~<      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~                              !"#$ % & ' ( ) * + , - . / 0 1 2 3 4 5 6 789:;: Safe-InferredNone < Alias for < to make sure it is inlined.  Why on earth GHC 7.4 doesn'Ht inline functions like ord?! They should normally compile to no-ops!!! =Faster > to ? conversion. + Top level function dealing with negation. @Value of a decimal digit. AStrict negation. BFirst helper function for fast  ByteString to ? conversion 3 This function deals with things before the comma. C Second helper function for fast  ByteString to ? conversion 2 This function deals with things after the comma. DFinalize parsing of E and construct result. FChecks that remaining part of  ByteString is pure spaces,  and return G2 if there is something else (for error handling.) HTrim spaces in front of the  ByteString. ITrim spaces at the end of the  ByteString. JDiscard last character within  ByteString without checking. K+Trim spaces in the front and at the end of  ByteString. <=@ABCDFHIJK=HK <=@ABCDFHIJKNone Read file contents as strict  ByteStringB. Uses mmap if possible. May decompress file contents, if needed. Write file contents as strict  ByteString.  LMNOPQ   LMNOPQNone /Unpacks an abstract 3D vector into a triple of Es. "Maps an operation that modifies a E onto a 3D vector. Maps an operation on a pair of Es 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. (asterisk - *2 - indicates side on which one can put a scalar.) Scalar product. (asterisk - *2 - 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. R RNone/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. $ADefault initial size of a mutable vector for structure contents. %(Appends an element to a mutable vector. &:Finalizes a mutable vector, and returns immutable vector. # [Does it shrink allocated space?] '' on immutable vectors. (( on immutable vectors. )) on immutable vectors. ** on immutable vectors. ++ on immutable vectors. ,, on immutable vectors. -- on immutable vectors. .. on immutable vectors. // on immutable vectors. 0+Conversion of an immutable vector to list. 1* on immutable vectors. 2.Concatenation of a list of immutable vectors. 3*Remove last element of immutable vectors. 4#First element of immutable vector. 5*Remove first element of immutable vector. 6Concatenation of two immutable 7!Indexing of an immutable vector. S !"#$%&'()*+,-./01234567T !"#$%&'()*+,-./01234567 %&!/*,'()-+.$"#01762354S !"#$%&'()*+,-./01234567T Safe-Inferred8We use only strict  ByteString as strings in PDB parser. 888 Safe-Inferred9"Enumeration of beta-strand sense. 9:;9:;9;:9;: Safe-Inferred<Enumeration 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 =helix2code converts a <% enumeration into an PDB CLASS code. >-helix2code converts an PDB CLASS code into a < enumeration. <UVWXYZ[\]^=><=><=>< ^]\[ZYXWVU=> Safe-Inferred?AEnumeration of experimental methods occuring in the PDB archive. I Generates an ? from words in PDB J Converts an ? back into text ?@ABCDEFGHIJ ?@ABCDEFGHIJ ?HGFEDCBA@IJ? HGFEDCBA@IJ Safe-InferredK$Datatype for event-based PDB parser DResidue id: residue name, chain, residue id, residue insertion code LAtom id: atom name, residue name, chain, residue id, residue insertion code KLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~89:;<?@ABCDEFGHKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~28K{zyuqpnjba^\YUNML|}~vwxrstrstoklmcdefghicdefklcd_`efkl]Z[VWXOPQRST9;:<?HGFEDCBA@K{zyuqpnjba^\YUNML|}~vwxrstrstoklmcdefghicdefklcd_`efkl]Z[VWXOPQRSTNone&_<A common type for shuttling parsed and typed record values. `3Splits a string into substrings by column numbers. a Converts a _ containing 8< into this string or an empty string if nothing was parsed. b4Construct an error message by concatenating list of  Bytestrings chParser for an optional single-character field, first argument is a name of a field, second is an input. d9Parser for an optional spacing, an argument is an input. eOld version of pSpc . NOTE: also slower than using new trimFront feParser for an optional integer field, first argument is a field name, a second argument is an input. gReports error from pInt. hdParser for an optional string field, first argument is a field name, a second argument is an input. ilParser for an optional floating-point field, first argument is a field name, a second argument is an input. j=A helper method for converting a parser of an optional field : into a parser of an optional field with a default value. kSParser for an optional single character field with a default value, arguments are:  field name  default value  input lJParser for an optional integer field with a default value, arguments are:  field name  default value  input mIParser for an optional string field with a default value, arguments are:  field name  default value  input nQParser for an optional floating-point field with a default value, arguments are:  field name  default value  input o]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 _ $A results is a function that takes:   field name  input and returns a _. p6Return error message when mandatory field is missing. qLParser