[Biopython-dev] [Biopython - Bug #3169] (Closed) to_one_letter_code in Bio.SCOP.Raf is old
redmine at redmine.open-bio.org
redmine at redmine.open-bio.org
Thu Apr 26 03:36:04 UTC 2012
Issue #3169 has been updated by Eric Talevich.
Status changed from New to Closed
% Done changed from 0 to 100
We've committed this fix now:
https://github.com/biopython/biopython/pull/35
----------------------------------------
Bug #3169: to_one_letter_code in Bio.SCOP.Raf is old
https://redmine.open-bio.org/issues/3169
Author: Hongbo Zhu
Status: Closed
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.56
URL:
Hi,
The dictionary to_one_letter_code in Bio.SCOP.Raf is a bit old now. The current dictionary is based on a table taken from the RAF release notes of ASTRAL. This is an old table and some new three-letter codes in the PDB are not found in it (e.g. M3L in 2X4W). ASTRAL does not use the table since v1.73. Rather, PDB Chemical Component Dictionary is used. See http://astral.berkeley.edu/seq.cgi?get=raf-edit-comments;ver=1.75
"Beginning with ASTRAL 1.73, the PDB's chemical dictionary is used to translate chemically modified residues, instead of the translation table from ASTRAL 1.55."
The PDB Chemical Component Dictionary can be obtained from: http://deposit.pdb.org/cc_dict_tut.html .
I have parsed the dictionary and there are 12054 three-letter codes (as of Jan 2011). Among them, most correspond to a one-letter code '?'. Still, there are 1245 three-letter codes corresponding to a one-letter code other than '?' (the list is attached in the end). Therefore, I suggest to update the to_one_letter_code dictionary in Bio.SCOP.Raf.
Best regards,
hongbo zhu
to_one_letter_code = {
'00C':'C','01W':'X','0A0':'D','0A1':'Y','0A2':'K',
'0A8':'C','0AA':'V','0AB':'V','0AC':'G','0AD':'G',
'0AF':'W','0AG':'L','0AH':'S','0AK':'D','0AM':'A',
'0AP':'C','0AU':'U','0AV':'A','0AZ':'P','0BN':'F',
'0C ':'C','0CS':'A','0DC':'C','0DG':'G','0DT':'T',
'0G ':'G','0NC':'A','0SP':'A','0U ':'U','0YG':'YG',
'10C':'C','125':'U','126':'U','127':'U','128':'N',
'12A':'A','143':'C','175':'ASG','193':'X','1AP':'A',
'1MA':'A','1MG':'G','1PA':'F','1PI':'A','1PR':'N',
'1SC':'C','1TQ':'W','1TY':'Y','200':'F','23F':'F',
'23S':'X','26B':'T','2AD':'X','2AG':'G','2AO':'X',
'2AR':'A','2AS':'X','2AT':'T','2AU':'U','2BD':'I',
'2BT':'T','2BU':'A','2CO':'C','2DA':'A','2DF':'N',
'2DM':'N','2DO':'X','2DT':'T','2EG':'G','2FE':'N',
