""" prosmart.py: CCP4 GUI Project Copyright (C) 2013 """ import os from CCP4PluginScript import CPluginScript from CCP4ErrorHandling import * class prosmart(CPluginScript): TASKMODULE = 'wrappers' # Where this plugin will appear on gui TASKNAME = 'prosmart' # Task name - should be same as class name TASKVERSION= 0.1 # Version of this plugin TASKCOMMAND = 'prosmart' # The command to run the executable MAINTAINER = 'nicholls@mrc-lmb.cam.ac.uk' ERROR_CODES = { 201 : { 'description' : 'No output restraint file from Prosmart' }, 202 : { 'description' : 'Log file does not report successful job completion' , 'severity' : SEVERITY_WARNING } } def processInputFiles(self): import os import shutil # Use temp input filename from which prosmart takes output restraints filename self.tempFile = os.path.splitext(str(self.container.outputData.RESTRAINTS))[0]+'_TARGET.pdb' print 'prosmart tempFile',self.tempFile shutil.copyfile(self.container.inputData.XYZIN.__str__(), self.tempFile) return CPluginScript.SUCCEEDED def makeCommandAndScript(self): self.appendCommandLine(['-p1',self.tempFile]) self.appendCommandLine(['-p2',self.container.inputData.REFERENCE_MODEL]) self.appendCommandLine(['-o',self.workDirectory]) # always output xml log self.appendCommandLine(['-xml',self.makeFileName('PROGRAMXML')]) if self.container.inputData.EXT_FILE.isSet(): self.appendCommandLine(['-f',self.container.inputData.EXT_FILE]) #if self.container.inputData.INPUTDIR.isSet(): #self.appendCommandLine(['-input_dir',self.container.inputData.INPUTDIR]) # (Don't yet know how to specify this sort of input - may or may not be specified multiple times) #if self.container.controlParameters.CHAIN1.isSet(): #self.appendCommandLine(['-c1',self.container.controlParameters.CHAIN1]) #if self.container.controlParameters.CHAIN2.isSet(): #self.appendCommandLine(['-c2',self.container.controlParameters.CHAIN2]) # (Don't yet know how to specify this sort of input - expects >1 value) #if self.container.controlParameters.INPUT_RANGE.isSet(): #self.appendCommandLine(['-align',self.container.controlParameters.INPUT_RANGE]) #if self.container.controlParameters.INPUT_RANGE_RM.isSet(): #self.appendCommandLine(['-align_rm',self.container.controlParameters.INPUT_RANGE_RM]) ### Program Options if self.container.controlParameters.PROGRAM_MODE == 'ALIGN_RESTRAIN': self.appendCommandLine(['-a','-r']) elif self.container.controlParameters.PROGRAM_MODE == 'ALIGN': self.appendCommandLine(['-a','-a']) elif self.container.controlParameters.PROGRAM_MODE == 'RESTRAIN': self.appendCommandLine(['-r','-r']) if not self.container.controlParameters.PROGRAM_MODE == 'RESTRAIN': if self.container.controlParameters.ALIGN_MODE == '1': self.appendCommandLine(['-a1','-a1']) elif self.container.controlParameters.ALIGN_MODE == '2': self.appendCommandLine(['-a2','-a2']) #if self.container.controlParameters.SEQ_IDENTICAL.isSet(): # self.appendCommandLine(['-id','-id']) #if self.container.controlParameters.ALL_ON_ALL.isSet(): # self.appendCommandLine(['-allonall','-allonall']) ### Fragment Options if self.container.controlParameters.LIB_MODE == 'LIB': self.appendCommandLine(['-lib','-lib']) elif self.container.controlParameters.LIB_MODE == 'HELIX': self.appendCommandLine(['-helix','-helix']) elif self.container.controlParameters.LIB_MODE == 'STRAND': self.appendCommandLine(['-strand','-strand']) # (other options - most probably don't