""" tasks/buccaneer_build_refine/CTaskbuccaneer_build_refine.py: CCP4 GUI Project Copyright (C) 2011 University of York 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. """ """ Liz Potterton Dec 2011 - copy and revise buccaneer gui Jon Agirre 2014 - Add new MR options, revise the gui and simplify it """ from PyQt4 import QtGui,QtCore import CCP4TaskWidget import CCP4Widgets def whatNext(jobId,childTaskName,childJobNumber,projectName): #print 'buccaneer_build_refine_mr.whatNext',projectName if childJobNumber is None: return ['coot_rebuild','edstats','prosmart_refmac','buccaneer_build_refine_mr'] elif childTaskName == 'refmac': return ['coot_rebuild','edstats','prosmart_refmac','buccaneer_build_refine_mr'] else: return [['prosmart_refmac','Refine this model before continuing']] # Subclass CTaskWidget to give specific task window class CTaskbuccaneer_build_refine_mr(CCP4TaskWidget.CTaskWidget): TASKNAME = 'buccaneer_build_refine_mr' TASKVERSION = 0.0 TASKMODULE='model_building' TASKTITLE='Autobuild protein - BUCCANEER' SHORTTASKTITLE='BUCCANEER' TASKLABEL = 'bucanr' DESCRIPTION = 'Iterations of model building (Buccaneer) and refinement (Refmac5, Prosmart and Coot)' MGDISPLAYFILES = ['XYZOUT'] WHATNEXT = ['coot_rebuild','prosmart_refmac','buccaneer_build_refine_mr', 'edstats'] PROGRAMHELP = ['cbuccaneer','refmac5'] RANK=1 EXPORTMTZPARAMS = [ 'F_SIGF','FPHIOUT', ['DIFFPHIOUT' ,'diff' ] , 'ABCDOUT' ] def __init__(self,parent): CCP4TaskWidget.CTaskWidget.__init__(self,parent) def drawContents(self): self.setProgramHelpFile('buccaneer') # Trying to handle if task is cloned and ABCD already set - then need to set ABCD_MR or ABCD_EXP if self.container.inputData.ABCD.isSet(): if self.container.controlParameters.BUCCANEER_PHSIN_TYPE == 'mr' : self.container.inputData.ABCD_MR.set(self.container.inputData.ABCD) else: self.container.inputData.ABCD_EXP.set(self.container.inputData.ABCD) self.container.inputData.ABCD.unSet() self.container.inputData.ABCD_EXP.setQualifier ( 'allowUndefined', False ) # the input data tab starts here folder = self.openFolder(folderFunction='inputData',title='Input Data') self.createLine( [ 'label', 'Build model with phases coming from ', 'widget', '-guiMode', 'radio', 'BUCCANEER_PHSIN_TYPE' ] ) self.createLine( [ 'subtitle', 'Input the molecular replacement model used to phase the data', 'A ' +\ 'refined molecular replacement solution provides best initial phases for the ' +\ 'autobuilding procedure; jelly body refinement will be done if the supplied model ' +\ 'has not been refined previously.' ], toggle=['BUCCANEER_PHSIN_TYPE', 'open', 'mr' ] ) self.openSubFrame(frame=[True], toggle= [ 'BUCCANEER_PHSIN_TYPE', 'open', 'mr' ] ) self.createLine( [ 'widget','BUCCANEER_MR_MODE_XYZIN' ] ) self.createLine( [ 'label', 'This model will be used to place and name chains, and','widget','BUCCANEER_MR_MODE' ] ) self.closeSubFrame() self.createLine( [ 'subtitle', 'Select experimental data', 'Looking for a way to input your pre-computed phases? You can find it under Advanced Buccaneer Options.' ] , toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'mr'] ) self.createLine( [ 'subtitle', 'Select experimental data', 'Experimental phases will no longer be used as restraints if Rwork < ' + str( self.getContainer().controlParameters.BUCCANEER_MLHL_RWORK_LIMIT ) ] , toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'experimental'] ) self.openSubFrame ( frame=[True] ) self.createLine( [ 'widget', 'F_SIGF' ] ) self.createLine( [ 'widget', 'ABCD_EXP' ], toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'experimental'] ) self.createLine( [ 'widget', 'FREERFLAG' ] ) self.closeSubFrame ( ) self.createLine( [ 'subtitle', 'Enter the sequence for the structure', 'Sequences may be input in any understandable format. ' +\ 'Click on Show list if you want to input more than one.' ] ) self.openSubFrame ( frame=[True] ) self.createLine( [ 'widget','SEQIN' ] ) self.closeSubFrame ( ) self.createLine( [ 'tip', 'Your model should contain confidently-built metals, ligands and/or protein parts', 'widget', 'XYZIN_MODE', 'label', 'Start from a partially built model' ] ) self.connect ( self.container.controlParameters.XYZIN_MODE, QtCore.SIGNAL('dataChanged'), self.updateRequirements ) self.connect ( self.container.controlParameters.BUCCANEER_PHSIN_TYPE, QtCore.SIGNAL('dataChanged'), self.updateRequirements ) self.openSubFrame( frame=[True], toggle=[ 'XYZIN_MODE', 'open', [True] ] ) self.createLine( [ 'widget','XYZIN' ] ) self.createLine( [ 'tip', 'Syntax reminder: /ch/res/at/:radius e.g. /A/*/*:2.0 for all atoms in chain A. You need not specify the radius.', 'label', 'Optionally keep part of the known structure fixed ','widget', 'KNOWN_STRUCTURE' ] ) self.closeSubFrame() self.closeFolder() # a control parameter tab with basic options starts here folder = self.openFolder( folderFunction='controlParameters', title='Options' , drawFolder= self.drawOptions ) # a control parameter tab with more advanced options starts here folder = self.openFolder(folderFunction='controlParameters',title='Advanced Buccaneer Options',drawFolder=self.drawAdvancedBuccaneer ) # a control parameter tab with coot and refmac options starts here folder = self.openFolder(folderFunction='controlParameters',title='Refinement options',drawFolder=self.drawRefinement) # the last tab, with the rarely used options for choosing reference structures folder = self.openFolder(folderFunction='controlParameters',title='Reference structures',drawFolder=self.drawReference) #for w in self.findChildren(CCP4TaskWidget.CStackedWidget): # print ' ',w,w.controlVar self.updateRequirements() self.updateViewFromModel() def updateRequirements ( self ) : if self.container.controlParameters.BUCCANEER_PHSIN_TYPE == 'mr' : self.container.inputData.BUCCANEER_MR_MODE_XYZIN.setQualifier ( 'allowUndefined', False ) self.container.inputData.BUCCANEER_MR_MODE_XYZIN.setQualifier ( 'toolTip', 'A molecular replacement model is required' ) else : self.container.inputData.BUCCANEER_MR_MODE_XYZIN.setQualifier ( 'allowUndefined', True ) self.getWidget ( 'BUCCANEER_MR_MODE_XYZIN' ).validate ( ) if self.container.controlParameters.XYZIN_MODE : self.container.inputData.XYZIN.setQualifier ( 'allowUndefined', False ) self.container.inputData.XYZIN.setQualifier ( 'toolTip', 'An initial atomic model is required' ) else : self.container.inputData.XYZIN.setQualifier ( 'allowUndefined', True ) self.getWidget ( 'XYZIN' ).validate ( ) return def fix(self): self.container.inputData.ABCD.unSet() if str(self.container.controlParameters.BUCCANEER_PHSIN_TYPE) == 'mr' : self.container.inputData.ABCD.set(self.container.inputData.ABCD_MR) else: self.container.inputData.ABCD.set(self.container.inputData.ABCD_EXP) self.container.inputData.ABCD_EXP.setQualifier ( 'allowUndefined', True ) self.getWidget('ABCD_EXP').validate() self.container.inputData.ABCD_EXP.unSet() self.container.inputData.ABCD_MR.unSet() return CCP4TaskWidget.CTaskWidget.fix(self) def drawOptions(self): self.createLine ( [ 'subtitle', 'Pipeline control', 'Warning: default values work best for most situations.' ] ) self.openSubFrame ( frame = [True] ) self.createLine( [ 'label', 'Iterate', 'widget', 'ITERATIONS', 'label', 'times over', 'widget', 'BUCCANEER_CYCLES_NEXT', 'label', 'cycles of build and', 'widget', 'REFMAC_CYCLES', 'label', 'of refinement, with', 'widget', 'BUCCANEER_CYCLES', 'label', 'initial build cycles' ] ) import multiprocessing, os self.getContainer().controlParameters.BUCCANEER_JOBS = int ( os.getenv ( 'OMP_NUM_THREADS', multiprocessing.cpu_count() ) ) self.createLine( [ 'tooltip', 'The default value shows the detected number of cores', 'label', 'Use up to', 'widget', 'BUCCANEER_JOBS', 'label', 'CPU cores whenever possible' ] ) self.closeSubFrame ( ) self.createLine( [ 'widget', 'BUCCANEER_BUILD_SEMET', 'label','Build methionines as selenomethionine' ] ) self.createLine( [ 'advice', 'The three-letter code MSE will be used instead of MET' ], toggle=[ 'BUCCANEER_BUILD_SEMET', 'open', [True] ] ) self.createLine( [ 'widget', 'BUCCANEER_FAST','label','Use fast mode - recommended' ] ) self.createLine( [ 'widget', 'BUCCANEER_ANISOTROPY_CORRECTION','label','Apply anisotropy correction' ] ) def drawAdvancedBuccaneer(self ): self.createLine( [ 'subtitle', 'Filtering', 'Buccaneer calculates the mean Bfactor distribution for all residues, and leaves out those showing values higher than a chosen σ level' ] ) self.openSubFrame ( frame=[True]) self.createLine( [ 'label', 'Filter the molecular replacement model