'2FI':'N','2FM':'M','2GT':'T','2HF':'H','2LU':'L',
'2MA':'A','2MG':'G','2ML':'L','2MR':'R','2MT':'P',
'2MU':'U','2NT':'T','2OM':'U','2OT':'T','2PI':'X',
'2PR':'G','2SA':'N','2SI':'X','2ST':'T','2TL':'T',
'2TY':'Y','2VA':'V','32S':'X','32T':'X','3AH':'H',
'3AR':'X','3CF':'F','3DA':'A','3DR':'N','3GA':'A',
'3MD':'D','3ME':'U','3NF':'Y','3TY':'X','3XH':'G',
'4AC':'N','4BF':'Y','4CF':'F','4CY':'M','4DP':'W',
'4F3':'GYG','4FB':'P','4FW':'W','4HT':'W','4IN':'X',
'4MF':'N','4MM':'X','4OC':'C','4PC':'C','4PD':'C',
'4PE':'C','4PH':'F','4SC':'C','4SU':'U','4TA':'N',
'5AA':'A','5AT':'T','5BU':'U','5CG':'G','5CM':'C',
'5CS':'C','5FA':'A','5FC':'C','5FU':'U','5HP':'E',
'5HT':'T','5HU':'U','5IC':'C','5IT':'T','5IU':'U',
'5MC':'C','5MD':'N','5MU':'U','5NC':'C','5PC':'C',
'5PY':'T','5SE':'U','5ZA':'TWG','64T':'T','6CL':'K',
'6CT':'T','6CW':'W','6HA':'A','6HC':'C','6HG':'G',
'6HN':'K','6HT':'T','6IA':'A','6MA':'A','6MC':'A',
'6MI':'N','6MT':'A','6MZ':'N','6OG':'G','70U':'U',
'7DA':'A','7GU':'G','7JA':'I','7MG':'G','8AN':'A',
'8FG':'G','8MG':'G','8OG':'G','9NE':'E','9NF':'F',
'9NR':'R','9NV':'V','A ':'A','A1P':'N','A23':'A',
'A2L':'A','A2M':'A','A34':'A','A35':'A','A38':'A',
'A39':'A','A3A':'A','A3P':'A','A40':'A','A43':'A',
'A44':'A','A47':'A','A5L':'A','A5M':'C','A5O':'A',
'A66':'X','AA3':'A','AA4':'A','AAR':'R','AB7':'X',
'ABA':'A','ABR':'A','ABS':'A','ABT':'N','ACB':'D',
'ACL':'R','AD2':'A','ADD':'X','ADX':'N','AEA':'X',
'AEI':'D','AET':'A','AFA':'N','AFF':'N','AFG':'G',
'AGM':'R','AGT':'X','AHB':'N','AHH':'X','AHO':'A',
'AHP':'A','AHS':'X','AHT':'X','AIB':'A','AKL':'D',
'ALA':'A','ALC':'A','ALG':'R','ALM':'A','ALN':'A',
'ALO':'T','ALQ':'X','ALS':'A','ALT':'A','ALY':'K',
'AP7':'A','APE':'X','APH':'A','API':'K','APK':'K',
'APM':'X','APP':'X','AR2':'R','AR4':'E','ARG':'R',
'ARM':'R','ARO':'R','ARV':'X','AS ':'A','AS2':'D',
'AS9':'X','ASA':'D','ASB':'D','ASI':'D','ASK':'D',
'ASL':'D','ASM':'X','ASN':'N','ASP':'D','ASQ':'D',
'ASU':'N','ASX':'B','ATD':'T','ATL':'T','ATM':'T',
'AVC':'A','AVN':'X','AYA':'A','AYG':'AYG','AZK':'K',
'AZS':'S','AZY':'Y','B1F':'F','B1P':'N','B2A':'A',
'B2F':'F','B2I':'I','B2V':'V','B3A':'A','B3D':'D',
'B3E':'E','B3K':'K','B3L':'X','B3M':'X','B3Q':'X',
'B3S':'S','B3T':'X','B3U':'H','B3X':'N','B3Y':'Y',
'BB6':'C','BB7':'C','BB9':'C','BBC':'C','BCS':'C',
'BCX':'C','BE2':'X','BFD':'D','BG1':'S','BGM':'G',
'BHD':'D','BIF':'F','BIL':'X','BIU':'I','BJH':'X',
'BLE':'L','BLY':'K','BMP':'N','BMT':'T','BNN':'A',
'BNO':'X','BOE':'T','BOR':'R','BPE':'C','BRU':'U',
'BSE':'S','BT5':'N','BTA':'L','BTC':'C','BTR':'W',
'BUC':'C','BUG':'V','BVP':'U','BZG':'N','C ':'C',
'C12':'TYG','C1X':'K','C25':'C','C2L':'C','C2S':'C',
'C31':'C','C32':'C','C34':'C','C36':'C','C37':'C',
'C38':'C','C3Y':'C','C42':'C','C43':'C','C45':'C',
'C46':'C','C49':'C','C4R':'C','C4S':'C','C5C':'C',
'C66':'X','C6C':'C','C99':'TFG','CAF':'C','CAL':'X',
'CAR':'C','CAS':'C','CAV':'X','CAY':'C','CB2':'C',
'CBR':'C','CBV':'C','CCC':'C','CCL':'K','CCS':'C',
'CCY':'CYG','CDE':'X','CDV':'X','CDW':'C','CEA':'C',
'CFL':'C','CFY':'FCYG','CG1':'G','CGA':'E','CGU':'E',
'CH ':'C','CH6':'MYG','CH7':'KYG','CHF':'X','CHG':'X',
'CHP':'G','CHS':'X','CIR':'R','CJO':'GYG','CLE':'L',
'CLG':'K','CLH':'K','CLV':'AFG','CM0':'N','CME':'C',
'CMH':'C','CML':'C','CMR':'C','CMT':'C','CNU':'U',
'CP1':'C','CPC':'X','CPI':'X','CQR':'GYG','CR0':'TLG',
'CR2':'GYG','CR5':'G','CR7':'KYG','CR8':'HYG','CRF':'TWG',
'CRG':'THG','CRK':'MYG','CRO':'GYG','CRQ':'QYG','CRU':'E',
'CRW':'ASG','CRX':'ASG','CS0':'C','CS1':'C','CS3':'C',
'CS4':'C','CS8':'N','CSA':'C','CSB':'C','CSD':'C',
'CSE':'C','CSF':'C','CSH':'SHG','CSI':'G','CSJ':'C',
'CSL':'C','CSO':'C','CSP':'C','CSR':'C','CSS':'C',
'CSU':'C','CSW':'C','CSX':'C','CSY':'SYG','CSZ':'C',
'CTE':'W','CTG':'T','CTH':'T','CUC':'X','CWR':'S',
'CXM':'M','CY0':'C','CY1':'C','CY3':'C','CY4':'C',
'CYA':'C','CYD':'C','CYF':'C','CYG':'C','CYJ':'X',
'CYM':'C','CYQ':'C','CYR':'C','CYS':'C','CZ2':'C',
'CZO':'GYG','CZZ':'C','D11':'T','D1P':'N','D3 ':'N',
'D33':'N','D3P':'G','D3T':'T','D4M':'T','D4P':'X',
'DA ':'A','DA2':'X','DAB':'A','DAH':'F','DAL':'A',
'DAR':'R','DAS':'D','DBB':'T','DBM':'N','DBS':'S',
'DBU':'T','DBY':'Y','DBZ':'A','DC ':'C','DC2':'C',
'DCG':'G','DCI':'X','DCL':'X','DCT':'C','DCY':'C',
'DDE':'H','DDG':'G','DDN':'U','DDX':'N','DFC':'C',
'DFG':'G','DFI':'X','DFO':'X','DFT':'N','DG ':'G',
'DGH':'G','DGI':'G','DGL':'E','DGN':'Q','DHA':'A',
'DHI':'H','DHL':'X','DHN':'V','DHP':'X','DHU':'U',
'DHV':'V','DI ':'I','DIL':'I','DIR':'R','DIV':'V',
'DLE':'L','DLS':'K','DLY':'K','DM0':'K','DMH':'N',
'DMK':'D','DMT':'X','DN ':'N','DNE':'L','DNG':'L',
'DNL':'K','DNM':'L','DNP':'A','DNR':'C','DNS':'K',
'DOA':'X','DOC':'C','DOH':'D','DON':'L','DPB':'T',
'DPH':'F','DPL':'P','DPP':'A','DPQ':'Y','DPR':'P',
'DPY':'N','DRM':'U','DRP':'N','DRT':'T','DRZ':'N',
'DSE':'S','DSG':'N','DSN':'S','DSP':'D','DT ':'T',
'DTH':'T','DTR':'W','DTY':'Y','DU ':'U','DVA':'V',
'DXD':'N','DXN':'N','DYG':'DYG','DYS':'C','DZM':'A',
'E ':'A','E1X':'A','EDA':'A','EDC':'G','EFC':'C',
'EHP':'F','EIT':'T','ENP':'N','ESB':'Y','ESC':'M',
'EXY':'L','EY5':'N','EYS':'X','F2F':'F','FA2':'A',
'FA5':'N','FAG':'N','FAI':'N','FCL':'F','FFD':'N',
'FGL':'G','FGP':'S','FHL':'X','FHO':'K','FHU':'U',
'FLA':'A','FLE':'L','FLT':'Y','FME':'M','FMG':'G',
'FMU':'N','FOE':'C','FOX':'G','FP9':'P','FPA':'F',
'FRD':'X','FT6':'W','FTR':'W','FTY':'Y','FZN':'K',
'G ':'G','G25':'G','G2L':'G','G2S':'G','G31':'G',
'G32':'G','G33':'G','G36':'G','G38':'G','G42':'G',
'G46':'G','G47':'G','G48':'G','G49':'G','G4P':'N',
'G7M':'G','GAO':'G','GAU':'E','GCK':'C','GCM':'X',
'GDP':'G','GDR':'G','GFL':'G','GGL':'E','GH3':'G',
'GHG':'Q','GHP':'G','GL3':'G','GLH':'Q','GLM':'X',
'GLN':'Q','GLQ':'E','GLU':'E','GLX':'Z','GLY':'G',
'GLZ':'G','GMA':'E','GMS':'G','GMU':'U','GN7':'G',
'GND':'X','GNE':'N','GOM':'G','GPL':'K','GS ':'G',
'GSC':'G','GSR':'G','GSS':'G','GSU':'E','GT9':'C',
'GTP':'G','GVL':'X','GYC':'CYG','GYS':'SYG','H2U':'U',
'H5M':'P','HAC':'A','HAR':'R','HBN':'H','HCS':'X',
'HDP':'U','HEU':'U','HFA':'X','HGL':'X','HHI':'H',
'HHK':'AK','HIA':'H','HIC':'H','HIP':'H','HIQ':'H',
'HIS':'H','HL2':'L','HLU':'L','HMF':'A','HMR':'R',
'HOL':'N','HPC':'F','HPE':'F','HPQ':'F','HQA':'A',
'HRG':'R','HRP':'W','HS8':'H','HS9':'H','HSE':'S',
'HSL':'S','HSO':'H','HTI':'C','HTN':'N','HTR':'W',
'HV5':'A','HVA':'V','HY3':'P','HYP':'P','HZP':'P',
'I ':'I','I2M':'I','I58':'K','I5C':'C','IAM':'A',
'IAR':'R','IAS':'D','IC ':'C','IEL':'K','IEY':'HYG',
'IG ':'G','IGL':'G','IGU':'G','IIC':'SHG','IIL':'I',
'ILE':'I','ILG':'E','ILX':'I','IMC':'C','IML':'I',
'IOY':'F','IPG':'G','IPN':'N','IRN':'N','IT1':'K',
'IU ':'U','IYR':'Y','IYT':'T','JJJ':'C','JJK':'C',
'JJL':'C','JW5':'N','K1R':'C','KAG':'G','KCX':'K',
'KGC':'K','KOR':'M','KPI':'K','KST':'K','KYQ':'K',
'L2A':'X','LA2':'K','LAA':'D','LAL':'A','LBY':'K',
'LC ':'C','LCA':'A','LCC':'N','LCG':'G','LCH':'N',
'LCK':'K','LCX':'K','LDH':'K','LED':'L','LEF':'L',
'LEH':'L','LEI':'V','LEM':'L','LEN':'L','LET':'X',
'LEU':'L','LG ':'G','LGP':'G','LHC':'X','LHU':'U',
'LKC':'N','LLP':'K','LLY':'K','LME':'E','LMQ':'Q',
'LMS':'N','LP6':'K','LPD':'P','LPG':'G','LPL':'X',
'LPS':'S','LSO':'X','LTA':'X','LTR':'W','LVG':'G',
'LVN':'V','LYM':'K','LYN':'K','LYR':'K','LYS':'K',
'LYX':'K','LYZ':'K','M0H':'C','M1G':'G','M2G':'G',
