yC      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~                              !"#$ % & ' ( ) * + , - . / 0 1 2 3 4 5 6 7 8 9:;<=>?@AB<NoneCIParallel folding like fold1, but assuming associativity and using O(n*lg)CCCSafeNone<N D Alias for D to make sure it is inlined. Why on earth GHC 7.4 doesn't inline functions like ord?! They should normally compile to no-ops!!!EFaster F to G7 conversion. Top level function dealing with negation.HValue of a decimal digit.IStrict negation.JFirst helper function for fast  ByteString to G> conversion This function deals with things before the comma.K Second helper function for fast  ByteString to G= conversion This function deals with things after the comma.LFinalize parsing of M and construct result.NChecks that remaining part of  ByteString is pure spaces, and return O1 if there is something else (for error handling.)PTrim spaces in front of the  ByteString.QTrim spaces at the end of the  ByteString.RDiscard last character within  ByteString without checking. S+Trim spaces in the front and at the end of  ByteString. DEHIJKLNPQRSEPS DEHIJKLNPQRSNone Read file contents as strict  ByteStringA. Uses mmap if possible. May decompress file contents, if needed.Write file contents as strict  ByteString. TUVWXY   TUVWXYSafe /Unpacks an abstract 3D vector into a triple of Ms."Maps an operation that modifies a M onto a 3D vector.Maps an operation on a pair of M.s 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.72-norm of a vector (also called a magnitude or length.)JCompute dihedral between three bond vectors using spherical angle formula.PScalar product. (asterisk - "*" - indicates side on which one can put a scalar.)PScalar product. (asterisk - "*" - indicates side on which one can put a scalar.)bFinds 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.QFinds a component of the vector v that is perpendicular to all vectors in a list. Z ZNone<.Type alias for a mutable sequence of elements.0Type alias for a immutable sequence of elements. Empty vector.Vector with a single elementCreate a new mutable vector. 0Allocate 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.$@Default initial size of a mutable vector for structure contents.%'Appends an element to a mutable vector.&^Finalizes a mutable vector, and returns immutable vector. [Does it shrink allocated space?]'' on immutable vectors.(( on immutable vectors.)) on immutable vectors.** on immutable vectors.++ on immutable vectors.,, on immutable vectors.-- on immutable vectors... on immutable vectors.// on immutable vectors.0*Conversion of an immutable vector to list.1* on immutable vectors.2-Concatenation of a list of immutable vectors.3)Remove last element of immutable vectors.4"First element of immutable vector.5)Remove first element of immutable vector.6Concatenation of two immutable7 Indexing of an immutable vector.[ !"#$%&'()*+,-./01234567\ !"#$%&'()*+,-./01234567 %&!/*,'()-+.$"#01762354[ !"#$%&'()*+,-./01234567\Safe8We use only strict  ByteString as strings in PDB parser.888Safe9!Enumeration of beta-strand sense.9:;9:;9:;9:;Safe<Enumeration of helix typesIPDB Class number in columns 39-40 for each type of helix in HELIX record: )Right-handed alpha (default, most common)Right-handed omegaRight-handed piRight-handed gammaRight-handed 3 - 10Left-handed alphaLeft-handed omegaLeft-handed gamma2 - 7 ribbon/helix Polyproline=helix2code converts a <$ enumeration into an PDB CLASS code.>-helix2code converts an PDB CLASS code into a < enumeration. <]^_`abcdef=><=><=>< ]^_`abcdef=>Safe?@Enumeration of experimental methods occuring in the PDB archive.I Generates an ? from words in PDBJ Converts an ? back into text ?@ABCDEFGHIJ ?@ABCDEFGHIJ ?@ABCDEFGHIJ? @ABCDEFGHIJSafeK#Datatype for event-based PDB parserCResidue id: residue name, chain, residue id, residue insertion codeKAtom id: atom name, residue name, chain, residue id, residue insertion codeKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~89:;<?@ABCDEFGHKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~28KL[\cdhloqrtvwxy{MNOPQRSTUVWXYZMNOPQRSTUVWXYMNOPQRS]^_`abWXYMNOPQRS]^_`abWXYePfgijkmnmpmpfsmumpffz|}~kP||P|ee~e||fPQe|||ee|~~9:;<?