cobot-io 0.1.3.16 → 0.1.3.17

raw patch · 5 files changed

+51/−42 lines, 5 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +4/−0
• cobot-io.cabal +2/−2
• src/Bio/PDB.hs +10/−7
• src/Bio/PDB/BondRestoring.hs +31/−32
• src/Bio/PDB/Type.hs +4/−1

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.17] - 2021-02-18+### Fixed+- PDB parsing.+ ## [0.1.3.16] - 2021-02-16 ### Fixed - Bad comment in GB parser.

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 7ba9dfa6aa8de04faf5d4aa77f0afaea9f338622fe927072726a1dc5c8178f52+-- hash: 17226c38dac49205091506cf77e5ab4bff45f9ec44f1882a95c33e15cdb47e4e  name:           cobot-io-version:        0.1.3.16+version:        0.1.3.17 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio

@@ -4,7 +4,8 @@   , modelsFromPDBFile, modelsToPDBFile   ) where -import           Bio.PDB.BondRestoring  (residueID, restoreChainLocalBonds,+import           Bio.PDB.BondRestoring  (residueID,+                                         restoreChainLocalBonds,                                          restoreModelGlobalBonds) import           Bio.PDB.Functions      (groupChainByResidue) import           Bio.PDB.Reader         (PDBWarnings, fromTextPDB)@@ -32,13 +33,15 @@     modelsOf PDB.PDB {..} = fmap mkModel models       where         mkModel :: PDB.Model -> Model-        mkModel model = Model (fmap mkChain model) (restoreModelGlobalBonds atomSerialToNilBasedIndex 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)           where-            atomSerialToNilBasedIndex :: Map Int Int-            atomSerialToNilBasedIndex = M.fromList $ allModelAtomSerials `zip` [0..]+            atomToNilBasedIndex :: Map PDB.Atom Int+            atomToNilBasedIndex = M.fromList $ allModelAtoms `zip` [0..] -            allModelAtomSerials :: [Int]-            allModelAtomSerials = sort . V.toList . fmap PDB.atomSerial . V.concat $ V.toList model+            allModelAtoms :: [PDB.Atom]+            allModelAtoms = sort . V.toList . V.concat $ V.toList model              mkChain :: PDB.Chain -> Chain             mkChain = uncurry Chain . (mkChainName &&& mkChainResidues)@@ -66,7 +69,7 @@                 firstResidueAtom = head atoms'              mkAtom :: PDB.Atom -> Atom-            mkAtom PDB.Atom{..} = Atom (GlobalID $ atomSerialToNilBasedIndex M.! atomSerial)+            mkAtom atom@PDB.Atom{..} = Atom (GlobalID $ atomToNilBasedIndex M.! atom)                                        atomSerial                                        (T.strip atomName)                                        atomElement

