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cobot-io 0.1.3.7 → 0.1.3.8

raw patch · 3 files changed

+44/−37 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

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ChangeLog.md view
@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.8] - 2020-10-22+### Fixed+- A couple of issues, that caused parametrization failures, fixed in bond restoring for PDB format.+ ## [0.1.3.7] - 2020-10-14 ### Added - Generic fasta parser.
cobot-io.cabal view
@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: eadbc12a962f0486f48dd57f8e72d5c4e7ea9528924b23e7b77ca0f67e9b0d4f+-- hash: c8e4ad988d6a9a2190936e54867ea81535c6b883ad6448fd8fbd16eab88715ca  name:           cobot-io-version:        0.1.3.7+version:        0.1.3.8 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio
src/Bio/PDB/BondRestoring.hs view
@@ -93,44 +93,47 @@   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-  where-    cystineSulfur :: [PDB.Atom]-    cystineSulfur = filter (("SG" ==) . T.strip . PDB.atomName) $ concat cystines-    cystines :: [[PDB.Atom]]-    cystines = filter cystinePredicate atomsGroupedByResidue-    cystinePredicate :: [PDB.Atom] -> Bool-    cystinePredicate residue = any (("SG" ==) . T.strip . PDB.atomName) residue && all (("HG" /=) . T.strip . PDB.atomName) residue-    coords :: PDB.Atom -> V3 Float-    coords PDB.Atom{..} = V3 atomX atomY atomZ+    where+      cystineSulfur :: [PDB.Atom]+      cystineSulfur = filter (("SG" ==) . T.strip . PDB.atomName) $ concat cystines+      cystines :: [[PDB.Atom]]+      cystines = filter cystinePredicate atomsGroupedByResidue+      cystinePredicate :: [PDB.Atom] -> Bool+      cystinePredicate residue = any (("SG" ==) . T.strip . PDB.atomName) residue && all (("HG" /=) . T.strip . PDB.atomName) residue +coords :: PDB.Atom -> V3 Float+coords PDB.Atom{..} = V3 atomX atomY atomZ+ sulfidicBondMaxLength :: Float sulfidicBondMaxLength = 2.56 +peptideBondMaxLength :: Float+peptideBondMaxLength = 1.5+ restoreChainPeptideBonds :: [[PDB.Atom]] -> [Bond GlobalID]-restoreChainPeptideBonds atomsGroupedByResidue = restoreChainPeptideBonds' atomsGroupedByResidue []+restoreChainPeptideBonds atomsGroupedByResidue = catMaybes $ restoreChainPeptideBonds' atomsGroupedByResidue mempty   where-    restoreChainPeptideBonds' :: [[PDB.Atom]] -> [Bond GlobalID] -> [Bond GlobalID]+    restoreChainPeptideBonds' :: [[PDB.Atom]] -> [Maybe (Bond GlobalID)] -> [Maybe (Bond GlobalID)]     restoreChainPeptideBonds' [] acc = acc     restoreChainPeptideBonds' [_] acc = acc     restoreChainPeptideBonds' (residue1:residue2:residues) acc =        restoreChainPeptideBonds' (residue2:residues) (constructBond residue1 residue2 : acc) -    constructBond :: [PDB.Atom] -> [PDB.Atom] -> Bond GlobalID-    constructBond residue1 residue2 = Bond (GlobalID $ getAtomIndex residue1 "C") (GlobalID $ getAtomIndex residue2 "N") 1-    -    getAtomIndex :: [PDB.Atom] -> Text -> Int-    getAtomIndex atoms atomNameToFind = case find ((atomNameToFind ==) . T.strip . PDB.atomName) atoms of -      Just PDB.Atom{..