Text.Molfile.Parser.Util

Definitions

isos : List Isotope

  Isotopes recognized directly by the parser.
  
  In addition to the regular element symbols, this includes "D" and "T"
  for deuterium and tritium.

Totality: total
Visibility: export

stringTillEOL : ByteString -> String

  Converts the given byte string to a string, removing any trailing
  end of line characters (`'\n'` and `'\r'`).

Totality: total
Visibility: export

coord : ByteString -> Coordinate

Totality: total
Visibility: export

0 ErrPair : Type

Totality: total
Visibility: public export

SPACE : Bits8

Totality: total
Visibility: public export

refineInt : Cast Integer a => (a -> Maybe b) -> (a -> MolErr) -> ByteString -> Either ErrPair b

Totality: total
Visibility: export

blockcharge : ByteString -> Either ErrPair Charge

Totality: total
Visibility: export

charge : ByteString -> Either ErrPair Charge

Totality: total
Visibility: export

massNr : ByteString -> Either ErrPair MassNr

Totality: total
Visibility: export

radical : ByteString -> Either ErrPair Radical

Totality: total
Visibility: export

sgroupType : ByteString -> SGroupType

Totality: total
Visibility: export

bondOrder : ByteString -> Either ErrPair BondOrder

Totality: total
Visibility: export

bondStereo : ByteString -> Either ErrPair BondStereo

Totality: total
Visibility: export

nat : ByteString -> Nat

Totality: total
Visibility: export

node : ByteString -> Either ErrPair (Fin k)

Totality: total
Visibility: export

uedge : Fin k -> ByteString -> Either ErrPair (Edge k ())

Totality: total
Visibility: export

setMass : MassNr -> Isotope -> Isotope

Totality: total
Visibility: export

groupLbl : SortedMap Nat String -> AtomGroup -> AtomGroup

Totality: total
Visibility: export

lkpNode : SortedMap Nat (Fin k) -> ByteString -> Either ErrPair (Fin k)

Totality: total
Visibility: export

lkpEdge : SortedMap Nat (Fin k) -> Fin k -> ByteString -> Either ErrPair (Edge k ())

Totality: total
Visibility: export

fill : Nat -> String -> List String

  From a given string, generates a list of string by badding
  it in all possible ways with spaces, so that each of them is
  exactly `n` characters long.
  
  For instance, `fill 3 "C"` will return `["  C", " C ", "C  "]`.

Totality: total
Visibility: export

newline : RExp True

  Expressions we recognize as line breaks.
  
  Note: To simplify things, we do currently not recognize a single
        line feed character (`'\r'`) as a valid line break.

Totality: total
Visibility: export

sdigit : RExp True

  A space or a decimal digit.

Totality: total
Visibility: export

zeroes : RExp True

  An arbitrary number of spaces and zeroes, followed by a linebreak.
  
  If we find this, it typically means we can stop interpreting a
  line of data and fill in default values (for instance, with V2000
  atom and bond definitions).

Totality: total
Visibility: export

spaces : RExp False

Totality: total
Visibility: export

m_end : RExp True

Totality: total
Visibility: public export

fail : CSTCK q => ErrPair -> F1' q

  Writes a custom error with proper bounds based on the given
  `ByteString`.
  
  The bounds are computed from the current position and the size
  and offset of the bytestring, which is supposed to be a substring
  of the one stored in the `bytes_` filed.

Totality: total
Visibility: export

failErr : CSTCK q => ErrPair -> F1 q CST

  Convenience alias for `fail p >> pure CErr`.

Totality: total
Visibility: export

h3 : CSTCK q => ByteString -> F1 q CST

Totality: total
Visibility: export

h2 : CSTCK q => ByteString -> F1 q CST

Totality: total
Visibility: export

h1 : CSTCK q => ByteString -> F1 q CST

Totality: total
Visibility: export

modAtom : CSTCK q => (MolAtom -> MolAtom) -> F1' q

  Modifies the current atom in the mol graph

Totality: total
Visibility: export

modBond : CSTCK q => (MolBond -> MolBond) -> F1' q

  Modifies the current atom in the mol graph

Totality: total
Visibility: export

inc : CSTCK q => Nat -> F1 q Nat

  Returns the current position in the bytestring
  and increases it by the given number of bytes.

Totality: total
Visibility: export

read : CSTCK q => (ByteString -> a) -> Nat -> F1 q a

  Converts the next `len` bytes of the recognized byte string
  using the given convertion function.

Totality: total
Visibility: export

remString : CSTCK q => F1 q String

  Converts the remainder of the recognized byte string to a `String`,
  trimming any newline characters from its end.

Totality: total
Visibility: export

end : CSTCK q => F1' q

  Finalizes the current molecule

Totality: total
Visibility: export

setIso : CST -> Isotope -> Step1 q CSz CSTCK

  Sets the isotope of the current atom

Totality: total
Visibility: export

sdata : Steps q CSz CSTCK

  Transition steps for structure data header entries.

Totality: total
Visibility: export

sdvalue : Steps q CSz CSTCK

  Transition steps for structure data value entries.

Totality: total
Visibility: export