diff --git a/AUTHORS b/AUTHORS --- a/AUTHORS +++ b/AUTHORS @@ -1,3 +1,6 @@ This parser and associated example programs were created by: Michal J. Gajda 2010-2013 In his free time, unencumbered by work duties. + +Thanks a lot to Ben Gamari for extensive analysis of the atom lookup problem: +https://ghc.haskell.org/trac/ghc/ticket/10565 diff --git a/Bio/PDB/Structure/Elements.hs b/Bio/PDB/Structure/Elements.hs --- a/Bio/PDB/Structure/Elements.hs +++ b/Bio/PDB/Structure/Elements.hs @@ -1,571 +1,594 @@ {-# LANGUAGE OverloadedStrings #-} -- | Basic properties of chemical 'Element's as suggested by Cambridge Structural Database. -module Bio.PDB.Structure.Elements(Element(..), - -- Finding element for a given atom - assignElement, - -- Guessing element name from atom name (for standard residues only.) - guessElement, - -- properties of elements - atomicNumber, atomicMass, - covalentRadius, maxCovalentRadius, - vanDerWaalsRadius, maxVanDerWaalsRadius) where - -import Prelude hiding (error, String) -import Data.ByteString.Char8 as BS -import System.IO.Unsafe(unsafePerformIO) -import System.IO(stderr) -import Bio.PDB.Structure(Atom(..)) - --- | Type alias for 'Element' names. -type Element = BS.ByteString --- TODO: May be better as a newtype, and make sure that other modules use this declaration - --- | Internal method that reports error to stderr, and return given default value. -defaulting e defaultValue = unsafePerformIO $ do BS.hPutStrLn stderr $ BS.concat e - return defaultValue - -{-# INLINE atomicNumber #-} --- | Atomic number of a given element -atomicNumber :: Element -> Int -atomicNumber "C" = 6 -atomicNumber "N" = 7 -atomicNumber "O" = 8 -atomicNumber "P" = 15 -atomicNumber "S" = 16 -atomicNumber "H" = 1 -atomicNumber "AC" = 89 -atomicNumber "AG" = 47 -atomicNumber "AL" = 13 -atomicNumber "AM" = 95 -atomicNumber "AR" = 18 -atomicNumber "AS" = 33 -atomicNumber "AT" = 85 -atomicNumber "AU" = 79 -atomicNumber "B" = 5 -atomicNumber "BA" = 56 -atomicNumber "BE" = 4 -atomicNumber "BH" = 107 -atomicNumber "BI" = 83 -atomicNumber "BK" = 97 -atomicNumber "BR" = 35 -atomicNumber "CA" = 20 -atomicNumber "CD" = 48 -atomicNumber "CE" = 58 -atomicNumber "CF" = 98 -atomicNumber "CL" = 17 -atomicNumber "CM" = 96 -atomicNumber "CO" = 27 -atomicNumber "CR" = 24 -atomicNumber "CS" = 55 -atomicNumber "CU" = 29 -atomicNumber "DB" = 105 -atomicNumber "DS" = 110 -atomicNumber "DY" = 66 -atomicNumber "ER" = 68 -atomicNumber "ES" = 99 -atomicNumber "EU" = 63 -atomicNumber "F" = 9 -atomicNumber "FE" = 26 -atomicNumber "FM" = 100 -atomicNumber "FR" = 87 -atomicNumber "GA" = 31 -atomicNumber "GD" = 64 -atomicNumber "GE" = 32 -atomicNumber "HE" = 2 -atomicNumber "HF" = 72 -atomicNumber "HG" = 80 -atomicNumber "HO" = 67 -atomicNumber "HS" = 108 -atomicNumber "I" = 53 -atomicNumber "IN" = 49 -atomicNumber "IR" = 77 -atomicNumber "K" = 19 -atomicNumber "KR" = 36 -atomicNumber "LA" = 57 -atomicNumber "LI" = 3 -atomicNumber "LR" = 103 -atomicNumber "LU" = 71 -atomicNumber "MD" = 101 -atomicNumber "MG" = 12 -atomicNumber "MN" = 25 -atomicNumber "MO" = 42 -atomicNumber "MT" = 109 -atomicNumber "NA" = 11 -atomicNumber "NB" = 41 -atomicNumber "ND" = 60 -atomicNumber "NE" = 10 -atomicNumber "NI" = 28 -atomicNumber "NO" = 102 -atomicNumber "NP" = 93 -atomicNumber "OS" = 76 -atomicNumber "PA" = 91 -atomicNumber "PB" = 82 -atomicNumber "PD" = 46 -atomicNumber "PM" = 61 -atomicNumber "PO" = 84 -atomicNumber "PR" = 59 -atomicNumber "PT" = 78 -atomicNumber "PU" = 94 -atomicNumber "RA" = 88 -atomicNumber "RB" = 37 -atomicNumber "RE" = 75 -atomicNumber "RF" = 104 -atomicNumber "RH" = 45 -atomicNumber "RN" = 86 -atomicNumber "RU" = 44 -atomicNumber "SB" = 51 -atomicNumber "SC" = 21 -atomicNumber "SE" = 34 -atomicNumber "SG" = 106 -atomicNumber "SI" = 14 -atomicNumber "SM" = 62 -atomicNumber "SN" = 50 -atomicNumber "SR" = 38 -atomicNumber "TA" = 73 -atomicNumber "TB" = 65 -atomicNumber "TC" = 43 -atomicNumber "TE" = 52 -atomicNumber "TH" = 90 -atomicNumber "TI" = 22 -atomicNumber "TL" = 81 -atomicNumber "TM" = 69 -atomicNumber "U" = 92 -atomicNumber "V" = 23 -atomicNumber "W" = 74 -atomicNumber "XE" = 54 -atomicNumber "Y" = 39 -atomicNumber "YB" = 70 -atomicNumber "ZN" = 30 -atomicNumber "ZR" = 40 -atomicNumber x = defaulting ["Unknown atomic number for element:", BS.pack $ show x] 0 - -{-# INLINE covalentRadius #-} --- | Covalent radius of an element with a given name. -covalentRadius "AC" = 2.15 -covalentRadius "AG" = 1.45 -covalentRadius "AL" = 1.21 -covalentRadius "AM" = 1.80 -covalentRadius "AR" = 1.51 -covalentRadius "AS" = 1.21 -covalentRadius "AT" = 1.21 -covalentRadius "AU" = 1.36 -covalentRadius "B" = 0.83 -covalentRadius "BA" = 2.15 -covalentRadius "BE" = 0.96 -covalentRadius "BH" = 1.50 -covalentRadius "BI" = 1.48 -covalentRadius "BK" = 1.54 -covalentRadius "BR" = 1.21 -covalentRadius "C" = 0.68 -covalentRadius "CA" = 1.76 -covalentRadius "CD" = 1.44 -covalentRadius "CE" = 2.04 -covalentRadius "CF" = 1.83 -covalentRadius "CL" = 0.99 -covalentRadius "CM" = 1.69 -covalentRadius "CO" = 1.26 -covalentRadius "CR" = 1.39 -covalentRadius "CS" = 2.44 -covalentRadius "CU" = 1.32 -covalentRadius "DB" = 1.50 -covalentRadius "DS" = 1.50 -covalentRadius "DY" = 1.92 -covalentRadius "ER" = 1.89 -covalentRadius "ES" = 1.50 -covalentRadius "EU" = 1.98 -covalentRadius "F" = 0.64 -covalentRadius "FE" = 1.52 -covalentRadius "FM" = 1.50 -covalentRadius "FR" = 2.60 -covalentRadius "GA" = 1.22 -covalentRadius "GD" = 1.96 -covalentRadius "GE" = 1.17 -covalentRadius "H" = 0.23 -covalentRadius "HE" = 1.50 -covalentRadius "HF" = 1.75 -covalentRadius "HG" = 1.32 -covalentRadius "HO" = 1.92 -covalentRadius "HS" = 1.50 -covalentRadius "I" = 1.40 -covalentRadius "IN" = 1.42 -covalentRadius "IR" = 1.41 -covalentRadius "K" = 2.03 -covalentRadius "KR" = 1.50 -covalentRadius "LA" = 2.07 -covalentRadius "LI" = 1.28 -covalentRadius "LR" = 1.50 -covalentRadius "LU" = 1.87 -covalentRadius "MD" = 1.50 -covalentRadius "MG" = 1.41 -covalentRadius "MN" = 1.61 -covalentRadius "MO" = 1.54 -covalentRadius "MT" = 1.50 -covalentRadius "N" = 0.68 -covalentRadius "NA" = 1.66 -covalentRadius "NB" = 1.64 -covalentRadius "ND" = 2.01 -covalentRadius "NE" = 1.50 -covalentRadius "NI" = 1.24 -covalentRadius "NO" = 1.50 -covalentRadius "NP" = 1.90 -covalentRadius "O" = 0.68 -covalentRadius "OS" = 1.44 -covalentRadius "P" = 1.05 -covalentRadius "PA" = 2.00 -covalentRadius "PB" = 1.46 -covalentRadius "PD" = 1.39 -covalentRadius "PM" = 1.99 -covalentRadius "PO" = 1.40 -covalentRadius "PR" = 2.03 -covalentRadius "PT" = 1.36 -covalentRadius "PU" = 1.87 -covalentRadius "RA" = 2.21 -covalentRadius "RB" = 2.20 -covalentRadius "RE" = 1.51 -covalentRadius "RF" = 1.50 -covalentRadius "RH" = 1.42 -covalentRadius "RN" = 1.50 -covalentRadius "RU" = 1.46 -covalentRadius "S" = 1.02 -covalentRadius "SB" = 1.39 -covalentRadius "SC" = 1.70 -covalentRadius "SE" = 1.22 -covalentRadius "SG" = 1.50 -covalentRadius "SI" = 1.20 -covalentRadius "SM" = 1.98 -covalentRadius "SN" = 1.39 -covalentRadius "SR" = 1.95 -covalentRadius "TA" = 1.70 -covalentRadius "TB" = 1.94 -covalentRadius "TC" = 1.47 -covalentRadius "TE" = 1.47 -covalentRadius "TH" = 2.06 -covalentRadius "TI" = 1.60 -covalentRadius "TL" = 