'M2L':'K','M2S':'M','M3L':'K','M5M':'C','MA ':'A',
'MA6':'A','MA7':'A','MAA':'A','MAD':'A','MAI':'R',
'MBQ':'Y','MBZ':'N','MC1':'S','MCG':'X','MCL':'K',
'MCS':'C','MCY':'C','MDH':'X','MDO':'ASG','MDR':'N',
'MEA':'F','MED':'M','MEG':'E','MEN':'N','MEP':'U',
'MEQ':'Q','MET':'M','MEU':'G','MF3':'X','MFC':'GYG',
'MG1':'G','MGG':'R','MGN':'Q','MGQ':'A','MGV':'G',
'MGY':'G','MHL':'L','MHO':'M','MHS':'H','MIA':'A',
'MIS':'S','MK8':'L','ML3':'K','MLE':'L','MLL':'L',
'MLY':'K','MLZ':'K','MME':'M','MMT':'T','MND':'N',
'MNL':'L','MNU':'U','MNV':'V','MOD':'X','MP8':'P',
'MPH':'X','MPJ':'X','MPQ':'G','MRG':'G','MSA':'G',
'MSE':'M','MSL':'M','MSO':'M','MSP':'X','MT2':'M',
'MTR':'T','MTU':'A','MTY':'Y','MVA':'V','N ':'N',
'N10':'S','N2C':'X','N5I':'N','N5M':'C','N6G':'G',
'N7P':'P','NA8':'A','NAL':'A','NAM':'A','NB8':'N',
'NBQ':'Y','NC1':'S','NCB':'A','NCX':'N','NCY':'X',
'NDF':'F','NDN':'U','NEM':'H','NEP':'H','NF2':'N',
'NFA':'F','NHL':'E','NIT':'X','NIY':'Y','NLE':'L',
'NLN':'L','NLO':'L','NLP':'L','NLQ':'Q','NMC':'G',
'NMM':'R','NMS':'T','NMT':'T','NNH':'R','NP3':'N',
'NPH':'C','NRP':'LYG','NRQ':'MYG','NSK':'X','NTY':'Y',
'NVA':'V','NYC':'TWG','NYG':'NYG','NYM':'N','NYS':'C',
'NZH':'H','O12':'X','O2C':'N','O2G':'G','OAD':'N',
'OAS':'S','OBF':'X','OBS':'X','OCS':'C','OCY':'C',
'ODP':'N','OHI':'H','OHS':'D','OIC':'X','OIP':'I',
'OLE':'X','OLT':'T','OLZ':'S','OMC':'C','OMG':'G',
'OMT':'M','OMU':'U','ONE':'U','ONL':'X','OPR':'R',
'ORN':'A','ORQ':'R','OSE':'S','OTB':'X','OTH':'T',
'OTY':'Y','OXX':'D','P ':'G','P1L':'C','P1P':'N',
'P2T':'T','P2U':'U','P2Y':'P','P5P':'A','PAQ':'Y',
'PAS':'D','PAT':'W','PAU':'A','PBB':'C','PBF':'F',
'PBT':'N','PCA':'E','PCC':'P','PCE':'X','PCS':'F',
'PDL':'X','PDU':'U','PEC':'C','PF5':'F','PFF':'F',
'PFX':'X','PG1':'S','PG7':'G','PG9':'G','PGL':'X',
'PGN':'G','PGP':'G','PGY':'G','PHA':'F','PHD':'D',
'PHE':'F','PHI':'F','PHL':'F','PHM':'F','PIV':'X',
'PLE':'L','PM3':'F','PMT':'C','POM':'P','PPN':'F',
'PPU':'A','PPW':'G','PQ1':'N','PR3':'C','PR5':'A',
'PR9':'P','PRN':'A','PRO':'P','PRS':'P','PSA':'F',
'PSH':'H','PST':'T','PSU':'U','PSW':'C','PTA':'X',
'PTH':'Y','PTM':'Y','PTR':'Y','PU ':'A','PUY':'N',
'PVH':'H','PVL':'X','PYA':'A','PYO':'U','PYX':'C',
'PYY':'N','QLG':'QLG','QUO':'G','R ':'A','R1A':'C',
'R1B':'C','R1F':'C','R7A':'C','RC7':'HYG','RCY':'C',
'RIA':'A','RMP':'A','RON':'X','RT ':'T','RTP':'N',
'S1H':'S','S2C':'C','S2D':'A','S2M':'T','S2P':'A',
'S4A':'A','S4C':'C','S4G':'G','S4U':'U','S6G':'G',
