from CCP4PluginScript import CPluginScript import CCP4Utils import CCP4ErrorHandling, CCP4XtalData import os, sys, shutil from xml.etree import ElementTree as ET class arp_warp_classic(CPluginScript): TASKTITLE = 'ARP/WARP classic' TASKNAME = 'arp_warp_classic' TASKVERSION = 0.0 COMTEMPLATE = None COMTEMPLATEFILE = None MAINTAINER = 'andrey.lebedev@stfc.ac.uk' PERFORMANCECLASS = 'CModelBuildPerformance' TASKHOME = os.path.join(CCP4Utils.getCCP4I2Dir(), 'wrappers', 'arp_warp_classic') TASKCOMMAND = os.path.join(TASKHOME, 'script', 'arp_warp_classic_xml.py') def processInputFiles(self): cinp = self.container.inputData cpar = self.container.controlParameters cols = list() self.script = list() arp_mode = cpar.AWA_ARP_MODE.get() free_is_set = cinp.AWA_FREE.isSet() seqin_is_set = cinp.AWA_SEQIN.isSet() ref_mode = cpar.AWA_REF_MODE.get() cols.append(['AWA_FOBS', CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN]) self.script.append(('fp', 'AWA_FOBS_F')) self.script.append(('sigfp', 'AWA_FOBS_SIGF')) if free_is_set: cols.append('AWA_FREE') self.script.append(('freelabin', 'AWA_FREE_FREER')) if arp_mode == 'WARPNTRACEPHASES': cols.append(['AWA_PHINI', CCP4XtalData.CPhsDataFile.CONTENT_FLAG_PHIFOM]) self.script.append(('phibest', 'AWA_PHINI_PHI')) self.script.append(('fom', 'AWA_PHINI_FOM')) else: self.script.append(('modelin', str(cinp.AWA_MODELIN))) if seqin_is_set: self.script.append(('seqin', str(cinp.AWA_SEQIN))) nres = cpar.AWA_NRES.get() nmol = cpar.AWA_NMOL.get() self.script.append(('residues', nmol* nres)) self.script.append(('cgr', nmol)) if ref_mode == 'AWA_SAD': cols.append(['AWA_FOBS', CCP4XtalData.CObsDataFile.CONTENT_FLAG_FPAIR]) self.script.append(('phaselabin', 'F+=AWA_FOBS_F(+) SIGF+=AWA_FOBS_SIGF(+) F-=AWA_FOBS_F(-) SIGF-=AWA_FOBS_SIGF(-)')) self.script.append(('heavyin', cinp.AWA_HEAVYIN.get())) ano_option = cpar.AWA_ANO_OPTION.get() if ano_option == 'LAMBDA': self.script.append(('sadcard', 'ANOM WAVE ' + str(cpar.AWA_SCAT_LAMBDA_AWA_SAD.get()))) elif ano_option == 'MEASURED': scat_atom = cpar.AWA_SCAT_ATOM.get() scat_fp_sad = cpar.AWA_SCAT_FP_AWA_SAD.get() scat_fdp_sad = cpar.AWA_SCAT_FDP_AWA_SAD.get() self.script.append(('sadcard', 'ANOM FORM %s %s %s' %(scat_atom, scat_fp_sad, scat_fdp_sad))) elif ref_mode == 'AWA_HL': cols.append(['AWA_PHREF', CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL]) self.script.append(('phaselabin', 'HLA=AWA_PHREF_HLA HLB=AWA_PHREF_HLB HLC=AWA_PHREF_HLC HLD=AWA_PHREF_HLD')) elif ref_mode == 'AWA_PHASED': cols.append(['AWA_PHREF', CCP4XtalData.CPhsDataFile.CONTENT_FLAG_PHIFOM]) self.script.append(('phaselabin', 'PHIB=AWA_PHREF_PHI FOM=AWA_PHREF_FOM')) self.hklin, columns, error = self.makeHklin0(cols) if error.maxSeverity() > CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED if arp_mode == 'MOLREP': self.script.append(('restrref', cpar.AWA_SMALL_CYCLES.get())) else: self.script.append(('buildingcycles', cpar.AWA_BIG_CYCLES.get())) small_cycles = cpar.AWA_SMALL_CYCLES.get() self.script.append(('restrref', small_cycles)) use_cond = cpar.AWA_USE_COND.get() force_cond = cpar.AWA_FORCE_COND.get() self.script.append(('restraints', 2 if force_cond and use_cond else 1 if use_cond else 0)) if cpar.AWA_FAKE_DATA.get(): self.script.append(('fakedata', '0.33 0.75 1')) self.script.append(('ncsrestraints', int(cpar.AWA_NCS_RESTRAINTS.get()))) self.script.append(('ncsextension', int(cpar.AWA_NCS_EXTENSION.get()))) self.script.append(('loops', int(cpar.AWA_LOOPS.get()))) self.script.append(('side', cpar.AWA_SIDE_AFTER.get() if seqin_is_set and cpar.AWA_BUILD_SIDE.get() else -1)) if ref_mode == 'AWA_SAD': self.script.append(('is_semet', int(cpar.AWA_IS_SEMET.get()))) self.script.append(('albe', int(cpar.AWA_ALBE.get()))) skip_build = cpar.AWA_SKIP_BUILD.get() skip_cycles = cpar.AWA_SKIP_CYCLES.get() self.script.append(('cycskip', skip_cycles* small_cycles if skip_build else 