1.45 -covalentRadius "TM" = 1.90 -covalentRadius "U" = 1.96 -covalentRadius "V" = 1.53 -covalentRadius "W" = 1.62 -covalentRadius "XE" = 1.50 -covalentRadius "Y" = 1.90 -covalentRadius "YB" = 1.87 -covalentRadius "ZN" = 1.22 -covalentRadius "ZR" = 1.75 -covalentRadius x = defaulting ["Unknown covalent radius for element:", BS.pack $ show x] 0.0 - -{-# INLINE maxCovalentRadius #-} --- | Upper bound of @covalentRadius@. -maxCovalentRadius :: Double -maxCovalentRadius = covalentRadius "FR" - -{-# INLINE atomicMass #-} --- | Atomic mass of a given element in g/mol -atomicMass :: Element -> Double -atomicMass "C" = 12.011 -atomicMass "N" = 14.007 -atomicMass "O" = 15.999 -atomicMass "P" = 30.974 -atomicMass "S" = 32.066 -atomicMass "H" = 1.008 -atomicMass "AC" = 227.000 -atomicMass "AG" = 107.868 -atomicMass "AL" = 26.982 -atomicMass "AM" = 243.000 -atomicMass "AR" = 39.948 -atomicMass "AS" = 74.922 -atomicMass "AT" = 210.000 -atomicMass "AU" = 196.967 -atomicMass "B" = 10.811 -atomicMass "BA" = 137.327 -atomicMass "BE" = 9.012 -atomicMass "BH" = 264.000 -atomicMass "BI" = 208.980 -atomicMass "BK" = 247.000 -atomicMass "BR" = 79.904 -atomicMass "CA" = 40.078 -atomicMass "CD" = 112.411 -atomicMass "CE" = 140.116 -atomicMass "CF" = 251.000 -atomicMass "CL" = 35.453 -atomicMass "CM" = 247.000 -atomicMass "CO" = 58.933 -atomicMass "CR" = 51.996 -atomicMass "CS" = 132.905 -atomicMass "CU" = 63.546 -atomicMass "DB" = 262.000 -atomicMass "DS" = 271.000 -atomicMass "DY" = 162.500 -atomicMass "ER" = 167.260 -atomicMass "ES" = 252.000 -atomicMass "EU" = 151.964 -atomicMass "F" = 18.998 -atomicMass "FE" = 55.845 -atomicMass "FM" = 257.000 -atomicMass "FR" = 223.000 -atomicMass "GA" = 69.723 -atomicMass "GD" = 157.250 -atomicMass "GE" = 72.610 -atomicMass "HE" = 4.003 -atomicMass "HF" = 178.490 -atomicMass "HG" = 200.590 -atomicMass "HO" = 164.930 -atomicMass "HS" = 269.000 -atomicMass "I" = 126.904 -atomicMass "IN" = 114.818 -atomicMass "IR" = 192.217 -atomicMass "K" = 39.098 -atomicMass "KR" = 83.800 -atomicMass "LA" = 138.906 -atomicMass "LI" = 6.941 -atomicMass "LR" = 262.000 -atomicMass "LU" = 174.967 -atomicMass "MD" = 258.000 -atomicMass "MG" = 24.305 -atomicMass "MN" = 54.938 -atomicMass "MO" = 95.940 -atomicMass "MT" = 268.000 -atomicMass "NA" = 22.991 -atomicMass "NB" = 92.906 -atomicMass "ND" = 144.240 -atomicMass "NE" = 20.180 -atomicMass "NI" = 58.693 -atomicMass "NO" = 259.000 -atomicMass "NP" = 237.000 -atomicMass "OS" = 190.230 -atomicMass "PA" = 231.036 -atomicMass "PB" = 207.200 -atomicMass "PD" = 106.420 -atomicMass "PM" = 145.000 -atomicMass "PO" = 210.000 -atomicMass "PR" = 140.908 -atomicMass "PT" = 195.078 -atomicMass "PU" = 244.000 -atomicMass "RA" = 226.000 -atomicMass "RB" = 85.468 -atomicMass "RE" = 186.207 -atomicMass "RF" = 261.000 -atomicMass "RH" = 102.906 -atomicMass "RN" = 222.000 -atomicMass "RU" = 101.070 -atomicMass "SB" = 121.760 -atomicMass "SC" = 44.956 -atomicMass "SE" = 78.960 -atomicMass "SG" = 266.000 -atomicMass "SI" = 28.086 -atomicMass "SM" = 150.360 -atomicMass "SN" = 118.710 -atomicMass "SR" = 87.620 -atomicMass "TA" = 180.948 -atomicMass "TB" = 158.925 -atomicMass "TC" = 98.000 -atomicMass "TE" = 127.600 -atomicMass "TH" = 232.038 -atomicMass "TI" = 47.867 -atomicMass "TL" = 204.383 -atomicMass "TM" = 168.934 -atomicMass "U" = 238.029 -atomicMass "V" = 50.942 -atomicMass "W" = 183.840 -atomicMass "XE" = 131.290 -atomicMass "Y" = 88.906 -atomicMass "YB" = 173.040 -atomicMass "ZN" = 65.390 -atomicMass "ZR" = 91.224 -atomicMass x = defaulting ["Unknown atomic mass for element:", BS.pack $ show x] 0.0 - -{-# INLINE