need to be used in this gui - probably never used by end users) #if self.container.controlParameters.LIB_CONFIG.isSet(): # self.appendCommandLine(['-library_config',self.container.controlParameters.LIB_CONFIG]) #if self.container.controlParameters.LIB_LOCATION.isSet(): # self.appendCommandLine(['-library',self.container.controlParameters.LIB_LOCATION]) #if self.container.controlParameters.LIB_SCORE.isSet(): # self.appendCommandLine(['-lib_score',self.container.controlParameters.LIB_SCORE]) #if self.container.controlParameters.LIB_FRAGLEN.isSet(): # self.appendCommandLine(['-lib_fraglen',self.container.controlParameters.LIB_FRAGLEN]) ### Alignment Options if self.container.controlParameters.FRAGLEN.isSet(): self.appendCommandLine(['-len',self.container.controlParameters.FRAGLEN]) if self.container.controlParameters.ALIGN_THRESHOLD.isSet(): self.appendCommandLine(['-score',self.container.controlParameters.ALIGN_THRESHOLD]) # (other options - far less important - may be unnecessary for this gui) if self.container.controlParameters.HELIX_CUTOFF.isSet(): self.appendCommandLine(['-helix_cutoff',self.container.controlParameters.HELIX_CUTOFF]) if self.container.controlParameters.HELIX_PENALTY.isSet(): self.appendCommandLine(['-helix_penalty',self.container.controlParameters.HELIX_PENALTY]) if not self.container.controlParameters.REWARD_SEQ: self.appendCommandLine(['-no_reward_seq','-no_reward_seq']) if not self.container.controlParameters.ALIGN_REFINE: self.appendCommandLine(['-skip_refine','-skip_refine']) ### Superposition Options if self.container.controlParameters.SUPERPOSE_THRESHOLD.isSet(): self.appendCommandLine(['-superpose',self.container.controlParameters.SUPERPOSE_THRESHOLD]) ### Scoring Options if self.container.controlParameters.INCLUDE_MAIN: self.appendCommandLine(['-main_dist','-main_dist']) if not self.container.controlParameters.PERFORM_FLIPS: self.appendCommandLine(['-no_fix_errors','-no_fix_errors']) ### Rigid Substructure Identification Options if not self.container.controlParameters.CLUSTER_PERFORM: self.appendCommandLine(['-cluster_skip','-cluster_skip']) if self.container.controlParameters.CLUSTER_SCORE.isSet(): self.appendCommandLine(['-cluster_score',self.container.controlParameters.CLUSTER_SCORE]) if self.container.controlParameters.CLUSTER_ANGLE.isSet(): self.appendCommandLine(['-cluster_angle',self.container.controlParameters.CLUSTER_ANGLE]) if self.container.controlParameters.CLUSTER_MIN.isSet(): self.appendCommandLine(['-cluster_min',self.container.controlParameters.CLUSTER_MIN]) if self.container.controlParameters.CLUSTER_LINK.isSet(): self.appendCommandLine(['-cluster_link',self.container.controlParameters.CLUSTER_LINK]) if self.container.controlParameters.CLUSTER_RIGID.isSet(): self.appendCommandLine(['-cluster_rigid',self.container.controlParameters.CLUSTER_RIGID]) #if self.container.controlParameters.PYMOL_CLUSTER_COLOR.isSet(): # self.appendCommandLine(['-cluster_color',self.container.controlParameters.CLUSTER_COLOR]) if self.container.controlParameters.OUTPUT_DM: self.appendCommandLine(['-output_dm','-output_dm']) ### Output Options """ if not self.container.controlParameters.OUTPUT_PDB_FILES: self.appendCommandLine(['-quick','-quick']) else: self.appendCommandLine(['-out_pdb','-out_pdb']) if self.container.controlParameters.OUTPUT_WHOLE_PDB: self.appendCommandLine(['-out_pdb_full','-out_pdb_full']) if