U4      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~                                  ! " # $ % & ' ( ) * + , - ./01237 Safe-InferredNone 456789:;<=>?5<? 456789:;<=>?None @ABCDE   @ABCDENone ?This module wraps 3D vector operations, and adds missing ones. 8Unpacks an abstract 3D vector into a triple of Doubles. ;Maps an operation that modifies a Double onto a 3D vector. AMaps an operation on a pair of Doubles onto a pair of 3D vectors  coordinatewise. <Normalises to a unit vector in the same direction as input. *Computes a dot product of two 3D vectors. 82-norm of a vector (also called a magnitude or length.) KCompute dihedral between three bond vectors using spherical angle formula. Scalar product. (F0 indicates side on which one can put a scalar.) Scalar product. (F0 indicates side on which one can put a scalar.) cFinds a vector component of the first vector that is a projection onto direction of second vector. @Returns a component of the vector v that is perpendicular to w. RFinds a component of the vector v that is perpendicular to all vectors in a list. G GNone/Type alias for a mutable sequence of elements. 1Type alias for a immutable sequence of elements. Empty vector. Vector with a single element Create a new mutable vector. 1Allocate initial space for a new mutable vector. !Length of mutable vector. "?Default initial size of a mutable vector for residue contents. #=Default initial size of a mutable vector for chain contents. $ADefault initial size of a mutable vector for structure contents. %(Appends an element to a mutable vector. &:Finalizes a mutable vector, and returns immutable vector. # [Does it shrink allocated space?] '' on immutable vectors. (( on immutable vectors. )) on immutable vectors. ** on immutable vectors. ++ on immutable vectors. ,, on immutable vectors. -- on immutable vectors. .. on immutable vectors. // on immutable vectors. 0+Conversion of an immutable vector to list. 1* on immutable vectors. 2!Indexing of an immutable vector. H !"#$%&'()*+,-./012I !"#$%&'()*+,-./012 %&!/*,'()-+.$"#012H !"#$%&'()*+,-./012I Safe-Inferred38We use only strict ByteString as strings in PDB parser. 333 Safe-Inferred4#Enumeration of beta-strand sense. 456456465465 Safe-Inferred7Enumeration of helix types JPDB Class number in columns 39-40 for each type of helix in HELIX record: + Right-handed alpha (default, most common)  Right-handed omega  Right-handed pi  Right-handed gamma  Right-handed 3 - 10  Left-handed alpha  Left-handed omega  Left-handed gamma  2 - 7 ribbon/helix  Polyproline 8helix2code converts a 7% enumeration into an PDB CLASS code. 9-helix2code converts an PDB CLASS code into a 7 enumeration. 7JKLMNOPQRS897897897 SRQPONMLKJ89 Safe-Inferred:AEnumeration of experimental methods occuring in the PDB archive. D)Generates an ExpMethod from words in PDB E%Converts an ExpMethod back into text :;<=>?@ABCDE :;<=>?@ABCDE :CBA@?>=<;DE: CBA@?>=<;DE Safe-InferredF$Datatype for event-based PDB parser DResidue id: residue name, chain, residue id, residue insertion code LAtom id: atom name, residue name, chain, residue id, residue insertion code FGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~34567:;<=>?@ABCFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~23Fvutplkie]\YWTPIHGwxyz{|}~qrsmnomnojfgh^_`abcd^_`afg^_Z[`afgXUVQRSJKLMNO4657:CBA@?>=<;Fvutplkie]\YWTPIHGwxyz{|}~qrsmnomnojfgh^_`abcd^_`afg^_Z[`afgXUVQRSJKLMNONone&T<A common type for shuttling parsed and typed record values. U3Splits a string into substrings by column numbers. V Converts a T containing 3< into this string or an empty string if nothing was parsed. W4Construct an error message by concatenating list of  Bytestrings XhParser for an optional single-character field, first argument is a name of a field, second is an input. Y9Parser for an optional spacing, an argument is an input. ZOld version of pSpc . NOTE: also slower than using new trimFront [eParser for an optional integer field, first argument is a field name, a second argument is an input. \Reports error from pInt. ]dParser for an optional string field, first argument is a field name, a second argument is an input. ^lParser for an optional floating-point field, first argument is a field name, a second argument is an input. _=A helper method for converting a parser of an optional field : into a parser of an optional field with a default value. `SParser for an optional single character field with a default value, arguments are:  field name  default value  input aJParser for an