""" crank2.py: CCP4 GUI Project Copyright (C) 2010 University of York, Leiden University 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. """ from CCP4PluginScript import CPluginScript import CCP4ErrorHandling, CCP4Utils, CCP4XtalData import CCP4Modules import crank2_basepipe import sys,os,shutil crank2_path=os.path.join(CCP4Utils.getCCP4I2Dir(),'pipelines','crank2','crank2') sys.path.append( crank2_path ) class crank2(CPluginScript): #TASKMODULE = 'expt_phasing' TASKTITLE = 'Crank2' SHORTTASKTITLE = 'CRANK2' TASKNAME = 'crank2' TASKCOMMAND = 'crank2.py' TASKVERSION = 0.02 PERFORMANCECLASS = 'CExpPhasPerformance' ERROR_CODES = { 0: {'description': ' '}, } MAINTAINER = 'skubakp@gmail.com' def CheckUse(self, cont, param): # use this function for all parameters that can be set by default or by user if getattr(cont,param).isSet() and ( not hasattr(cont,'USER_'+param) or getattr(cont,'USER_'+param) ): return True else: return False def GetProgramKeysOrArgs(self, key_str, args=False, onechar=False): keys = key_str.split(',') keys2 = [] for k in keys: key,sep,val = k.strip().partition(' ') key,val=key.strip(),val.strip() if args: key,val=key.strip('-'),val.strip('-') if len(key)>1 and val=='' and onechar: val=key[1:] key=key[0] if val=='': val = 'True' val = val.split() if key and args: for v in val: keys2.append('{};{}'.format(key,v)) if key and not args: for v in val: keys2.append('{}:{}'.format(key,v)) return keys2 def process(self, container=None): defaults = False if container: self.container = container defaults = True # fixbrokenpluginname: try: if self.parent() and self.parent().pluginName.startswith('crank2_'): self.container.saveDataToXml(self.parent().comFilePath) except RuntimeError: sys.exc_clear() basepipe = crank2_basepipe.crank2_basepipe() basepipe.SetBaseSteps(self.container) # for convenience inp = self.container.inputData ctrl = self.container.controlParameters crank_lines = [] fpfpp = {} cell, spgr = '', '' if inp.NON_MTZ and (inp.USER_CELL_A or inp.USER_CELL_B or inp.USER_CELL_C or inp.USER_CELL_D or inp.USER_CELL_E or inp.USER_CELL_F): cell = 'cell={},{},{},{},{},{}'.format(inp.CELL_A,inp.CELL_B,inp.CELL_C,inp.CELL_D,inp.CELL_E,inp.CELL_F) if inp.USER_SPACEGROUP and inp.NON_MTZ: spgr = '"spgr={}"'.format(inp.SPACEGROUP) for i in range(4): si = str(i+1) if i else '' sif = si+'_nonmtz' if inp.NON_MTZ else si anom = getattr(inp,'F_SIGFanom'+sif) dn = getattr(inp,'DNAME'+si) dnstr = "dname="+str(dn) if dn else "" if anom.fullPath.isSet() and (anom.contentFlag.isSet() or inp.NON_MTZ) and (not i or getattr(inp,'MAD'+si)): saved_fpm = getattr(inp,'SAVED_FPMFILE'+si) if saved_fpm and defaults and os.path.isfile(str(saved_fpm)): crank_lines.append("fsigf plus {1} f={2} sigf={3} \"file={0}\" {4} {5}".format( saved_fpm, dnstr, getattr(inp,'SAVED_FPLUS'+si),getattr(inp,'SAVED_SIGFPLUS'+si),cell,spgr )) crank_lines.append("fsigf minus {0} f={1} sigf={2} {3} {4}".format( dnstr, getattr(inp,'SAVED_FMIN'+si),getattr(inp,'SAVED_SIGFMIN'+si),cell,spgr )) crank_lines.append("fsigf average {0} f={2} sigf={3} \"file={1}\" {4} {5}".format( dnstr, getattr(inp,'SAVED_FAVFILE'+si), getattr(inp,'SAVED_FAVER'+si),getattr(inp,'SAVED_SIGFAVER'+si),cell,spgr )) elif anom.contentFlag.isSet() and anom.contentFlag == CCP4XtalData.CObsDataFile.CONTENT_FLAG_FPAIR: crank_lines.append("fsigf plus {} f=Fplus sigf=SIGFplus \"file={}\" {} {}".format(dnstr,anom.fullPath,cell,spgr)) crank_lines.append("fsigf minus {} f=Fminus sigf=SIGFminus {} {}".format(dnstr,cell,spgr)) elif inp.NON_MTZ or anom.contentFlag == CCP4XtalData.CObsDataFile.CONTENT_FLAG_IPAIR: crank_lines.append("fsigf plus {1} i=Iplus sigi=SIGIplus \"file={0}\" {2} {3}".format(anom.fullPath,dnstr,cell,spgr)) crank_lines.append("fsigf minus {} i=Iminus sigi=SIGIminus {} {}".format(dnstr,cell,spgr)) if self.CheckUse(inp,'WAVELENGTH'+si) and crank_lines: crank_lines[-1] += " wavel={}".format(getattr(inp,'WAVELENGTH'+si)) if self.CheckUse(inp,'FPRIME'+si) or self.CheckUse(inp,'FDPRIME'+si): fpfpp[dn] = [getattr(inp,'FPRIME'+si), getattr(inp,'FDPRIME'+si)] native = inp.F_SIGFnative_nonmtz if inp.NON_MTZ else inp.F_SIGFnative if inp.NATIVE and native.fullPath.isSet() and native.contentFlag.isSet(): saved_aver = getattr(inp,'SAVED_FAVFILE_NATIVE') if saved_aver and os.path.isfile(str(saved_aver)) and (defaults or not '.mtz' in native.fullPath): crank_lines.append("fsigf average xname=native dname=nat f={} sigf={} \"file={}\" {}".format( \ inp.SAVED_FAVER_NATIVE,inp.SAVED_SIGFAVER_NATIVE,inp.SAVED_FAVFILE_NATIVE,cell,spgr)) elif native.contentFlag == CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN: crank_lines.append("fsigf average xname=native dname=nat f=F sigf=SIGF \"file={}\" {} {}".format(native.fullPath,cell,spgr)) if native.contentFlag == CCP4XtalData.CObsDataFile.CONTENT_FLAG_IMEAN: crank_lines.append("fsigf average xname=native dname=nat i=I sigi=SIGI \"file={}\" {} {}".format(native.fullPath,cell,spgr)) elif native.contentFlag == CCP4XtalData.CObsDataFile.CONTENT_FLAG_IPAIR: crank_lines.append("fsigf plus xname=native dname=nat i=Iplus sigi=SIGIplus \"file={0}\" {1} {2}".format(native.fullPath,cell,spgr)) crank_lines.append("fsigf minus xname=native dname=nat i=Iminus sigi=SIGIminus {} {}".format(cell,spgr)) elif native.contentFlag == CCP4XtalData.CObsDataFile.CONTENT_FLAG_FPAIR: crank_lines.append("fsigf plus xname=native dname=nat f=Fplus sigf=SIGFplus \"file={0}\" {1} {2}".format(native.fullPath,cell,spgr)) crank_lines.append("fsigf minus xname=native dname=nat f=Fminus sigf=SIGFminus {} {}".format(cell,spgr)) #else: # print 'WARNING: Native inputted as anomalous pairs, mean is needed! Data ignored.' if inp.INPUT_PARTIAL: model = "model unknown" if inp.XYZIN.isSet(): model += " \"file={0}\"".format(inp.XYZIN.fullPath) if self.CheckUse(ctrl,'COMB_PHDMMB_NCS_DET_MR') and