vanDerWaalsRadius #-} --- | Van der Waals radius of the given element -vanDerWaalsRadius :: Element -> Double -vanDerWaalsRadius "C" = 1.70 -vanDerWaalsRadius "N" = 1.55 -vanDerWaalsRadius "O" = 1.52 -vanDerWaalsRadius "P" = 1.80 -vanDerWaalsRadius "S" = 1.80 -vanDerWaalsRadius "AC" = 2.00 -vanDerWaalsRadius "AG" = 1.72 -vanDerWaalsRadius "AL" = 2.00 -vanDerWaalsRadius "AM" = 2.00 -vanDerWaalsRadius "AR" = 1.88 -vanDerWaalsRadius "AS" = 1.85 -vanDerWaalsRadius "AT" = 2.00 -vanDerWaalsRadius "AU" = 1.66 -vanDerWaalsRadius "B" = 2.00 -vanDerWaalsRadius "BA" = 2.00 -vanDerWaalsRadius "BE" = 2.00 -vanDerWaalsRadius "BH" = 2.00 -vanDerWaalsRadius "BI" = 2.00 -vanDerWaalsRadius "BK" = 2.00 -vanDerWaalsRadius "BR" = 1.85 -vanDerWaalsRadius "CA" = 2.00 -vanDerWaalsRadius "CD" = 1.58 -vanDerWaalsRadius "CE" = 2.00 -vanDerWaalsRadius "CF" = 2.00 -vanDerWaalsRadius "CL" = 1.75 -vanDerWaalsRadius "CM" = 2.00 -vanDerWaalsRadius "CO" = 2.00 -vanDerWaalsRadius "CR" = 2.00 -vanDerWaalsRadius "CS" = 2.00 -vanDerWaalsRadius "CU" = 1.40 -vanDerWaalsRadius "DB" = 2.00 -vanDerWaalsRadius "DS" = 2.00 -vanDerWaalsRadius "DY" = 2.00 -vanDerWaalsRadius "ER" = 2.00 -vanDerWaalsRadius "ES" = 2.00 -vanDerWaalsRadius "EU" = 2.00 -vanDerWaalsRadius "F" = 1.47 -vanDerWaalsRadius "FE" = 2.00 -vanDerWaalsRadius "FM" = 2.00 -vanDerWaalsRadius "FR" = 2.00 -vanDerWaalsRadius "GA" = 1.87 -vanDerWaalsRadius "GD" = 2.00 -vanDerWaalsRadius "GE" = 2.00 -vanDerWaalsRadius "H" = 1.09 -vanDerWaalsRadius "HE" = 1.40 -vanDerWaalsRadius "HF" = 2.00 -vanDerWaalsRadius "HG" = 1.55 -vanDerWaalsRadius "HO" = 2.00 -vanDerWaalsRadius "HS" = 2.00 -vanDerWaalsRadius "I" = 1.98 -vanDerWaalsRadius "IN" = 1.93 -vanDerWaalsRadius "IR" = 2.00 -vanDerWaalsRadius "K" = 2.75 -vanDerWaalsRadius "KR" = 2.02 -vanDerWaalsRadius "LA" = 2.00 -vanDerWaalsRadius "LI" = 1.82 -vanDerWaalsRadius "LR" = 2.00 -vanDerWaalsRadius "LU" = 2.00 -vanDerWaalsRadius "MD" = 2.00 -vanDerWaalsRadius "MG" = 1.73 -vanDerWaalsRadius "MN" = 2.00 -vanDerWaalsRadius "MO" = 2.00 -vanDerWaalsRadius "MT" = 2.00 -vanDerWaalsRadius "NA" = 2.27 -vanDerWaalsRadius "NB" = 2.00 -vanDerWaalsRadius "ND" = 2.00 -vanDerWaalsRadius "NE" = 1.54 -vanDerWaalsRadius "NI" = 1.63 -vanDerWaalsRadius "NO" = 2.00 -vanDerWaalsRadius "NP" = 2.00 -vanDerWaalsRadius "OS" = 2.00 -vanDerWaalsRadius "PA" = 2.00 -vanDerWaalsRadius "PB" = 2.02 -vanDerWaalsRadius "PD" = 1.63 -vanDerWaalsRadius "PM" = 2.00 -vanDerWaalsRadius "PO" = 2.00 -vanDerWaalsRadius "PR" = 2.00 -vanDerWaalsRadius "PT" = 1.72 -vanDerWaalsRadius "PU" = 2.00 -vanDerWaalsRadius "RA" = 2.00 -vanDerWaalsRadius "RB" = 2.00 -vanDerWaalsRadius "RE" = 2.00 -vanDerWaalsRadius "RF" = 2.00 -vanDerWaalsRadius "RH" = 2.00 -vanDerWaalsRadius "RN" = 2.00 -vanDerWaalsRadius "RU" = 2.00 -vanDerWaalsRadius "SB" = 2.00 -vanDerWaalsRadius "SC" = 2.00 -vanDerWaalsRadius "SE" = 1.90 -vanDerWaalsRadius "SG" = 2.00 -vanDerWaalsRadius "SI" = 2.10 -vanDerWaalsRadius "SM" = 2.00 -vanDerWaalsRadius "SN" = 2.17 -vanDerWaalsRadius "SR" = 2.00 -vanDerWaalsRadius "TA" = 2.00 -vanDerWaalsRadius "TB" = 2.00 -vanDerWaalsRadius "TC" = 2.00 -vanDerWaalsRadius "TE" = 2.06 -vanDerWaalsRadius "TH" = 2.00 -vanDerWaalsRadius "TI" = 2.00 -vanDerWaalsRadius "TL" = 1.96 -vanDerWaalsRadius "TM" = 2.00 -vanDerWaalsRadius "U" = 1.86 -vanDerWaalsRadius "V" = 2.00 -vanDerWaalsRadius "W" = 2.00 -vanDerWaalsRadius "XE" = 2.16 -vanDerWaalsRadius "Y" = 2.00 -vanDerWaalsRadius "YB" = 2.00 -vanDerWaalsRadius "ZN" = 1.39 -vanDerWaalsRadius "ZR" = 2.00 -vanDerWaalsRadius e = defaulting ["Do not know van der Waals radius of", BS.pack $ show e] 0.0 - -{-# INLINE