optional integer field with a default value, arguments are:  field name  default value  input bIParser for an optional string field with a default value, arguments are:  field name  default value  input cQParser for an optional floating-point field with a default value, arguments are:  field name  default value  input d]Converts an optional field parser into a mandatory field parser that bails on missing input. Arguments are:   name of the field type @ a parser function that takes field name, and input and returns T $A results is a function that takes:   field name  input and returns a T. e6Return error message when mandatory field is missing. fLParser for a mandatory character field with a default value, arguments are:  field name  input gQParser for a mandatory floating-point field with a default value, arguments are:  field name  input hIParser for a mandatory string field with a default value, arguments are:  field name  input iJParser for a mandatory integer field with a default value, arguments are:  field name j5Parser for a mandatory spacing field, arguments are:  number of columns for spacing  input kVParser for a fixed field that can be filled with one of many keywords, arguments are:  field name  a list of valid keywords  input l8Parser for a fixed single keyword field, arguments are:  field name  keyword  input mSDissects columns from stage 1 parsing, and applies converters from stage 2 parsing * list of string parsers that return typed T values @ list of column numbers that indicate a beginning of each field  input n"Finds IFError values in a list of T values, and returns / a list of error events in case there are any. * list of string parsers that return typed T values @ list of column numbers that indicate a beginning of each field . line number to be injected into error events  input oCUses field declarations that are list of (column number, parser to T, ...) 1 tuples and applies it to a given line of input. Arguments are:  field declarations list  input line ! ordinal number of an input line pReturns if a given T/ value _certainly_ represents a missing value. qReturns if a given T/ value _certainly_ represents a present value. rCMerges a set of values that corresponds to a residue description. Arguments are:  B boolean indicating, if the field group may omit a residue number  field group name (description) 9 column number beginning the residue description entries  T. containing a three letter residue identifier  T- containing a single letter chain identifier  T containing a residue number  T% containing a residue insertion code A result is a s/ of pair with column number and error message,  or # value with a residue description. tLMerges a set of values that corresponds to an optional residue description. Arguments are:  B boolean indicating, if the field group may omit a residue number  field group name (description) 9 column number beginning the residue description entries  T. containing a three letter residue identifier  T- containing a single letter chain identifier  T containing a residue number  T% containing a residue insertion code A result is a s/ of pair with column number and error message,  or u / value that may contain a residue description. vHMerges a set of values that correspond to a mandatory atom description. Arguments are:   field group name (description) 9 column number beginning the residue description entries  T+ containing a three letter atom identifier  T. containing a three letter residue identifier  T- containing a single letter chain identifier  T containing a residue number  T% containing a residue insertion code A result is a s/ of pair with column number and error message,  or - value that may contain an atom description. wHMerges a set of values that correspond to an optional atom description. Arguments are:   field group name (description) 9 column number beginning the residue description entries  T+ containing a three letter atom identifier  T. containing a three letter residue identifier  T- containing a single letter chain identifier  T containing a residue number  T% containing a residue insertion code A result is a s/ of pair with column number and error message,  or u - value that may contain an atom description. xChanges a list of s& values, into a list of all values in y entries. z\Extracts Left (column_number, error_message) values from a list of results in a given line,  to form HC events with a given line number, column number and error message.  