ctrl.COMB_PHDMMB_NCS_DET_MR: model += " custom=ncs" if inp.ATOM_TYPE.isSet(): model += " atomtype={0}".format(inp.ATOM_TYPE) if self.CheckUse(inp,'FPRIME') and self.CheckUse(inp,'FDPRIME'): model += " fp={0} fpp={1}".format(inp.FPRIME, inp.FDPRIME) crank_lines.append("{0}".format(model)) # why was this code here? it inputs the partial model if partial model was unclicked... #elif inp.XYZIN.isSet(): # crank_lines.append("model partial \"file={0}\"".format(inp.XYZIN.fullPath)) if inp.ATOM_TYPE.isSet(): model = "model substr atomtype={0}".format(inp.ATOM_TYPE) if inp.XYZIN_SUB.isSet(): #substr_file = str(inp.XYZIN_SUB) #if os.path.basename(str(inp.XYZIN_SUB.fullPath)).startswith('SHELX_fa'): # substr_file = os.path.join(self.workDirectory,'SHELX_fa.res') # shutil.copy(str(inp.XYZIN_SUB),substr_file) model += " \"file={}\"".format(inp.XYZIN_SUB) if inp.XYZIN_SUB_RES.isSet(): model += " \"file={}\"".format(inp.XYZIN_SUB_RES) for dn,f in fpfpp.iteritems(): if dn: model += " d_name={}".format(dn) model += " fp={} fpp={}".format(f[0], f[1]) #if self.CheckUse(inp,'NUMBER_SUBSTRUCTURE') and inp.MONOMERS_ASYM.isSet(): # model += " exp_num_atoms={0}".format(inp.NUMBER_SUBSTRUCTURE*inp.MONOMERS_ASYM) if self.CheckUse(inp,'NUMBER_SUBSTRUCTURE'): model += " exp_num_atoms={0}".format(inp.NUMBER_SUBSTRUCTURE) if self.CheckUse(inp,'RESIDUES_MON'): model += " residues_mon={0}".format(inp.RESIDUES_MON) if self.CheckUse(inp,'MONOMERS_ASYM'): model += " monomers_asym={0}".format(inp.MONOMERS_ASYM) if self.CheckUse(inp,'SOLVENT_CONTENT'): model += " solvent_content={0}".format(inp.SOLVENT_CONTENT) crank_lines.append("{0}".format(model)) # *** NSP - what about DNA??? if inp.SEQIN.isSet() and inp.INPUT_SEQUENCE: sequence = "sequence \"file={0}\"".format(inp.SEQIN.fullPath) crank_lines.append("{0}".format(sequence)) if inp.FPHIN_HL.isSet() and inp.INPUT_PHASES: if inp.FPHIN_HL.contentFlag==CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL: phases = "mapcoef \"file={0}\" hla=HLA hlb=HLB hlc=HLC hld=HLD".format(inp.FPHIN_HL.fullPath) else: phases = "mapcoef \"file={0}\" ph=PHI fom=FOM".format(inp.FPHIN_HL.fullPath) crank_lines.append(phases) if self.CheckUse(inp,'EXPTYPE'): crank_lines.append("target::{0}".format(inp.EXPTYPE)) #if inp.REPLACE_MET_MSE.isSet() and inp.REPLACE_MET_MSE: # crank_lines.append("replace_met_mse::1") if str(inp.FREE)=='new': no_out_next = 'no_output_to_next_step::True' if not inp.INPUT_PARTIAL else '' crank_lines.append("createfree {} fraction::{}".format(no_out_next, inp.FREE_RATIO*0.01)) self.i2_shelxdir = None if hasattr(CCP4Modules.PREFERENCES(),'SHELXDIR') and CCP4Modules.PREFERENCES().SHELXDIR: self.i2_shelxdir = str(CCP4Modules.PREFERENCES().SHELXDIR) if basepipe.ToggleDetection() or (basepipe.ToggleShelxCDE() and (inp.XYZIN_SUB.isSet() or inp.XYZIN_SUB_RES.isSet())): faest = "faest" # this should be removed once we have