Geom.Mol

The geometry of molecules

Definitions

BondLengthInAngstrom : Scale

  Desired bond length in a .mol file in Angstrom

Totality: total
Visibility: public export

BondLengthInPixels : Scale

  Desired bond length in the UI

Totality: total
Visibility: public export

ScalingFactor : Scale

  Scaling factor when drawing molecules.
  
  Note: This must not be applied as part of the overall transformations of
        the canvas when drawing the molecule, because this would also scale
        the bond thickness and font sizes.
  
        The points corresponding to the atoms in a molecule are therefore
        indexed by the inverse of this scaling factor. That way, when we
        convert a molecule to a canvas `Scene` - where we will always
        require `Point Id`s for the positions - the correct scaling happens
        automatically.

Totality: total
Visibility: public export

Mol : AffineTransformation

  Describes the affine space a molecule loaded from a molfile
  (and after normalization, see `normalizeMol`) lives in.
  
  See also @ScalingFactor for some more details.

Totality: total
Visibility: export

0 MolPoint : Type

Totality: total
Visibility: public export

0 MolVector : Type

Totality: total
Visibility: public export

toCoords : Point Mol -> Vect 3 Coordinate -> Vect 3 Coordinate

  Adjust the 3-D coordinates of an atom by setting the x- and y-
  coordinate from the given `Point Mol`.

Totality: total
Visibility: export

bondLength : GetPoint a => IGraph k b a -> Edge k b -> Double

  Calculate the length of an edge in a molecule

Totality: total
Visibility: export

averageBondLength : GetPoint a => IGraph k b a -> Maybe Double

  Calculate the average length of bonds in a molecule.

Totality: total
Visibility: export

normalizeMol : {auto mod : ModPoint a} -> {auto get : GetPoint a} -> {auto 0 _ : mtrans = Mol} -> {auto 0 _ : gtrans = Mol} -> IGraph k b a -> IGraph k b a

  Normalize a molecule to an average bond length of 1.25 Angstrom.

Totality: total
Visibility: export