maxVanDerWaalsRadius #-} --- | Upper bound of @vanDerWaalsRadius@. -maxVanDerWaalsRadius :: Double -maxVanDerWaalsRadius = vanDerWaalsRadius "K" - -{-# INLINE assignElement #-} --- | Given a PDB 'Atom' extract or guess its 'Element' name. -assignElement :: Atom -> Element -assignElement at = case element at of - "" -> guessElement . atName $ at - code -> code - -{-# INLINE guessElement #-} --- | Guessing an 'Element' name from PDB 'Atom' name. --- Returns empty string, if 'Element' can't be guessed. -guessElement :: BS.ByteString -> Element -guessElement "C" = "C" -guessElement "C1'" = "C" -guessElement "C2" = "C" -guessElement "C2'" = "C" -guessElement "C3'" = "C" -guessElement "C4" = "C" -guessElement "C4'" = "C" -guessElement "C5" = "C" -guessElement "C5'" = "C" -guessElement "C6" = "C" -guessElement "C8" = "C" -guessElement "CA" = "C" -guessElement "CB" = "C" -guessElement "CD" = "C" -guessElement "CD1" = "C" -guessElement "CD2" = "C" -guessElement "CE" = "C" -guessElement "CE1" = "C" -guessElement "CE2" = "C" -guessElement "CE3" = "C" -guessElement "CG" = "C" -guessElement "CG1" = "C" -guessElement "CG2" = "C" -guessElement "CH2" = "C" -guessElement "CZ" = "C" -guessElement "CZ2" = "C" -guessElement "CZ3" = "C" -guessElement "N" = "N" -guessElement "N1" = "N" -guessElement "N2" = "N" -guessElement "N3" = "N" -guessElement "N4" = "N" -guessElement "N6" = "N" -guessElement "N7" = "N" -guessElement "N9" = "N" -guessElement "ND1" = "N" -guessElement "ND2" = "N" -guessElement "NE" = "N" -guessElement "NE1" = "N" -guessElement "NE2" = "N" -guessElement "NH1" = "N" -guessElement "NH2" = "N" -guessElement "NZ" = "N" -guessElement "O" = "O" -guessElement "O2" = "O" -guessElement "O2'" = "O" -guessElement "O3'" = "O" -guessElement "O4" = "O" -guessElement "O4'" = "O" -guessElement "O5'" = "O" -guessElement "O6" = "O" -guessElement "OD1" = "O" -guessElement "OD2" = "O" -guessElement "OE1" = "O" -guessElement "OE2" = "O" -guessElement "OG" = "O" -guessElement "OG1" = "O" -guessElement "OH" = "O" -guessElement "OP1" = "O" -guessElement "OP2" = "O" -guessElement "OXT" = "O" -guessElement "P" = "P" -guessElement "SD" = "S" -guessElement "SG" = "S" -guessElement _ = "" -- not a standard residue of protein or nucleic acid +-- +-- NOTE: This module contains functions that could use hash tables for the lookup instead. +-- See https://ghc.haskell.org/trac/ghc/ticket/10565 +module Bio.PDB.Structure.Elements(Element(..), + -- Finding element for a given atom + assignElement, + -- Guessing element name from atom name (for standard residues only.) + guessElement, + -- properties of elements + atomicNumber, atomicMass, + covalentRadius, maxCovalentRadius, + vanDerWaalsRadius, maxVanDerWaalsRadius) where + +import Prelude hiding (error, String) +import Data.ByteString.Char8 as BS +import System.IO.Unsafe(unsafePerformIO) +import System.IO(stderr) +import Bio.PDB.Structure(Atom(..)) +import Data.HashMap.Strict as M +import Data.Maybe + +-- | Type alias for 'Element' names. +type Element = BS.ByteString +-- TODO: May be better as a newtype, and make sure that other modules use this declaration + +-- | Internal method that reports error to stderr, and return given default value. +defaultingLookup :: BS.ByteString -> v -> HashMap Element v -> Element -> v +defaultingLookup msg defaultValue dict e = + fromMaybe withWarning + $ M.lookup (BS.unpack e) dict + where + withWarning = unsafePerformIO $ do BS.hPutStrLn stderr $ BS.concat [msg, BS.pack . show . BS.unpack $ e] + return defaultValue + +-- | Atomic number of a given element +atomicNumber :: Element -> Int +atomicNumber = defaultingLookup "Unknown atomic number for element:" + 0 dict + where + dict = M.fromList [ + ( "C", 6) + ,( "N", 7) + ,( "O", 8) + ,( "P", 15) + ,( "S", 16) + ,( "H", 1) + ,("AC", 89) + ,("AG", 47) + ,("AL", 13) + ,("AM", 95) + ,("AR", 18) + ,("AS", 33) + ,("AT", 85) + ,("AU", 79) + ,( "B", 5) + ,("BA", 56) + ,("BE", 4) + ,("BH", 107) + ,("BI", 83) + ,("BK", 97) + ,("BR", 35) + ,("CA", 20) + ,("CD", 48) + ,("CE", 58) + ,("CF", 98) + ,("CL", 17) + ,("CM", 96) + ,("CO", 27) + ,("CR", 24) + ,("CS", 55) + ,("CU", 29) + ,("DB", 105) + ,("DS", 110) + ,("DY", 66) + ,("ER", 68) + ,("ES", 99) + ,("EU", 63) + ,( "F", 9) + ,("FE", 26) + ,("FM", 100) + ,("FR", 87) + ,("GA", 31) + ,("GD", 64) + ,("GE", 32) + ,("HE", 2) + ,("HF", 72) + ,("HG", 80) + ,("HO", 67) + ,("HS", 108) + ,( "I", 53) + ,("IN", 49) + ,("IR", 77) + ,( "K", 19) + ,("KR", 36) + ,("LA", 57) + ,("LI", 3) + ,("LR", 103) + ,("LU", 71) + ,("MD", 101) + ,("MG", 12) + ,("MN", 25) + ,("MO", 42) + ,("MT", 109) + ,("NA", 11) + ,("NB", 41) + ,("ND", 60) + ,("NE", 10) + ,("NI", 28) + ,("NO", 102) + ,("NP", 93) + ,("OS", 76) + ,("PA", 91) + ,("PB", 82) + ,("PD", 46) + ,("PM", 61) + ,("PO", 84) + ,("PR", 59) + ,("PT", 78) + ,("PU", 94) + ,("RA", 88) + ,("RB", 37) + ,("RE", 75) + ,("RF", 104) + ,("RH", 45) + ,("RN", 86) + ,("RU", 44) + ,("SB", 51) + ,("SC", 21) + ,("SE", 34) + ,("SG", 106) + ,("SI", 14) + ,("SM", 62) + ,("SN", 50) + ,("SR", 38) + ,("TA", 73) + ,("TB", 65) + ,("TC", 43) + ,("TE", 52) + ,("TH", 90) + ,("TI", 22) + ,("TL", 81) + ,("TM", 69) + ,( "U", 92) + ,( "V", 23) + ,( "W", 74) + ,("XE", 54) + ,( "Y", 39) + ,("YB", 70) + ,("ZN", 30) + ,("ZR", 40) + ] + +-- | Covalent radius of an element with a given name. +covalentRadius = defaultingLookup "Unknown covalent radius for element:" + 0.0 dict + where + dict = M.fromList [ + ("AC", 2.15) + , ("AG", 1.45) + , ("AL", 1.21) + , ("AM", 1.80) + , ("AR", 1.51) + , ("AS", 1.21) + , ("AT", 1.21) + , ("AU", 1.36) + , ( "B", 0.83) + , ("BA", 2.15) + , ("BE", 0.96) + , ("BH", 1.50) + , ("BI", 1.48) + , ("BK", 1.54) + , ("BR", 1.21) + , ( "C", 0.68) + , ("CA", 1.76) + , ("CD", 1.44) + , ("CE", 2.04) + , ("CF", 1.83) + , ("CL", 0.99) + , ("CM", 1.69) + , ("CO", 1.26) + , ("CR", 1.39) + , ("CS", 2.44) + , ("CU", 1.32) + , ("DB", 1.50) + , ("DS", 1.50) + , ("DY", 1.92) + , ("ER", 1.89) + , ("ES", 1.50) + , ("EU", 1.98) + , ( "F", 0.64) + , ("FE", 1.52) + , ("FM", 1.50) + , ("FR", 2.60) + , ("GA", 1.22) + , ("GD", 1.96) + , ("GE", 1.17) + , ( "H", 0.23) + , ("HE", 1.50) + , ("HF", 1.75) + , ("HG", 1.32) + , ("HO", 1.92) + , ("HS", 1.50) + , ( "I", 1.40) + , ("IN", 1.42) + , ("IR", 1.41) + , ( "K", 2.03) + , ("KR", 1.50) + , ("LA", 2.07) + , ("LI", 1.28) + , ("LR", 1.50) + , ("LU", 1.87) + , ("MD", 1.50) + , ("MG", 1.41) + , ("MN", 1.61) + , ("MO", 1.54) + , ("MT", 1.50) + , ( "N", 0.68) + , ("NA", 1.66) + , ("NB", 1.64) + , ("ND", 2.01) + , ("NE", 1.50) + , ("NI", 1.24) + , ("NO", 1.50) + , ("NP", 1.90) + , ( "O", 0.68) + , ("OS", 1.44) + , ( "P", 1.05) + , ("PA", 2.00) + , ("PB", 1.46) + , ("PD", 1.39) + , ("PM", 1.99) + , ("PO", 1.40) + , ("PR", 2.03) + , ("PT", 1.36) + , ("PU", 1.87) + , ("RA", 2.21) + , ("RB", 2.20) + , ("RE", 1.51) + , ("RF", 1.50) + , ("RH", 1.42) + , ("RN", 1.50) + , ("RU", 1.46) + , ( "S", 1.02) + , ("SB", 1.39) + , ("SC", 1.70) + , ("SE", 1.22) + , ("SG", 1.50) + , ("SI", 1.20) + , ("SM", 1.98) + , ("SN", 1.39) + , ("SR", 1.95) + , ("TA", 1.70) + , ("TB", 1.94) + , ("TC", 1.47) + , ("TE", 1.47) + , ("TH", 2.06) + , ("TI", 1.60) + , ("TL", 1.45) + , ("TM", 1.90) + , ( "U", 1.96) + , ( "V", 1.53) + , ( "W", 1.62) + , ("XE", 