Arguments:   line number  list of s6 (column_number, error_message_string) result values,  where y. entries are used to generate error messages. Result is a list of F entries that contain H s (if any.) {Changes a list of s& values, into a list of all values in | entries. }Utility: Changes a list of u s to a list of values hidden in ~ _ records. ,TUVWXYZ[\]^_`abcdefghijklmnopqrtvwxz{}"?TVXY[]^`abcfghijklortvwxz{}&TUVWXYZ[\]^_`abcdefghijklmnopqrtvwxz{}NoneParses an ATOM record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. {-@ SPECIALIZE parseATOM :: Bool -> String -> Int -> IO [PDBEvent] -} Parses an ANISOU record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a HEADER record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a TITLE record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. None'Parses a record with a single integer.  Arguments:   constructor  input line  input line number -Result is a monad action returning a list of Fs. Parses a NUMMDL record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a MODEL record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a REVDAT record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a CONECT record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a SEQRES record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a CRYST1 record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a HET record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. NoneParses a SHEET record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs.  NoneParses a TER record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. !NoneFields of the MASTER record Parses a MASTER record.  Arguments:   input line  input line number .Result is a mionad action returning a list of Fs. "NoneParses a MODRES record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. #NoneParses a SEQADV record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. $NoneParses a CAVEAT record.  Arguments:  input line  input line number %NoneParses a SPLIT record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. &NoneDParses a JRNL or REMARK 1 record that contains a journal reference.  Arguments:  E boolean indicating, if it is first reference for a structure (JRNL)  or any other (REMARK 1.)  input line  input line number -Result is a monad action returning a list of Fs. 8Parses a JRNL record that contains a journal reference.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. <Parses a REMARK 1 record that contains a journal reference.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 'None"Parses a _generic_ REMARK record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. (NoneFields of a DBREF record. Parses a DBREF record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. List of fields in DBREF1 line List of fields in DBREF2 line. ,Checks agreement between DBREF1 and DBREF2. ,Parses a pair of DBREF1 and DBREF2 records.  Arguments:   two input lines as a tuple  input line number -Result is a monad action returning a list of Fs. )None"Parses a HETNAM or HETSYN record.  Arguments:  & boolean indicating, if it is HETNAM ( ) or HETSYN ( ) record  input line  input line number -Result is a monad action returning a list of Fs. *NoneParses a HET record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. +NoneParses a FORMUL record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. ,NoneParses a CISPEP record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. -NoneParses a SSBOND record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. .NoneParses a LINK record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. /NoneParses a SLTBRG record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 0NoneParses a HYDBND record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 1NoneParses a SITE record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 2None#Parses an OBSLTE or SPRSDE record:  Arguments:   a PDBEvent constructor:  OBSLTE or  SPRSDE   input line  input line number -Result is a monad action returning a list of Fs. Parses a OBSLTE record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a SPRSDE record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 3NoneParses a COMPND record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a SOURCE record:  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. .NOTE: SOURCE record values are always Strings 4None'String type used all over the library. 9Fields of the KEYWDS, AUTHOR, EXPDTA and MDLTYP records. 0Parses a record that contains a list of values.  