@ABCDEFGHKL[\cdhloqrtvwxy{MNOPQRSTUVWXYZMNOPQRSTUVWXYMNOPQRS]^_`abWXYMNOPQRS]^_`abWXYePfgijkmnmpmpfsmumpffz|}~kP||P|ee~e||fPQe|||ee|~~None GN&g;A common type for shuttling parsed and typed record values.h2Splits a string into substrings by column numbers.i Converts a g containing 8; into this string or an empty string if nothing was parsed.j4Construct an error message by concatenating list of  BytestringskgParser for an optional single-character field, first argument is a name of a field, second is an input.l8Parser for an optional spacing, an argument is an input.mAOld version of pSpc NOTE: also slower than using new trimFrontndParser for an optional integer field, first argument is a field name, a second argument is an input.oReports error from pInt.pcParser for an optional string field, first argument is a field name, a second argument is an input.qkParser for an optional floating-point field, first argument is a field name, a second argument is an input.rvA helper method for converting a parser of an optional field into a parser of an optional field with a default value.sRParser for an optional single character field with a default value, arguments are:  field name default valueinputtIParser for an optional integer field with a default value, arguments are:  field name default valueinputuHParser for an optional string field with a default value, arguments are:  field name default valueinputvPParser for an optional floating-point field with a default value, arguments are:  field name default valueinputw\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 g#A results is a function that takes:  field nameinputand returns a g.x5Return error message when mandatory field is missing.yKParser for a mandatory character field with a default value, arguments are:  field nameinputzPParser for a mandatory floating-point field with a default value, arguments are:  field nameinput{HParser for a mandatory string field with a default value, arguments are:  field nameinput|IParser for a mandatory integer field with a default value, arguments are:  field name}4Parser for a mandatory spacing field, arguments are: number of columns for spacinginput~UParser for a fixed field that can be filled with one of many keywords, arguments are:  field namea list of valid keywordsinput7Parser for a fixed single keyword field, arguments are:  field namekeywordinputRDissects columns from stage 1 parsing, and applies converters from stage 2 parsing )list of string parsers that return typed g values>list of column numbers that indicate a beginning of each fieldinput"Finds IFError values in a list of gC values, and returns a list of error events in case there are any. )list of string parsers that return typed g values>list of column numbers that indicate a beginning of each field,line number to be injected into error eventsinputCUses field declarations that are list of (column number, parser to g7, ...) tuples and applies it to a given line of input.Arguments are: field declarations list input lineordinal number of an input lineReturns if a given g. value _certainly_ represents a missing value.Returns if a given g. value _certainly_ represents a present value.BMerges a set of values that corresponds to a residue description. Arguments are: @boolean indicating, if the field group may omit a residue numberfield group name (description)7column number beginning the residue description entriesg- containing a three letter residue identifierg, containing a single letter chain identifierg containing a residue numberg$ containing a residue insertion codeA result is a 3 of pair with column number and error message, or " value with a residue description.KMerges a set of values that corresponds to an optional residue description.Arguments are: @boolean indicating, if the field group may omit a residue numberfield group name (description)7column number beginning the residue description entriesg- containing a three letter residue identifierg, containing a single letter chain identifierg containing a residue numberg$ containing a residue insertion codeA result is a 3 of pair with column number and error message, or  . value that may contain a residue description.GMerges a set of values that correspond to a mandatory atom description.Arguments are: field group name (description)7column number beginning the residue description entriesg* containing a three letter atom identifierg- containing a three letter residue identifierg, containing a single letter chain identifierg containing a residue numberg$ containing a residue insertion codeA result is a 3 of pair with column number and error message, or , value that may contain an atom description.GMerges a set of values that correspond to an optional atom description.Arguments are: field group name (description)7column number beginning the residue description entriesg* containing a three letter atom identifierg- containing a three letter residue identifierg, containing a single letter chain identifierg containing a residue