0)) self.script.append(('multit', cpar.AWA_MULTITRACE.get())) if arp_mode == 'WARPNTRACEMODEL': self.script.append(('freebuild', int(cpar.AWA_FREEBUILD.get()))) self.script.append(('flatten', int(cpar.AWA_FLATTEN.get()))) self.script.append(('fsig', cpar.AWA_ADDATOM_SIGMA.get())) self.script.append(('rsig', cpar.AWA_REMATOM_SIGMA.get())) self.script.append(('upmore', cpar.AWA_UP_UPDATE.get())) if ref_mode != 'AWA_SAD': self.script.append(('twin', int(cpar.AWA_TWIN.get()))) self.script.append(('rrcyc', cpar.AWA_NCYCLES.get())) if ref_mode in ('AWA_HL', 'AWA_PHASED'): self.script.append(('phaseref', 'PHAS SCBL ' + str(cpar.AWA_PHASE_BLUR.get()))) weight_mode = cpar.AWA_WEIGHT_MODE.get() self.script.append(('wmat', 'AUTO' if weight_mode == 'AUTO' else 'MATRIX')) if weight_mode != 'AUTO': self.script.append(('weightv', cpar.AWA_WMAT.get())) self.script.append(('ridgerestraints', int(cpar.AWA_RIDGE_RESTRAINTS.get()))) scale = cpar.AWA_SCALE.get() self.script.append(('scaleopt', scale + ' LSSC ANIS' if cpar.AWA_SCANIS.get() else scale)) self.script.append(('scalml', 'SCAL MLSC FREE' if free_is_set and cpar.AWA_REFMAC_REF_SET.get() else 'SCAL MLSC')) self.script.append(('solvent', int(cpar.AWA_SOLVENT.get()))) if cpar.AWA_MOCKYES.get(): self.script.append(('mockdir', os.path.join(self.TASKHOME, 'mock_data', 'PSP'))) self.script.append(('pause', cpar.AWA_MOCKPAUSE.get())) self.script.append(('jsrview', '1' if cpar.AWA_JSRVIEW.get() else None)) self.script.append(('workdir', self.workDirectory)) self.script.append(('jobId', 'PSP')) self.script.append(('datafile', self.hklin)) self.script.append(('xmlout', self.makeFileName('PROGRAMXML'))) return CPluginScript.SUCCEEDED def makeCommandAndScript(self): for key, value in self.script: if not value is None: tvalue = str(value).strip() if tvalue: self.appendCommandScript(key + ' ' + tvalue) return CPluginScript.SUCCEEDED def processOutputFiles(self): annotation = self.jobNumberString() + ' 2mFo-DFc map coefficients from ARP/WARP' self.container.outputData.FPHIOUT.annotation = annotation self.container.outputData.FPHIOUT.subType = 1 annotation = self.jobNumberString() + ' mFo-DFc map coefficients from ARP/WARP' self.container.outputData.DIFFPHIOUT.annotation = annotation self.container.outputData.DIFFPHIOUT.subType = 2 xyzwrk = os.path.join(self.workDirectory,'PSP','PSP_warpNtrace.pdb') if os.path.isfile(xyzwrk): with open(xyzwrk) as istream: pdb_records = istream.read() import re match_dummy = re.search('^ATOM .+ DUM +DUM ', pdb_records, flags=re.M) if match_dummy: xyzdum = str(self.container.outputData.XYZDUM.fullPath) annotation = self.jobNumberString() + ' ARP/WARP model with dummy atoms' self.container.outputData.XYZDUM.annotation = annotation self.container.outputData.XYZDUM.subType = 1 with open(xyzdum, 'w') as ostream: ostream.write(pdb_records) pdb_records = pdb_records[:match_dummy.start()] xyzout = str(self.container.outputData.XYZOUT.fullPath) annotation = self.jobNumberString() + ' ARP/WARP model' self.container.outputData.XYZOUT.annotation = annotation self.container.outputData.XYZOUT.subType = 1 with open(xyzout, 'w') as ostream: ostream.write(pdb_records) else: return CPluginScript.FAILED hklawa = os.path.join(self.workDirectory,'PSP','PSP_warpNtrace.mtz') outputFiles = ['FPHIOUT','DIFFPHIOUT'] outputColumns = ['FWT,PHWT','DELFWT,PHDELWT'] error = self.splitHklout(outputFiles, outputColumns, infile=hklawa) if error.maxSeverity() > CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED try: cycles = list() e0 = ET.parse(self.makeFileName('PROGRAMXML')).getroot() for e3 in e0.findall('./BuildRefineCycle'): cycles.append((int(e3.findtext('Number')), float(e3.find('RefmacResult').findtext('r_factor')))) self.container.outputData.PERFORMANCE.RFactor = sorted(cycles)[-1][1] # self.container.outputData.PERFORMANCE.completeness = 0.89 # broken? return CPluginScript.SUCCEEDED except: return CPluginScript.FAILED