1.50) + , ( "Y", 1.90) + , ("YB", 1.87) + , ("ZN", 1.22) + , ("ZR", 1.75) + ] + +{-# INLINE maxCovalentRadius #-} +-- | Upper bound of @covalentRadius@. +maxCovalentRadius :: Double +maxCovalentRadius = covalentRadius "FR" + +-- | Atomic mass of a given element in g/mol +atomicMass :: Element -> Double +atomicMass = defaultingLookup "Unknown atomic mass for element:" + 0.0 dict + where + dict = M.fromList [ + ( "C", 12.011) + ,( "N", 14.007) + ,( "O", 15.999) + ,( "P", 30.974) + ,( "S", 32.066) + ,( "H", 1.008) + ,("AC", 227.000) + ,("AG", 107.868) + ,("AL", 26.982) + ,("AM", 243.000) + ,("AR", 39.948) + ,("AS", 74.922) + ,("AT", 210.000) + ,("AU", 196.967) + ,( "B", 10.811) + ,("BA", 137.327) + ,("BE", 9.012) + ,("BH", 264.000) + ,("BI", 208.980) + ,("BK", 247.000) + ,("BR", 79.904) + ,("CA", 40.078) + ,("CD", 112.411) + ,("CE", 140.116) + ,("CF", 251.000) + ,("CL", 35.453) + ,("CM", 247.000) + ,("CO", 58.933) + ,("CR", 51.996) + ,("CS", 132.905) + ,("CU", 63.546) + ,("DB", 262.000) + ,("DS", 271.000) + ,("DY", 162.500) + ,("ER", 167.260) + ,("ES", 252.000) + ,("EU", 151.964) + ,( "F", 18.998) + ,("FE", 55.845) + ,("FM", 257.000) + ,("FR", 223.000) + ,("GA", 69.723) + ,("GD", 157.250) + ,("GE", 72.610) + ,("HE", 4.003) + ,("HF", 178.490) + ,("HG", 200.590) + ,("HO", 164.930) + ,("HS", 269.000) + ,( "I", 126.904) + ,("IN", 114.818) + ,("IR", 192.217) + ,( "K", 39.098) + ,("KR", 83.800) + ,("LA", 138.906) + ,("LI", 6.941) + ,("LR", 262.000) + ,("LU", 174.967) + ,("MD", 258.000) + ,("MG", 24.305) + ,("MN", 54.938) + ,("MO", 95.940) + ,("MT", 268.000) + ,("NA", 22.991) + ,("NB", 92.906) + ,("ND", 144.240) + ,("NE", 20.180) + ,("NI", 58.693) + ,("NO", 259.000) + ,("NP", 237.000) + ,("OS", 190.230) + ,("PA", 231.036) + ,("PB", 207.200) + ,("PD", 106.420) + ,("PM", 145.000) + ,("PO", 210.000) + ,("PR", 140.908) + ,("PT", 195.078) + ,("PU", 244.000) + ,("RA", 226.000) + ,("RB", 85.468) + ,("RE", 186.207) + ,("RF", 261.000) + ,("RH", 102.906) + ,("RN", 222.000) + ,("RU", 101.070) + ,("SB", 121.760) + ,("SC", 44.956) + ,("SE", 78.960) + ,("SG", 266.000) + ,("SI", 28.086) + ,("SM", 150.360) + ,("SN", 118.710) + ,("SR", 87.620) + ,("TA", 180.948) + ,("TB", 158.925) + ,("TC", 98.000) + ,("TE", 127.600) + ,("TH", 232.038) + ,("TI", 47.867) + ,("TL", 204.383) + ,("TM", 168.934) + ,( "U", 238.029) + ,( "V", 50.942) + ,( "W", 183.840) + ,("XE", 131.290) + ,( "Y", 88.906) + ,("YB", 173.040) + ,("ZN", 65.390) + ,("ZR", 91.224) + ] + +-- | Van der Waals radius of the given element +vanDerWaalsRadius :: Element -> Double +vanDerWaalsRadius = defaultingLookup "Do not know van der Waals radius of " + 0.0 dict + where + dict = M.fromList [ + ( "C", 1.70) + ,( "N", 1.55) + ,( "O", 1.52) + ,( "P", 1.80) + ,( "S", 1.80) + ,("AC", 2.00) + ,("AG", 1.72) + ,("AL", 2.00) + ,("AM", 2.00) + ,("AR", 1.88) + ,("AS", 1.85) + ,("AT", 2.00) + ,("AU", 1.66) + , ("B", 2.00) + ,("BA", 2.00) + ,("BE", 2.00) + ,("BH", 2.00) + ,("BI", 2.00) + ,("BK", 2.00) + ,("BR", 1.85) + ,("CA", 2.00) + ,("CD", 1.58) + ,("CE", 2.00) + ,("CF", 2.00) + ,("CL", 1.75) + ,("CM", 2.00) + ,("CO", 2.00) + ,("CR", 2.00) + ,("CS", 2.00) + ,("CU", 1.40) + ,("DB", 2.00) + ,("DS", 2.00) + ,("DY", 2.00) + ,("ER", 2.00) + ,("ES", 2.00) + ,("EU", 2.00) + ,( "F", 1.47) + ,("FE", 2.00) + ,("FM", 2.00) + ,("FR", 2.00) + ,("GA", 1.87) + ,("GD", 2.00) + ,("GE", 2.00) + ,( "H", 1.09) + ,("HE", 1.40) + ,("HF", 2.00) + ,("HG", 1.55) + ,("HO", 2.00) + ,("HS", 2.00) + ,( "I", 1.98) + ,("IN", 1.93) + ,("IR", 2.00) + ,( "K", 2.75) + ,("KR", 2.02) + ,("LA", 2.00) + ,("LI", 1.82) + ,("LR", 2.00) + ,("LU", 2.00) + ,("MD", 