numberg$ containing a residue insertion codeA result is a 3 of pair with column number and error message, or  , value that may contain an atom description.Changes a list of & values, into a list of all values in  entries.eExtracts Left (column_number, error_message) values from a list of results in a given line, to form B events with a given line number, column number and error message. Arguments:  line numberlist of = (column_number, error_message_string) result values, where - entries are used to generate error messages.Result is a list of K entries that contain  s (if any.)Changes a list of & values, into a list of all values in  entries.Utility: Changes a list of  s to a list of values hidden in  _ records.,ghijklmnopqrstuvwxyz{|}~"Sgiklnpqstuvyz{|}~&ghijklmnopqrstuvwxyz{|}~NoneNParses an ATOM record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks. {-@ SPECIALIZE parseATOM :: Bool -> String -> Int -> IO [PDBEvent] -}Parses an ANISOU record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a HEADER record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a TITLE record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneN&Parses a record with a single integer. Arguments:  constructor input lineinput line number-Result is a monad action returning a list of Ks.Parses a NUMMDL record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a MODEL record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a REVDAT record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a CONECT record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a SEQRES record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a CRYST1 record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.NoneNParses a HET record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks. NoneNParses a SHEET record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.!NoneNParses a TER record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks."NoneNFields of the MASTER recordParses a MASTER record. Arguments:  input lineinput line number.Result is a mionad action returning a list of Ks.#NoneNParses a MODRES record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.$NoneNParses a SEQADV record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.%NoneNParses a CAVEAT record. Arguments:  input lineinput line number&NoneNParses a SPLIT record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.'NoneNCParses a JRNL or REMARK 1 record that contains a journal reference. Arguments: ]boolean indicating, if it is first reference for a structure (JRNL) or any other (REMARK 1.) input lineinput line number-Result is a monad action returning a list of Ks.7Parses a JRNL record that contains a journal reference. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.;Parses a REMARK 1 record that contains a journal reference. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.(NoneN!Parses a _generic_ REMARK record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.)NoneNFields of a DBREF record.Parses a DBREF record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.List of fields in DBREF1 lineList 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 tupleinput line number-Result is a monad action returning a list of Ks.*NoneN!Parses a HETNAM or HETSYN record. Arguments: %boolean indicating, if it is HETNAM ( ) or HETSYN () record input lineinput line number-Result is a monad action returning a list of Ks.+NoneNParses a HET record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.,NoneNParses a FORMUL record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.-NoneNParses a CISPEP record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks..NoneNParses a SSBOND record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks./NoneNParses a LINK record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.0NoneNParses a SLTBRG record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.1NoneNParses a HYDBND record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.2NoneNParses a SITE record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.3NoneN"Parses an OBSLTE or SPRSDE record: Arguments: a PDBEvent constructor: OBSLTE orSPRSDE  input lineinput line number-Result is a monad action returning a list of Ks.Parses a OBSLTE record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a SPRSDE record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.4NoneNParses a COMPND record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a SOURCE record: Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.