by a', 'widget', 'BUCCANEER_MR_MODE_SIGMA', 'label', 'σ threshold'], toggle=['BUCCANEER_PHSIN_TYPE', 'open', 'mr' ] ) self.createLine( [ 'label', 'Filter the model between cycles by a', 'widget', 'BUCCANEER_MODEL_SIGMA', 'label', 'σ threshold' ] ) self.createLine( [ 'tooltip', '(Using data beyond 2A is slow and seldom helps)', 'label','Leave out reflection data beyond a','widget','BUCCANEER_RESOLUTION', 'label', 'Å resolution limit'] ) self.createLine( [ 'widget' , 'BUCCANEER_USE_FREER', 'label', 'exclude Free R reflections from map calculation' ] ) self.closeSubFrame ( ) self.createLine( [ 'subtitle', 'Input a heavy atom model to aid with sequencing', 'You may input, for instance, Selenium atoms to aid in placing SeMet residues.' ] ) self.openSubFrame ( frame = [True] ) self.createLine( [ 'widget', 'XYZIN_SEQ' ] ) self.closeSubFrame ( ) self.createLine( [ 'subtitle', 'Pre-computed phases', 'If you have already refined your model, you may input your phase probabilities here.' ], toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'mr'] ) self.openSubFrame ( frame=[True], toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'mr']) self.createLine( [ 'widget', 'ABCD_MR' ] ) self.closeSubFrame ( ) self.createLine( [ 'widget','BUCCANEER_FIX_POSITION','label','Build the new model in the same place as the input model' ] ) self.createLine( [ 'label','Residue name for unsequenced residues','widget','BUCCANEER_NEW_RESIDUE_NAME' ] ) def drawRefinement(self): self.createLine( [ 'subtitle', 'Real space refinement', 'A number of operations are available to be performed between the building and reciprocal-space refinement steps' ] ) self.openSubFrame( frame=[True] ) self.createLine( [ 'label', 'Perform ','widget','COOT_REALSPACE_OPERATION' , 'label', ' on the built model'] ) self.createLine( [ 'label', '       when Rwork is ', 'widget', 'BUCCANEER_RSR_RWORK_LIMIT', 'label', ' or lower' ], toggle = [ 'COOT_REALSPACE_OPERATION','open', [ 'coot_stepped_refine','coot_fit_residues', 'coot_script_lines', 'coot_add_waters' ] ] ) self.createLine( [ 'widget', 'USERAMA', 'label', 'Use ramachandran restraints' ], toggle = [ 'COOT_REALSPACE_OPERATION','open', [ 'coot_stepped_refine','coot_fit_residues' ] ] ) self.createLine( [ 'label','Script to run' ], toggle = [ 'COOT_REALSPACE_OPERATION','open', [ 'coot_script_lines' ] ] ) self.createLine( [ 'widget', '-guiMode','multiLine','SCRIPT' ], toggle = [ 'COOT_REALSPACE_OPERATION','open', [ 'coot_script_lines' ] ] ) self.closeSubFrame() self.createLine( [ 'subtitle', 'Reciprocal space refinement', 'Note:
Default options need to be changed very rarely. Use with caution' ] ) self.openSubFrame( frame=[True] ) self.createLine( [ 'tip', 'This option will be turned off automatically if the generated model is very fragmented', 'widget', 'REFMAC_LOCAL_NCS', 'label', 'Exploit local non-crystallographic symmetry' ] ) #self.createLine( [ 'advice', 'This option will be turned off automatically if the generated model is very fragmented' ], toggle=['REFMAC_LOCAL_NCS', 'open', [True] ] ) self.createLine( [ 'widget', 'REFMAC_EXP_USEPHI', 'label', 'Use experimental phases as restraints in refinement' ], toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'experimental' ] ) self.createLine( [ 'label', '       but drop them if Rwork goes below', 'widget', 'BUCCANEER_MLHL_RWORK_LIMIT' ], toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'experimental' ] ) self.createLine( [ 'widget', 'REFMAC_MR_USEPHI', 'label', 'Use molecular replacement phases as restraints in refinement' ], toggle=[ 'BUCCANEER_PHSIN_TYPE', 'open', 'mr' ] ) self.createLine( [ 'widget', 'USE_PROSMART', 'label', 'Use a higher-resolution restraint target' ] ) self.createLine( [ 'widget', 'TARGET' ], toggle=[ 'USE_PROSMART', 'open', [True]] ) self.createLine( [ 'widget', 'DICT' ] ) self.createLine( [ 'widget', '-guiMode','multiLine','EXTRAREFMACKEYWORDS' ] ) self.closeSubFrame() def drawReference(self): self.createLine( [ 'subtitle', 'Reference structures', 'You should normally let Buccaneer to choose reference structures'] ) self.openSubFrame ( frame=[True] ) self.createLine( [ 'widget', 'F_SIGF_REF' ] ) self.createLine( [ 'widget', 'ABCD_REF' ] ) self.createLine( [ 'widget', 'XYZIN_REF' ] ) self.closeSubFrame ()