2.00) + ,("MG", 1.73) + ,("MN", 2.00) + ,("MO", 2.00) + ,("MT", 2.00) + ,("NA", 2.27) + ,("NB", 2.00) + ,("ND", 2.00) + ,("NE", 1.54) + ,("NI", 1.63) + ,("NO", 2.00) + ,("NP", 2.00) + ,("OS", 2.00) + ,("PA", 2.00) + ,("PB", 2.02) + ,("PD", 1.63) + ,("PM", 2.00) + ,("PO", 2.00) + ,("PR", 2.00) + ,("PT", 1.72) + ,("PU", 2.00) + ,("RA", 2.00) + ,("RB", 2.00) + ,("RE", 2.00) + ,("RF", 2.00) + ,("RH", 2.00) + ,("RN", 2.00) + ,("RU", 2.00) + ,("SB", 2.00) + ,("SC", 2.00) + ,("SE", 1.90) + ,("SG", 2.00) + ,("SI", 2.10) + ,("SM", 2.00) + ,("SN", 2.17) + ,("SR", 2.00) + ,("TA", 2.00) + ,("TB", 2.00) + ,("TC", 2.00) + ,("TE", 2.06) + ,("TH", 2.00) + ,("TI", 2.00) + ,("TL", 1.96) + ,("TM", 2.00) + ,( "U", 1.86) + ,( "V", 2.00) + ,( "W", 2.00) + ,("XE", 2.16) + ,( "Y", 2.00) + ,("YB", 2.00) + ,("ZN", 1.39) + ,("ZR", 2.00) + ] + +{-# INLINE maxVanDerWaalsRadius #-} +-- | Upper bound of @vanDerWaalsRadius@. +maxVanDerWaalsRadius :: Double +maxVanDerWaalsRadius = vanDerWaalsRadius "K" + +-- | Given a PDB 'Atom' extract or guess its 'Element' name. +assignElement :: Atom -> Element +assignElement at = case element at of + "" -> guessElement . atName $ at + code -> code + +-- | Guessing an 'Element' name from PDB 'Atom' name. +-- Returns empty string, if 'Element' can't be guessed. +guessElement :: BS.ByteString -> BS.ByteString +guessElement = \e -> fromMaybe "" $ M.lookup (BS.unpack e) els + where + els = M.fromList + [ ("C" , "C"), + ("C1'" , "C"), + ("C2" , "C"), + ("C2'" , "C"), + ("C3'" , "C"), + ("C4" , "C"), + ("C4'" , "C"), + ("C5" , "C"), + ("C5'" , "C"), + ("C6" , "C"), + ("C8" , "C"), + ("CA" , "C"), + ("CB" , "C"), + ("CD" , "C"), + ("CD1" , "C"), + ("CD2" , "C"), + ("CE" , "C"), + ("CE1" , "C"), + ("CE2" , "C"), + ("CE3" , "C"), + ("CG" , "C"), + ("CG1" , "C"), + ("CG2" , "C"), + ("CH2" , "C"), + ("CZ" , "C"), + ("CZ2" , "C"), + ("CZ3" , "C"), + ("N" , "N"), + ("N1" , "N"), + ("N2" , "N"), + ("N3" , "N"), + ("N4" , "N"), + ("N6" , "N"), + ("N7" , "N"), + ("N9" , "N"), + ("ND1" , "N"), + ("ND2" , "N"), + ("NE" , "N"), + ("NE1" , "N"), + ("NE2" , "N"), + ("NH1" , "N"), + ("NH2" , "N"), + ("NZ" , "N"), + ("O" , "O"), + ("O2" , "O"), + ("O2'" , "O"), + ("O3'" , "O"), + ("O4" , "O"), + ("O4'" , "O"), + ("O5'" , "O"), + ("O6" , "O"), + ("OD1" , "O"), + ("OD2" , "O"), + ("OE1" , "O"), + ("OE2" , "O"), + ("OG" , "O"), + ("OG1" , "O"), + ("OH" , "O"), + ("OP1" , "O"), + ("OP2" , "O"), + ("OXT" , "O"), + ("P" , "P"), + ("SD" , "S"), + ("SG" , "S")] + diff --git a/changelog b/changelog --- a/changelog +++ b/changelog @@ -1,4 +1,9 @@ -*-Changelog-*- +1.2.0.7 Jun 2016 + * Use hashmap for element properties. + Great thanks to Ben Gamari: + https://ghc.haskell.org/trac/ghc/ticket/917 + 1.2.0.6 Jun 2016 * Updated bounds again. diff --git a/hPDB.cabal b/hPDB.cabal --- a/hPDB.cabal +++ b/hPDB.cabal @@ -1,5 +1,5 @@ name: hPDB -version: 1.2.0.6 +version: 1.2.0.7 synopsis: Protein Databank file format library homepage: https://github.com/BioHaskell/hPDB stability: stable @@ -57,7 +57,24 @@ Library ghc-options: -fspec-constr-count=4 -O3 - build-depends: base>=4.0, base <4.10, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, iterable >= 3.0, tagged >= 0.7, parallel >= 3.0.0.0, bytestring, zlib, Octree>= 0.5 + build-depends: base>=4.0 && <4.10, + ghc-prim, + directory, + mtl, + template-haskell, + vector, + AC-Vector, + containers, + unordered-containers >= 0.2.5.0, + deepseq, + QuickCheck >= 2.5.0.0, + text>=0.11.1.13, + iterable >= 3.0, + tagged >= 0.7, + parallel >= 3.0.0.0, + bytestring, + zlib, + Octree>= 0.5 if flag(have-sse2) ghc-options: -msse2 if flag(have-mmap)