cobot-io 0.1.3.17 → 0.1.3.18

raw patch · 10 files changed

+98/−33 lines, 10 filesPVP: minor bump suggested

API additions: PVP suggests at least a minor version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +4/−0
• cobot-io.cabal +4/−2
• src/Bio/MAE.hs +7/−6
• src/Bio/PDB.hs +29/−15
• src/Bio/PDB/Functions.hs +13/−7
• src/Bio/Structure/Functions.hs +4/−3
• src/Bio/Utils/Map.hs +13/−0
• src/Bio/Utils/Vector.hs +17/−0
• test/PDBSpec.hs +6/−0
• test/Spec.hs +1/−0

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.18] - 2021-03-09+### Fixed+- Lowercase insertion code parsing in PDB.+ ## [0.1.3.17] - 2021-02-18 ### Fixed - PDB parsing.

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 17226c38dac49205091506cf77e5ab4bff45f9ec44f1882a95c33e15cdb47e4e+-- hash: fe5f3bd32c503a44c34349ccfa5bf4ef5ec52540df5c2ce4637127a0b33394df  name:           cobot-io-version:        0.1.3.17+version:        0.1.3.18 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio@@ -69,6 +69,8 @@       Bio.Uniprot       Bio.Uniprot.Parser       Bio.Uniprot.Type+      Bio.Utils.Map+      Bio.Utils.Vector   other-modules:       Paths_cobot_io   hs-source-dirs:

@@ -21,6 +21,7 @@                                          Model (..), Residue (..),                                          SecondaryStructure (..),                                          StructureModels (..))+import qualified Bio.Utils.Map          as M ((!?!)) import           Control.Monad          (join) import           Control.Monad.IO.Class (MonadIO, liftIO) import           Data.Attoparsec.Text   (parseOnly)@@ -28,7 +29,7 @@ import           Data.Function          (on) import qualified Data.List              as L (find, groupBy, sortOn) import           Data.Map.Strict        (Map)-import qualified Data.Map.Strict        as M (fromList, lookup, (!))+import qualified Data.Map.Strict        as M (fromList, lookup) import           Data.Maybe             (catMaybes, fromJust) import           Data.Text              (Text) import qualified Data.Text              as T (head, init, last, null, pack,@@ -62,7 +63,7 @@   modelsOf Mae{..} = V.fromList $ fmap blockToModel blocks     where       unsafeGetFromContentsMap :: FromMaeValue a => Map Text [MaeValue] -> Text -> Int -> a-      unsafeGetFromContentsMap m name i = unsafeFromMaeValue $ (m M.! name) !! i+      unsafeGetFromContentsMap m name i = unsafeFromMaeValue $ (m M.!?! name) !! i        getFromContentsMap :: FromMaeValue a => Map Text [MaeValue] -> Text -> Int -> Maybe a       getFromContentsMap m name i = join $ fromMaeValue . (!! i) <$> name `M.lookup` m@@ -71,7 +72,7 @@       blockToModel Block{..} = Model (atomsTableToChains atomsTable) bonds         where           atomsTable    = findTable "m_atom"-          numberOfAtoms = length $ atomsTable M.! "r_m_x_coord"+          numberOfAtoms = length $ atomsTable M.!?! "r_m_x_coord"            bondsTable         = findTable "m_bond"           (bondGraph, bonds) = bondsTableToGlobalBonds bondsTable@@ -89,7 +90,7 @@           bondsTableToGlobalBonds :: Map Text [MaeValue] -> (Map Int [(Int, Int)], Vector (Bond GlobalID))           bondsTableToGlobalBonds m = bimap toMap V.fromList bonds'             where-              numberOfBonds = length $ m M.! "i_m_from"+              numberOfBonds = length $ m M.!?! "i_m_from"               bonds'        = unzip $ fmap indexToBond [0 .. numberOfBonds - 1]                toMap :: [(Int, (Int, Int))] -> Map Int [(Int, Int)]@@ -150,7 +151,7 @@                    toLocalBond :: Int -> (Int, Int) -> [Bond LocalID]                   toLocalBond x (y, o) | y `elem` group = pure $ Bond (LocalID x)-                                                                      (LocalID $ globalToLocal M.! y)+                                                                      (LocalID $ globalToLocal M.!?! y)                                                                       o                                        | otherwise          = [] @@ -161,7 +162,7 @@               indexToAtom i = Atom (GlobalID i)                                    (i + 1)                                    (stripQuotes $ getFromContentsI "s_m_pdb_atom_name")-                                   (elIndToElement M.! getFromContentsI "i_m_atomic_number")+                                   (elIndToElement M.!?! getFromContentsI "i_m_atomic_number")                                    coords                                    (getFromContents 0 "i_m_formal_charge" i)                                    (getFromContents 0 "r_m_pdb_tfactor" i)