-NOTE: SOURCE record values are always Strings5NoneN&String type used all over the library.8Fields of the KEYWDS, AUTHOR, EXPDTA and MDLTYP records./Parses a record that contains a list of values. Arguments: a matrix constructor2a separator characteristic for this type of record input lineinput line number-Result is a monad action returning a list of Ks.Parses a KEYWDS record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a AUTHOR record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a EXPDTA record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a MDLTYP record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.6NoneN7Parses a single line with matrix or vector information. Arguments: *record constructor: SCALEn, ORIGXn, MTRIXn input lineinput line number-Result is a monad action returning a list of Ks.Parses a SCALEn record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a ORIGXn record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.Parses a MTRIXn record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks.7NoneNParses a TVECT record. Arguments:  input lineinput line number-Result is a monad action returning a list of Ks. NoneNParses 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 accC after all actions are performed in an order consistent with input.Parses a strict ByteString contents named fname and performs action^ on events given by parsing chunks, returning accumulated results. Accumulator is primed by acc.6Checks whether line was ignored as unknown record type None0PSingle atom position | NOTE: disordered atoms are now reported as multiplicatesdResidue groups all atoms assigned to the same aminoacid or nucleic acid base within a polymer chain.8Single linear polymer chain of protein, or nucleic acidsRPDB entry may contain multiple models, with slight differences in coordinates etc.7Structure holds all data parsed from a single PDB entry!     %8     %8           8None3457       9None3457Takes a first model. )Number of all atoms within the structure.!,Number of all residues within the structure."*Number of all chains within the structure.#*Number of all models within the structure. !"# !"# !"#None   !"#  !"# None47 Standard nucleic acid codes QList of all correspondences between FASTA 1-letter codes, and PDB 3-letter codes.Standard protein codes5List of both standard and non-standard protein codes.[Dictionary of translations from all 3-letter PDB codes into 1-letter FASTA aminoacid codes.mDictionary of translations from 1-letter FASTA aminoacid (standard protein) codes into 3-letter PDB codes.$5Three-letter PDB code for an unknown type of residue.%9One-letter aminoacid code for an unknown type of residue.&ODictionary mapping three-letter PDB residue code to a single-letter FASTA code.'TDictionary mapping single-letter FASTA standard aminoacid code to a PDB residue name Converts a  :% into a one character aminoacid code.( Converts an   yielding /s into a list of aminoacid one-character codes.) Converts an   yielding /s into a list of aminoacid one-character codes.Scans 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.rConvert a filename and Chain into a text of FASTA format record. First argument tells if we want gaps included.*Returns F' with ungapped sequence of a given PDB .+Returns F% with gapped sequence of a given PDB Y. Gaps are placed to assure consistent numbering of residues and indices in the output F.  $%&'()*+$%&'()*+&'$%()*+  $%&'()*+ None ,Type alias for , names.MInternal method that reports error to stderr, and return given default value.- Atomic number of a given element.0Covalent radius of an element with a given name./Upper bound of covalentRadius.0'Atomic mass of a given element in g/mol1)Van der Waals radius of the given element2Upper bound of vanDerWaalsRadius.3 Given a PDB  extract or guess its , name.4 Guessing an , name from PDB " name. Returns empty string, if , can't be guessed. ,-./01234 ,-./01234 ,34-0./12 ,-./01234 None475 Octree of s.#Preparing atom to be inserted into Octree.6Make an Octree of s7 Find all %s within a given radius from a point.8Find an s closest to a point.5678567867855678;None 47IN?Record holding a current state of the structure record builder.9Shorthand for the State monad in which parsing is done.  is existential phantom& type to keep ST effects from escaping|Parses PDB records given as ByteString, given filename fileContents and a monadic action to be executed for each PDB event.9Given 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..Initial state of the structure record builder.Checks that a residue with a given identification tuple is current, | or if not, then closes previous residue (if present), | and marks a new ,,current'' residue in a state of builder.Checks that a chain with a given identification character is current, | and if not, creates one. Also checks that we have any model in which | to assign the chain.dChecks that a current model has been declared, and creates zeroth model, | if no such model exists.