[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
Wed Apr 25 23:36:04 EDT 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' }
--
You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here and login: http://redmine.open-bio.org
More information about the Biopython-dev
mailing list