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* Residue index supported in PDB * Residue number and insertion code: the proper way * HETATMs now parsed from PDB * Insertion code support in mae * PDBSpec renamed to PDBParserSpec * Bond restoring first version. Doesn't work correctly for now * Global bond restoring work correctly * Fixed text * Type * Bond restoring works correctly. Input data must be slightly fixed * Added missing disulfide bridges to mae structures * Local bond for PDB, with no tests yet * Fuck, nothing works * Everything works! * pedantation * Fetching from REST API avoided in MMTF test * Changelog, version * Removed some strange comments in a test * Changes after the review * Added atomInputIndex. GlobalID is 0-based now * Changelog and formatting
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| name: cobot-io | ||
| version: 0.1.2.10 | ||
| version: 0.1.3.0 | ||
| github: "less-wrong/cobot-io" | ||
| license: BSD3 | ||
| category: Bio | ||
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| {-# OPTIONS_GHC -fno-warn-orphans #-} | ||
| module Bio.PDB | ||
| ( | ||
| ( modelsFromPDBText | ||
| , modelsFromPDBFile | ||
| ) where | ||
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| import qualified Bio.PDB.Type as PDB | ||
| import qualified Bio.PDB.Type as PDB | ||
| import Bio.PDB.Reader (fromTextPDB, PDBWarnings) | ||
| import Bio.PDB.BondRestoring (restoreModelGlobalBonds, restoreChainLocalBonds, residueID) | ||
| import Bio.PDB.Functions (groupChainByResidue) | ||
| import Bio.Structure | ||
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| import Control.Arrow ((&&&)) | ||
| import Data.Coerce (coerce) | ||
| import Data.Foldable (Foldable (..)) | ||
| import Data.Text as T (Text, singleton, unpack) | ||
| import qualified Data.Vector as V | ||
| import Linear.V3 (V3 (..)) | ||
| import Control.Arrow ((&&&)) | ||
| import Control.Monad.IO.Class (MonadIO, liftIO) | ||
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| import Data.Text as T (Text, singleton, unpack, strip) | ||
| import Data.Text.IO as TIO (readFile) | ||
| import Data.Map (Map) | ||
| import qualified Data.Map as M ((!), fromList) | ||
| import qualified Data.Vector as V | ||
| import Data.List (sort) | ||
| import Data.Maybe (fromMaybe) | ||
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| import Text.Read (readMaybe) | ||
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| import Linear.V3 (V3 (..)) | ||
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| instance StructureModels PDB.PDB where | ||
| modelsOf PDB.PDB {..} = fmap mkModel models | ||
| where | ||
| mkModel :: PDB.Model -> Model | ||
| mkModel = flip Model V.empty . fmap mkChain | ||
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| mkChain :: PDB.Chain -> Chain | ||
| mkChain = uncurry Chain . (mkChainName &&& mkChainResidues) | ||
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| mkChainName :: PDB.Chain -> Text | ||
| mkChainName = T.singleton . PDB.atomChainID . safeFirstAtom | ||
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| mkChainResidues :: PDB.Chain -> V.Vector Residue | ||
| mkChainResidues = V.fromList . fmap mkResidue . flip groupByResidue [] . pure . toList | ||
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| -- can be rewritten with sortOn and groupBy | ||
| groupByResidue :: [[PDB.Atom]] -> [PDB.Atom] -> [[PDB.Atom]] | ||
| groupByResidue res [] = res | ||
| groupByResidue [] (x : xs) = groupByResidue [[x]] xs | ||
| groupByResidue res@(lastList : resultTail) (x : xs) | ||
| | (PDB.atomResSeq x, PDB.atomICode x) == (PDB.atomResSeq (head lastList), PDB.atomICode (head lastList)) | ||
| = groupByResidue ((x : lastList) : resultTail) xs | ||
| | otherwise = groupByResidue ([x] : res) xs | ||
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| safeFirstAtom :: V.Vector PDB.Atom -> PDB.Atom | ||
| safeFirstAtom arr | V.length arr > 0 = arr V.! 0 | ||
| | otherwise = error "Could not pick first atom" | ||
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| mkResidue :: [PDB.Atom] -> Residue | ||
| mkResidue [] = error "Cound not make residue from empty list" | ||
| mkResidue atoms' = Residue (PDB.atomResName . head $ atoms') | ||
| (V.fromList $ mkAtom <$> atoms') | ||
| V.empty -- now we do not read bonds | ||
| Undefined -- now we do not read secondary structure | ||
| "" -- chemical component type?! | ||
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| mkAtom :: PDB.Atom -> Atom | ||
| mkAtom PDB.Atom{..} = Atom (coerce atomSerial) | ||
| atomName | ||
| atomElement | ||
| (V3 atomX atomY atomZ) | ||
| (read $ T.unpack atomCharge) | ||
| atomTempFactor | ||
| atomOccupancy | ||
| mkModel model = Model (fmap mkChain model) (restoreModelGlobalBonds atomSerialToNilBasedIndex model) | ||
| where | ||
| atomSerialToNilBasedIndex :: Map Int Int | ||
| atomSerialToNilBasedIndex = M.fromList $ allModelAtomSerials `zip` [0..] | ||
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| allModelAtomSerials :: [Int] | ||
| allModelAtomSerials = sort . V.toList . fmap PDB.atomSerial . V.concat $ V.toList model | ||
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| mkChain :: PDB.Chain -> Chain | ||
| mkChain = uncurry Chain . (mkChainName &&& mkChainResidues) | ||
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| mkChainName :: PDB.Chain -> Text | ||
| mkChainName = T.singleton . PDB.atomChainID . safeFirstAtom | ||
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| mkChainResidues :: PDB.Chain -> V.Vector Residue | ||
| mkChainResidues chain = V.fromList . fmap (mkResidue (restoreChainLocalBonds chain)) $ groupChainByResidue chain | ||
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| safeFirstAtom :: V.Vector PDB.Atom -> PDB.Atom | ||
| safeFirstAtom arr | V.length arr > 0 = arr V.! 0 | ||
| | otherwise = error "Could not pick first atom" | ||
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| mkResidue :: Map Text (V.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) | ||
| Undefined -- now we do not read secondary structure | ||
| "" -- chemical component type?! | ||
| where | ||
| firstResidueAtom = head atoms' | ||
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| mkAtom :: PDB.Atom -> Atom | ||
| mkAtom PDB.Atom{..} = Atom (GlobalID $ atomSerialToNilBasedIndex M.! atomSerial) | ||
| atomSerial | ||
| (T.strip atomName) | ||
| atomElement | ||
| (V3 atomX atomY atomZ) | ||
| (fromMaybe 0 . readMaybe $ T.unpack atomCharge) | ||
| atomTempFactor | ||
| atomOccupancy | ||
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| modelsFromPDBFile :: (MonadIO m) => FilePath -> m (Either Text ([PDBWarnings], V.Vector Model)) | ||
| modelsFromPDBFile = liftIO . fmap modelsFromPDBText . TIO.readFile | ||
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| modelsFromPDBText :: Text -> Either Text ([PDBWarnings], V.Vector Model) | ||
| modelsFromPDBText pdbText = do | ||
| (warnings, parsedPDB) <- fromTextPDB pdbText | ||
| let models = modelsOf parsedPDB | ||
| pure (warnings, models) |
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