a "dummy" 'program' keyowrd in crank2! if not ctrl.FAEST_PROGRAM.isSet() and self.i2_shelxdir and os.path.isfile(os.path.join(self.i2_shelxdir,'shelxc')): ctrl.FAEST_PROGRAM.set('shelxc') if ctrl.FAEST_PROGRAM.isSet(): faest += " {}".format(ctrl.FAEST_PROGRAM) if ctrl.FAEST_PROGRAM.startswith('shelx') and self.i2_shelxdir: faest += ' "binary::{}"'.format(os.path.join(self.i2_shelxdir,str(ctrl.FAEST_PROGRAM))) crank_lines.append(faest) if basepipe.ToggleDetection(): substrdet = "substrdet" if self.CheckUse(ctrl,'SUBSTRDET_HIGH_RES_CUTOFF'): substrdet += " high_res_cutoff::{0}".format(ctrl.SUBSTRDET_HIGH_RES_CUTOFF) if self.CheckUse(ctrl,'SUBSTRDET_HIGH_RES_CUTOFF_CCHALF'): substrdet += " high_res_cutoff_cchalf::{0}".format(bool(ctrl.SUBSTRDET_HIGH_RES_CUTOFF_CCHALF)) if self.CheckUse(ctrl,'SUBSTRDET_HIGH_RES_CUTOFF_RADIUS') and str(ctrl.SUBSTRDET_PROGRAM)=='prasa': substrdet += " high_res_cutoff_radius::{0}".format(ctrl.SUBSTRDET_HIGH_RES_CUTOFF_RADIUS) if self.CheckUse(ctrl,'SUBSTRDET_HIGH_RES_CUTOFF_STEP'): substrdet += " high_res_cutoff_step::{0}".format(ctrl.SUBSTRDET_HIGH_RES_CUTOFF_STEP) if self.CheckUse(ctrl,'SUBSTRDET_THRESHOLD_STOP'): substrdet += ' threshold_stop::{0}'.format(ctrl.SUBSTRDET_THRESHOLD_STOP) if self.CheckUse(ctrl,'SUBSTRDET_THRESHOLD_WEAK'): substrdet += ' threshold_weak::{0}'.format(ctrl.SUBSTRDET_THRESHOLD_WEAK) if self.CheckUse(ctrl,'SUBSTRDET_NUM_TRIALS'): substrdet += " num_trials::{0}".format(ctrl.SUBSTRDET_NUM_TRIALS) if self.CheckUse(ctrl,'SUBSTRDET_MIN_DIST_ATOMS'): minus='-' if not str(ctrl.SUBSTRDET_MIN_DIST_ATOMS).startswith('-') else '' substrdet += " min_dist_atoms::{}{}".format(minus,ctrl.SUBSTRDET_MIN_DIST_ATOMS) if self.CheckUse(ctrl,'SUBSTRDET_MIN_DIST_SYMM_ATOMS'): substrdet += " min_dist_symm_atoms::{}".format(-0.1 if ctrl.SUBSTRDET_MIN_DIST_SYMM_ATOMS else 3) if ctrl.PRASA_NUM_ATOMS_RESTR and inp.NUMBER_SUBSTRUCTURE: substrdet += " num_atoms::{}".format(inp.NUMBER_SUBSTRUCTURE) # this should be removed once we have a "dummy" 'program' keyowrd in crank2! if not ctrl.SUBSTRDET_PROGRAM.isSet() and self.i2_shelxdir and os.path.isfile(os.path.join(self.i2_shelxdir,'shelxd')): ctrl.SUBSTRDET_PROGRAM.set('shelxd') if ctrl.SUBSTRDET_PROGRAM.isSet(): if ctrl.SUBSTRDET_PROGRAM.startswith('shelx') and self.CheckUse(inp,'SUBSTRDET_NUM_DSUL'): substrdet += " num_dsul::{}".format(inp.SUBSTRDET_NUM_DSUL) substrdet += " {0}".format(ctrl.SUBSTRDET_PROGRAM) if ctrl.SUBSTRDET_PROGRAM.startswith('shelx') and self.i2_shelxdir: substrdet += ' "binary::{}"'.format(os.path.join(self.i2_shelxdir,str(ctrl.SUBSTRDET_PROGRAM))) if ctrl.KEYWORDS_SUBSTRDET.isSet(): substrdet += ' '+' '.join( self.GetProgramKeysOrArgs(ctrl.KEYWORDS_SUBSTRDET) ) #substrdet += ' - \n \"keywords={0}\"'.format(ctrl.KEYWORDS_SUBSTRDET) crank_lines.append(substrdet) if basepipe.TogglePeakSearch(): refatompick = "refatompick" if self.CheckUse(ctrl,'REFATOMPICK_NUM_ITER'): refatompick += " num_iter::{0}".format(ctrl.REFATOMPICK_NUM_ITER) if self.CheckUse(ctrl,'REFATOMPICK_REFCYC'): refatompick += " refcyc::{0}".format(ctrl.REFATOMPICK_REFCYC) if self.CheckUse(ctrl,'REFATOMPICK_RMS_THRESHOLD'): refatompick += " rms_threshold::{0}".format(ctrl.REFATOMPICK_RMS_THRESHOLD) #if self.CheckUse(ctrl,'REFATOMPICK_REF_PROGRAM'): # refatompick += " ref {0}".format(ctrl.REFATOMPICK_REF_PROGRAM) #else: # refatompick += " ref" # Do we need this?? ***NSP crank_lines.append(refatompick) if inp.INPUT_PARTIAL and inp.PARTIAL_AS_SUBSTR: crank_lines.append("sepsubstrprot") if basepipe.ToggleShelxCDE(): phdmmb = "phdmmb" if self.CheckUse(ctrl,'PHDMMB_DMCYC'): phdmmb += " dmcyc::{0}".format(ctrl.PHDMMB_DMCYC) if self.CheckUse(ctrl,'PHDMMB_BIGCYC'): phdmmb += " bigcyc::{0}".format(ctrl.PHDMMB_BIGCYC) if self.CheckUse(ctrl,'PHDMMB_THRESHOLD_STOP'): phdmmb += " threshold_stop::{0}".format(ctrl.PHDMMB_THRESHOLD_STOP) if self.CheckUse(ctrl,'PHDMMB_THRESHOLD_HAND_STOP'): phdmmb += " threshold_hand_stop::{0}".format(ctrl.PHDMMB_THRESHOLD_HAND_STOP) if self.CheckUse(ctrl,'PHDMMB_THOROUGH_BUILD'): phdmmb += " thorough_build::{0}".format(bool(ctrl.PHDMMB_THOROUGH_BUILD)) if self.CheckUse(inp,'SUBSTR_ATOMS_NATIVE'): phdmmb += " substr_in_native::{}".format(str(inp.SUBSTR_ATOMS_NATIVE)) phdmmb += " shelxe" if self.i2_shelxdir: phdmmb += ' "binary::{}"'.format(os.path.join(self.i2_shelxdir,'shelxe')) if ctrl.ARGUMENTS_SHELXE.isSet(): phdmmb += ' '+' '.join( self.GetProgramKeysOrArgs(ctrl.ARGUMENTS_SHELXE,args=True,onechar=True) ) crank_lines.append(phdmmb) if basepipe.TogglePhasing(): phas = "phas" if self.CheckUse(ctrl,'PHAS_CYCLES'): phas += " cycles::{0}".format(ctrl.PHAS_CYCLES) if ctrl.PHAS_PROGRAM.isSet(): phas += " {0}".format(ctrl.PHAS_PROGRAM) if ctrl.KEYWORDS_PHAS.isSet(): phas += ' - \n \" keywords={0}\"'.format(ctrl.KEYWORDS_PHAS) crank_lines.append(phas) if basepipe.ToggleHandDetermination() and ctrl.DO_HANDDET: handdet = "handdet dmfull" #if ctrl.HANDDET_DMCYC.isSet(): # handdet += " dmcyc::{0}".format(ctrl.HANDDET_DMCYC) if ctrl.HANDDET_DMFULL_DM_PROGRAM.isSet(): handdet += " dm {0}".format(ctrl.HANDDET_DMFULL_DM_PROGRAM) else: handdet += " dm" # Do we need this?? ***NSP if ctrl.KEYWORDS_HANDDET_DM.isSet(): handdet += ' - \n \" keywords={0}\"\n'.format(ctrl.KEYWORDS_HANDDET_DM) if ctrl.HANDDET_DMFULL_PHCOMB_PROGRAM.isSet(): handdet += " phcomb {0}".format(ctrl.HANDDET_DMFULL_PHCOMB_PROGRAM) else: handdet += " phcomb" # Do we need this?? ***NSP if ctrl.KEYWORDS_HANDDET_PHCOMB.isSet(): handdet += ' - \n \" keywords={0}\"'.format(ctrl.KEYWORDS_HANDDET_PHCOMB) crank_lines.append(handdet) if basepipe.ToggleDensityModification(): dmfull = "dmfull" if self.CheckUse(ctrl,'DMFULL_DMCYC'): dmfull += " dmcyc::{0}".format(ctrl.DMFULL_DMCYC) if self.CheckUse(ctrl,'DMFULL_THRESHOLD_STOP'): dmfull += " threshold_stop::{0}".format(ctrl.DMFULL_THRESHOLD_STOP) if ctrl.DMFULL_DM_PROGRAM.isSet(): dmfull += " dm {0}".format(ctrl.DMFULL_DM_PROGRAM) else: dmfull += " dm" # Do we need this?? ***NSP # We do. ***PS if ctrl.KEYWORDS_DMFULL_DM.isSet(): dmfull += ' '+' '.join( self.GetProgramKeysOrArgs(ctrl.KEYWORDS_DMFULL_DM,args=str(ctrl.DMFULL_DM_PROGRAM)!