IJ Ic@sdZddlmZddlTddlmZidd6dd6d d 6d d 6d d6dd6dd6dd6dd6dd6dd6dd6dd6dd 6d!d"6d#d$6d%d&6d'd(6d)d*6d+d,6dd-6d!d.6dd/6dd06dd16dd26dd36dd46dd56dd66dd76dd86dd96dd:6dd;6d#d<6dd=6dd>6dd?6d#d@6ddA6d#dB6d#dC6d#dD6d#dE6ddF6ddG6d#dH6ddI6d#dJ6d#dK6d#dL6d#dM6d dN6d#dO6d#dP6d#dQ6d#dR6d#dS6d dT6ddU6ddV6ddW6d#dX6ddY6d'dZ6dd[6d!d\6dd]6dd^6dd_6dd`6dda6d db6d dc6ddd6dde6ddf6d)dg6ddh6ddi6d#dj6ddk6d dl6ddm6d+dn6ddo6d+dp6ddq6ddr6d!ds6d!dt6ddu6d dv6d)dw6d dx6ddy6ddz6dd{6dd|6dd}6d)d~6dd6dd6dd6d%d6d!d6dd6dd6d+d6d+d6d d6dd6d!d6d!d6dd6dd6dd6d+d6dd6d#d6d d6dd6dd6d#d6d d6d d6d#d6dd6dd6dd6d+d6d#d6d#d6d#d6dd6dd6dd6d#d6dd6d#d6dd6dd6dd6d)d6dd6dd6dd6d)d6dd6dd6dd6dd6dd6d+d6d#d6dd6dd6d#d6dd6dd6ZdZdefdYZdddYZdddYZ dZ dddYZ dddYZ dS(sASTRAL RAF (Rapid Access Format) Sequence Maps. The ASTRAL RAF Sequence Maps record the relationship between the PDB SEQRES records (representing the sequence of the molecule used in an experiment) to the ATOM records (representing the atoms experimentally observed). This data is derived from the Protein Data Bank CIF files. Known errors in the CIF files are corrected manually, with the original PDB file serving as the final arbiter in case of discrepancies. Residues are referenced by residue ID. This consists of a the PDB residue sequence number (upto 4 digits) and an optional PDB insertion code (an ascii alphabetic character, a-z, A-Z). e.g. "1", "10A", "1010b", "-1" See "ASTRAL RAF Sequence Maps":http://astral.stanford.edu/raf.html to_one_letter_code -- A mapping from the 3-letter amino acid codes found in PDB files to 1-letter codes. The 3-letter codes include chemically modified residues. i(tcopy(t*(tResiduestAtALAtVtVALtFtPHEtPtPROtMtMETtItILEtLtLEUtDtASPtEtGLUtKtLYStRtARGtStSERtTtTHRtYtTYRtHtHIStCtCYStNtASNtQtGLNtWtTRPtGtGLYt2ASt3AHt5HPtACLtAIBtALMtALOtALYtARMtASAtASBtASKtASLtASQtAYAtBCStBHDtBMTtBNNtBUCtBUGtC5CtC6CtCCStCEAtCHGtCLEtCMEtCSDtCSOtCSPtCSStCSWtCXMtCY1tCY3tCYGtCYMtCYQtDAHtDALtDARtDAStDCYtDGLtDGNtDHAtDHItDILtDIVtDLEtDLYtDNPtDPNtDPRtDSNtDSPtDTHtDTRtDTYtDVAtEFCtFLAtFMEtGGLtGLZtGMAtGSCtHACtHARtHICtHIPtHMRtHPQtHTRtHYPtIILtIYRtKCXtLLPtLLYtLTRtLYMtLYZtMAAtMENtMHStMIStMLEtMPQtMSAtMSEtMVAtNEMtNEPtNLEtNLNtNLPtNMCtOAStOCStOMTtPAQtPCAtPECtPHItPHLtPR3tPRRtPTRtSACtSARtSCHtSCStSCYtSELtSEPtSETtSHCtSHRtSOCtSTYtSVAtTIHtTPLtTPOtTPQtTRGtTROtTYBtTYQtTYStTYYtAGMtGL3tSMCtBtASXtCGUtCSXtZtGLXtXtUNKcCs|dkrdS|jSdS(sConvert RAF one-letter amino acid codes into IUPAC standard codes. Letters are uppercased, and "." ("Unknown") is converted to "X". t.RN(tupper(tone_letter_code((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Raf.pytnormalize_lettersIs t SeqMapIndexcBs)eZdZdZdZdZRS(sIAn RAF file index. The RAF file itself is about 50 MB. This index provides rapid, random access of RAF records without having to load the entire file into memory. The index key is a concatenation of the PDB ID and chain ID. e.g "2drcA", "155c_". RAF uses an underscore to indicate blank chain IDs. cCstj|||_t|j}z_d}xRtr|j}|sMPn|dd!}|dkrs|||sX ################################  W $