Search.setIndex({objects:{"modpipe.sequence.SPTRFile":{read:[16,2,1]},"modpipe.tmalign":{TMAlign:[1,3,1]},"modpipe.fold_assignment":{SequenceSequence:[9,3,1],Hit:[9,3,1],ProfileSequence:[9,3,1]},"modpipe.ce":{CE:[1,3,1],Error:[1,4,1]},"modpipe.ce.CE":{write_program_output:[1,2,1],calculate_superpositions:[1,2,1],parse_output:[1,2,1],read_program_output:[1,2,1],fix_alignment:[1,2,1],write_alignment:[1,2,1],get_alignment:[1,2,1]},"modpipe.fold_assignment.Hit":{get_modeling_alignment:[9,2,1]},"modpipe.sequence.FASTAFile":{write:[16,2,1],read:[16,2,1]},"modpipe.sequence.UniqueFile":{write:[16,2,1],add_sequence:[16,2,1],file_name_from_seqfile:[16,2,1]},"modpipe.tmalign.TMAlign":{write_program_output:[1,2,1],calculate_superpositions:[1,2,1],parse_output:[1,2,1],read_program_output:[1,2,1],fix_alignment:[1,2,1],write_alignment:[1,2,1],get_alignment:[1,2,1]},"modpipe.sequence.PIRFile":{write:[16,2,1],read:[16,2,1]},"modpipe.binaries":{get_ce_mkdb:[10,1,1],get_cd_hit:[10,1,1],get_ce:[10,1,1],get_jess:[10,1,1],get_seg:[10,1,1],get_tess2jess:[10,1,1],get_blast:[10,1,1],get_spasm:[10,1,1],get_tmalign:[10,1,1]},"modpipe.cdhit":{CDHit:[1,3,1]},"modpipe.version":{message:[10,1,1],get:[10,1,1]},"modpipe.matrix2d.Matrix2D":{write:[14,2,1]},"modpipe.config":{Config:[10,3,1],read_file:[10,1,1]},"modpipe.crc64":{digest:[14,1,1]},"modpipe.test.TestCase":{get_modpipe_binary_path:[6,2,1],require_clean_exit:[6,2,1],run_script:[6,2,1],run_perl_code:[6,2,1],run_binary:[6,2,1]},modpipe:{sequence:[16,0,1],serialize:[0,0,1],fold_assignment:[9,0,1],ce:[1,0,1],cdhit:[1,0,1],crc64:[14,0,1],Error:[18,4,1],version:[10,0,1],FileFormatError:[18,4,1],filesystem:[10,0,1],test:[6,0,1],MissingBinaryError:[18,4,1],binaries:[10,0,1],config:[10,0,1],matrix2d:[14,0,1],tmalign:[1,0,1]},"modpipe.matrix2d":{Matrix2D:[14,3,1]},"modpipe.sequence.Sequence":{get_id:[16,2,1],clean:[16,2,1]},"modpipe.filesystem":{FileSystem:[10,3,1]},"modpipe.config.Config":{parse_file:[10,2,1]},"modpipe.fold_assignment.ProfileSequence":{search:[9,2,1]},"modpipe.filesystem.FileSystem":{get_sequence_dir:[10,2,1],get_selected_file:[10,2,1],get_sequence_file:[10,2,1],add_sequence:[10,2,1],get_alignment_dir:[10,2,1],get_model_dir:[10,2,1]},"modpipe.sequence":{FASTAFile:[16,3,1],PIRFile:[16,3,1],Sequence:[16,3,1],SPTRFile:[16,3,1],UniqueFile:[16,3,1]},"modpipe.cdhit.CDHit":{cluster:[1,2,1],parse_clusters:[1,2,1]},"modpipe.serialize":{read_models_file:[0,1,1],Hit:[0,3,1],write_models_file:[0,1,1],read_hits_file:[0,1,1],Model:[0,3,1],write_hits_file:[0,1,1]},"modpipe.fold_assignment.SequenceSequence":{search:[9,2,1]},"modpipe.test":{TestCase:[6,3,1]}},terms:{represent:[0,16],all:[21,9,12,19,20,11,2,13,3,7,22,4],code:[12,19,6,10,2,13,16],chain:[2,3,12],scratch:4,add_sequ:[16,10],four:[2,3],supplement:21,prffile:9,follow:[12,11,2,13,3,7,17],disk:10,