Arguments:   a matrix constructor 4 a separator characteristic for this type of record  input line  input line number -Result is a monad action returning a list of Fs. Parses a KEYWDS record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a AUTHOR record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a EXPDTA record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a MDLTYP record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 5None8Parses a single line with matrix or vector information.  Arguments:  , record constructor: SCALEn, ORIGXn, MTRIXn  input line  input line number -Result is a monad action returning a list of Fs. Parses a SCALEn record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a ORIGXn record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. Parses a MTRIXn record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs. 6NoneParses a TVECT record.  Arguments:   input line  input line number -Result is a monad action returning a list of Fs.  NoneParses an input stream input with name fname at line line_no, and uses parsed input evts to perform an action on them and accumulator acc. 9Returns the ultimate value of the accumulated results in acc Cafter all actions are performed in an order consistent with input. Parses a strict ByteString contents named fname and performs action O on events given by parsing chunks, returning accumulated results. Accumulator  is primed by acc. 7Checks whether line was ignored as unknown record type  NoneSingle atom position < | NOTE: disordered atoms are now reported as multiplicates  eResidue groups all atoms assigned to the same aminoacid or nucleic acid base within a polymer chain. 9Single linear polymer chain of protein, or nucleic acids SPDB entry may contain multiple models, with slight differences in coordinates etc. 8Structure holds all data parsed from a single PDB entry !     %3     %3           None   NoneStandard nucleic acid codes RList of all correspondences between FASTA 1-letter codes, and PDB 3-letter codes. Standard protein codes 6List of both standard and non-standard protein codes. \Dictionary of translations from all 3-letter PDB codes into 1-letter FASTA aminoacid codes. CDictionary of translations from 1-letter FASTA aminoacid (standard + protein) codes into 3-letter PDB codes. 6Three-letter PDB code for an unknown type of residue. :One-letter aminoacid code for an unknown type of residue. PDictionary mapping three-letter PDB residue code to a single-letter FASTA code. UDictionary mapping single-letter FASTA standard aminoacid code to a PDB residue name  Converts a  7& into a one character aminoacid code.  Converts an   yielding  0s into a list of aminoacid one-character codes.  Converts an   yielding  0s into a list of aminoacid one-character codes. BScans a list and applies first argument to all consecutive pairs, + and second argument to the beginning or ` lone wolf` , mapping to  a list of the same length. AConvert a filename and Chain into a text of FASTA format record. 2 First argument tells if we want gaps included.  ! ! ! !8None"#$%&"#$%&"#$%& None'0Basic elemental parameters as suggested by CSD. XTODO: May be better as a newtype, and make sure that other modules use this declaration NInternal method that reports error to stderr, and return given default value. (!Atomic number of a given element *#Atomic mass of a given element in g/mol +*Van der Waals radius of the given element '()*+,-'()*+,-',-(*)+'()*+,-None@Record holding a current state of the structure record builder. .RGiven filename, and contents, parses a whole PDB file, returning a monadic action ( | with a tuple of (Structure, [PDBEvent])), where the list of events contains all # | parsing or construction errors. Uparse :: (State.MonadState BState m) => FilePath -> String -> m (Structure, [PDBEvent]) /Initial state of the structure record builder. DChecks that a residue with a given identification tuple is current, 9 | or if not, then closes previous residue (if present),  | and marks a new ,,current'' residue in a state of builder. FChecks that a chain with a given identification character is current, H | and if not, creates one. Also checks that we have any model in which  | to assign the chain. IChecks that a current model has been declared, and creates zeroth model,  | if no such model exists. T TODO: when createing a dummy model, check that there are no models declared before / [Otherwise one needs to report an error!] hCloses construction of a current residue and appends this residue to a current chain. (Monadic action.) &closeResidue :: State.State BState ()  JFinalizes construction of current chain, and appends it to current model. $closeChain :: State.State BState ()  :Reports error during building of structure for PDB entry. . TODO: This should be probably monadic action  TODO: forgot about line/column number passing!  (Finalizes construction of current model  9Finalizes construction of record holding PDB entry data. P NOTE: this one is different and should only be used after parsing is complete!  ePerforms a match on a single PDBEvent and performs relevant change to a BState of structure builder. ?parseStep :: (State.MonadState BState m) => PDBEvent -> m () BCreates a new model within structure builder. (For internal use.) 6 WARNING: And forgets anything that was there before! [Finalizes state of structure builder, and returns pair of a structure, and list of errors. w NOTE: should have a monadic action for each error instead. Then possibly default monad that accumulates these errors. .     .. .     None/#Prints a PDBEvent to a filehandle. 08Reports whether a given PDB record is already printable ) [temporary method, they all should be.]  Including errors. /0 !"/0/0/0 !"None#ShowS like type for a list of Fs. 14Writes a structure in a PDB format to a filehandle. $Generates list of Fs from a given Structure. %Generates list of Fs from a given Model. &Generates list of Fs from a given Chain. 'Generates list of F&s from a given Residue and its Chain. (Generates list of F1s from a given Atom, its Residue, and its Chain. #1$%&'(11#1$%&'(None2Parse a .pdb file and return . )#Default exception handler that for ` IO (Maybe a)`? just prints nice error message to stderr, and returns Nothing *JPrints a catenated list of ByteStrings to stderr. (Convenience function.) +Show error message from  PDBParser. 3 Write structure to a .pdb file. ,-2)*+32323,-2)*+3 None6      "#$%&'()*+,23623      #$%&"',(*)+.9:;9:<9:=9:>9:>?@A?@B?@C?@D?@E?@F?@G?@HIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~      !"#$%&'()*+,-./012345566 7 8 8 9 : ; < / = 1 3 4 7 7 > ?  @ @ A B B C D E E F G H I J K L M N8O8P8Q8R8S T U V W X Y Z[\]^[^_`abcdefghijklmnopqrstWuvwxyz{|}~qqqqq  !!""##$$%%&&&&''(((((())**++,,--..//0011222233334o444444555 5 56 6        ! " # $ % & ' ( ) * +,-./012345678,9:;<=>?@ABCDEFGHIJKLMNOPQRSoTU hPDB-0.999Bio.PDB.Structure.VectorBio.PDB.IterableBio.PDB.IO.OpenAnyFileBio.PDB.Structure.ListBio.PDB.EventParser.PDBEventsBio.PDB.EventParser.StrandSenseBio.PDB.EventParser.HelixTypes'Bio.PDB.EventParser.ExperimentalMethods"Bio.PDB.EventParser.PDBEventParserBio.PDB.Structure Bio.PDB.FastaBio.PDBBio.PDB.Structure.ElementsBio.PDB.StructureBuilder#Bio.PDB.EventParser.PDBEventPrinterBio.PDB.StructurePrinter Bio.PDB.IOBio.PDB.Util.MissingInstancesBio.PDB.EventParser.FastParseBio.PDB.Common*Bio.PDB.EventParser.PDBParsingAbstractionsBio.PDB.EventParser.ParseATOMBio.PDB.EventParser.ParseHEADERBio.PDB.EventParser.ParseTITLE"Bio.PDB.EventParser.ParseIntRecordBio.PDB.EventParser.ParseREVDATBio.PDB.EventParser.ParseCONECTBio.PDB.EventParser.ParseSEQRESBio.PDB.EventParser.ParseCRYST1Bio.PDB.EventParser.ParseHELIXBio.PDB.EventParser.ParseSHEETBio.PDB.EventParser.ParseTERBio.PDB.EventParser.ParseMASTERBio.PDB.EventParser.ParseMODRESBio.PDB.EventParser.ParseSEQADVBio.PDB.EventParser.ParseCAVEATBio.PDB.EventParser.ParseSPLITBio.PDB.EventParser.ParseJRNLBio.PDB.EventParser.ParseREMARKBio.PDB.EventParser.ParseDBREFBio.PDB.EventParser.ParseHETNAMBio.PDB.EventParser.ParseHETBio.PDB.EventParser.ParseFORMULBio.PDB.EventParser.ParseCISPEPBio.PDB.EventParser.ParseSSBONDBio.PDB.EventParser.ParseLINKBio.PDB.EventParser.ParseSLTBRGBio.PDB.EventParser.ParseHYDBNDBio.PDB.EventParser.ParseSITE#Bio.PDB.EventParser.ParseObsoleting'Bio.PDB.EventParser.ParseSpecListRecord#Bio.PDB.EventParser.ParseListRecord%Bio.PDB.EventParser.ParseMatrixRecordBio.PDB.EventParser.ParseTVECTResidueBio.PDB.Iterable.UtilsAC-Vector-2.3.2Data.Vector.V3v3zv3yv3xVector3 iterable-1.0 Data.Iterableilengthifoldl'ifoldlifoldrifoldMimapimapMIterablereadFile writeFile unpackVector3vmapvzip vnormalisevdotvnorm vdihedral*||*vprojvperpend vperpendsTempListListempty singletonnew initialNew tempLengthresidueVectorSizechainVectorSize defaultSizeaddfinalizefoldlfoldl'foldrmapfiltermapMfoldMlengthlasttoListvimap!String StrandSenseT AntiparallelParallelHelixT helix2code code2helix ExpMethodOtherExpMethodSolutionScattering SolutionNMR