Chem.AtomType

Definitions

record AtomType : Type

  CDK atom types

Totality: total
Visibility: public export
Constructor: 

AT : String -> Nat -> Hybridization -> Nat -> Nat -> Nat -> AtomType

Projections:

.double : AtomType -> Nat

.hybridization : AtomType -> Hybridization

.lonePairCount : AtomType -> Nat

.name : AtomType -> String

.single : AtomType -> Nat

.triple : AtomType -> Nat

Hints:

Eq AtomType

Show AtomType

.name : AtomType -> String

Totality: total
Visibility: public export

name : AtomType -> String

Totality: total
Visibility: public export

.lonePairCount : AtomType -> Nat

Totality: total
Visibility: public export

lonePairCount : AtomType -> Nat

Totality: total
Visibility: public export

.hybridization : AtomType -> Hybridization

Totality: total
Visibility: public export

hybridization : AtomType -> Hybridization

Totality: total
Visibility: public export

.single : AtomType -> Nat

Totality: total
Visibility: public export

single : AtomType -> Nat

Totality: total
Visibility: public export

.double : AtomType -> Nat

Totality: total
Visibility: public export

double : AtomType -> Nat

Totality: total
Visibility: public export

.triple : AtomType -> Nat

Totality: total
Visibility: public export

triple : AtomType -> Nat

Totality: total
Visibility: public export

record Bonds : Type

  Counts of bond types connected to an atom

Totality: total
Visibility: public export
Constructor: 

BS : Nat -> Nat -> Nat -> Bonds

Projections:

.double : Bonds -> Nat

.single : Bonds -> Nat

.triple : Bonds -> Nat

Hints:

Eq Bonds

Monoid Bonds

Ord Bonds

Semigroup Bonds

Show Bonds

.single : Bonds -> Nat

Totality: total
Visibility: public export

single : Bonds -> Nat

Totality: total
Visibility: public export

.double : Bonds -> Nat

Totality: total
Visibility: public export

double : Bonds -> Nat

Totality: total
Visibility: public export

.triple : Bonds -> Nat

Totality: total
Visibility: public export

triple : Bonds -> Nat

Totality: total
Visibility: public export

toBonds : BondOrder -> Bonds

  Converts a single bond to a value of type `Bonds`

Totality: total
Visibility: export

addH : HCount -> Bonds -> Bonds

  Add single bonds from implicit hydrogens to the list of bonds
  connected to an atom

Totality: total
Visibility: export

unknown : AtomType

  Placeholder for unknown atom types
  
  We use this instead of returning an error type such
  as a `Maybe` or an `Either` because it facilitates
  writing algorithms with a certain tolerance for invalid
  molecules

Totality: total
Visibility: export

hasPiBonds : Bonds -> Bool

Totality: total
Visibility: export

atomType : Elem -> Radical -> Charge -> Bonds -> AtomType

  Perceiving atom types
  
  This is to be used if no implicit hydrogen atoms are given.
  Implicit hydrogen count can then be determined from the atom type.

Totality: total
Visibility: export

atomTypeAndHydrogens : Elem -> Radical -> Charge -> Bonds -> (HCount, AtomType)

  General purpose atom type perception
  
  This is to be used if no implicit hydrogen atoms are given
  and these should be perceived from the atom type as well.

Totality: total
Visibility: export

exactAtomType : Elem -> Radical -> Charge -> Bonds -> AtomType

  Utility for those cases where the number of implict hydrogens
  (if any) is already included in the number of bonds.
  
  This returns `unknown` if the number of single bonds do not
  match exactly.

Totality: total
Visibility: export

isInvalid : AtomType -> Bool

  True, if the given atom type is considered to be invalid.
  
  Currently, the following atom types are considered to be invalid:
  "unknown", "N.oxide", "N.sp2.3"

Totality: total
Visibility: export