salilab:8,scr:11,compact:12,profil:[5,9,21,2,13,3,22,4],depend:[11,3],get_tess2jess:10,send:19,program:[5,0,1,10,11,3,7,4,17],those:3,under:[11,3,7],aris:7,surfnet:3,unit:[6,19],modbas:[5,3,20],merchant:7,gurusami:7,digit:[2,12],sourc:[8,5,3,11],everi:[21,3,4,22],string:[12,14,3],fals:0,util:[14,17,15],mechan:21,whether:[4,7],sequence_ident:[12,1],veri:[11,12],blast:[18,5,21,11,2,3,22,4],relev:[11,3],level:[11,3],list:[9,12,0,11,2,22,16,4],upload:20,fewer:2,"try":18,adjust:17,stderr:[6,1],small:3,missingbinaryerror:[18,10],modpipe_id:16,dir:6,pleas:[20,19],x86_64:11,impli:7,procheck:[11,5,3],dimens:14,fold:[5,9,12,21,11,2,13,3,15,4],rate:[12,0],design:2,pass:[6,3,14],download:[11,3,22],howev:[3,19],acid:[16,15],tmpdir:4,even:7,index:[5,22],what:[3,4],sub:3,compar:[2,3,5],sum:2,asid:21,abl:3,calcul:[5,13,1,3,4],current:[8,13,1],mplib:17,version:[0,12,19,10,11,2,3,7,15],aux:3,get_modeling_align:9,"new":[19,10,2,3,22,4],row:[2,14],method:[5,0,12,21,14,1,9,11,2,3,22,15,4],cutoff_rm:2,full:[2,6,3,13],deriv:21,num_equiv_po:2,variat:3,gener:[18,0,12,19,20,11,2,13,7,22],here:[3,4,15],water:[12,0,3],read_hits_fil:0,let:19,symlink:11,ratio:12,get_model_dir:10,modifi:7,sinc:[2,3,4],valu:[21,2,3,12],ncbiseqdb:4,convert:[2,13,22],hdf5:[4,22],popen:6,chn1:1,chn0:1,permit:[12,7],action:7,typic:[21,2,4,19],matrix2d:[14,15],tmalign:[1,15],although:[8,21],extra:2,target_len:12,modul:[5,0,1,10,12,6,7,15,17],foundat:7,deprec:19,printf:17,select_by_region:2,instal:[11,5,3,10,17],conf_fil:[2,13,4],highli:4,bookkeep:3,from:[5,0,13,19,21,1,9,10,11,2,6,3,7,22,16,17],describ:[13,3,14,4],sarathi:7,sake:[13,3],chi:12,two:[11,2,13,21,17],coverag:12,subvers:[3,19],websit:[11,22],superposit:[2,1],live:8,blastpgp:11,call:[11,13,1,3,17],usr:11,recommend:[8,3,19],type:3,more:[5,21,2,13,3,7],exit:6,desir:3,mean_num_equiv_po:2,comparison:[2,3],appendic:5,benchmark:[2,6,5],notic:7,everydai:3,flag:4,parse_fil:10,templat:[5,9,12,0,21,2,13,3,22,4],particular:7,known:2,rare:11,herebi:7,harvest:3,must:[11,2],mergepairwisetomultipl:3,none:14,jess:3,setup:[11,3,10],work:[3,19],uniqu:[12,20,2,13,3,16],can:[5,12,21,14,11,2,13,3,7,22,17],clutter:6,purpos:7,root:[2,3,10],fetch:3,associ:[3,7],claim:7,pdb1abc:22,conf:[2,13],tar:[11,3],scan:[21,3,22],process:[3,4],indic:[5,12],crc64:[14,15],hitsprfprf:3,want:[3,20,22],serial:[12,0,17,15],read_fil:10,surfac:12,multipl:[21,2,3,4,12],csh:3,divid:22,rather:2,seq_id:2,buildprofil:3,i686:11,snippet:6,how:3,swissprot:16,ent:22,env:9,subdirectori:[8,13,3,22],verifi:3,config:[10,15],sequence_db:22,map:[16,2,13,3],modelsfil:[],tcsh:3,prodir:11,max:[21,2],after:[2,12],runbinari:11,lab:[8,19,20,11,3,22,4],befor:[0,4],wrong:18,mai:[11,2,3,19,12],end:[2,3,12],redund:[14,22,21,13,3,15,4],data:[5,0,12,20,11,2,13,3,15,16,4],averag:2,"short":[6,4],essenti:3,bind:3,grant:7,correspond:[2,10],inform:[15,13,3,4,10],"switch":11,maintain:[3,19],combin:[12,3],allow:3,anoth:2,exclus:2,volum:3,ga341:12,order:[12,4],furnish:7,origin:2,gathermodmp:[2,5],help:[11,2,3],cutoff:2,over:19,move:11,ia64:11,i386:11,through:22,nrdbtag:4,hierarchi:[5,3],still:22,digest:[14,3],paramet:[13,4],raw:[1,22],modsvn:11,style:19,ligand:3,fit:7,binari:[18,22,1,10,11,6,15,4],makemodel:3,align_cod:16,better:[12,3],tort:7,main:[5,13,2,6,3,17],fin:20,easier:3,non:[11,21,6,4],good:[2,12],"return":[9,14,1,0,10,2,6,3,16],thei:[8,21,4],python:[5,19,12,3,15,17],cover:2,pdb0:1,pdb1:1,"break":[12,3],framework:[6,15],somebodi:19,facilit:3,front:3,introduct:[5,3],assess:[12,3],term:7,name:[14,1,2,13,3,16,4],simonov:7,edit:11,simpl:[2,14,15],separ:[11,0],easili:[8,3],exampl:[5,0,14,11,2,13,3,4,17],mode:3,each:[21,0,12,11,2,13,3,22,4,17],found:[0,3,4,22],intervent:5,higher:12,"97d910a766e44b11cb232a8b78312180mnifyknl":3,mean:2,compil:11,everyth:3,domain:2,pllib:17,weight:21,individu:[2,12],kiril:7,procedur:3,realli:0,combinatori:3,redistribut:7,connect:7,our:19,energi:12,patch:19,extract:[11,3],event:7,special:[3,4],out:[0,19,14,1,2,3,7],variabl:[11,2,13,3,4],accomplish:2,network:4,space:4,seqfil:[16,1],num_equiv_pos_35:2,publish:7,content:13,laid:19,suitabl:[9,14,10,11,3,16],length_differ:1,print:[14,1,17],correct:11,matric:14,statist:12,state:3,parse_clust:1,manipul:2,differ:2,free:7,standard:[12,14,3],reason:3,base:[14,3,4],put:11,org:8,"byte":14,bash:3,md5:3,precompil:3,pyyaml:7,topdir:11,frequenc:[21,2],could:3,xprf_pssmdb:4,filter:[12,13],thing:19,length:[2,3,12],place:3,pieper:20,outsid:[8,11,3],write_models_fil:0,assign:[5,9,12,21,14,11,2,13,3,15,4],first:[19,11,2,13,3,17],oper:14,softwar:[5,7],directli:3,unq_fil:2,onc:[14,19],independ:[2,4],qualiti:[12,3],number:[5,12,21,14,1,10,11,2,13,3,4],yourself:[22,19],restrict:7,instruct:[11,3],alreadi:[0,3,4,19],done:[21,2,0,17],messag:10,stabl:3,native_chain:2,open:17,primari:[16,3],get_c:10,pirfil:16,superpos:2,given:[9,1,0,10,13,2,6,3,22,16],fuller:12,script:[19,10,11,12,6,3,17],arch:11,top:[11,3,10],trembl:16,system:[8,2],wrapper:[1,3,15],attach:19,exetyp:11,conveni:[1,3,17],"final":[2,13,3],store:[9,3,13],low:3,shell:3,require_clean_exit:6,option:[5,10,11,2,13,3,17],relationship:3,modenv:1,tool:[2,22,3,5],copi:[11,13,3,7],specifi:[1,11,2,13,3,4],part:[3,4,22],pars:[2,1,17],holder:7,than:[11,2,3],methodnam:6,kind:7,ben:[3,19],target:[9,12,21,2,3,4],uniquefil:16,cyclic:[14,15],provid:[1,10,2,6,7,4,17],native_benchmark:2,remov:[13,3,4,22],offici:19,clusterali:[2,4],biolog:[16,15],structur:[5,0,22,21,2,3,15],charact:3,get_align:1,get_spasm:10,"97d":3,sens:2,posit:[21,2,4],initi:13,pre:3,prf:[4,22],fastafil:[16,10],ga341_scor:12,pdb95_prf:22,ani:[0,3,19,7,17],mean_cutoff_rm:2,packag:[11,7],width:16,have:[20,11,2,3,4,17],tabl:[2,5],need:[22,3,4,19],seem:19,turn:[2,14],sell:7,depict:3,probabl:11,squar:[2,12],lib:[3,17],note:[19,20,11,12,13,3,22],also:[8,21,0,19,10,20,11,2,13,14,22,4],without:[3,7],build:[21,2,13,3,4],which:[12,14,10,11,2,3,22,4],environ:[13,3],methodolog:[5,3],singl:[0,9,2,13,3,22,16],modweb:[8,5,3,20],compat:20,begin:12,sure:[0,3,19],unless:[3,4],distribut:[8,11,12,13,3,7],shall:7,licens:[11,5,7],compress:22,most:[11,2,21],regular:21,sublicens:7,stereochem:3,blastal:11,"class":[9,1,0,10,12,6,14,15,16],charg:7,throw_away_seq_length:1,sali:[8,19,20,11,3,7,22,4],renam:11,get_cd_hit:10,doc:19,later:11,request:2,pwd:13,highest_sequence_ident:[12,0],ext:[11,3],runtim:11,clean:[16,1],usual:[21,12,10,11,2,3,22,4],target_cod:9,modpi:11,alphanumer:3,subprocess:6,fold_assign:[9,15],percentage_gap:12,checkprofil:3,permiss:7,threshold:[1,3],protocol:3,next:[13,3],find:[21,2,13,4],get_tmalign:10,redirect:6,onli:[11,2,13,4],locat:[22,10,11,13,3,15,4,17],copyright:[5,10,7,15],configur:[5,18,22,10,20,11,2,13,3,15,4,17],activ:19,prfupdat:4,should:[19,20,10,13,3,22,4],read_program_output:1,"1abc":2,local:[3,4],addseqmp:[2,13,3,17,5],hope:7,flexibl:3,output_filenam:2,hit:[5,0,12,21,1,9,11,2,13,3,15,4],variou:[12,9,1,3,10],get:[5,19,10,11,6,3],dope:[2,17,12],express:7,autom:[5,3],nativ:2,cannot:[8,11,3],report:2,liabl:7,requir:[11,2,6,3,13],hits_mod:[2,13],scene:15,global_rm:2,yield:2,"public":[3,7],irrespect:4,crc:14,common:[2,16,3,4,5],contain:[8,0,19,12,1,2,13,3,22,16,4],modpip:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22],where:11,summari:[13,3],calculate_superposit:1,set:[0,12,22,10,11,2,13,3,15,4],seq:[16,10],seg:3,see:[0,12,19,10,2,13,3,7,4],result:[13,3,20,19],arg:6,testcas:6,close:[8,17],modweb_templatebas:3,get_modpipe_binary_path:6,best:[2,3],subject:[3,7],"9v5":11,statu:6,detect:[21,12,9],extend:3,correctli:3,databas:[5,9,21,3,22,16,4],someth:[13,19],"97e":13,label:[],written:[0,3,19],score:[0,12,21,2,3,4,17],between:[2,13,3,12],"import":[5,20,17],cdhit:[1,15],email:19,altern:19,accord:3,bourn:3,get_ce_mkdb:10,kei:[],get_jess:10,extens:[12,3],job:3,entir:[2,19],outfil:1,addit:21,both:[21,2],profilesequ:9,waterman:3,last:3,ncbi:3,get_seg:10,region:[2,0,3,12],alon:3,contract:7,etc:3,instanc:[13,3],uniprot:[3,4,22],mani:[3,4],whole:[2,3,12],pdb:[5,12,2,3,22,4],load:[3,20],simpli:[11,2,3,17],stream:[0,16],point:[11,13,3,4],guidelin:19,cutoff_rms_35:2,executable_typexxx:11,residu:[21,2,3,12],header:[12,0,3],templatebas:3,path:[6,10,17],respect:17,hitsseqseq:3,assum:[11,0,13],duplic:3,liabil:7,modpipebas:11,evalu:3,second:[2,17],yaml:[2,0,12],convertseq:[2,13,5],three:3,been:3,compon:[5,3,12],whom:7,much:15,treat:3,interest:19,basic:3,popul:[2,13,3],"97e075794f588a59e8a0fb8a945814b1mlgikikp":13,sptrfile:16,sequence_fil:13,unq:[2,13,3],final_models_bi:2,xxx:11,search:[5,9,21,2,13,3,22,4,17],append:[0,17],argument:[11,2,6,13,4],andrej:7,get_id:16,zero:6,togeth:22,input:[5,14,1,2,13,3,16],present:[3,10],"case":[11,2,3,5],ident:[2,1,12],look:[11,2,13,19,17],gnu:7,align:[9,12,1,0,10,2,13,3,16,4],defin:[2,1,3,12],"while":[2,13,22],parse_output:1,pairwis:[12,3],abov:7,error:[18,6,1,15],observ:12,opt:9,motif:3,advantag:3,stdout:[6,1],almost:5,demo:13,therefor:2,site:3,worri:3,cluster:[8,1,2,3,22,4],modinstallxxx:11,itself:7,breaksw:11,against:[21,9,3],substanti:7,protein:[5,13,3],routin:1,fasta:[1,2,13,3,22,16],sever:[3,22],pdb_repositori:[2,4],develop:[5,19],author:7,perform:[2,3],make:[11,2,0,3,19],same:[2,22,19,7,12],check:[0,3,14,15],handl:[12,22,16,10,15],complex:3,pdb95:[21,5,4,22],document:[19,11,12,3,7,15],complet:[5,3,19],endsw:11,write_program_output:1,swiss:14,uniprot90:[21,4,22],modxxx:11,pick:2,rais:[18,6,1,10],user:3,extern:[5,18,1,10,11,3,15],accumul:13,implement:[21,14,3,15],built:13,noninfring:7,task:2,off:[3,4],equival:[2,17],run_perl_cod:6,pssm:[21,2,22],entri:[16,1],thu:[8,2],well:[3,22],inherit:3,col:14,person:7,addseq:3,contact:[3,20,19],command:[5,10,13,2,6,3,4,17],thi:[21,0,19,13,12,14,1,10,11,2,6,3,7,22,4,17],filesystem:[5,10,2,13,3,15,4],undefin:[],model:[5,0,12,21,14,1,9,11,2,13,3,22,4,17],latest:19,chore:3,construct:[4,22],identifi:[5,12,20,2,13,3,16],conform:19,nrseqdb:4,obtain:[11,7],rest:11,select:[2,13,3,12],interim:3,model_len:12,behind:15,sptr:16,speed:13,get_sequence_dir:10,web:[8,5,20],cut:3,miscellan:3,smith:3,except:[18,1],add:[19,10,11,13,3,16],valid:0,overview:[5,13],els:19,netapp:[3,4],match:[2,3,4],take:[5,13,1,3],bin:[11,10],getfullseq:3,psi:[21,2,3,4,22],around:3,format:[5,0,18,12,14,1,2,13,3,16],read:[18,0,21,1,10,11,12,14,16,17],consensu:[21,3],molecul:3,distanc:[2,12],get_sequence_fil:10,traffic:4,know:[3,4,19],readmodelsfil:17,bit:14,amino:[16,15],mod:[20,11,12,13,3,17],measur:12,like:[0,19,13,17],specif:[21,3,4],manual:[5,22],server:[3,19],collect:3,necessari:[11,17],either:[2,10],output:[1,6,2,13,4,17],write_hits_fil:0,page:5,openfil:17,right:7,often:2,deal:[3,7],some:[0,19,1,11,3,22,15,4],pipelin:5,percentag:12,intern:[6,3],get_alignment_dir:10,sampl:[3,4],guarante:21,fix_align:1,guess:11,librari:[3,17],spasm:3,ursula:[20,19],nummodel:4,avoid:3,normal:12,pep:19,file_name_from_seqfil:16,per:[2,13],substitut:21,larg:[5,3,12],iso:14,caviti:3,condit:7,damag:7,reproduc:3,refer:[5,3,15],machin:[11,4],plu:12,object:[0,1,9,10,12,14,16],run:[5,21,1,13,20,11,2,6,3,4],run_script:6,uncompress:22,genom:3,usag:3,agreement:12,normalized_dope_scor:12,backbon:3,uniprotkb:16,step:[13,3],sel:12,ixhash:7,repositori:[5,3,22],d18b74a08d8b83e15835daaf76471976fcghgnvv:17,appli:2,src:[2,13,3,5],about:[13,3,19],actual:[12,3],hitsprfseq:3,column:14,http:8,addition:3,fileformaterror:18,stand:3,discard:2,produc:[5,13,3,22],deviat:2,own:[5,0,3,17],effici:3,setenv:11,primarili:13,within:[2,3],encod:14,automat:20,warranti:7,seqid:10,alpha:2,chang:[13,3],updat:3,perl:[19,14,6,3,7,17],your:[5,0,19,20,11,2,13,3,17],merg:7,span:2,wai:[3,17],area:12,support:2,question:3,"long":3,sequencesequ:9,avail:21,start:[0,19,11,2,3,12],reli:[11,21,13,22],interfac:[8,5,20],includ:[21,12,13,7],suit:[6,3],resolut:3,unam:11,"function":[19,10,11,12,6,3,15],reduc:4,properli:3,form:22,happen:2,criteria:2,mycod:19,sequence_id:[2,13],link:11,newer:[3,22],atom:[2,3],don:3,line:[5,13,12,10,11,2,6,3,4,17],highest:[21,2],"true":[0,14],runtest:6,flowchart:3,consist:[2,22,19],possibl:[21,19,17],"default":[11,2],wish:8,displai:[2,10],hetatm:[12,0],crystal:2,below:[11,3,22],limit:7,fundament:0,otherwis:7,embed:[5,7],remaind:3,similar:[2,3,4,17],expect:[12,22],reserv:7,creat:[21,12,14,10,11,2,13,3,4],"int":11,get_selected_fil:10,dure:[21,3],parser:[12,10],checkpdb:3,repres:[0,22],strongli:19,templateseqdb:4,exist:[11,1,4,19],file:[5,0,18,12,14,1,9,10,11,2,13,3,19,7,15,22,16,20,4,17],pir:[2,16,1,3,22],doe:[13,4],simplest:5,pdb_95:[4,22],formatdb:[11,22],again:[11,3],readi:[2,3],hex:14,when:[11,12,3,4,18],detail:[2,1,7,22],field:[2,12],other:[8,2,3,11,7],angstrom:2,spatial:2,test:[19,14,13,11,6,3,15],you:[8,19,20,11,2,13,3,7,22,4,17],procomp:11,architectur:[11,3],poor:12,repeat:11,sequence_file_nam:13,fulli:20,sequenc:[5,0,12,1,9,10,21,2,13,3,22,15,16,20,4],datdir:[3,4],releas:3,queri:[2,3],eval:11,gap:[2,12],matrix:[21,14,4,15],svn:[3,19],fsa:13,xprf_list:4,write_align:1,longer:19,fold_assignment_method:[12,0],directori:[5,19,11,2,13,3,22,4,17],run_binari:6,descript:12,read_models_fil:[0,17],get_blast:10,them:[11,0,3,19,17],portion:7,write:[0,19,1,10,2,6,14,16],potenti:[2,13],time:12,"export":13},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:class","4":"py:exception"},titles:["Data structures","Wrappers for external binaries","ModPipe command line tools","Introduction","The ModPipe configuration file","ModPipe","Testing","Copyright and license","The ModWeb web interface","Fold assignment methods","Configuration","Installing external programs","File formats","Running ModPipe","Utilities","Python modules","Handling of biological data","Using ModPipe from your own programs","Errors","Developing ModPipe","Importing data into ModBase","Fold assignment methods","Databases used by ModPipe"],objnames:{"0":"Python module","1":"Python function","2":"Python method","3":"Python class","4":"Python exception"},filenames:["modules/structures","modules/external","cmdline","intro","configurationfile","index","modules/test","copying","modweb","modules/fold_assignment","modules/configuration","install-ext","file-formats","running","modules/utilities","modules/index","modules/biodata","using-lib","modules/errors","developing","modbase-import","fold-assignments","databases"]})