@@ -11,21 +11,35 @@ import           Bio.PDB.Reader         (PDBWarnings, fromTextPDB) import qualified Bio.PDB.Type           as PDB import           Bio.PDB.Writer         (pdbToFile, pdbToText)-import           Bio.Structure+import           Bio.Structure         (Residue(..),+                                        Bond,+                                        Atom(..),+                                        LocalID,+                                        GlobalID(GlobalID, getGlobalID),+                                        SecondaryStructure(Undefined),+                                        Chain(..),+                                        Model(Model, modelChains),+                                        StructureSerializable(..),+                                        StructureModels(..))+import qualified Bio.Utils.Map          as M ((!?!))+import qualified Bio.Utils.Vector       as V ((!?!)) import           Control.Arrow          ((&&&)) import           Control.Lens           ((^.)) import           Control.Monad          (join) import           Control.Monad.IO.Class (MonadIO, liftIO) import           Data.List              (sort)-import           Data.Map               (Map)-import qualified Data.Map               as M (fromList, (!))+import           Data.Map.Strict        (Map)+import qualified Data.Map.Strict        as M (fromList) import           Data.Maybe             (fromMaybe) import           Data.Text              (Text) import qualified Data.Text              as T (head, pack, singleton, strip,                                               unpack) import           Data.Text.IO           as TIO (readFile) import           Data.Vector            (Vector)-import qualified Data.Vector            as V+import qualified Data.Vector            as V (toList,+                                              concat,+                                              fromList,+                                              length) import           Linear.V3              (V3 (..), _x, _y, _z) import           Text.Read              (readMaybe) @@ -33,9 +47,9 @@     modelsOf PDB.PDB {..} = fmap mkModel models       where         mkModel :: PDB.Model -> Model-        mkModel model = case length atomToNilBasedIndex == length allModelAtoms of-            False -> error "Mapping from PDB id to nil based index must be a bijection."-            True  -> Model (fmap mkChain model) (restoreModelGlobalBonds atomToNilBasedIndex model)+        mkModel model = if length atomToNilBasedIndex == length allModelAtoms+                          then Model (fmap mkChain model) (restoreModelGlobalBonds atomToNilBasedIndex model)+                          else error "Mapping from PDB id to nil based index must be a bijection."           where             atomToNilBasedIndex :: Map PDB.Atom Int             atomToNilBasedIndex = M.fromList $ allModelAtoms `zip` [0..]@@ -49,27 +63,27 @@             mkChainName :: PDB.Chain -> Text             mkChainName = T.singleton . PDB.atomChainID . safeFirstAtom -            mkChainResidues :: PDB.Chain -> V.Vector Residue+            mkChainResidues :: PDB.Chain -> Vector Residue             mkChainResidues chain = V.fromList . fmap (mkResidue (restoreChainLocalBonds chain)) $ groupChainByResidue chain -            safeFirstAtom :: V.Vector PDB.Atom -> PDB.Atom-            safeFirstAtom arr | V.length arr > 0 = arr V.! 0+            safeFirstAtom :: Vector PDB.Atom -> PDB.Atom+            safeFirstAtom arr | V.length arr > 0 = arr V.!?! 0                               | otherwise        = error "Could not pick first atom" -            mkResidue :: Map Text (V.Vector (Bond LocalID)) -> [PDB.Atom] -> Residue+            mkResidue :: Map Text (Vector (Bond LocalID)) -> [PDB.Atom] -> Residue             mkResidue _ []    = error "Cound not make residue from empty list"             mkResidue localBondsMap atoms' = Residue (T.strip $ PDB.atomResName firstResidueAtom)                                                      (PDB.atomResSeq firstResidueAtom)                                                      (PDB.atomICode firstResidueAtom)                                                      (V.fromList $ mkAtom <$> atoms')-                                                     (localBondsMap M.! residueID firstResidueAtom)+                                                     (localBondsMap M.!?! residueID firstResidueAtom)                                                      Undefined -- now we do not read secondary structure                                                      ""        -- chemical component type?!               where                 firstResidueAtom = head atoms'              mkAtom :: PDB.Atom -> Atom-            mkAtom atom@PDB.Atom{..} = Atom (GlobalID $ atomToNilBasedIndex M.! atom)+            mkAtom atom@PDB.Atom{..} = Atom (GlobalID $ atomToNilBasedIndex M.!?! atom)                                        atomSerial                                        (T.strip atomName)                                        atomElement@@ -78,10 +92,10 @@                                        atomTempFactor                                        atomOccupancy -modelsFromPDBFile :: (MonadIO m) => FilePath -> m (Either Text ([PDBWarnings], V.Vector Model))+modelsFromPDBFile :: (MonadIO m) => FilePath -> m (Either Text ([PDBWarnings], Vector Model)) modelsFromPDBFile = liftIO . fmap modelsFromPDBText . TIO.readFile -modelsFromPDBText :: Text -> Either Text ([PDBWarnings], V.Vector Model)+modelsFromPDBText :: Text -> Either Text ([PDBWarnings], Vector Model) modelsFromPDBText pdbText = do   (warnings, parsedPDB) <- fromTextPDB pdbText   let models = modelsOf parsedPDB