} -> atomSerial-      Nothing           -> error ("Atom with name " ++ T.unpack atomNameToFind ++ " wasn't found in residue " ++ residueId atoms ++ ", chain: " ++ chainId atoms)-    residueId :: [PDB.Atom] -> String-    residueId [] = error "cobot-io: it's impossible to form a residue ID on a residue with no atoms"-    residueId (PDB.Atom{..}:_) = T.unpack atomResName ++ show atomResSeq ++ show atomICode-    -    chainId :: [PDB.Atom] -> String-    chainId [] = error "cobot-io: it's impossible to get a chain ID on a chain with no atoms"-    chainId (PDB.Atom{..}:_) = show atomChainID+    constructBond :: [PDB.Atom] -> [PDB.Atom] -> Maybe (Bond GlobalID)+    constructBond residue1 residue2 = do+        carbonAtom1   <- getAtomByName residue1 "C"+        nitrogenAtom2 <- getAtomByName residue2 "N"++        -- check if the atoms are close enough+        -- 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     +    getAtomByName :: [PDB.Atom] -> Text -> Maybe PDB.Atom+    getAtomByName atoms atomNameToFind = find ((atomNameToFind ==) . T.strip . PDB.atomName) atoms + restoreChainIntraResidueBonds :: [[PDB.Atom]] -> [Bond GlobalID] restoreChainIntraResidueBonds = concatMap restoreIntraResidueBonds @@ -160,8 +163,8 @@  caCbBonds :: Text -> [(Text, Text)] caCbBonds aminoacid = case aminoacid of-  "GLY" -> bwhMany [("CA", ["HA2", "HA3"])]-  _     -> [("CA", "CB"), ("CA", "HA")]+  "GLY" -> bwhMany [("CA", ["HA1", "HA2", "HA3"])]+  _     -> [("CA", "CB"), ("CA", "HA"), ("CA", "HA1"), ("CA", "HA2"), ("CA", "HA3")]  sideChainBonds :: Text -> [(Text, Text)] sideChainBonds "ALA" = bwhMany [("CB", ["HB1", "HB2", "HB3"])]@@ -170,20 +173,20 @@ sideChainBonds "ASP" = [("CB", "CG"), ("CG", "OD1"), ("CG", "OD2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("OD2", ["HD2"])] sideChainBonds "CYS" = [("CB", "SG")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("SG", ["HG"])] sideChainBonds "GLN" = [("CB", "CG"), ("CG", "CD"), ("CD", "OE1"), ("CD", "NE2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG3", "HG2"]), ("NE2", ["HE22", "HE21"])]-sideChainBonds "GLU" = [("CB", "CG"), ("CG", "CD"), ("CD", "OE1"), ("CD", "OE2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG3", "HG2"]), ("OE2", ["HE2"])]+sideChainBonds "GLU" = [("CB", "CG"), ("CG", "CD"), ("CD", "OE1"), ("CD", "OE2")] ++ bwhMany [("CB", ["HB1", "HB2", "HB3"]), ("CG", ["HG3", "HG2"]), ("OE2", ["HE2"])] sideChainBonds "GLY" = [] -- nothing sideChainBonds "HIS" = [("CB", "CG"), ("CG", "ND1"), ("ND1", "CE1"), ("CE1", "NE2"), ("NE2", "CD2"), ("CD2", "CG")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("ND1", ["HD1"]), ("CE1", ["HE1"]), ("NE2", ["HE2"]), ("CD2", ["HD2"])]-sideChainBonds "ILE" = [("CB", "CG1"), ("CB", "CG2"), ("CG1", "CD1")] ++ bwhMany [("CB", ["HB"]), ("CG1", ["HG13", "HG12"]), ("CG2", ["HG21", "HG22", "HG23"]), ("CD1", ["HD11", "HD12", "HD13"])]-sideChainBonds "LEU" = [("CB", "CG"), ("CG", "CD1"), ("CG", "CD2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG"]), ("CD1", ["HD11", "HD12", "HD13"]), ("CD2", ["HD21", "HD22", "HD23"])]-sideChainBonds "LYS" = [("CB", "CG"), ("CG", "CD"), ("CD", "CE"), ("CE", "NZ")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG3", "HG2"]), ("CD", ["HD3", "HD2"]), ("CE", ["HE3", "HE2"]), ("NZ", ["HZ1", "HZ2", "HZ3"])]+sideChainBonds "ILE" = [("CB", "CG1"), ("CB", "CG2"), ("CG1", "CD1")] ++ bwhMany [("CB", ["HB", "HB2", "HB3"]), ("CG1", ["HG13", "HG12"]), ("CG2", ["HG21", "HG22", "HG23"]), ("CD1", ["HD11", "HD12", "HD13"])]+sideChainBonds "LEU" = [("CB", "CG"), ("CG", "CD1"), ("CG", "CD2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG", "HG2"]), ("CD1", ["HD11", "HD12", "HD13"]), ("CD2", ["HD21", "HD22", "HD23"])]+sideChainBonds "LYS" = [("CB", "CG"), ("CG", "CD"), ("CD", "CE"), ("CE", "NZ")] ++ bwhMany [("CB", ["HB1", "HB2", "HB3"]), ("CG", ["HG1", "HG2", "HG3"]), ("CD", ["HD3", "HD2"]), ("CE", ["HE3", "HE2"]), ("NZ", ["HZ1", "HZ2", "HZ3"])] sideChainBonds "MET" = [("CB", "CG"), ("CG", "SD"), ("SD", "CE")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG3", "HG2"]), ("CE", ["HE1", "HE2", "HE3"])] sideChainBonds "PHE" = [("CB", "CG"), ("CG", "CD1"), ("CD1", "CE1"), ("CE1", "CZ"), ("CZ", "CE2"), ("CE2", "CD2"), ("CD2", "CG")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CD1", ["HD1"]), ("CE1", ["HE1"]), ("CZ", ["HZ"]), ("CE2", ["HE2"]), ("CD2", ["HD2"])]-sideChainBonds "PRO" = [("CB", "CG"), ("CG", "CD"), ("CD", "N")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CG", ["HG3", "HG2"]), ("CD", ["HD2", "HD3"])]-sideChainBonds "SER" = [("CB", "OG")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("OG", ["HG"])]-sideChainBonds "THR" = [("CB", "OG1"), ("CB", "CG2")] ++ bwhMany [("CB", ["HB"]), ("OG1", ["HG1"]), ("CG2", ["HG21", "HG22", "HG23"])]+sideChainBonds "PRO" = [("CB", "CG"), ("CG", "CD"), ("CD", "N")] ++ bwhMany [("CB", ["HB1", "HB2", "HB3"]), ("CG", ["HG3", "HG2"]), ("CD", ["HD2", "HD3"])]+sideChainBonds "SER" = [("CB", "OG")] ++ bwhMany [("CB", ["HB3", "HB2", "HB1"]), ("OG", ["HG"])]+sideChainBonds "THR" = [("CB", "OG1"), ("CB", "CG2")] ++ bwhMany [("CB", ["HB", "HB3"]), ("OG1", ["HG1"]), ("CG2", ["HG21", "HG22", "HG23"])] sideChainBonds "TRP" = [("CB", "CG"), ("CG", "CD1"), ("CD1", "NE1"), ("NE1", "CE2"), ("CE2", "CD2"), ("CD2", "CG"), ("CD2", "CE3"), ("CE3", "CZ3"), ("CZ3", "CH2"), ("CH2", "CZ2"), ("CZ2", "CE2")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CD1", ["HD1"]), ("NE1", ["HE1"]), ("CE3", ["HE3"]), ("CZ3", ["HZ3"]), ("CH2", ["HH2"]), ("CZ2", ["HZ2"])] sideChainBonds "TYR" = [("CB", "CG"), ("CG", "CD1"), ("CD1", "CE1"), ("CE1", "CZ"), ("CZ", "CE2"), ("CE2", "CD2"), ("CD2", "CG"), ("CZ", "OH")] ++ bwhMany [("CB", ["HB3", "HB2"]), ("CD1", ["HD1"]), ("CE1", ["HE1"]), ("CE2", ["HE2"]), ("CD2", ["HD2"]), ("OH", ["HH"])]-sideChainBonds "VAL" = [("CB", "CG1"), ("CB", "CG2")] ++ bwhMany [("CB", ["HB"]), ("CG1", ["HG11", "HG12", "HG13"]), ("CG2", ["HG21", "HG22", "HG23"])]+sideChainBonds "VAL" = [("CB", "CG1"), ("CB", "CG2")] ++ bwhMany [("CB", ["HB", "HB3"]), ("CG1", ["HG11", "HG12", "HG13"]), ("CG2", ["HG21", "HG22", "HG23"])] sideChainBonds unknownResidue = error . T.unpack $ "cobot-io: we don't know what to do with residue " <> unknownResidue  bwhMany :: [(Text, [Text])] -> [(Text, Text)]