""" pipelines/refmac_ii2/Crefmac.py: CCP4 GUI Project Copyright (C) 2012 STFC This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ """ Andrey Lebedev September 2011 - refmac_martin gui Liz Potterton Aug 2012 - convert for MTZ ADO's demo Liz Potterton Oct 2012 - Moved mini-MTZ version to refmac_martin """ from PyQt4 import QtGui,QtCore import CCP4TaskWidget import CCP4Widgets def whatNext(jobId=None,childTaskName=None,childJobNumber=None,projectName=None): import os from lxml import etree import CCP4Modules, CCP4Utils, CCP4File, CCP4Container, CCP4Data, CCP4PluginScript jobStatus = CCP4Modules.PROJECTSMANAGER().db().getJobInfo(jobId,'status') if jobStatus == 'Unsatisfactory': returnList = ['LidiaAcedrg', 'prosmart_refmac'] else: returnList = ['prosmart_refmac', 'coot_rebuild', 'buccaneer_build_refine_mr'] return returnList class Cprosmart_refmac(CCP4TaskWidget.CTaskWidget): TASKTITLE='Refinement - REFMAC5' SHORTTASKTITLE='REFMAC5' DESCRIPTION='Refine (Refmac5) with optional restraints (Prosmart)' TASKNAME = 'prosmart_refmac' TASKLABEL = 'refmac' TASKVERSION = 0.0 TASKMODULE = 'refinement' MGDISPLAYFILES = ['XYZOUT','FPHIOUT','DIFFPHIOUT'] AUTOPOPULATEINPUT = True RANK=1 def __init__(self,parent): CCP4TaskWidget.CTaskWidget.__init__(self,parent) def ToggleWeightAuto(self): return str(self.container.controlParameters.WEIGHT_OPT) == 'MANUAL' def ToggleTLS(self): return self.container.inputData.TLSIN.isSet() def ToggleTLSNot(self): return not self.container.inputData.TLSIN.isSet() def ToggleTLSUsed(self): return self.container.inputData.TLSIN.isSet() or self.container.controlParameters.AUTOTLS def ToggleTLSNotUsed(self): return not self.container.inputData.TLSIN.isSet() and not self.container.controlParameters.AUTOTLS def drawContents(self): self.setProgramHelpFile('refmac') indent = '      ' #- -------------------- -------------------- -------------------- folder = self.openFolder(folderFunction='inputData',title='Input Data') #self.createLine( [ 'advice',' '] ) self.createLine( [ 'subtitle', 'Main inputs' ]) self.openSubFrame(frame=[True]) self.createLine( [ 'widget', '-browseDb', True, 'XYZIN' ] ) self.createLine( [ 'widget', '-browseDb', True, 'F_SIGF' ]) self.createLine( [ 'label','Use anomalous data for ', 'widget', 'USEANOMALOUSFOR', 'stretch', 'label', 'Wavelength', 'widget', 'WAVELENGTH'],toggleFunction=[self.anomalousAvailable,['F_SIGF']]) if self.isEditable(): self.connect(self.container.inputData.F_SIGF, QtCore.SIGNAL('dataChanged'), self.F_SIGFChanged) if not self.container.controlParameters.WAVELENGTH.isSet(): self.getWavelength() self.createLine( [ 'widget', '-browseDb', True, 'FREERFLAG' ] ) self.closeSubFrame() #self.createLine( [ 'advice',' '] ) self.createLine( [ 'subtitle', 'Optional additional inputs' ]) self.openSubFrame(frame=[True]) self.createLine( [ 'widget', '-browseDb', True, 'ABCD' ] ) self.createLine( [ 'widget', '-browseDb', True, 'TLSIN'] ) self.createLine( [ 'widget', '-browseDb', True, 'DICT' ] ) self.createLine( [ 'widget', '-browseDb', True, 'REFERENCE_MODEL' ] ) self.closeSubFrame() #- -------------------- -------------------- -------------------- folder = self.openFolder(folderFunction='controlParameters',title='Options', drawFolder=self.drawControlParameters) #- -------------------- -------------------- -------------------- folder = self.openFolder(folderFunction='controlParameters',title='Advanced Options', drawFolder=self.drawAdvancedOptions) #- -------------------- -------------------- -------------------- def drawControlParameters( self ): indent = '      ' self.createLine( [ 'subtitle', 'Main refinement options'] ) self.openSubFrame(frame=[True]) self.createLine( [ 'label', 'Number of refinement cycles:', 'stretch', 'widget', 'NCYCLES' ] ) auto_weight = self.createLine( [ 'label', 'Weight restaints versus experimental data using', 'widget', 'WEIGHT_OPT', 'label', 'weight'] ) self.createLine( [ 'label', ':', 'widget', 'WEIGHT' ], toggleFunction=[self.ToggleWeightAuto, ['WEIGHT_OPT']], appendLine=auto_weight ) use_twin = self.createLine( [ 'widget', 'USE_TWIN', 'label', 'Crystal is twinned' ] ) self.createLine( [ 'label', 'Perform twin refinement using observed', 'widget', 'TWIN_TYPE' ], toggle = ['USE_TWIN', 'open', [ True ] ],appendLine=use_twin ) #- OLD KEYWORD: self.createLine( [ 'label', 'Set of hydrogen atoms to model', 'stretch', 'widget', 'HYDROGENS' ] ) use_hydr = self.createLine( [ 'widget', 'HYDR_USE', 'label', 'Use hydrogens during refinement'] ) self.createLine( [ 'widget', 'HYDR_ALL' ], toggle = ['HYDR_USE', 'open', [ True ] ], appendLine=use_hydr ) self.closeSubFrame() self.createLine( [ 'subtitle', 'Parameters' ] ) self.openSubFrame(frame=[True]) self.createLine( [ 'label','Use','widget', 'B_REFINEMENT_MODE', 'label','B-factors'] ) self.createLine( [ 'label', 'TLS input file has been provided. Number of TLS refinement cycles:', 'stretch', 'widget', 'NTLSCYCLES' ], toggleFunction=[self.ToggleTLS, ['TLSIN']]) tls_cycles = self.createLine( [ 'widget', 'AUTOTLS', 'label', 'Use TLS parameters' ], toggleFunction=[self.ToggleTLSNot, ['TLSIN']]) self.createLine( [ 'label', 'Number of TLS refinement cycles:', 'widget', 'NTLSCYCLES_AUTO' ], toggleFunction=[self.ToggleTLSUsed, ['TLSIN','AUTOTLS']], appendLine=tls_cycles) reset_bfac_tls = self.createLine( [ 'label', indent, 'widget', 'TLSBFACSETUSE', 'label', 'Reset all B-factors at start' ], toggleFunction=[self.ToggleTLSUsed, ['TLSIN','AUTOTLS']]) self.createLine( [ 'label', ' to fixed value:', 'widget', 'TLSBFACSET' ], toggle = ['TLSBFACSETUSE', 'open', [ True ] ], appendLine=reset_bfac_tls ) self.closeSubFrame() self.createLine( [ 'subtitle', 'Restraints' ] ) self.openSubFrame(frame=[True]) #- OLD KEYWORD: self.createLine( [ 'widget', 'USE_LOCAL_SYMMETRY','label', 'Use local symmetry' ] ) self.createLine( [ 'widget', 'USE_NCS', 'label', 'Use non-crystallographic symmetry (NCS) restraints' ] ) self.createLine( [ 'label', indent+'Use', 'widget', 'NCS_TYPE', 'label', 'NCS restraints, generated', 'widget', 'NCS_AUTO' ], toggle = ['USE_NCS', 'open', [ True ] ] ) use_jellybody = self.createLine( [ 'widget', 'USE_JELLY', 'label', 'Use jelly-body restraints' ] ) self.createLine( [ 'label', ' with sigma:', 'widget', 'JELLY_SIGMA', 'label', 'and max distance:', 'widget', 'JELLY_DIST' ], toggle = ['USE_JELLY', 'open', [ True ] ], appendLine=use_jellybody) self.closeSubFrame() self.createLine( [ 'subtitle', 'Scaling' ] ) self.openSubFrame(frame=[True]) self.createLine( [ 'widget', 'SCALETYPE', 'label', 'Specify scaling model' ] ) self.closeSubFrame() self.createLine( [ 'subtitle', 'Output options']) self.openSubFrame(frame=[True]) self.createLine( [ 'widget', 'MAP_SHARP', 'label', 'Perform map sharpening when calculating maps' ] ) use_mapsharp = self.createLine( [ 'label', indent, 'widget', 'MAP_SHARP_CUSTOM', 'label', 'Use custom sharpening parameter (B-factor)' ], toggle = ['MAP_SHARP', 'open', [ True ] ] ) self.createLine( [ 'label', ':', 'widget', 'BSHARP' ], toggle = ['MAP_SHARP_CUSTOM', 'open', [ True ] ], appendLine=use_mapsharp) self.closeSubFrame() def drawAdvancedOptions( self ): indent = '      ' #- REMOVED: self.createLine( [ 'label','Exit if new ligand encountered','stretch','widget', 'MAKE_NEW_LIGAND_EXIT'] ) #- OLD KEYWORD: self.createLine( [ 'label', 'Resolution limits', 'stretch', 'widget', 'RESOLUTION' ] ) custom_res = self.createLine( [ 'widget', 'RES_CUSTOM', 'label', 'Use custom resolution limits' ] ) self.createLine( [ 'label', indent+indent+'min:', 'widget', 'RES_MIN', 'label', ' max:', 'widget', 'RES_MAX' ], toggle = ['RES_CUSTOM', 'open', [ True ] ], appendLine=custom_res ) reset_bfac = self.createLine( [ 'widget', 'BFACSETUSE', 'label', 'Reset all B-factors at start' ], toggleFunction=[self.ToggleTLSNotUsed, ['TLSIN','AUTOTLS']]) self.createLine( [ 'label', ' to fixed value:', 'widget', 'BFACSET' ], toggle = ['BFACSETUSE', 'open', [ True ] ], appendLine=reset_bfac ) self.createLine( [ 'widget', 'TLSOUT_ADDU', 'label', 'Add TLS contribution to output B-factors (only for analysis and deposition)' ] ) self.createLine( [ 'widget', 'OPTIMISE_WEIGHT', 'label', 'Execute multiple refinement runs in order to optimise X-ray/geometry weight' ] ) self.createLine( [ 'widget', '-guiMode','multiLine','EXTRAREFMACKEYWORDS' ] ) def anomalousAvailable(self): if not self.container.inputData.F_SIGF.isSet(): return False if not self.isEditable(): return True #Peak to see if we can make F+/F- self.container.inputData.F_SIGF.setContentFlag(reset=True) canConvertString, toType = self.container.inputData.F_SIGF.conversion(2) print 'Can convert ?',self.container.inputData.F_SIGF.contentFlag, canConvertString, toType self.validate() if canConvertString == 'no': self.container.controlParameters.USEANOMALOUSFOR.set('NOTHING') return False else: return True def F_SIGFChanged(self): self.getWavelength() self.setTwinMode() def setTwinMode(self): if self.container.inputData.F_SIGF.isSet(): columnLabelsInFile = [column.columnLabel.__str__() for column in self.container.inputData.F_SIGF.fileContent.listOfColumns] if not 'I' in columnLabelsInFile and not 'Iplus' in columnLabelsInFile: self.container.controlParameters.TWIN_TYPE.setQualifiers({'enumerators':['F'],'menuText':['SF Amplitudes (F)']}) self.container.controlParameters.TWIN_TYPE.set('F') else: self.container.controlParameters.TWIN_TYPE.setQualifiers({'enumerators':['I','F'],'menuText':['Intensities (I)','SF Amplitudes (F)']}) self.container.controlParameters.TWIN_TYPE.set('I') try: self.getWidget('TWIN_TYPE').populateComboBox(self.container.controlParameters.TWIN_TYPE) self.getWidget('TWIN_TYPE').updateViewFromModel() except: pass self.validate() def getWavelength(self): if self.container.inputData.F_SIGF.isSet(): wavelengths = self.container.inputData.F_SIGF.fileContent.getListOfWavelengths() if len(wavelengths)>0: self.container.controlParameters.WAVELENGTH = round(wavelengths[-1],3) try: self.getWidget('WAVELENGTH').updateViewFromModel() except: print 'prosmart_refmac - WAVELENGTH widget updateViewFromModel failed'