@@ -2,19 +2,25 @@   ( groupChainByResidue   ) where -import qualified Bio.PDB.Type as PDB (Atom (..))-import           Data.Map            (Map)-import qualified Data.Map as M       (fromList, (!))-import           Data.List           (groupBy, sortOn)-import           Data.Vector         (Vector)-import qualified Data.Vector as V    (toList)+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.! atomICode)+    sortOnResidue PDB.Atom{..} = atomSerial * 100 + (insertionCodeSortingCorrections M.!?! toUpper atomICode)+         insertionCodeSortingCorrections :: Map Char Int     insertionCodeSortingCorrections = M.fromList $ zip (' ':['A'..'Z']) [0..]

@@ -12,7 +12,8 @@                                   localBonds, residues) import           Control.Lens    (Traversal', each, (%~), (&)) import           Data.Map.Strict (Map)-import qualified Data.Map.Strict as M (fromList, (!), (!?))+import qualified Data.Map.Strict as M (fromList, (!?))+import qualified Bio.Utils.Map   as M ((!?!)) import           Data.Set        (Set) import qualified Data.Set        as S (fromList, notMember, unions) import           Data.Text       (Text)@@ -84,8 +85,8 @@     leaveBond (Bond (LocalID l) (LocalID r) _) = l `notElem` indsToDelete && r `notElem` indsToDelete      modifyBond :: Bond LocalID -> Bond LocalID-    modifyBond (Bond (LocalID l) (LocalID r) t) = Bond (LocalID $ oldIndsToNew M.! l)-                                                       (LocalID $ oldIndsToNew M.! r)+    modifyBond (Bond (LocalID l) (LocalID r) t) = Bond (LocalID $ oldIndsToNew M.!?! l)+                                                       (LocalID $ oldIndsToNew M.!?! r)                                                        t      newInd :: Int -> Int

@@ -0,0 +1,13 @@+module Bio.Utils.Map +  ( (!?!)+  ) where+++import GHC.Stack       (HasCallStack)+import Data.Map.Strict (Map, +                        (!?))+import Data.Maybe      (fromMaybe)++infix 9 !?!+(!?!) :: (HasCallStack, Ord k, Show k, Show a) => Map k a -> k -> a+(!?!) m k = fromMaybe (error $ "cobot-io: No key " ++ show k ++ " in Map: " ++ show m) $ m !? k

@@ -0,0 +1,17 @@+module Bio.Utils.Vector +  ( (!?!)+  ) where+++import GHC.Stack             (HasCallStack)+import Data.Vector           (Vector)+import qualified Data.Vector as V ((!?),+                                   length)+import Data.Maybe            (fromMaybe)++infix 9 !?!+(!?!) :: (HasCallStack, Show a) => Vector a -> Int -> a+(!?!) v i = fromMaybe (error msg) $ v V.!? i+  where+    msg :: String+    msg = "cobot-io: index " ++ show i ++ " is out of bounds. Vector length is : " ++ show (V.length v)

@@ -130,6 +130,12 @@         formAtomId :: (Text, Atom) -> Text         formAtomId (chainId, Atom{..}) = chainId <> "_" <> atomName <> "_" <> T.pack (show $ getGlobalID atomId) +lowercaseInsertionCodeSpec :: SpecWith ()+lowercaseInsertionCodeSpec = describe "Lowercase insertion code in PDB" $ do+    it "should be processed normally" $ do+        model <- firstPDBModel "test/PDB/6a0z.HLHL.pdb" >>= ef++        V.length (modelChains model) `shouldBe` 2  getStats :: Model -> (Int, Int, Int, Int) getStats model = (globalBondCount, localBondCount, chainCount, atomCount)

@@ -59,6 +59,7 @@          bondsRestoringTripeptideSpec          bondsRestoringBiggerMoleculesSpec          withSegmentIdentifierModelSpecP+         lowercaseInsertionCodeSpec          pdbWriterSpec          -- Structure          structureSpec