from PyQt4 import QtGui,QtCore import CCP4TaskWidget import CCP4Widgets def whatNext(jobId=None): return [ 'buccaneer_build_refine_mr' ] class Cmrbump_basic(CCP4TaskWidget.CTaskWidget): TASKNAME = 'mrbump_basic' TASKVERSION = 0.1 TASKMODULE='molecular_replacement' TASKTITLE='Automated structure solution - MrBUMP' DESCRIPTION='Run a quick MrBUMP job with streamlined settings' RANK=1 WHATNEXT = ['prosmart_refmac','buccaneer_build_refine_mr','coot_rebuild'] def __init__(self,parent): CCP4TaskWidget.CTaskWidget.__init__(self,parent) def drawContents(self): self.setProgramHelpFile('mrbump_basic') #- -------------------- -------------------- -------------------- folder = self.openFolder(folderFunction='inputData',title='Input Data') self.createLine( [ 'subtitle', 'Target Sequence', 'Sequence of your target structure' ] ) self.createLine( [ 'widget', 'SEQIN' ] ) self.createLine( [ 'label', 'The number of monomers to search for', 'widget', 'NMON' ] ) self.createLine( [ 'subtitle', 'Experimental Data', 'Observed intensities or amplitudes, and Free-R flags' ] ) self.createLine( [ 'widget', 'F_SIGF' ] ) self.createLine( [ 'widget', 'FREERFLAG' ] ) #- -------------------- -------------------- -------------------- folder = self.openFolder(folderFunction='controlParameters',title='Options') # self.createLine( [ 'advice', 'Tick box to open a folder and define parameter(s) manually' ] ) self.createLine( [ 'label', 'Expected number of copies', 'widget', 'NMASU'] )#, toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) self.closeFolder() #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_PRF', 'advice', 'Search method' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'SAPTF = Spherically Averaged Phased Translation Function' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'PRF = Phased Rotation Function' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'RF(M) = Rotation Function (f-obs from the density outside of the fixed Model)' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'RF(S) = Rotation Function (f-obs from the density inside a Sphere)' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) # self.setMenuText( 'PRF', { # 'n': 'RF(M) + PTF', # 'y': 'SAPTF + PRF + PTF', # 's': 'SAPTF + RF(S) + PTF', # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'PRF' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_PRF', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_NPEAKS', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_NPEAKS', 'advice', 'Number of peaks to analyse' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_NPEAKS', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'Number of Rotation Function peaks', 'widget', 'NP'], toggle=[ 'OPEN_NPEAKS', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'Number of Translation Function peaks', 'widget', 'NPT'], toggle=[ 'OPEN_NPEAKS', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_NPEAKS', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_SCORE', 'advice', 'Scoring putative solutions' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'CC = Correlation Coefficient' ], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'PF = Packing Function' ], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) # self.setMenuText( 'SCORE', { # 'y': 'Use CC times PF as a score and stop translation search if contrast is > 3.0', # 'n': 'Use CC times PF and do not stop', # 'c': 'Use CC and do not stop', # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'SCORE' ], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'label', 'Expected number of copies (for contrast calculation only)', 'widget', 'NMON_EXP'], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SCORE', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_ANISO', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_ANISO', 'advice', 'Scaling' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_ANISO', 'open', [ True ] ] ) # self.setMenuText( 'ANISO', { # 'y': 'anisotropic', # 'n': 'isotropic', # 'k': 'none', # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'ANISO' ], toggle=[ 'OPEN_ANISO', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_ANISO', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_HIGH_PATH_VAR', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_HIGH_PATH_VAR', 