{-# LANGUAGE ScopedTypeVariables, OverloadedStrings #-} -- | Contains function that parse ATOM and ANISOU records module Bio.PDB.EventParser.ParseATOM( parseATOM, parseANISOU ) where import qualified Data.ByteString.Char8 as BS import Text.Printf(hPrintf) import Prelude hiding(String) import Bio.PDB.EventParser.PDBEvents import Bio.PDB.EventParser.PDBParsingAbstractions --------------- {{{ ATOM/HETATM records {-- From http://deposit.rcsb.org/adit/docs/pdb_atom_format.html: 1 - 6 Record name "ATOM " 7 - 11 Int Atom serial number. 13 - 16 Atom Atom name. 17 Character Alternate location indicator. 18 - 20 Residue name Residue name. 22 Character Chain identifier. 23 - 26 Int Residue sequence number. 27 AChar Code for insertion of residues. 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms. 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms. 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms. Following is optional for my parser: 55 - 60 Real(6.2) Occupancy. 61 - 66 Real(6.2) Temperature factor (Default = 0.0). Following is optional in PDB format? 73 - 76 LString(4) Segment identifier, left-justified. 77 - 78 LString(2) Element symbol, right-justified. 79 - 80 LString(2) Charge on the atom. Some programs treat 67-80 as generic "notes" Example line ATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S --} -- SHOULD BE ABSTRACTED - but this breaks optimization, and makes code 4x-5x slower -- List of pairs (ending column, field parser) --{-# INLINE commonFields #-} -- fields common to ATOM/HETATM and ANISOU records {-commonFields keywords middle = [( 6, mKeywords "Record declaration" keywords), -- Atom description (11, mInt "atom id"), (16, mStr "atom name"), (17, mChr "altloc"), -- Residue and chain description (20, mStr "residue name"), -- three letter code (21, mSpc 1), -- spacing (22, mChr "chain id"), (26, mInt "residue number"), (27, mChr "residue insertion code")] ++ middle ++ -- Trailing fields optional according to PDB [(76, pStr "SegId"), (78, pStr "element"), (80, pStr "charge") -- useful for MD ]-} --{-# INLINE atomFields #-} {-atomFields = commonFields ["ATOM ", "HETATM"] [ -- Coordinates (38, mDouble "X coordinate"), (46, mDouble "Y coordinate"), (54, mDouble "Z coordinate"), -- Fields below must be present in a proper PDB entry, -- but may be absent in theoretical models: (60, dDouble "occupancy" 1.00), (66, dDouble "B-factor" 99.99), (73, pSpc)] -- spacing -} {-# INLINE atomFields #-} atomFields = [ ( 6, mKeywords "Record declaration" ["ATOM ", "HETATM", "SIGATM"]), -- Atom description (11, mInt "atom id"), (16, mStr "atom name"), (17, mChr "altloc"), -- Residue and chain description (20, mStr "residue name"), -- three letter code (21, mSpc 1), -- spacing (22, mChr "chain id"), (26, mInt "residue number"), (27, mChr "residue insertion code"), (38, mDouble "X coordinate"), (46, mDouble "Y coordinate"), (54, mDouble "Z coordinate"), -- Fields below must be present in a proper PDB entry, -- but may be absent in theoretical models: (60, dDouble "occupancy" 1.00), (66, dDouble "B-factor" 99.99), --(73, pStr "<spaces>"), -- Use with GHC 6.12 and earlier to avoid broken optimization: should be pSpc 7 --(73, pSpc ), -- non-standard, but used by some programs, so we catenate it with SegId field (76, pStr "SegId"), (78, pStr "element"), (80, pStr "charge")] --{- ### INLINE parseATOM #-} -- strangely makes code 7x slower!!! -- | Parses an ATOM record. -- -- Arguments: -- -- (1) input line -- -- (2) input line number -- -- Result is a monad action returning a list of 'PDBEvent's. --{-# SPECIALIZE parseATOM :: Bool -> String -> Int -> IO [PDBEvent] #-} parseATOM :: (Monad m) => String -> Int -> m [PDBEvent] parseATOM line line_no = return $ if null errs then [result] else errs where -- parse (fields, errs) = parseFields atomFields line line_no [fRecTag, fAtId, fAtNam, fAltLoc, fResNam, _fSpace, fChain, fResId, fInsid, fX, fY, fZ, fOcc, fBFact, fSegid, fElt, fCharge] = fields -- unpack fields IFStr rectag = fRecTag IFInt atid = fAtId IFStr atnam = fAtNam IFChar altloc = fAltLoc IFStr resnam = fResNam IFChar chain = fChain IFInt resid = fResId IFChar insid = fInsid IFDouble x = fX IFDouble y = fY IFDouble z = fZ IFDouble occ = fOcc IFDouble bFact = fBFact segid = unstr fSegid elt = unstr fElt charge = unstr fCharge -- assemble record coords = Vector3 x y z result = case rectag of "ATOM " -> ATOM atid atnam resnam chain resid insid altloc coords occ bFact segid elt charge False "HETATM" -> ATOM atid atnam resnam chain resid insid altloc coords occ bFact segid elt charge True "SIGATM" -> SIGATM atid atnam resnam chain resid insid altloc coords occ bFact segid elt charge --------------- }}} ATOM/HETATM records --------------- {{{ ANISOU records {- COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------------------------- 1 - 6 Record name "ANISOU" 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Insertion code. 29 - 35 Integer u[0][0] U(1,1) 36 - 42 Integer u[1][1] U(2,2) 43 - 49 Integer u[2][2] U(3,3) 50 - 56 Integer u[0][1] U(1,2) 57 - 63 Integer u[0][2] U(1,3) 64 - 70 Integer u[1][2] U(2,3) 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom. -} --{-# INLINE anisouFields #-} {-anisouFields = commonFields ["ANISOU"] [ (29, mSpc 2), (35, mInt "U(1,1)"), (42, mInt "U(2,2)"), (49, mInt "U(3,3)"), (56, mInt "U(1,2)"), (63, mInt "U(1,3)"), (70, mInt "U(2,3)"), (76, mSpc 6)]-} {-# INLINE anisouFields #-} anisouFields = [ ( 6, mKeywords "Record declaration" ["ANISOU", "SIGUIJ"]), -- Atom description (11, mInt "atom id"), (16, mStr "atom name"), (17, mChr "altloc"), -- Residue and chain description (20, mStr "residue name"), -- three letter code (21, mSpc 1), -- spacing (22, mChr "chain id"), (26, mInt "residue number"), (27, mChr "residue insertion code"), (29, mSpc 2), (35, mInt "U(1,1)"), (42, mInt "U(2,2)"), (49, mInt "U(3,3)"), (56, mInt "U(1,2)"), (63, mInt "U(1,3)"), (70, mInt "U(2,3)"), (75, pSpc ), -- use pStr "<spaces>" with GHC<=6.12 to avoid broken optimization (76, pStr "SegId"), (78, pStr "element"), (80, pStr "charge")] {-# INLINE parseANISOU #-} -- | Parses an ANISOU record. -- -- Arguments: -- -- (1) input line -- -- (2) input line number -- -- Result is a monad action returning a list of 'PDBEvent's. parseANISOU :: (Monad m) => String -> Int -> m [PDBEvent] parseANISOU line line_no = return $ if null errs then result `seq` [result] else errs where -- parse (fields, errs) = parseFields anisouFields line line_no [fRecTag, fAtId, fAtNam, fAltLoc, fResNam, _fSpace, fChain, fResId, fInsid, _, fU_1_1, fU_2_2, fU_3_3, fU_1_2, fU_1_3, fU_2_3, _, fSegid, fElt, fCharge] = fields -- unpack fields IFStr rectag = fRecTag IFInt atid = fAtId IFStr atnam = fAtNam IFChar altloc = fAltLoc IFStr resnam = fResNam IFChar chain = fChain IFInt resid = fResId IFChar insid = fInsid IFInt u_1_1 = fU_1_1 IFInt u_2_2 = fU_2_2 IFInt u_3_3 = fU_3_3 IFInt u_1_2 = fU_1_2 IFInt u_1_3 = fU_1_3 IFInt u_2_3 = fU_2_3 segid = unstr fSegid elt = unstr fElt charge = unstr fCharge -- assemble record cons = case rectag of "ANISOU" -> ANISOU "SIGUIJ" -> SIGUIJ result = cons atid atnam resnam chain resid insid altloc u_1_1 u_2_2 u_3_3 u_1_2 u_1_3 u_2_3 segid elt charge --------------- }}} ANISOU records