import warnings class ATOM(object): def setATOM_BFACTOR_WILSON(self): warnings.warn( "Deprecated function: use setATOM_CHANGE_BFAC", DeprecationWarning ) self.setATOM_CHANGE_BFAC( true ) def setATOM_PDB_SCAT(self,x,w,e): warnings.warn( "Deprecated function: use setATOM_CHANGE_SCAT", DeprecationWarning ) self.setATOM_CHANGE_SCAT( true ) self.setATOM_SCAT( e ) class COMP(object): def addPROT(self, mw, num): warnings.warn( "Deprecated function: use addCOMP_PROT_MW_NUM", DeprecationWarning ) self.addCOMP_PROT_MW_NUM( mw, num ) def addNUCL(self, mw, num): warnings.warn( "Deprecated function: use addCOMP_NUCL_MW_NUM", DeprecationWarning ) self.addCOMP_NUCL_MW_NUM( mw, num ) def addPROT_SEQ(self, seq, num): warnings.warn( "Deprecated function: use addCOMP_PROT_SEQ_NUM", DeprecationWarning ) self.addCOMP_PROT_SEQ_NUM( seq, num ) def addNUCL_SEQ(self, seq, num): warnings.warn( "Deprecated function: use addCOMP_NUCL_SEQ_NUM", DeprecationWarning ) self.addCOMP_NUCL_SEQ_NUM( seq, num ) class CRYS(object): def setCRYS_MILLER(self, m): warnings.warn( "Deprecated function: use setCRYS_SAD_DATA", DeprecationWarning ) self.setCRYS_MILLER(m) def addCRYS_ANOM_DATA(self, x,w,a,b,c,d,e,f): warnings.warn( "Deprecated function: use setCRYS_SAD_DATA", DeprecationWarning ) self.setCRYS_ANOM_DATA(a,b,c,d,e,f) class EIGE(object): def setREAD_EIGENFILE(self, eigenfile): warnings.warn( "Deprecated function: use setEIGE_READ", DeprecationWarning ) self.setEIGE_READ(modlid, frac) def setWRITE_EIGENFILE(self, eigenfile): warnings.warn( "Deprecated function: use setEIGE_WRITE", DeprecationWarning ) self.setEIGE_WRITE( modlid, frac ) class ENSE(object): def addPDB(self, modlid, pdbfile, homology_as_rms, rms_identity): warnings.warn( "Deprecated function: use addENSE_PDB_RMS or addENSE_PDB_ID", DeprecationWarning ) if homology_as_rms: self.addENSE_PDB_RMS( modlid, pdbfile, rms_identity ) else: self.addENSE_PDB_ID( modlid, rms_identity ) def addPDB_RMS(self, modlid, pdbfile, rms_identity): warnings.warn( "Deprecated function: use addENSE_PDB_RMS", DeprecationWarning ) self.addENSE_PDB_RMS( modlid, pdbfile, rms_identity ) def addPDB_ID(self, modlid, pdbfile, rms_identity): warnings.warn( "Deprecated function: use addENSE_PDB_ID", DeprecationWarning ) self.addENSE_PDB_ID( modlid, pdbfile, rms_identity ) def setMAP_MW(self, modlid, hklin, sf, phase, extent, rms, centre, protmw, nuclmw): warnings.warn( "Deprecated function: use addENSE_MAP", DeprecationWarning ) self.addENSE_MAP( modlid, hklin, sf, phase, extent, rms, centre, protmw, nuclmw ) def setENSE_MAP_MW(self, modlid, hklin, sf, phase, extent, rms, centre, protmw, nuclmw): warnings.warn( "Deprecated function: use addENSE_MAP", DeprecationWarning ) self.addENSE_MAP( modlid, hklin, sf, phase, extent, rms, centre, protmw, nuclmw ) class FINA(object): def setFINA_SELE_PERCENT(self, rot, tra, step, num): warnings.warn( "Deprecated function: use setPEAK_[ROT|TRA]_SELE_PERC", DeprecationWarning ) if rot: self.setPEAK_ROT_SELE_PERC( num ) if tra: self.setPEAK_TRA_SELE_PERC( num ) def setFINA_SELE_SIGMA(self, rot, tra, step, num): warnings.warn( "Deprecated function: use