for a mandatory character field with a default value, arguments are:  field name  input rQParser for a mandatory floating-point field with a default value, arguments are:  field name  input sIParser for a mandatory string field with a default value, arguments are:  field name  input tJParser for a mandatory integer field with a default value, arguments are:  field name u5Parser for a mandatory spacing field, arguments are:  number of columns for spacing  input vVParser for a fixed field that can be filled with one of many keywords, arguments are:  field name  a list of valid keywords  input w8Parser for a fixed single keyword field, arguments are:  field name  keyword  input xSDissects columns from stage 1 parsing, and applies converters from stage 2 parsing * list of string parsers that return typed _ values @ list of column numbers that indicate a beginning of each field  input y"Finds IFError values in a list of _ values, and returns / a list of error events in case there are any. * list of string parsers that return typed _ values @ list of column numbers that indicate a beginning of each field . line number to be injected into error events  input zCUses field declarations that are list of (column number, parser to _, ...) 1 tuples and applies it to a given line of input. Arguments are:  field declarations list  input line ! ordinal number of an input line {Returns if a given _/ value _certainly_ represents a missing value. |Returns if a given _/ value _certainly_ represents a present value. }CMerges 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  _. containing a three letter residue identifier  _- containing a single letter chain identifier  _ containing a residue number  _% containing a residue insertion code A result is a ~/ of pair with column number and error message,  or # value with a residue description. LMerges 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  _. containing a three letter residue identifier  _- containing a single letter chain identifier  _ containing a residue number  _% containing a residue insertion code A result is a ~/ of pair with column number and error message,  or  / value that may contain a residue description. HMerges 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  _+ containing a three letter atom identifier  _. containing a three letter residue identifier  _- containing a single letter chain identifier  _ containing a residue number  _% containing a residue insertion code A result is a ~/ of pair with column number and error message,  or - value that may contain an atom description. HMerges 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  _+ containing a three letter atom identifier  _. containing a three letter residue identifier  _- containing a single letter chain identifier  _ containing a residue number  _% containing a residue insertion code A result is a ~/ 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. \Extracts Left (column_number, error_message) values from a list of results in a given line,  to form MC events with a given line number, column number and error message.  Arguments:   line number  list of ~6 (column_number, error_message_string) result values,  where . entries are used to generate error messages. Result is a list of K entries that contain M 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. ,_`abcdefghijklmnopqrstuvwxyz{|}"K_acdfhiklmnqrstuvwz}&_`abcdefghijklmnopqrstuvwxyz{|}NoneParses an ATOM record.  Arguments:   input line  input 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 line  input line number -Result is a monad action returning a list of Ks. NoneParses a HEADER record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a TITLE record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. None'Parses a record with a single integer.  Arguments:   constructor  input line  input line number -Result is a monad action returning a list of Ks. Parses a NUMMDL record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a MODEL record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a REVDAT record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a CONECT record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a SEQRES record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a CRYST1 record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a HET record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a SHEET record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. NoneParses a TER record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks.  NoneFields of the MASTER record Parses a MASTER record.  Arguments:   input line  input line number .Result is a mionad action returning a list of Ks. !NoneParses a MODRES record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. "NoneParses a SEQADV record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. #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 Ks. %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 Ks. 8Parses a JRNL record that contains a journal reference.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. <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 Ks. &None"Parses a _generic_ REMARK record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 'NoneFields of a DBREF record. Parses a DBREF record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 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 Ks. (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 Ks. )NoneParses a HET record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. *NoneParses a FORMUL record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. +NoneParses a CISPEP record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. ,NoneParses a SSBOND record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. -NoneParses a LINK record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. .NoneParses a SLTBRG record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. /NoneParses a HYDBND record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 0NoneParses a SITE record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 1None#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 Ks. Parses a OBSLTE record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a SPRSDE record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 2NoneParses a COMPND record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a SOURCE record:  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. .NOTE: SOURCE record values are always Strings 3None'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 Ks. Parses a KEYWDS record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a AUTHOR record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a EXPDTA record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a MDLTYP record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 4None8Parses 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 Ks. Parses a SCALEn record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a ORIGXn record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. Parses a MTRIXn record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks. 5NoneParses a TVECT record.  Arguments:   input line  input line number -Result is a monad action returning a list of Ks.  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 !     %8     %8           6None 7NoneTakes 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   !"#  !"# 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  8& 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. *Returns >' with ungapped sequence of a given PDB . +Returns >% with gapped sequence of a given PDB . @ Gaps are placed to assure consistent numbering of residues and  indices in the output >.  $%&' ()  *+$%&'()*+&'$%()*+ $%&' ()  *+ None,Type alias for , names.  NInternal method that reports error to stderr, and return given default value. -!Atomic number of a given element .1Covalent radius of an element with a given name. /#Atomic mass of a given element in g/mol 0*Van der Waals radius of the given element 1 Given a PDB  extract or guess its , name. 2 Guessing an , name from PDB  name.  Returns empty string, if , can't be guessed. , -./012,-./012,12-/.0, -./0129None@Record holding a current state of the structure record builder. 8Shorthand for the State monad in which parsing is done.   is existential phantom' type to keep ST effects from escaping RParses PDB records given as ByteString, given filename fileContents and a monadic + action to be executed for each PDB event. 3RGiven 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. 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. hCloses construction of a current residue and appends this residue to a current chain. (Monadic action.) &closeResidue :: State.State BState () T TODO: when createing a dummy model, check that there are no models declared before / [Otherwise one needs to report an error!] ?Default model id, in case none was indicated (for comparison.) JFinalizes construction of current chain, and appends it to current model. $closeChain :: State.State BState () :Reports error during building of structure for PDB entry. . TODO: This should be probably monadic action  TODO: forgot about line/column number passing! (Finalizes construction of current model 9Finalizes construction of record holding PDB entry data. P NOTE: this one is different and should only be used after parsing is complete! ePerforms a match on a single PDBEvent and performs relevant change to a BState of structure builder. ?parseStep :: (State.MonadState BState m) => PDBEvent -> m () BCreates a new model within structure builder. (For internal use.) 6 WARNING: And forgets anything that was there before! [Finalizes state of structure builder, and returns pair of a structure, and list of errors. w NOTE: should have a monadic action for each error instead. Then possibly default monad that accumulates these errors.  !"#$%&'3() !"#$%&'3()  !"#$%&'3():None */Intermediate result from parsing of PDB chunk. +NParse a fragment of PDB file, returning final line number (within the chunk.) 4EParse file in parallel with as many threads as we have capabilities. ,Joins *0 from two different chunks and returns a single *. -Joins !s resulting from partial parses. .Joins !s resulting from partial parses. /Joins !s resulting from partial parses. 0Joins !s resulting from partial parses. 1Produce joinX function, given: . * getter for subordinate component vector, . * setter for subordinate component vector, 3 * getter for the id of a subordinate component, \ * matcher for ids of subordinate components that decides whether they have to be joined, O * and joining function for subordinate objects (if they share the same id.) 2This joining function merges two data structures. 2Increments line numbers in M records by a given value. 5*Parse input file with N parallel threads. 3JSplits a ByteString into chunks of given size, and ending at end of line. *+4,-./012534,-5 *+4,-./01253 None6;Default parser - uses parallel capabilities, if available. 6345663456None7#Prints a PDBEvent to a filehandle. 4XFor indicating continuation of the record in previous line as a digit with line number. 5DFor indicating continuation of the text in previous line by indent. 88Reports whether a given PDB record is already printable ) [temporary method, they all should be.]  Including errors. 65Prints a list of words as a PDB speclist record (see ;<.) 71Prints a list of words as a PDB list record (see ;<.) 8#Prints a matrix given as a list of s. 745867878787458678None9ShowS like type for a list of Ks. 94Writes a structure in a PDB format to a filehandle. :Generates list of Ks from a given Structure. ;Generates list of Ks from a given Model. <Generates list of Ks from a given Chain. =Generates list of K&s from a given Residue and its Chain. >Generates list of K1s from a given Atom, its Residue, and its Chain. 99:;<=>9999:;<=>None? Type alias. @1Alias to a function present in newer versions of A library. :Parse a .pdb file and return . B#Default exception handler that for ` IO (Maybe a)`? just prints nice error message to stderr, and returns Nothing CJPrints a catenated list of ByteStrings to stderr. (Convenience function.) DShow error message from  PDBParser. ; Write structure to a .pdb file. ?@:BCD;:;:;?@:BCD;=None6       !"#&',-./01:;6:;      !"#&',1-/.0E>?@>?A>?B>?C>?CDEFDEGDEHDEIDEJDEKDELDEMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~      !"#$%&'()*+,-./0123456789:;<=>??@@ A B B C D E F 9 G ; = > 8 8 H I  J J K L L M N O O P7Q7R7S7T7U V W X Y Z [ \ ] ^ _ ` a b c d9e:f:g hijkhklmnoypqrstuvwpqxynz{|}~\nnznnnz  !!""##$$%%%%&&''''''(pqpq())**++,,--..//0011 1 1 2 2 223y3333334444455       !6"6#6$6%6&6'6(6)6*6+6,6-6.6/60 1 2 3 4 5 6 7 8 9 :9;9<9=9>9?9@9A9B9C9D9E9F9G9H9I9;9J9K9L9M9N9O9P9Q9R9S9T9U:V:W:X:Y:Z:[:\:]:^:_`abcdefghijyklmnopqr hPDB-0.9999Bio.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.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.ParseTVECTBio.PDB.Iterable.InstancesBio.PDB.Iterable.UtilsResidue"Bio.PDB.StructureBuilder.Internals!Bio.PDB.StructureBuilder.ParallelBio.PDB.EventParserParseSpecListRecordBio.PDBAC-Vector-2.3.2Data.Vector.V3v3zv3yv3xVector3 iterable-2.0 Data.Iterableitlengthitfoldl'itfoldlitfoldritfoldMitmapitmapMIterablereadFile writeFile unpackVector3vmapvzip vnormalisevdotvnorm vdihedral*||*vprojvperpend vperpendsTempListListempty singletonnew initialNew tempLengthresidueVectorSizechainVectorSize defaultSizeaddfinalizefoldlfoldl'foldrmapfiltermapMfoldMlengthlasttoListvimapconcatinitheadtail++!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 Structuremodels firstModelnumAtoms numResidues numChains numModelsdefaultResnamedefaultFastaCoderesname2fastacodefastacode2resname fastaSequencefastaGappedSequence fastaRecordfastaGappedRecordElement atomicNumbercovalentRadius atomicMassvanDerWaalsRadius assignElement guessElement parseSerial parseParallelparseWithNParallelparseprint isPrintablewriteordstrtofbaseGHC.Baseghc-prim GHC.TypesFloat digitValuefinalstrtof0strtof1 makeDoubleDouble checkSpaces Data.MaybeNothing trimFronttrimRearbutlasttrim readFile' throwNotFoundgetCodec gzipParams isReadable simpleRead$fArbitraryVector3$fNFDataTempList Polyproline Ribbon2_7 LeftGamma LeftOmega LeftAlpha Right3_10 RightGammaRightPi RightOmega RightAlpha ParsedFieldsplitByColumnsunstrifErrorpChrpSpcpSpcOpIntpIntErrpStrpDoubledConvdChrdIntdStrdDouble mandFieldmandFieldErrMsgmChrmDoublemStrmIntmSpc mKeywordsmKeywordconvertColumnsfindColumnErrors parseFields nonEmptyIFfullIF fgResidue Data.EitherEithermaybeFgResidueMaybefgAtom 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 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' defaultingBState ParsingMonad parsePDBRecinitializeState checkResidue checkChain checkModeldefaultModelId closeChainaddError closeModelcloseStructure parseStep openModel parseFinishcurrentResidue currentModel currentChaincurrentStructureresidueContents chainContents modelContentsstructureContentserrorslineNo closeResiduenextLine ParseResult partialParse joinResult joinStructure joinModel joinChain joinResiduejoinerupdateErrorLine chunkStringshowContinuationcontd printSpecList printList printMatrix PDBEventSstructureEvents modelEvents chainEvents residueEvents atomEventsforcedeepseq-1.3.0.1Control.DeepSeqdeepseqexceptionHandler printError showError