'SAC':'S','SAH':'C','SAR':'G','SBL':'S','SC ':'C',
'SCH':'C','SCS':'C','SCY':'C','SD2':'X','SDG':'G',
'SDP':'S','SEB':'S','SEC':'A','SEG':'A','SEL':'S',
'SEM':'X','SEN':'S','SEP':'S','SER':'S','SET':'S',
'SGB':'S','SHC':'C','SHP':'G','SHR':'K','SIB':'C',
'SIC':'DC','SLA':'P','SLR':'P','SLZ':'K','SMC':'C',
'SME':'M','SMF':'F','SMP':'A','SMT':'T','SNC':'C',
'SNN':'N','SOC':'C','SOS':'N','SOY':'S','SPT':'T',
'SRA':'A','SSU':'U','STY':'Y','SUB':'X','SUI':'DG',
'SUN':'S','SUR':'U','SVA':'S','SVX':'S','SVZ':'X',
'SYS':'C','T ':'T','T11':'F','T23':'T','T2S':'T',
'T2T':'N','T31':'U','T32':'T','T36':'T','T37':'T',
'T38':'T','T39':'T','T3P':'T','T41':'T','T48':'T',
'T49':'T','T4S':'T','T5O':'U','T5S':'T','T66':'X',
'T6A':'A','TA3':'T','TA4':'X','TAF':'T','TAL':'N',
'TAV':'D','TBG':'V','TBM':'T','TC1':'C','TCP':'T',
'TCQ':'X','TCR':'W','TCY':'A','TDD':'L','TDY':'T',
'TFE':'T','TFO':'A','TFQ':'F','TFT':'T','TGP':'G',
'TH6':'T','THC':'T','THO':'X','THR':'T','THX':'N',
'THZ':'R','TIH':'A','TLB':'N','TLC':'T','TLN':'U',
'TMB':'T','TMD':'T','TNB':'C','TNR':'S','TOX':'W',
'TP1':'T','TPC':'C','TPG':'G','TPH':'X','TPL':'W',
'TPO':'T','TPQ':'Y','TQQ':'W','TRF':'W','TRG':'K',
'TRN':'W','TRO':'W','TRP':'W','TRQ':'W','TRW':'W',
'TRX':'W','TS ':'N','TST':'X','TT ':'N','TTD':'T',
'TTI':'U','TTM':'T','TTQ':'W','TTS':'Y','TY2':'Y',
'TY3':'Y','TYB':'Y','TYI':'Y','TYN':'Y','TYO':'Y',
'TYQ':'Y','TYR':'Y','TYS':'Y','TYT':'Y','TYU':'N',
'TYX':'X','TYY':'Y','TZB':'X','TZO':'X','U ':'U',
'U25':'U','U2L':'U','U2N':'U','U2P':'U','U31':'U',
'U33':'U','U34':'U','U36':'U','U37':'U','U8U':'U',
'UAR':'U','UCL':'U','UD5':'U','UDP':'N','UFP':'N',
'UFR':'U','UFT':'U','UMA':'A','UMP':'U','UMS':'U',
'UN1':'X','UN2':'X','UNK':'X','UR3':'U','URD':'U',
'US1':'U','US2':'U','US3':'T','US5':'U','USM':'U',
'V1A':'C','VAD':'V','VAF':'V','VAL':'V','VB1':'K',
'VDL':'X','VLL':'X','VLM':'X','VMS':'X','VOL':'X',
'X ':'G','X2W':'E','X4A':'N','X9Q':'AFG','XAD':'A',
'XAE':'N','XAL':'A','XAR':'N','XCL':'C','XCP':'X',
'XCR':'C','XCS':'N','XCT':'C','XCY':'C','XGA':'N',
'XGL':'G','XGR':'G','XGU':'G','XTH':'T','XTL':'T',
'XTR':'T','XTS':'G','XTY':'N','XUA':'A','XUG':'G',
'XX1':'K','XXY':'THG','XYG':'DYG','Y ':'A','YCM':'C',
'YG ':'G','YOF':'Y','YRR':'N','YYG':'G','Z ':'C',
'ZAD':'A','ZAL':'A','ZBC':'C','ZCY':'C','ZDU':'U',
'ZFB':'X','ZGU':'G','ZHP':'N','ZTH':'T','ZZJ':'A' }
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