setPEAK_[ROT|TRA]_SELE_SIG", DeprecationWarning ) if rot: self.setPEAK_ROT_SELE_SIG( num ) if tra: self.setPEAK_TRA_SELE_SIG( num ) def setFINA_SELE_NUMBER(self, rot, tra, step, num): warnings.warn("Deprecated function: use setPEAK_[ROT|TRA]_SELE_NUM", DeprecationWarning ) if rot: self.setPEAK_ROT_SELE_NUM( num ) if tra: self.setPEAK_TRA_SELE_NUM( num ) def setFINA_SELE_ALL(self, rot, tra, step, num): warnings.warn( "Deprecated function: use setPEAK_[ROT|TRA]_SELE_ALL", DeprecationWarning ) if rot: self.setPEAK_ROT_SELE_ALL() if tra: self.setPEAK_TRA_SELE_ALL() class LABI(object): def addLABI(self, f, sigf): warnings.warn( "Deprecated function: use setLABI", DeprecationWarning ) self.setLABI( f, sigf ) class LLGC(object): def setLLGC_CRYS_COMPLETE(self, xtalid, tmp): warnings.warn( "Deprecated function: use setLLGC_COMPLETE", DeprecationWarning ) self.setLLGC_COMPLETE(tmp) def setLLGC_CRYS_CLASH_DEFAULT(self, xtalid): warnings.warn( "Deprecated function: use setLLGC_CLASH_DEFAULT", DeprecationWarning ) self.setLLGC_CLASH_COMPLETE() def setLLGC_CRYS_CLASH_DISTANCE(self, xtalid): warnings.warn( "Deprecated function: use setLLGC_CLASH_DISTANCE", DeprecationWarning ) self.setLLGC_CLASH_DISTANCE() def setLLGC_CRYS_SIGMA(self, xtalid, tmp): warnings.warn( "Deprecated function: use setLLGC_SIGMA", DeprecationWarning ) self.setLLGC_SIGMA(tmp) def setLLGC_CRYS_SCAT_ELEMENT(self, xtalid, tmp): warnings.warn( "Deprecated function: use addLLGC_ATOM", DeprecationWarning ) self.addLLGC_ELMENET(tmp) def setLLGC_CRYS_SCAT_CLUSTER(self, xtalid): warnings.warn( "Deprecated function: use addLLGC_CLUSTER", DeprecationWarning ) self.addLLGC_CLUSTER() def setLLGC_CRYS_SCAT_REAL(self, xtalid): warnings.warn( "Deprecated function: use addLLGC_SCAT_REAL", DeprecationWarning ) self.addLLGC_REAL() def setLLGC_CRYS_SCAT_ANOM(self, xtalid): warnings.warn( "Deprecated function: use addLLGC_SCAT_ANOM", DeprecationWarning ) self.addLLGC_ANOM() def setLLGC_MAPS(self): warnings.warn( "Deprecated function: use setLLGM", DeprecationWarning ) self.setLLGM() class OUTL(object): def setOUTL(self, on_off): warnings.warn( "Deprecated function: use setOUTL_REJECT", DeprecationWarning ) self.setOUTL_REJECT( on_off ) class PART(object): def setPART_PDB(self, filename): warnings.warn( "Deprecated function: use setPART_PDB_RMS or setPART_PDB_ID", DeprecationWarning ) self.filename = filename if hasattr( self, "num" ): if self.homology_as_rms: self.setPART_PDB_RMS(self.filename, self.num ) else: self.setPART_PDB_ID( self.filename, self.num ) def setPART_RMS(self, homology_as_rms, num): warnings.warn( "Deprecated function: use setPART_PDB_RMS or setPART_PDB_ID", DeprecationWarning ) self.homology_as_rms = homology_as_rms self.num = num if hasattr( self, "filename" ): if self.homology_as_rms: self.setPART_PDB_RMS( self.filename, self.num ) else: self.setPART_PDB_ID( self.filename, self.num ) class PURG(object): def setPURGE(self, on_off): warnings.warn( "Deprecated function: use setPURG_SELECT", DeprecationWarning ) self.setPURG( on_off ) def setPURGE_PERCENT(self, perc): warnings.warn( "Deprecated function: use setPURG_PERCENT", DeprecationWarning ) self.setPURG_PERCENT( perc) class PACK(object): def setPACK_ALLOW(self, cutoff): warnings.warn( "Deprecated function: use setPACK_ALLOW and setPACK_CUTOFF", DeprecationWarning ) self.setPACK_ALLOW() self.setPACK_CUTOFF(cutoff) def setPACK_BEST_MAX(self, cutoff): warnings.warn( "Deprecated function: use setPACK_CUTOFF", DeprecationWarning ) self.setPACK_CUTOFF( perc) class RESC(object): def setRESCORE(self, rot, tra, b): warnings.warn( "Deprecated function: use setRESC_ROT or setRESC_TRA", DeprecationWarning ) if rot: self.setRESC_ROT( b ) if tra: self.setRESC_TRA( b ) class SEAR(object): def addSEAR(self, ensembles): warnings.warn( "Deprecated function: use addSEAR_ENSE_OR_ENSE_NUM", DeprecationWarning ) self.addSEAR_ENSE_OR_ENSE_NUM( ensembles, 1 ) def setSEAR(self, ensembles): warnings.warn( "Deprecated function: use addSEAR_ENSE_OR_ENSE_NUM", DeprecationWarning ) self.addSEAR_ENSE_OR_ENSE_NUM( ensembles, 1 ) def addSEAR_NUM(self, ensembles, num): warnings.warn( "Deprecated function: use addSEAR_ENSE_OR_ENSE_NUM", DeprecationWarning ) self.addSEAR_ENSE_OR_ENSE_NUM( ensembles, num ) class TRAN(object): def setFULL(self): warnings.warn( "Deprecated function: use setTRAN_FULL", DeprecationWarning ) self.setTRAN_FULL() def setREGI(self, frac, corner1, corner2): warnings.warn( "Deprecated function: use setTRAN_REGI", DeprecationWarning ) self.setTRAN_REGI( frac, corner1, corner2 ) def setLINE(self, frac, line_start, line_end): warnings.warn( "Deprecated function: use setTRAN_LINE", DeprecationWarning ) self.setTRAN_LINE( frac, line_start, line_end ) def setAROU(self, frac,line_start,range): warnings.warn( "Deprecated function: use setTRAN_AROU", DeprecationWarning ) self.setTRAN_AROU( frac, line_start, range ) def setDEGE(self, string_value): warnings.warn( "Deprecated function: use setTRAN_DEGE", DeprecationWarning ) self.setTRAN_DEGE( string_value ) class NMAP(object): def setNMAP_MODE(self, tmp): warnings.warn( "Deprecated function: use addLLGC_MODE", DeprecationWarning ) self.addLLGC_MODE(tmp[0]) def setNMAP_DQ(self, tmp): warnings.warn( "Deprecated function: use addLLGC_DQ", DeprecationWarning ) self.addLLGC_DQ(tmp[0]) def setNMAP_RMS(self, tmp): warnings.warn( "Deprecated function: use setLLGC_RMS_STEP", DeprecationWarning ) self.setLLGC_RMS_STEP(tmp) def setNMAP_STRETCH(self, tmp): warnings.warn( "Deprecated function: use setLLGC_RMS_STRETCH", DeprecationWarning ) self.setLLGC_RMS_STRETCH(tmp) def setNMAP_CLASH(self, tmp): warnings.warn( "Deprecated function: use setLLGC_RMS_CLASH", DeprecationWarning ) self.setLLGC_RMS_CLASH(tmp) def setNMAP_MAXRMS(self, tmp): warnings.warn( "Deprecated function: use setLLGC_RMS_MAX", DeprecationWarning ) self.setLLGC_RMS_MAX(tmp) def setNMAP_BACKWARD(self): warnings.warn( "Deprecated function: use setLLGC_RMS_DIR_BACKWARD", DeprecationWarning ) self.setLLGC_RMS_DIR_BACKWARD(tmp) def setNMAP_FORWARD(self): warnings.warn( "Deprecated function: use setLLGC_RMS_DIR_FORWARD", DeprecationWarning ) self.setLLGC_RMS_DIR_FORWARD(tmp) def setNMAP_TO_AND_FRO(self): warnings.warn( "Deprecated function: use setLLGC_RMS_DIR_TOFRO", DeprecationWarning ) self.setLLGC_RMS_DIR_TOFRO(tmp)