>Default model id, in case none was indicated (for comparison.)gCloses construction of a current residue and appends this residue to a current chain. (Monadic action.) mFinalizes 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#Finalizes construction of record holding PDB entry data. NOTE: this one is different and should only be used after parsing is complete!$Updates line counter.%Performs a match on a single PDBEvent and performs relevant change to a BState of structure builder. parseStep :: (State.MonadState BState m) => PDBEvent -> m ()&wCreates a new model within structure builder. (For internal use.) WARNING: And forgets anything that was there before!'Finalizes state of structure builder, and returns pair of a structure, and list of errors. NOTE: should have a monadic action for each error instead. Then possibly default monad that accumulates these errors.()*+,-./0129 !"#$%&'()*+,-./0129 !"#$%&' ()*+,-./0129 !"#$%&'<NoneG 3.Intermediate result from parsing of PDB chunk.4MParse a fragment of PDB file, returning final line number (within the chunk.):DParse file in parallel with as many threads as we have capabilities.5Joins 30 from two different chunks and returns a single 3.6Joins  s resulting from partial parses.7Joins  s resulting from partial parses.8Joins  s resulting from partial parses.9Joins  s resulting from partial parses.:XProduce joinX function, given: * getter for subordinate component vector, * setter for subordinate component vector, * getter for the id of a subordinate component, * matcher for ids of subordinate components that decides whether they have to be joined, * and joining function for subordinate objects (if they share the same id.)1This joining function merges two data structures.;Increments line numbers in  records by a given value.;)Parse input file with N parallel threads.<ISplits a ByteString into chunks of given size, and ending at end of line. 34:56789:;;<:56; 34:56789:;;<None<:Default parser - uses parallel capabilities, if available.<9:;<<9:;<SafeG="Prints a PDBEvent to a filehandle.=WFor indicating continuation of the record in previous line as a digit with line number.>CFor indicating continuation of the text in previous line by indent.>wReports whether a given PDB record is already printable [temporary method, they all should be.] Including errors.?5Prints a list of words as a PDB speclist record (see =>.)@1Prints a list of words as a PDB list record (see =>.)A#Prints a matrix given as a list of s.==>>?@A=>=>==>>?@ANone ?4Class generating events for PDB structure fragments.BShowS like type for a list of Ks.@?Writes a structure or its part in a PDB format to a filehandle.CIHelper: blank chain in case we don't know which chain residue belongs to.DMHelper blank residue in case we don't know which residue the atom belongs to.EGenerates list of Ks from a given Structure.FGenerates list of Ks from a given Model.GGenerates list of Ks from a given Chain.HGenerates list of K%s from a given Residue and its Chain.IGenerates list of K0s from a given Atom, its Residue, and its Chain.?JKB@CDEFGHILMNOP?@@??JKB@CDEFGHILMNOPNoneQ Type alias.R1Alias to a function present in newer versions of S library.AParse a .pdb file and return .ToDefault exception handler that for `IO (Maybe a)` just prints nice error message to stderr, and returns NothingUIPrints a catenated list of ByteStrings to stderr. (Convenience function.)VShow error message from  PDBParser.BWrite structure to a .pdb file.QRATUVB?ABAB?QRATUVB?None7       !"#&',-.013?AB7AB?      !"#&',3-0.1W@AB@AC@AD@AE@AEFGHFGIFGJFGKFGLFGMFGNFGOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~      !"#$%&'()*+,-./0123456789:;<=>?@AABB C D D E F G H I : : J K L L M  N N O P Q Q R9S9T9U9V9W X Y Z [ \ ] ^ _ ` a b c d e f g h i j k l;m<n<opqrstptuvwxy{z{|}~z{xy^xxyxxxy  !!""##$$%%&&''''(())))))*z{z{*++,,--../ / 0 0 1 122333344445{55555566 6!6"67#7 $ % & ' ( ) *8+8,8-8.8/80818283848586878889 : ; < = > ? @ A B C D;E;F;G;H;I;J;K;L;M;N;O;P;Q;R;S;T;U;E;V;W;X;Y;Z;[;\;];^;_<`<a<b<c<d<e<f<g<h<ijklmnopqrstuvwxyz{|}{~hPDB_B3WHGzTja715wYaDTwRuOHBio.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.PDB.Structure.ElementsBio.PDB.Structure.NeighboursBio.PDB.StructureBuilder#Bio.PDB.EventParser.PDBEventPrinterBio.PDB.StructurePrinter Bio.PDB.IOBio.PDB.Util.ParFoldBio.