'advice', 'High pass filter parameter' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_HIGH_PATH_VAR', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'advice', '(B-add, the B-factor applied to input structure amplitudes)' ], toggle=[ 'OPEN_HIGH_PATH_VAR', 'open', [ True ] ] ) # self.setMenuText( 'HIGH_PATH_VAR', { # 's': 'From identity between model and sequence (if sequence given)', # 'i': 'From identity specified manually', # 'r': 'From high resolution limit', # 'b': 'Directly as the value of additional B-factor', # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'HIGH_PATH_VAR' ], toggle=[ 'OPEN_HIGH_PATH_VAR', 'open', [ True ] ] ) # lab1 = 'Identity between search and target sequences (from 0 to 1)' # self.createLine( [ 'label', ' ', 'label', lab1, 'widget', 'SIM' ], toggleFunction=[ self.openSIM, [ 'OPEN_HIGH_PATH_VAR', 'HIGH_PATH_VAR' ] ] ) # lab1 = 'High resolution limit, Ang' # self.createLine( [ 'label', ' ', 'label', lab1, 'widget', 'RESMAX' ], toggleFunction=[ self.openRESMAX, [ 'OPEN_HIGH_PATH_VAR', 'HIGH_PATH_VAR' ] ] ) # lab1 = 'B-add' # self.createLine( [ 'label', ' ', 'label', lab1, 'widget', 'BADD' ], toggleFunction=[ self.openBADD, [ 'OPEN_HIGH_PATH_VAR', 'HIGH_PATH_VAR' ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_HIGH_PATH_VAR', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_LOW_PATH_VAR', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_LOW_PATH_VAR', 'advice', 'Low pass filter parameter' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_LOW_PATH_VAR', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'advice', '(B-off, the B-factor of the removed fraction of structure amplitudes)' ], toggle=[ 'OPEN_LOW_PATH_VAR', 'open', [ True ] ] ) # self.setMenuText( 'LOW_PATH_VAR', { # 'c': 'From completeness of the search model', # 'r': 'From low resolution limit', # 'b': 'Directly as the value of additional B-factor', # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'LOW_PATH_VAR' ], toggle=[ 'OPEN_LOW_PATH_VAR', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_LOW_PATH_VAR', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SEQ', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_SEQ', 'advice', 'Sequence modification options' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SEQ', 'open', [ True ] ] ) # self.createLine( [ 'label', ' ', 'advice', 'Perform alignment and use it to rename residues and trimm side chains' ], toggle=[ 'OPEN_SEQ', 'open', [ True ] ] ) # self.setMenuText( 'SEQ', { # 'y': 'always', # 'd': 'only for sequence identity > 20%', # 'n': 'never' # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'SEQ' ], toggle=[ 'OPEN_SEQ', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SEQ', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SURF', 'open', [ True ] ] ) # self.createLine( [ 'widget', 'OPEN_SURF', 'advice', 'B-factors modification options' ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SURF', 'open', [ True ] ] ) # self.setMenuText( 'SURF', { # 'y': 'Increase B-factor on the molecular surface for all functions', # 'c': 'Increase B-factor on the surface for Packing function only', # 'n': 'Do not do anything', # '2': 'Set B-factors of all atoms to 20', # 'a': 'Use poly-alanine model with all B-factors 20', # } ) # self.createLine( [ 'label', ' ', 'widget', '-guiMode', 'multiLineRadio', 'SURF' ], toggle=[ 'OPEN_SURF', 'open', [ True ] ] ) #- self.createLine( [ 'advice', '' ], toggle=[ 'OPEN_SURF', 'open', [ True ] ] ) #- -------------------- -------------------- -------------------- print 'CTaskMolrep stackedWidgets' for w in self.findChildren( CCP4TaskWidget.CStackedWidget ) : print ' ', w, w.controlVar self.updateViewFromModel() #- -------------------- -------------------- -------------------- def openSIM( self ) : gui = self.container.guiParameters if gui.OPEN_HIGH_PATH_VAR and str( gui.HIGH_PATH_VAR ) == 'i' : return True else: return False def openRESMAX( self ) : gui = self.container.guiParameters if gui.OPEN_HIGH_PATH_VAR and str( gui.HIGH_PATH_VAR ) == 'r' : return True else: return False def openBADD( self ) : gui = self.container.guiParameters if gui.OPEN_HIGH_PATH_VAR and str( gui.HIGH_PATH_VAR ) == 'b' : return True else: return False