cobot-io-0.1.3.18: src/Bio/PDB/Functions.hs

module Bio.PDB.Functions
  ( groupChainByResidue
  ) where

import qualified Bio.PDB.Type  as PDB (Atom (..))
import qualified Bio.Utils.Map as M ((!?!))

import           Data.Map.Strict (Map)
import qualified Data.Map.Strict as M (fromList)
import           Data.List       (groupBy, 
                                  sortOn)
import           Data.Vector     (Vector)
import qualified Data.Vector      as V (toList)
import           Data.Char       (toUpper)

groupChainByResidue :: Vector PDB.Atom -> [[PDB.Atom]]
groupChainByResidue = sortOn (sortOnResidue . head) . groupBy atomsFromSameResidue . V.toList
  where 
    atomsFromSameResidue :: PDB.Atom -> PDB.Atom -> Bool
    atomsFromSameResidue atom1 atom2 = PDB.atomResSeq atom1 == PDB.atomResSeq atom2 && PDB.atomICode atom1 == PDB.atomICode atom2
    
    sortOnResidue :: PDB.Atom -> Int
    sortOnResidue PDB.Atom{..} = atomSerial * 100 + (insertionCodeSortingCorrections M.!?! toUpper atomICode)
    
    insertionCodeSortingCorrections :: Map Char Int
    insertionCodeSortingCorrections = M.fromList $ zip (' ':['A'..'Z']) [0..]