@@ -45,54 +45,54 @@       let _residueID = residueID $ head residueAtoms       pure (_residueID, localBonds)     -    intraResidueGlobalBonds :: [[Bond GlobalID]]+    intraResidueGlobalBonds :: [[Bond PDB.Atom]]     intraResidueGlobalBonds = fmap restoreIntraResidueBonds chainAtomsGroupedByResidue          chainAtomsGroupedByResidue :: [[PDB.Atom]]     chainAtomsGroupedByResidue = groupChainByResidue chainAtoms     -    convertGlobalsToLocals :: [PDB.Atom] -> [Bond GlobalID] -> [Bond LocalID]+    convertGlobalsToLocals :: [PDB.Atom] -> [Bond PDB.Atom] -> [Bond LocalID]     convertGlobalsToLocals residueAtoms = map convertGlobalToLocal       where-        convertGlobalToLocal :: Bond GlobalID -> Bond LocalID-        convertGlobalToLocal (Bond (GlobalID from) (GlobalID to) order) = -          Bond (LocalID $ globalToLocalIdxMap ! from) (LocalID $ globalToLocalIdxMap ! to) order+        convertGlobalToLocal :: Bond PDB.Atom -> Bond LocalID+        convertGlobalToLocal (Bond from to order) = +          Bond (LocalID $ atomToLocalIdMap ! from) (LocalID $ atomToLocalIdMap ! to) order         -        globalToLocalIdxMap :: Map Int Int-        globalToLocalIdxMap = M.fromList $ zip sortedGlobalIndices [0..]+        atomToLocalIdMap :: Map PDB.Atom Int+        atomToLocalIdMap = M.fromList $ zip sortedAtoms [0..]         -        sortedGlobalIndices :: [Int]-        sortedGlobalIndices = map PDB.atomSerial $ sort residueAtoms+        sortedAtoms :: [PDB.Atom]+        sortedAtoms = sort residueAtoms  -restoreModelGlobalBonds :: Map Int Int -> Vector (Vector PDB.Atom) -> Vector (Bond GlobalID)-restoreModelGlobalBonds atomSerialToNilBasedIndex chains = convertGlobalIDs atomSerialToNilBasedIndex . V.fromList $ _intraResidueBonds ++ peptideBonds ++ disulfideBonds+restoreModelGlobalBonds :: Map PDB.Atom Int -> Vector (Vector PDB.Atom) -> Vector (Bond GlobalID)+restoreModelGlobalBonds atomToNilBasedIndex chains = convertToGlobalIDs atomToNilBasedIndex . V.fromList $ _intraResidueBonds ++ peptideBonds ++ disulfideBonds   where-    convertGlobalIDs :: Map Int Int -> Vector (Bond GlobalID) -> Vector (Bond GlobalID)-    convertGlobalIDs mapping = reindexBonds (\(GlobalID v) -> GlobalID $ mapping ! v)+    convertToGlobalIDs :: Map PDB.Atom Int -> Vector (Bond PDB.Atom) -> Vector (Bond GlobalID)+    convertToGlobalIDs mapping = reindexBonds (\atom -> GlobalID $ mapping ! atom)     -    reindexBonds :: (a -> a) -> Vector (Bond a) -> Vector (Bond a)+    reindexBonds :: (a -> b) -> Vector (Bond a) -> Vector (Bond b)     reindexBonds convertID = fmap (\(Bond from to order) -> Bond (convertID from) (convertID to) order)      chainAtomsGroupedByResidue :: Vector [[PDB.Atom]]     chainAtomsGroupedByResidue = fmap groupChainByResidue chains     -    _intraResidueBonds :: [Bond GlobalID]+    _intraResidueBonds :: [Bond PDB.Atom]     _intraResidueBonds = concatMap restoreChainIntraResidueBonds chainAtomsGroupedByResidue     -    peptideBonds :: [Bond GlobalID]+    peptideBonds :: [Bond PDB.Atom]     peptideBonds = concatMap restoreChainPeptideBonds chainAtomsGroupedByResidue     -    disulfideBonds :: [Bond GlobalID]+    disulfideBonds :: [Bond PDB.Atom]     disulfideBonds = restoreDisulfideBonds . concat $ V.toList chainAtomsGroupedByResidue -restoreDisulfideBonds :: [[PDB.Atom]] -> [Bond GlobalID]+restoreDisulfideBonds :: [[PDB.Atom]] -> [Bond PDB.Atom] restoreDisulfideBonds atomsGroupedByResidue = do   atom1 <- cystineSulfur   atom2 <- cystineSulfur   guard (PDB.atomSerial atom1 < PDB.atomSerial atom2)   guard $ distance (coords atom1) (coords atom2) < sulfidicBondMaxLength-  