self.container.controlParameters.OUTPUT_COLOUR_SCRIPTS: self.appendCommandLine(['-out_colour','-out_colour']) if self.container.controlParameters.COLOUR_SCORE.isSet(): self.appendCommandLine(['-colour_score',self.container.controlParameters.COLOUR_SCORE]) if self.container.controlParameters.SIDE_COLOUR_SCORE.isSet(): self.appendCommandLine(['-side_score',self.container.controlParameters.SIDE_COLOUR_SCORE]) """ # (Don't yet know how to specify this sort of input - expects >1 value) #if self.container.controlParameters.COLOUR_SIMILAR.isSet(): # self.appendCommandLine(['-col1',self.container.controlParameters.COLOUR_SIMILAR]) #if self.container.controlParameters.COLOUR_DISSIMILAR.isSet(): # self.appendCommandLine(['-col2',self.container.controlParameters.COLOUR_DISSIMILAR]) if not self.container.controlParameters.DISPLAY_AS_DEGREES: self.appendCommandLine(['-cosine','-cosine']) ### Restraint Options if self.container.controlParameters.RESTRAIN_SELF: self.appendCommandLine(['-self_restrain','-self_restrain']) if self.container.controlParameters.RESTRAIN_ALL_VS_BEST.isSet(): if self.container.controlParameters.RESTRAIN_ALL_VS_BEST == 'ALL': self.appendCommandLine(['-restrain_all','-restrain_all']) else: self.appendCommandLine(['-restrain_best','-restrain_best']) if self.container.controlParameters.RESTRAIN_TO_SELF: self.appendCommandLine(['-restrain_to_self','-restrain_to_self']) if self.container.controlParameters.RESTRAIN_RMAX.isSet(): self.appendCommandLine(['-rmax',self.container.controlParameters.RESTRAIN_RMAX]) if self.container.controlParameters.RESTRAIN_RMIN.isSet(): self.appendCommandLine(['-rmin',self.container.controlParameters.RESTRAIN_RMIN]) if self.container.controlParameters.RESTRAIN_SIGMA.isSet(): self.appendCommandLine(['-sigma',self.container.controlParameters.RESTRAIN_SIGMA]) if self.container.controlParameters.RESTRAIN_MIN_SIGMA.isSet(): self.appendCommandLine(['-minsigma',self.container.controlParameters.RESTRAIN_MIN_SIGMA]) if self.container.controlParameters.RESTRAIN_SIGMATYPE.isSet(): if self.container.controlParameters.RESTRAIN_SIGMATYPE == 'DEFAULT': self.appendCommandLine(['-sigmatype','0']) elif self.container.controlParameters.RESTRAIN_SIGMATYPE == 'CONSTANT': self.appendCommandLine(['-sigmatype','1']) else: self.appendCommandLine(['-sigmatype','2']) if self.container.controlParameters.RESTRAIN_MAIN_CUTOFF.isSet(): self.appendCommandLine(['-cutoff',self.container.controlParameters.RESTRAIN_MAIN_CUTOFF]) if self.container.controlParameters.RESTRAIN_SIDE_CUTOFF.isSet(): self.appendCommandLine(['-side_cutoff',self.container.controlParameters.RESTRAIN_SIDE_CUTOFF]) if self.container.controlParameters.RESTRAIN_OUTLIER_THRESHOLD.isSet(): self.appendCommandLine(['-multiplier',self.container.controlParameters.RESTRAIN_OUTLIER_THRESHOLD]) if self.container.controlParameters.RESTRAIN_SCALE_SIGMAS.isSet(): self.appendCommandLine(['-weight',self.container.controlParameters.RESTRAIN_SCALE_SIGMAS]) if self.container.controlParameters.RESTRAIN_RM_BONDS: self.appendCommandLine(['-rm_bonds','-rm_bonds']) if self.container.controlParameters.RESTRAIN_MAIN_VS_SIDE.isSet(): if self.container.controlParameters.RESTRAIN_MAIN_VS_SIDE == 'MAIN': self.appendCommandLine(['-main','-main']) else: self.appendCommandLine(['-side','-side']) if self.container.controlParameters.RESTRAIN_REFMAC_TYPE.isSet(): if self.container.controlParameters.RESTRAIN_REFMAC_TYPE == 'TYPE0': self.appendCommandLine(['-type','0']) elif self.container.controlParameters.RESTRAIN_REFMAC_TYPE == 'TYPE1': self.appendCommandLine(['-type','1']) else: self.appendCommandLine(['-type','2']) # (Don't yet know how to specify this sort of input - expects >1 values #if self.container.controlParameters.RESTRAIN_RANGE.isSet(): # self.appendCommandLine(['-restrain',self.container.controlParameters.RESTRAIN_RANGE]) #if self.container.controlParameters.RESTRAIN_RM.isSet(): # self.appendCommandLine(['-restrain_rm',self.container.controlParameters.RESTRAIN_RANGE]) # (other options - less important - may be unnecessary this gui) if self.container.controlParameters.OUTPUT_PDB_CHAIN_RESTRAINTS: self.appendCommandLine(['-output_pdb_chain_restraints','-output_pdb_chain_restraints']) ### Generic Bond (H-Bond) Restraint Options if self.container.controlParameters.H_BOND: self.appendCommandLine(['-h','-h']) if self.container.controlParameters.H_HELIX: self.appendCommandLine(['-h_helix','-h_helix']) if self.container.controlParameters.H_SHEET: self.appendCommandLine(['-h_sheet','-h_sheet']) if self.container.controlParameters.H_310: self.appendCommandLine(['-3_10','-3_10']) if self.container.controlParameters.H_ALPHA: self.appendCommandLine(['-alpha','-alpha']) if self.container.controlParameters.H_PI: self.appendCommandLine(['-pi','-pi']) if self.container.controlParameters.H_STRICT: self.appendCommandLine(['-h_strict','-h_strict']) if self.container.controlParameters.H_DIST.isSet(): self.appendCommandLine(['-bond_dist',self.container.controlParameters.H_DIST]) if self.container.controlParameters.H_MIN.isSet(): self.appendCommandLine(['-bond_min',self.container.controlParameters.H_MIN]) if self.container.controlParameters.H_MAX.isSet(): self.appendCommandLine(['-bond_max',self.container.controlParameters.H_MAX]) if self.container.controlParameters.H_MIN_SEP.isSet(): self.appendCommandLine(['-min_sep',self.container.controlParameters.H_MIN_SEP]) if self.container.controlParameters.H_MAX_SEP.isSet(): self.appendCommandLine(['-max_sep',self.container.controlParameters.H_MAX_SEP]) # (Don't yet know how to specify this sort of input - expects >1 values #if self.container.controlParameters.H_ALLOW_SEP.isSet(): # self.appendCommandLine(['-allow_sep',self.container.controlParameters.H_ALLOW_SEP]) #if self.container.controlParameters.H_RM_SEP.isSet(): # self.appendCommandLine(['-rm_sep',self.container.controlParameters.H_RM_SEP]) if self.container.controlParameters.H_BOND_OPT.isSet(): if self.container.controlParameters.H_BOND_OPT == 'TYPE1': self.appendCommandLine(['-bond_opt','1']) elif self.container.controlParameters.H_BOND_OPT == 'TYPE2': self.appendCommandLine(['-bond_opt','2']) else: self.appendCommandLine(['-bond_opt','3']) if self.container.controlParameters.H_BOND_OVERRIDE.isSet(): self.appendCommandLine(['-bond_override',self.container.controlParameters.H_BOND_OVERRIDE]) ### Advanced Options #if self.container.controlParameters.THREADS.isSet(): # self.appendCommandLine(['-threads',self.container.controlParameters.THREADS]) if self.container.controlParameters.MERGE_CHAINS: self.appendCommandLine(['-merge','-merge']) if self.container.controlParameters.IS_NMR_MD_ENSEMBLE: self.appendCommandLine(['-nmr','-nmr']) if self.container.controlParameters.RENAME_CHAIN.isSet(): self.appendCommandLine(['-rename_chain',self.container.controlParameters.RENAME_CHAIN]) def processOutputFiles(self): import os,glob,shutil try: #Remove potentially confusing tempFile os.remove(self.tempFile) except: pass if not self.container.outputData.RESTRAINTS.exists(): resFileList = glob.glob(os.path.splitext(self.container.outputData.RESTRAINTS.