.py Copyright (C) 2011 STFC Author: Martyn Winn """ from CCP4TaskWidget import CTaskWidget from PyQt4 import QtCore #------------------------------------------------------------------- class CTaskPhaser_mr(CTaskWidget): #------------------------------------------------------------------- # Subclass CTaskWidget to give specific task window TASKNAME = 'phaser_mr' TASKVERSION = 0.1 TASKMODULE='test' TASKTITLE='MR using Phaser' def __init__(self,parent): CTaskWidget.__init__(self,parent) def drawContents(self): print 'Whoops' self.setProgramHelpFile('phaser') self.openFolder(folderFunction='inputData') self.openSubFrame() self.createLine ( ['label', '\n ']) self.createLine ( [ 'widget', 'F_SIGF' ] ) self.closeSubFrame() self.setMenuText('COMP_BY',{ 'DEFAULT':'Provide no guidance to Phaser', 'MW':'Provide an estimate of the molecular weight of protein and nucleic acid in ASU', 'ASU':'Provide a full specification of the ASU content by sequence' }) self.createLine(['advice','']) self.createLine(['advice','']) self.createLine(['advice',"Phaser's maximum likelihood estimates will be best if you provide guidance about the contents of the asymmetric unit"]) self.createLine(['advice',"Phaser also uses this information to carry out its cell content analysis, to suggest how many copies to expect"]) self.createLine ( ['label', 'For estimating asymmetric unit contents:','widget','COMP_BY']) self.createLine ( ['label', '\n '], toggle=['COMP_BY','open',['DEFAULT']]) self.createLine ( [ 'widget', '-title','Contents of asymmetric unit - click "Show list" if more than one type of chain is present', 'ASU_COMPONENTS' ], toggle=['COMP_BY','open',['ASU']]) self.createLine ( [ 'label','Molecular weight (Da) of protein in the ASU','stretch','widget', 'ASU_PROTEIN_MW' ], toggle=['COMP_BY','open',['MW']]) self.createLine ( [ 'label','Molecular weight (Da) of nucleic acid','stretch','widget', 'ASU_NUCLEICACID_MW' ], toggle=['COMP_BY','open',['MW']]) #The validity of the ASU_COMPONENTS widget contents are dependent on COMP_BY self.connect(self.container.controlParameters.COMP_BY,QtCore.SIGNAL('dataChanged'),self.getWidget('ASU_COMPONENTS').validate) self.createLine(['advice','']) self.createLine ( [ 'widget', '-title','Search model(s) - click "Show list" if more than one copy or more than one search model','ENSEMBLES' ] ) self.createLine ( [ 'label', 'Use the ensembles above as', 'widget' , '-guiMode', 'radio', 'SEARCHMODE' ] ) self.createLine(['advice','']) self.createLine(['advice','']) self.createLine(['advice','If some part of the structure has already been positioned in the unit cell, you can enter it in the "Known structure" tab']) self.openFolder(title='Known structure') self.createLine ( ['label', '\n ']) self.createLine ( [ 'widget', '-title','Already positioned structure - click "Show list" if more than one copy or more than one search model','FIXED_STRUCTURE' ] ) self.openFolder(title='Main Options') self.setMenuText('MODE',{ 'MR_AUTO':'fully automated', 'MR_FRF':'rotation function only', 'MR_FTF':'translation function only', 'MR_RNP':'refine ensembles in a solution and phase accounting for anisotropy and tNCS', 'MR_RGR':'refine chains in an ensemble of a solution and phase accounting for anisotropy and tNCS' }) self.createLine( [ 'label', 'MR method', 'widget', 'MODE', ] ) self.setMenuText('SGALT_SELECT',{ 'NONE':'Use input spacegroup only', 'HAND':'Test spacegroup and enantiomorph', 'ALL':'Test all spacegroups in point group', 'LIST':'Select from list'}) self.createLine( [ 'label', 'Choice of spacegroups to test', 'widget', 'SGALT_SELECT', ] ) self.setToolTip('SGALT_TEST','Enter a list of space-separated spacegroups') self.createLine( [ 'widget', 'SGALT_TEST' ], toggle=['SGALT_SELECT','open',['LIST']]) #The validity of the SGALT_TEST widget contents are dependent on SGALT_SELECT self.connect(self.container.controlParameters.SGALT_SELECT,QtCore.SIGNAL('dataChanged'),self.getWidget('SGALT_TEST').validate) self.openFolder(title='Extra Options') self.setToolTip('RESOLUTION_HIGH','Limiting the resolution will make the job faster but less sensitive') self.createLine ( [ 'label' , 'Set high resolution limit to ', 'widget', 'RESOLUTION_HIGH' ] ) self.createLine ( [ 'label' , 'Set high resolution limit for final stage of AUTO_MR', 'widget', 'RESOLUTION_AUTO_HIGH' ] ) self.setToolTip('PEAKS_ROT_CUTOFF','Lower this to try more rotation solutions (slower)') self.createLine ( [ 'label' , 'Select rotation peaks over', 'widget', 'PEAKS_ROT_CUTOFF', 'label', 'percent.' ] ) self.setToolTip('PACK_CUTOFF','Increase this if inaccurate loops are causing packing test to fail') self.createLine ( [ 'label' , 'Maximum clashes allowed as percentage of total Calpha', 'widget', 'PACK_CUTOFF' ] ) self.openFolder(title='Advanced Options') self.createLine ( [ 'advice', 'Use more local processors if available' ] ) self.createLine ( [ 'label', 'Number of processors', 'widget', 'NJOBS' ] ) self.createLine ( [ 'label' , 'Number of top solutions to output', 'widget', 'NUM_SOL_OUT' ] ) self.createLine ( [ 'widget', 'PERMUTATIONS', 'label', 'Permute search set' ] ) def isValid(self): #Here override logic of whether this is a valid task to allow for CSeqDataFile from the #CASUComponentList being required ONLY IF COMP_BY has the value "ASU" invalidElements = CTaskWidget.isValid(self) import CCP4ModelData, CCP4XtalData widgLib = {"COMP_BY":"Not set yet"} self.getParams(widgLib) if widgLib["COMP_BY"] != "ASU": invalidElements = [invalidElement for invalidElement in invalidElements if (type(invalidElement) != CCP4XtalData.CAsuComponent and type(invalidElement) != CCP4ModelData.CSeqDataFile)] return invalidElements