='solomon') ) # dmfull += ' - \n \" keywords={0}\"\n'.format(ctrl.KEYWORDS_DMFULL_DM) if ctrl.DMFULL_PHCOMB_PROGRAM.isSet(): dmfull += " phcomb {0}".format(ctrl.DMFULL_PHCOMB_PROGRAM) else: dmfull += " phcomb" # Do we need this?? ***NSP if ctrl.KEYWORDS_DMFULL_PHCOMB.isSet(): dmfull += ' - \n \" keywords={0}\"'.format(ctrl.KEYWORDS_DMFULL_PHCOMB) crank_lines.append(dmfull) if basepipe.ToggleModelBuilding(): if basepipe.ToggleUseComb(): model_build = "comb_phdmmb target::SAD" if self.CheckUse(ctrl,'COMB_PHDMMB_MINBIGCYC'): model_build += " minbigcyc::{0}".format(ctrl.COMB_PHDMMB_MINBIGCYC) if self.CheckUse(ctrl,'COMB_PHDMMB_MAXBIGCYC'): model_build += " maxbigcyc::{0}".format(ctrl.COMB_PHDMMB_MAXBIGCYC) if self.CheckUse(ctrl,'COMB_PHDMMB_NCS_DET') and basepipe.ToggleNCS(): model_build += " ncs_det::{0}".format(ctrl.COMB_PHDMMB_NCS_DET._value) if self.CheckUse(ctrl,'COMB_PHDMMB_NCS_DET_MR') and basepipe.ToggleNCS(): model_build += " ncs_det_mr::{0}".format(ctrl.COMB_PHDMMB_NCS_DET_MR._value) if self.CheckUse(ctrl,'COMB_PHDMMB_SKIP_INITIAL_BUILD'): model_build += " skip_initial_build::{0}".format(ctrl.COMB_PHDMMB_SKIP_INITIAL_BUILD._value) if self.CheckUse(ctrl,'COMB_PHDMMB_REBUILD_ONLY'): model_build += " rebuild_only::{0}".format(ctrl.COMB_PHDMMB_REBUILD_ONLY._value) if self.CheckUse(ctrl,'COMB_PHDMMB_START_SHELXE'): model_build += " start_shelxe::{0}".format(bool(ctrl.COMB_PHDMMB_START_SHELXE)) if ctrl.COMB_PHDMMB_EXCLUDE_FREE!='never': if ctrl.COMB_PHDMMB_EXCLUDE_FREE=='last': model_build += " always_exclude_free::False" model_build += self.SetFree() if self.CheckUse(ctrl,'COMB_PHDMMB_DMFULL_DM_PROGRAM'): model_build += " dmfull dm {0}".format(ctrl.COMB_PHDMMB_DMFULL_DM_PROGRAM) else: model_build += " dmfull dm" # Do we need this?? ***NSP if ctrl.KEYWORDS_COMB_DM.isSet(): model_build += ' '+' '.join( self.GetProgramKeysOrArgs(ctrl.KEYWORDS_COMB_DM,args=str(ctrl.COMB_PHDMMB_DMFULL_DM_PROGRAM)!='solomon') ) #model_build += ' - \n \" keywords={0}\"\n'.format(ctrl.KEYWORDS_COMB_DM) if ctrl.KEYWORDS_MB.isSet(): model_build += ' mb buccaneer '+' '.join( self.GetProgramKeysOrArgs(ctrl.KEYWORDS_MB,args=True) ) if ctrl.KEYWORDS_COMB_SHELXE.isSet() and self.CheckUse(ctrl,'COMB_PHDMMB_START_SHELXE'): model_build += ' shelxe \" keywords={0}\"\n'.format(self.GetProgramKeysOrArgs(ctrl.KEYWORDS_COMB_SHELXE,args=True,onechar=True)) else: model_build = "mbref" if ctrl.MBREF_EXCLUDE_FREE: model_build += self.SetFree() if self.CheckUse(ctrl,'MBREF_BIGCYC'): model_build += " bigcyc::{0}".format(ctrl.MBREF_BIGCYC) if ctrl.MB_PROGRAM.isSet() and str(ctrl.MB_PROGRAM)=='arpwarp': model_build += " arpwarp" else: if ctrl.MBREF_REF_PROGRAM.isSet(): model_build += " ref {0}".format(ctrl.MBREF_REF_PROGRAM) else: model_build += " ref" # Do we need this?? ***NSP if ctrl.KEYWORDS_MB.isSet(): model_build += ' - \n \" keywords={0}\"\n'.format(ctrl.KEYWORDS_MB_REF) if ctrl.MB_PROGRAM.isSet(): model_build += " mb {0}".format(ctrl.MB_PROGRAM) else: model_build += " mb" # Do we need this?? ***NSP if ctrl.KEYWORDS_MB.isSet(): model_build += ' - \n \" keywords={0}\"\n'.format(ctrl.KEYWORDS_MB) if ctrl.KEYWORDS_COMB_SHELXE.isSet() and self.CheckUse(ctrl,'COMB_PHDMMB_START_SHELXE'): model_build += ' shelxe \" keywords={0}\"\n'.format(self.GetProgramKeysOrArgs(ctrl.KEYWORDS_COMB_SHELXE,args=True,onechar=True)) crank_lines.append(model_build) if basepipe.ToggleRefine(): ref = "ref target::mlhl" if self.CheckUse(ctrl,'REF_CYCLES'): ref += " cycles::{0}".format(ctrl.REF_CYCLES) # ***NSP when rfree is allowed from input, we need to allow it to be input here... if ctrl.REF_EXCLUDE_FREE: ref += self.SetFree() if ctrl.REF_PROGRAM.isSet(): ref += " {0}".format(ctrl.REF_PROGRAM) if ctrl.KEYWORDS_REF.isSet(): ref += ' - \n \" keywords={0}\"\n'.format(ctrl.KEYWORDS_REF) crank_lines.append(ref) inpfile = os.path.join(self.workDirectory, 'crank.inp') with open(inpfile,'w') as g: g.write( '\n'.join(crank_lines) ) if (inp.F_SIGFanom.fullPath.isSet() or inp.F_SIGFanom_nonmtz.fullPath.isSet()) or (defaults and inp.SEQIN.isSet()): # (inp.SEQIN.isSet() or inp.RESIDUES_MON.isSet()): rvapi_style = str(ctrl.PRESENT_STYLE) if (ctrl,'PRESENT_STYLE') else 'rvapi_tree' i2natfile = os.path.join(self.workDirectory, 'i2_native_present') self.rvapi_converter=False if rvapi_style == 'i2_bigpage': with open(i2natfile,'w') as g: g.write('using i2 native presentation') self.rvapi_converter=True elif os.path.isfile(i2natfile): os.remove(i2natfile) import ccp4i2crank,common,traceback try: return ccp4i2crank.CallCrankFromCCP4i2(self, inpfile=inpfile, defaults=defaults, rvapi_style=rvapi_style) # except common.CrankError as e: # self.appendErrorReport(1000, str(e)) # try: # self.reportStatus(CPluginScript.FAILED) # except RuntimeError: # raise e except common.Unsuccessful as e: self.appendErrorReport(1000, str(e)) try: self.reportStatus(CPluginScript.UNSATISFACTORY) except RuntimeError: raise e, None, sys.exc_info()[2] except Exception as e: err = str(e) +'\n\n'+str(traceback.format_exc()) self.appendErrorReport(0, err) try: self.reportStatus(CPluginScript.FAILED) except RuntimeError: raise e, None, sys.exc_info()[2] else: return 0 def SetFree(self): inp = self.container.inputData if str(inp.FREE)=='new': return " exclude obj_from=0,typ=freeR" elif str(inp.FREE)=='existing' and inp.FREERFLAG.isSet(): return " exclude typ=freeR free=FREER \"file={}\"".format(inp.FREERFLAG.fullPath) return "" def setProgramVersion(self): with open(os.path.join(crank2_path,'VERSION')) as f: return f.read()