__str__())[0]+'*.txt') if len(resFileList)==0: self.appendErrorReport(201,str(self.container.outputData.RESTRAINTS)) return CPluginScript.FAILED else: shutil.copyfile(resFileList[0],self.container.outputData.RESTRAINTS.__str__()) self.container.outputData.RESTRAINTS.annotation = 'Restraints to ' + str(self.container.inputData.XYZIN.annotation) #htmlFilePath = os.path.join(self.workDirectory.__str__(),'ProSMART_Results.html') xmlPath = self.makeFileName('PROGRAMXML') from lxml import etree xmlRoot = etree.Element('PROSMART') xmlString = etree.tostring(xmlRoot,pretty_print=True) xmlFile=open( xmlPath,'w') xmlFile.write( xmlString ) xmlFile.close() # sanity check that prosmart has produced something ok = False logText = self.logFileText() pyListLogLines = logText.split("\n") for j, pyStrLine in enumerate(pyListLogLines): if "ProSMART completed." in pyStrLine: ok = True if not ok: self.appendErrorReport(202) return CPluginScript.SUCCEEDED #====================================================== # PLUGIN TESTS # See Python documentation on unittest module import unittest class testprosmart(unittest.TestCase): def setUp(self): import CCP4Modules self.app = CCP4Modules.QTAPPLICATION() # make all background jobs wait for completion # this is essential for unittest to work CCP4Modules.PROCESSMANAGER().setWaitForFinished(10000) def tearDown(self): import CCP4Modules CCP4Modules.PROCESSMANAGER().setWaitForFinished(-1) def test_1(self): import CCP4Modules, CCP4Utils, os workDirectory = CCP4Utils.getTestTmpDir() # this needs to agree with name attribute below logFile = os.path.join(workDirectory,'prosmart_test1.log') # Delete any existing log file if os.path.exists(logFile): os.remove(logFile) self.wrapper = prosmart(parent=CCP4Modules.QTAPPLICATION(),name='prosmart_test1',workDirectory=workDirectory) self.wrapper.container.loadDataFromXml(os.path.join(CCP4Utils.getCCP4I2Dir(),'wrappers','prosmart','test_data','prosmart_test1.data.xml')) self.wrapper.setWaitForFinished(1000000) pid = self.wrapper.process() self.wrapper.setWaitForFinished(-1) if len(self.wrapper.errorReport)>0: print self.wrapper.errorReport.report() #self.assertTrue(os.path.exists(logFile),'No log file found') def test_2(self): import CCP4Modules, CCP4Utils, os workDirectory = CCP4Utils.getTestTmpDir() # this needs to agree with name attribute below logFile = os.path.join(workDirectory,'prosmart_test2.log') # Delete any existing log file if os.path.exists(logFile): os.remove(logFile) self.wrapper = prosmart(parent=CCP4Modules.QTAPPLICATION(),name='prosmart_test2',workDirectory=workDirectory) self.wrapper.container.loadDataFromXml(os.path.join(CCP4Utils.getCCP4I2Dir(),'wrappers','prosmart','test_data','prosmart_test2.data.xml')) self.wrapper.setWaitForFinished(1000000) pid = self.wrapper.process() self.wrapper.setWaitForFinished(-1) if len(self.wrapper.errorReport)>0: print self.wrapper.errorReport.report() #self.assertTrue(os.path.exists(logFile),'No log file found') def TESTSUITE(): suite = unittest.TestLoader().loadTestsFromTestCase(testprosmart) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite)