Update convert test & check

src/Makefile

@@ -8,13 +8,13 @@ OBJDIR := o
 BINPATH := $(BINDIR)/reseek
 
 CC = gcc
-CFLAGS := $(CFLAGS)  -ffast-math -march=native --std=c++17 -O3 -DNDEBUG -fopenmp
+CFLAGS := $(CFLAGS)  -ffast-math -march=native -O3 -DNDEBUG
 
 CXX = g++
-CXXFLAGS := $(CFLAGS)  -ffast-math -march=native --std=c++17 -O3 -DNDEBUG -fopenmp
+CXXFLAGS := $(CFLAGS)  -ffast-math -march=native -O3 -DNDEBUG
 
 UNAME_S := $(shell uname -s)
-LDFLAGS := $(LDFLAGS)  -ffast-math -march=native -O3 -fopenmp
+LDFLAGS := $(LDFLAGS)  -ffast-math -march=native -O3
 ifeq ($(UNAME_S),Linux)
     LDFLAGS += -static
 endif

test_data/chains.fa

@@ -215,34 +215,13 @@ IYRALEQSALPIHAVQLIEDTSRETAKELFTLNDGLDVLIPRGGKKLIDLVVRESTVPVLETGAGNCHIFIDETAKPQMA
 EKVVVNAKTQRPSVCNAIESLLIHKAWARQHGKELLDQLENAGVEIRGDELVCELHPSSKQASKEDWETEFLAPVLSVKT
 VENVQEAVKHIQQYGTNHSEAILTENDKNAVYFQTAVDAAAVYHNASTRFTDGFEFGYGAEIGISTQKLHARGPMGLPAL
 TSTKYIIKGTGQIRE
->AFDB_Q839W3:A
-MKVTDLKQLGQQAKEASYTLGLMDTRQKNTLLNKMAAAIEANAPRILQANALDLEQAATHGISETMQDRLRLTEERITAM
-AEGIRQVATLPDPIGEVDKMWRNEAGLLIGQQRVPLGVIGIIYESRPNVTTDAASLCFKSGNAVILRGGKEAFHSNQILV
-TILQEALIQEAVSPHLIQFVDDTSRETAQQLMRLNDYLDVLIPRGGANLIKTVLTTATVPVIETGTGNCHIYVDKDAQLT
-MATEIIVNAKCQRPSVCNAAETLLIHQEVAEAFLPTIEKALKEFHVELRADERALAIFEEAIPATEQDWETEFLDFILAV
-KVVDSLDEAIQHINRYNTKHSESIISDNYFATQQFLQQVDAAAVYANASTRFTDGFEFGFGAEIGISTQKLHARGPMGLA
-ELTSTKYVIYGNGQARS
->AFDB_Q890J4:A
-MVDLEQLGQQAQQASYTLGLLSTAQKNQVLTAMATALTSHQDEILAANAQDLENPQVPVKFVDRLRLTADRIQDMAIGLK
-QVVSLPDPIGNVDRAWRNEAGLMIAKERVPLGVIGMIFEARPNVTVDASALCFKTGNAVILRGGKEALHSNQALVQVLRG
-ALRAEAVDENAIQLITDTSHATAAKFMQLTDYVDVLIPRGSARLIQTVLAKATVPVIETGAGNCHVYVDKDAQLQMATDI
-VINGKVQRPSVCNATEKLLIHREVAADYLPSMIQALREQGVEVRGDAATQAIVPDVVPATDADWGTEYNDLIIAVKVVDS
-EAAAITHINRYNTQHSEAIVTDNYQAGKLFQQRVNAACVYINASTRFTDGFEFGFGAEIGISTQKLHARGPMGLAELTSY
-KYVIDGNGQIRH
 >AFDB_Q896G4:A
 MDDLNKYLINKGKKAKEASRFLSSVDSNFKNKALHKMGEDLKANMNKIIAANKIDMEKGKEKGLSKSLLDRLLIDEKRVN
 DMVNGLIEVAELPDPIGEVLNMWKRPNGINIGVKRVPLGVIGIIYEARPNVTVDATALCLKSGNAVILRGGSEAINTNKA
 IGKILENSAIESGLPEGTIQLIETTDREIVNKMLKLNEYIDVLIPRGGRGLIDNVVKNSTVPVIQTGVGLCHVYVDGSAN
 LKMAQDIIVNAKTQRPGVCNALETLLVHKDVANSFLPEIVSEISKYGVESKLCEKSFEVVKGSIKDAKVLSLISEATEED
 WDTEYLDLILSIKIVNSLDEALNHIYDHGTKHSEAIITENYTNSQRFLNEVDAAAVYVNASTRFTDGSQFGFGAEIGIST
 QKLHARGPMGLTQLTTTKYIIYGNGQIR
->AFDB_Q8CUQ4:A
-MSEVIEKAKRAKQASFKMALSTTDDKNEALQLISQAIINHKQEILTANALDIEEGKKKGLSEAVIDRIRLNEERLQDIAD
-AILQVTILTDPIGEALEIIEKDNGLFITKKRVPIGVIGMVYEARPNVTVDAASLAIKTGNSVVLRGSSSAIESNKALIQV
-IHQSLASSSIPKEAVQLIEDTRREVANQFFQLNEYLDVLIPRGGKQLIDTVIKQSTVPVIETGAGNCHVYLDESAKVEMA
-TEIVLNAKLQRPSVCNAIESLIIHRQWFEDHGLELLKTMQSHDIKIHGDSVVMEKFPPAIKAVERDWEKEYLSSEISVKI
-VDSVSEAIDHINRYGTRHSEAIITENKMNAEQFQLQVDAAAVYHNASTRFTDGFEFGYGAEIGISTQKLHARGPMGLEAL
-TSTKFVISGSGQIRE
 >PDB_1hhs:A
 PRRAPAFPLSDIKAQMLFANNIKAQQASKRSFKEGAIETYEGLLSVDPRFLSFKNELSRYLTDHFPANVDEYGRVYGNGV
 RTNFFGMRHMNGFPMIPATWPLASNLKKRADADLADGPVSERDNLLFRAAVRLMFSDLEPVPLKIRKGSSTCIPYFSNDM
@@ -273,50 +252,10 @@ MGTLLMSITYLVMQLDHTAPHLNSRIKDMPSACRFLDSYWQGHEEIRQISKSDDAMLGWTKGRALVGGHRLFEMLKEGKV
 NPSPYMKISYEHGGAFLGDILLYDSRREPGSAIFVGNINSMLNNQFSPEYGVQSGVRDRSKRKRPFPGLAWASMKDTYGA
 CPIYSDVLEAIERCWWNAFGESYRAYREDMLKRDTLELSRYVASMARQAGLAELTPIDLEVLADPNKLQYKWTEADVSAN
 IHEVLMHGVSVEKTERFLRSVMPR
->PDB_2ckw:A
-DEFQWKGLPVVKSGLDVGGMPTGTRYHRSPAWPEEQPGETHAPAPFGSGDKRYTFSQTEMLVNGLKPYTEPTAGVPPQLL
-SRAVTHVRSYIETIIGTHRSPVLTYHQACELLERTTSCGPFVQGLKGDYWDEEQQQYTGVLANHLEQAWDKANKGIAPRN
-AYKLALKDELRPIEKNKAGKRRLLWGCDAATTLIATAAFKAVATRLQVVTPMTPVAVGINMDSVQMQVMNDSLKGGVLYC
-LDYSKWDSTQNPAVTAASLAILERFAEPHPIVSCAIEALSSPAEGYVNDIKFVTRGGLPSGMPFTSVVNSINHMIYVAAA
-ILQAYESHNVPYTGNVFQVETIHTYGDDCMYSVCPATASIFHTVLANLTSYGLKPKPTNTPVFLKRTFTQTPHGIRALLD
-ITSITRQFYWLKANRTSDPSSPPAFDRQARSAQLENALAYASQHGPVMFDTVRQIAIKTAQGEGLVLVNTNYDQALATYN
-AWFIGGT
 >PDB_3h5y:A
 KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLE
 AAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGA
 LKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYS
 RWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEV
 TNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQS
 SILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELDFYVPRQEPMFRWMRFS
->PDB_4gzk:A
-HAETRIVTDAPRNSESVGDHLFNGGVNHHDEDPDAYTKMYGPLVGYDPRNPTTLFANARQTGTQLVAPRKAREILTGIYS
-FEPTVLAFQREFVKRANAVAQPDLNSDGFSLNGLHTTFDSIRSVSGYPQWPVSALPKSNVGLLRDDLKLQERMTARQVVI
-AREIWKRVWGHMKPTAIKIPKMMSTSGPPRNVNDAEMKLQYALALFSGNRYNGYLDAFKSGDLSRFYRDYEAAVIMGTTN
-NVRWQVDNNPGKKRDDYWAQADIERELAPSKRPITTKVEINGTVYDDFAAMRTRLLVNAGPWTINVALQQPFATTGCMNA
-MFELYRATWHPDEDKIAGFLEGKHAFFGDVSSYDHSFSEEKIDLSLEVGKEFISPEIMELASSLFYAAYFTRPLGPDDGP
-QLVGNPNRYLEKQVKAGNRSGHAFTSLFAKVWKVIDTVSKFDQMGYDVVANMDAILKGDMPFGCINNGDDEIVWFKSERD
-YRLFLRLLETQPQEQRMFKVGPEEGAVFSGSVYQLIGPLKYQAVERITTPFQRIICPERSIGGNFRKFWPLGILERYNKR
-NSHPVLEEVWRVFDDDTYATLMEPHYGSFLGIVQRAHKEIPFSVDDLSWKEIMVLDDPNKMYHRFTDEEIRDQVQESAFR
-KLQPIFFERMFKEHYKGNYV
->PDB_5amq:A
-MDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDN
-YLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQ
-FFDLKQLLYEKFGDDEEFLLKVAHGDFTLTAPWCKTGCPEFWKHPIYKEFKMSMPVPERRLFEESVKFNAYESERWNTNL
-VKIREYTKKDYSEHISKSAKNIFLASGFYKQPNKNEISEGWTLMVERVQDQREISKSLHDQKPSIHFIWGAHNPGNSNNA
-TFKLILLSKSLQSIKGISTYTEAFKSLGKMMDIGDKAIEYEEFCMSLKSKARSSWKQIMNKKLEPKQINNALVLWEQQFM
-INNDLIDKSEKLKLFKNFCGIGKHDLEVSKPKILDFDDANMYLASLTMMEQSKKILSKSNGLKPDNFILNEFGSRIKDAN
-KETYDNMHKIFETGYWQCISDFSTLMKNILSVSQYNRHNTFRIAMCANNNVFAIVFPSADTVVYSIIVLHKEEENIFNPG
-CLHGTFKCMNGYISISRAIRLDKERCQRIVSSPGLFLTTCLLFKHDNPTLVMSDIMNFSIYTSLSITKSVLSLTEPARYM
-IMNSLAISSNVKDYIAEKFSPYTKTLFSVYMTRLIKNACFDAYDQRQRVQLRQKGIKDNRELTSIWFPGSVTLKEYLTQI
-YLPFYFNAKGLHEKHHVMVDLAKTILEIECEQRENIKEIWSTNCTKQTVNLKILIHSLCKNLLADTSRHNHLRNRIENRN
-NFRRSITTISTFTSSKSCLKIGDFRKEKELQSVKQKKILEVQSRKMRLANNYEMLRNAMPNYTDYISTKVFDRLYELLDK
-KVLTDKPVIEQIMDMMIDHKKFYFTFFNKGQKTSKDREIFVGEYEAKMCMYAVERIAKERCKLNPDEMISEPGDGKLKVL
-EQKSEQEIRFLVETTRQKNREIDEAIEALATEGYESNLGKIEKLSLGKAKGLKMEINADMSKWSAQDVFYKYFWLIALDP
-ILYPQEKERILYFMCNYMDKELILPDELLFNLLDQKVAYQNDIIATMTNQLNSNTVLIKRNWLQGNFNYTSSYVHSCAMS
-VYKEILKEAITLLDGSILVNSLVHSDDNQTSITIVQDKMENDKIIDFAMKEFERACLTFGCQANMKKTYVTNCIKEFVSL
-FNLYGEPFSIYGRFLLTSVGDCAYIGPYEDLASRISSAQTAIKHGCPPSLAWVSIAISHWMTSLTYNMLPGQSNDPIDYF
-PAENRKDIPIELNGVLDAPLSMISTVGLESGNLYFLIKLLSKYTPVMQKRESVVNQIAEVKNWKVEDLTDNEIFRLKILR
-YLVLDASILTPRKFTTAGSLRKLYSFSKYQDRLSSPGGMVELFTYLLEKPELLVTKGEDMKDYMESVIFRYNSKRFKESL
-SIQNPAQLFIEQILFSHKPVIDFSGIRDKYINGKVTFTEAYRLLMRDLSSLELTNDDIQVIYSYIILNDPMMITIANTHI
-LSIYGSPQRRMGMSCSTMPEFRNSPALVLRAYSKNNPDIQGAPTEMARDLVHLKEFVENTNLEEKMKVRIAMNEAEKGQR
-DIVFELKEMTRFYQVCYEYVKSTEHKIKVFILPAKSYTTTDFCSLMQGNLIKDKEWYTVHYLKQIL

test_scripts/check_convert.py

@@ -30,7 +30,10 @@ def check_fasta(fn):
             errors += 1
             print("ERROR %s not found in %s" % (label, fn))
             return
-        if seq != seq2:
+        if seq == seq2:
+            if 0:
+                print("seq ok %s" % label)
+        else:
             errors += 1
             print("ERROR %s different %s" % (label, fn))
             return

test_scripts/convert.bash

@@ -11,13 +11,15 @@ ls ../test_structures/* \
 	-fasta files.fa \
 	-cal files.cal \
 	-bca files.bca \
+	-chainsep : \
 	-log convert_files.log
 
 ../bin/reseek \
 	-convert ../test_structures/ \
 	-fasta dir.fa \
 	-cal dir.cal \
 	-bca dir.bca \
+	-chainsep : \
 	-log convert_dir.log
 
 function cvt() {