pure $ Bond (GlobalID $ PDB.atomSerial atom1) (GlobalID $ PDB.atomSerial atom2) 1+  pure $ Bond atom1 atom2 1     where       cystineSulfur :: [PDB.Atom]       cystineSulfur = filter (("SG" ==) . T.strip . PDB.atomName) $ concat cystines@@ -110,16 +110,16 @@ peptideBondMaxLength :: Float peptideBondMaxLength = 1.5 -restoreChainPeptideBonds :: [[PDB.Atom]] -> [Bond GlobalID]+restoreChainPeptideBonds :: [[PDB.Atom]] -> [Bond PDB.Atom] restoreChainPeptideBonds atomsGroupedByResidue = catMaybes $ restoreChainPeptideBonds' atomsGroupedByResidue mempty   where-    restoreChainPeptideBonds' :: [[PDB.Atom]] -> [Maybe (Bond GlobalID)] -> [Maybe (Bond GlobalID)]+    restoreChainPeptideBonds' :: [[PDB.Atom]] -> [Maybe (Bond PDB.Atom)] -> [Maybe (Bond PDB.Atom)]     restoreChainPeptideBonds' [] acc = acc     restoreChainPeptideBonds' [_] acc = acc     restoreChainPeptideBonds' (residue1:residue2:residues) acc =        restoreChainPeptideBonds' (residue2:residues) (constructBond residue1 residue2 : acc) -    constructBond :: [PDB.Atom] -> [PDB.Atom] -> Maybe (Bond GlobalID)+    constructBond :: [PDB.Atom] -> [PDB.Atom] -> Maybe (Bond PDB.Atom)     constructBond residue1 residue2 = do         carbonAtom1   <- getAtomByName residue1 "C"         nitrogenAtom2 <- getAtomByName residue2 "N"@@ -128,27 +128,26 @@         -- in order not to restore a wrong peptide bond in case of absent residues (gaps)         guard $ distance (coords carbonAtom1) (coords nitrogenAtom2) < peptideBondMaxLength -        pure $ Bond (GlobalID $ PDB.atomSerial carbonAtom1) (GlobalID $ PDB.atomSerial nitrogenAtom2) 1+        pure $ Bond carbonAtom1 nitrogenAtom2 1          getAtomByName :: [PDB.Atom] -> Text -> Maybe PDB.Atom     getAtomByName atoms atomNameToFind = find ((atomNameToFind ==) . T.strip . PDB.atomName) atoms --restoreChainIntraResidueBonds :: [[PDB.Atom]] -> [Bond GlobalID]+restoreChainIntraResidueBonds :: [[PDB.Atom]] -> [Bond PDB.Atom] restoreChainIntraResidueBonds = concatMap restoreIntraResidueBonds -restoreIntraResidueBonds :: [PDB.Atom] -> [Bond GlobalID]+restoreIntraResidueBonds :: [PDB.Atom] -> [Bond PDB.Atom] restoreIntraResidueBonds residueAtoms = catMaybes $ constructBond <$> residueBonds   where     -- TODO: support bond order somehow-    constructBond :: (Text, Text) -> Maybe (Bond GlobalID)-    constructBond (fromAtomName, toAtomName) = Bond <$> constructGlobalID fromAtomName <*> constructGlobalID  toAtomName <*> Just 1+    constructBond :: (Text, Text) -> Maybe (Bond PDB.Atom)+    constructBond (fromAtomName, toAtomName) = Bond <$> constructAtom fromAtomName <*> constructAtom toAtomName <*> Just 1     -    constructGlobalID :: Text -> Maybe GlobalID-    constructGlobalID atomName = GlobalID <$> atomNameToIndex !? atomName+    constructAtom :: Text -> Maybe PDB.Atom+    constructAtom atomName = atomNameToAtom !? atomName     -    atomNameToIndex :: Map Text Int-    atomNameToIndex = M.fromList $ (\PDB.Atom{..} -> (T.strip atomName, atomSerial)) <$> residueAtoms+    atomNameToAtom :: Map Text PDB.Atom+    atomNameToAtom = M.fromList $ (\atom@PDB.Atom{..} -> (T.strip atomName, atom)) <$> residueAtoms          residueBonds :: [(Text, Text)]     residueBonds = intraResidueBonds . T.strip . PDB.atomResName $ head residueAtoms

@@ -93,5 +93,8 @@                  }   deriving (Show, Eq, Generic, NFData) +-- | We cannot use only atomSerial as key because there+-- | can be two atoms with the same atomSerial in different chains+-- instance Ord Atom where-  a1 <= a2 = atomSerial a1 <= atomSerial a2+  a1 <= a2 = (atomSerial a1, atomChainID a1) <= (atomSerial a2, atomChainID a2)