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.ParseTVECTBio.PDB.Iterable.InstancesBio.PDB.Iterable.UtilsResidue"Bio.PDB.StructureBuilder.Internals!Bio.PDB.StructureBuilder.ParallelBio.PDB.EventParserParseSpecListRecordBio.PDBACVec_28GP9v21kog3qFBqtyTMnBData.Vector.V3v3zv3yv3xVector3itera_5z4DB2pfVMmLasVhosvCqe Data.Iterableitlengthitfoldl'itfoldlitfoldritfoldMitmapitmapMIterablereadFile writeFile unpackVector3vmapvzip vnormalisevdotvnorm vdihedral*||*vprojvperpend vperpendsTempListListempty singletonnew initialNew tempLengthresidueVectorSizechainVectorSize defaultSizeaddfinalizefoldlfoldl'foldrmapfiltermapMfoldMlengthlasttoListvimapconcatinitheadtail++!String StrandSenseTParallel AntiparallelHelixT helix2code code2helix ExpMethodXRayDiffractionFiberDiffractionNeutronDiffractionElectronCrystallographyElectronMicroscopy SolidStateNMR SolutionNMRSolutionScatteringOtherExpMethod mkExpMethod showExpMethodPDBEventATOMnoatomtyperestypechainresidresinsaltloccoords occupancybfactorsegideltchargehetatmSIGATMANISOUu_1_1u_2_2u_3_3u_1_2u_1_3u_2_3SIGUIJSEQRESserialnumresListHEADERclassificationdepDateidCodeTITLE continuationtitleKEYWDSaListAUTHORREMARKtextEXPDTA expMethodsMDLTYPNUMMDLMODELCONECTatomsCAVEATcontpdbidcommentDBREF iniSeqNumPDB iniInsCodePDB endSeqNumPDB endInsCodePDB seqDbName seqDbAccCode seqDbIdCode iniSeqNumInDbiniInsCodeInPDBRef endSeqNumInDbendInsCodeInPDBRefREVDATmodNummodDatmodIdmodTypdetailsHETNAMhetIdname notSynonymHETseqNuminsCodeatmNum descriptionFORMULcompNumisWaterformulaCISPEPres1res2angleHELIXiniResendRes helixClasslenSHEETstrandIdsheetId numStrandssensecurAtprevAtORIGXnnotSCALEnMTRIXnrelMolCRYST1abcalphabetagammaspcGrpzValueCOMPNDtokensSOURCETERresnameMASTER numRemarknumHetnumHelixnumSheetnumTurnnumSitenumXformnumAts numMaster numConect numSeqresENDENDMDLSITEsiteidnumresresiduesOBSLTEdatethisentriesSPRSDESPLITcodesSSBONDsymOp1symOp2bondLenLINKat1altloc1at2altloc2symop1symop2linkdistSLTBRGHYDBNDatHaltlocHTVECTvecJRNLcontentisFirstMODRESpdbCoderesiduestdResSEQADVpdbId advResiduedatabase accessionCode dbResnamedbSeqNum PDBParseErrorPDBIgnoredLineRESIDATIDparsePDBRecordsAtomatNameatSerialcoordbFactorelementresNameresSeqChainchainIdModelmodelIdchains Structuremodels firstModelnumAtoms numResidues numChains numModelsdefaultResnamedefaultFastaCoderesname2fastacodefastacode2resname fastaSequencefastaGappedSequence fastaRecordfastaGappedRecordElement atomicNumbercovalentRadiusmaxCovalentRadius atomicMassvanDerWaalsRadiusmaxVanDerWaalsRadius assignElement guessElement AtomOctree makeOctree findInRadius findNearest parseSerial parseParallelparseWithNParallelparseprint isPrintable PDBWritablewriteparFold1ordstrtofbaseGHC.Baseghc-prim GHC.TypesFloat digitValuefinalstrtof0strtof1 makeDoubleDouble checkSpacesNothing trimFronttrimRearbutlasttrim readFile' throwNotFoundgetCodec gzipParams isReadable simpleRead$fArbitraryVector3$fNFDataTempList RightAlpha RightOmegaRightPi RightGamma Right3_10 LeftAlpha LeftOmega LeftGamma Ribbon2_7 Polyproline ParsedFieldsplitByColumnsunstrifErrorpChrpSpcpSpcOpIntpIntErrpStrpDoubledConvdChrdIntdStrdDouble mandFieldmandFieldErrMsgmChrmDoublemStrmIntmSpc mKeywordsmKeywordconvertColumnsfindColumnErrors parseFields nonEmptyIFfullIF fgResidue Data.EitherEithermaybeFgResidueMaybefgAtom maybeFgAtomleftsLeft liftFgErrsrightsRight maybeListJustIFIntIFStrIFCharIFDoubleIFErrorIFNone 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 parseHETNAMTrueFalse 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$fIterableChainAtomcodebookNucleicAcidscodebookcodebookStandardProteincodebookProteinresname2fastacodeDictionaryfastacode2resnameDictionaryres2codescan2 fastaRecord' defaultingextractBState ParsingMonad parsePDBRecinitializeState checkResidue checkChain checkModeldefaultModelId closeResidue closeChainaddError closeModelcloseStructurenextLine parseStep openModel parseFinishcurrentResidue currentModel currentChaincurrentStructureresidueContents chainContents modelContentsstructureContentserrorslineNo ParseResult partialParse joinResult joinStructure joinModel joinChain joinResiduejoinerupdateErrorLine chunkStringshowContinuationcontd printSpecList printList printMatrix PDBEventS blankChain blankResiduestructureEvents modelEvents chainEvents residueEvents atomEvents pdbEvents pdbEventS$fPDBWritableAtom$fPDBWritableResidue$fPDBWritableChain$fPDBWritableModel$fPDBWritableStructureforcedeeps_6vMKxt5sPFR0XsbRWvvq59Control.DeepSeqdeepseqexceptionHandler printError showError