SolidStateNMRElectronMicroscopyElectronCrystallographyNeutronDiffractionFiberDiffractionXRayDiffraction mkExpMethod showExpMethodPDBEventPDBIgnoredLine PDBParseErrorSEQADVpdbId advResiduedatabase accessionCode dbResnamedbSeqNumMODRESpdbCoderesiduestdResJRNLcontentisFirstTVECTvecHYDBNDatHaltlocHSLTBRGLINKat1altloc1at2altloc2symop1symop2linkdistSSBONDsymOp1symOp2bondLenSPLITcodesSPRSDEOBSLTEdatethisentriesSITEsiteidnumresresiduesENDMDLENDMASTER numRemarknumHetnumHelixnumSheetnumTurnnumSitenumXformnumAts numMaster numConect numSeqresTERresnameSOURCECOMPNDtokensCRYST1abcalphabetagammaspcGrpzValueMTRIXnrelMolSCALEnORIGXnnotSHEETstrandIdsheetId numStrandssensecurAtprevAtHELIXiniResendRes helixClasslenCISPEPres1res2angleFORMULcompNumisWaterformulaHETseqNuminsCodeatmNum descriptionHETNAMhetIdname notSynonymREVDATmodNummodDatmodIdmodTypdetailsDBREF iniSeqNumPDB iniInsCodePDB endSeqNumPDB endInsCodePDB seqDbName seqDbAccCode seqDbIdCode iniSeqNumInDbiniInsCodeInPDBRef endSeqNumInDbendInsCodeInPDBRefCAVEATcontpdbidcommentCONECTatomsMODELNUMMDLMDLTYPEXPDTA expMethodsREMARKtextAUTHORKEYWDSaListTITLE continuationtitleHEADERclassificationdepDateidCodeSEQRESserialnumresListSIGUIJANISOUu_1_1u_2_2u_3_3u_1_2u_1_3u_2_3SIGATMATOMnoatomtyperestypechainresidresinsaltloccoords occupancybfactorsegideltchargehetatmRESIDATIDparsePDBRecordsAtomatNameatSerialcoordbFactorelementresNameresSeqChainchainIdModelmodelIdchains StructuremodelsdefaultResnamedefaultFastaCoderesname2fastacodefastacode2resname fastaSequencefastaGappedSequence fastaRecordfastaGappedRecord firstModelnumAtoms numResidues numChains numModelsElement atomicNumbercovalentRadius atomicMassvanDerWaalsRadius assignElement guessElementparseprint isPrintablewriteordstrtof digitValuefinalstrtof0strtof1 makeDouble checkSpaces trimFronttrimRearbutlasttrim readFile' throwNotFoundgetCodec gzipParams isReadable simpleReadbaseGHC.Num*$fArbitraryVector3$fNFDataTempList Polyproline Ribbon2_7 LeftGamma LeftOmega LeftAlpha Right3_10 RightGammaRightPi RightOmega RightAlpha ParsedFieldsplitByColumnsunstrifErrorpChrpSpcpSpcOpIntpIntErrpStrpDoubledConvdChrdIntdStrdDouble mandFieldmandFieldErrMsgmChrmDoublemStrmIntmSpc mKeywordsmKeywordconvertColumnsfindColumnErrors parseFields nonEmptyIFfullIF fgResidue Data.EitherEithermaybeFgResidue Data.MaybeMaybefgAtom maybeFgAtomleftsLeft liftFgErrsrightsRight maybeListJustIFNoneIFErrorIFDoubleIFCharIFStrIFInt parseATOM parseANISOU atomFields anisouFields parseHEADER headerFields parseTITLE titleFieldsparseIntRecord parseNUMMDL parseMODEL nummdlFields parseREVDAT revdatFieldspStrList strListErrs parseCONECT conectFieldsintList parseSEQRES seqresFields splitResidues parseCRYST1 crystFields parseHELIX helixFields parseSHEETparseTER terFields masterFields parseMASTER parseMODRES modresFields parseSEQADV parseCAVEAT caveatFields parseSPLITparseJournalRef parseJRNL parseREMARK1 parseREMARK remarkFields dbrefFields parseDBREF dbref1Fields dbref2FieldscheckEqs parseDBREF12 parseHETNAMghc-prim GHC.TypesTrueFalse hetnamFieldsparseHET hetFields parseFORMUL formulFields parseCISPEP cispepFields parseSSBOND ssbondFields parseLINK linkFields parseSLTBRG sltbrgFields parseHYDBND hydbndFields parseSITE siteFieldsparseObsoleting parseOBSLTE parseSPRSDEobsoletingFields parseCOMPND parseSOURCEspecListRecordFieldsparseSpecListRecord listFieldsparseListRecord parseKEYWDS parseAUTHOR parseEXPDTA parseMDLTYPparseMatrixRecord parseSCALEn parseORIGXn parseMTRIXn parseTVECT parsePDBLines ignoreLine $fNFDataAtom$fNFDataResidue $fNFDataChain $fNFDataModel$fNFDataStructure$fIterableStructureModel$fIterableModelChain$fIterableChainResidue$fIterableResidueAtom$fIterableStructureStructure$fIterableModelModel$fIterableChainChain$fIterableResidueResidue$fIterableAtomAtom$fIterableStructureChain$fIterableStructureResidue$fIterableStructureAtom$fIterableModelResidue$fIterableModelAtom$fIterableChainAtomcodebook_nucleic_acidscodebookcodebook_standard_proteincodebook_proteinresname2fastacodeDictionaryfastacode2resnameDictionaryres2codescan2 fastaRecord' defaultingBStateinitializeState checkResidue checkChain checkModel closeResidue closeChainaddError closeModelcloseStructure parseStep openModel parseFinishcurrentResidue currentModel currentChaincurrentStructureresidueContents chainContents modelContentsstructureContentserrorslineNo ParsingMonad parsePDBRecnextLineshowContinuationcontd printSpecList printList printMatrix PDBEventSstructureEvents modelEvents chainEvents residueEvents atomEventsexceptionHandler printError showErrorforce