Source file ptable.ml

module A = BatArray
module Ht = BatHashtbl
module L = BatList
module Log = Dolog.Log

(* Statistics for ChEMBL-34:
#atom_count symbol prime
61440436 H    2
53818425 C    3
 8561288 O    5
 8478199 N    7
 1040693 F   11
  932402 S   13
  584961 Cl  17
  122574 Br  19
   55866 P   23
   20896 I   29
   15555 Na  31
    5937 B   37
    3924 Si  41
    3432 Se  43
    1557 K   47
     555 Li  53
     281 As  59
     220 Te  61
     165 Zn  67
     155 Ca  71
     130 Mg  73
     120 Al  79
      42 Ag  83
      18 Sr  89
      12 Rb  97
      12 Ba 101
       8 Cs 103
       6 At 107
       5 Bi 109
       4 Xe 113
       4 Ra 127
       2 Kr 131
       2 Be 137
       1 He 139
       1 Ga 149
*)
let symbol2prime =
  Ht.of_list [("H",2);
              ("C",3);
              ("O",5);
              ("N",7);
              ("F",11);
              ("S",13);
              ("Cl",17);
              ("Br",19);
              ("P",23);
              ("I",29);
              ("Na",31);
              ("B",37);
              ("Si",41);
              ("Se",43);
              ("K",47);
              ("Li",53);
              ("As",59);
              ("Te",61);
              ("Zn",67);
              ("Ca",71);
              ("Mg",73);
              ("Al",79);
              ("Ag",83);
              ("Sr",89);
              ("Rb",97);
              ("Ba",101);
              ("Cs",103);
              ("At",107);
              ("Bi",109);
              ("Xe",113);
              ("Ra",127);
              ("Kr",131);
              ("Be",137);
              ("He",139);
              ("Ga",149)]

let prime2symbol =
  Ht.of_list [(2  ,"H" );
              (3  ,"C" );
              (5  ,"O" );
              (7  ,"N" );
              (11 ,"F" );
              (13 ,"S" );
              (17 ,"Cl");
              (19 ,"Br");
              (23 ,"P" );
              (29 ,"I" );
              (31 ,"Na");
              (37 ,"B" );
              (41 ,"Si");
              (43 ,"Se");
              (47 ,"K" );
              (53 ,"Li");
              (59 ,"As");
              (61 ,"Te");
              (67 ,"Zn");
              (71 ,"Ca");
              (73 ,"Mg");
              (79 ,"Al");
              (83 ,"Ag");
              (89 ,"Sr");
              (97 ,"Rb");
              (101,"Ba");
              (103,"Cs");
              (107,"At");
              (109,"Bi");
              (113,"Xe");
              (127,"Ra");
              (131,"Kr");
              (137,"Be");
              (139,"He");
              (149,"Ga")]
  
(* Enough primes to cover the whole periodic table
   $> primes 2 | head -118 | tr '\n' ';'
*)
let all_primes =
  [|2;3;5;7;11;13;17;19;23;29;31;37;41;43;47;53;59;61;67;71;73;79;83;89;97;101;
    103;107;109;113;127;131;137;139;149;151;157;163;167;173;179;181;191;193;
    197;199;211;223;227;229;233;239;241;251;257;263;269;271;277;281;283;293;
    307;311;313;317;331;337;347;349;353;359;367;373;379;383;389;397;401;409;
    419;421;431;433;439;443;449;457;461;463;467;479;487;491;499;503;509;521;
    523;541;547;557;563;569;571;577;587;593;599;601;607;613;617;619;631;641;
    643;647|]

let prime_for_symbol (s: string): int =
  try Ht.find symbol2prime s
  with Not_found ->
    (Log.fatal "Ptable.prime_for_symbol: no prime assigned to %s" s;
     exit 1)

let symbol_for_prime (p: int): string =
  try Ht.find prime2symbol p
  with Not_found ->
    (Log.fatal "Ptable.symbol_for_prime: no symbol assigned to %d" p;
     exit 1)

let max_atomic_number = 118

(* the first atomic number (0) is FAKE but necessary for tabulation *)
let anums = A.of_list (L.range 0 `To max_atomic_number)

let elements_regexp = Str.regexp "He\\|Li\\|Be\\|Ne\\|Na\\|Mg\\|Al\\|Si\\|Cl\\|Ar\\|Ca\\|Sc\\|Ti\\|Cr\\|Mn\\|Fe\\|Co\\|Ni\\|Cu\\|Zn\\|Ga\\|Ge\\|As\\|Se\\|Br\\|Kr\\|Rb\\|Sr\\|Zr\\|Nb\\|Mo\\|Tc\\|Ru\\|Rh\\|Pd\\|Ag\\|Cd\\|In\\|Sn\\|Sb\\|Te\\|Xe\\|Cs\\|Ba\\|La\\|Ce\\|Pr\\|Nd\\|Pm\\|Sm\\|Eu\\|Gd\\|Tb\\|Dy\\|Ho\\|Er\\|Tm\\|Yb\\|Lu\\|Hf\\|Ta\\|Re\\|Os\\|Ir\\|Pt\\|Au\\|Hg\\|Tl\\|Pb\\|Bi\\|Po\\|At\\|Rn\\|Fr\\|Ra\\|Ac\\|Th\\|Pa\\|Np\\|Pu\\|Am\\|Cm\\|Bk\\|Cf\\|Es\\|Fm\\|Md\\|No\\|Lr\\|Rf\\|Db\\|Sg\\|Bh\\|Hs\\|Mt\\|Ds\\|Rg\\|Cn\\|Nh\\|Fl\\|Mc\\|Lv\\|Ts\\|Og\\|H\\|B\\|C\\|N\\|O\\|F\\|P\\|S\\|K\\|V\\|Y\\|I\\|W\\|U"

(* chemical symbols; 1st elt. is also for tabulation reasons only *)
let symbols =
  [|"";"H";"He";"Li";"Be";"B";"C";"N";"O";"F";"Ne";"Na";"Mg";"Al";"Si";"P";
    "S";"Cl";"Ar";"K";"Ca";"Sc";"Ti";"V";"Cr";"Mn";"Fe";"Co";"Ni";"Cu";"Zn";
    "Ga";"Ge";"As";"Se";"Br";"Kr";"Rb";"Sr";"Y";"Zr";"Nb";"Mo";"Tc";"Ru";"Rh";
    "Pd";"Ag";"Cd";"In";"Sn";"Sb";"Te";"I";"Xe";"Cs";"Ba";"La";"Ce";"Pr";"Nd";
    "Pm";"Sm";"Eu";"Gd";"Tb";"Dy";"Ho";"Er";"Tm";"Yb";"Lu";"Hf";"Ta";"W";"Re";
    "Os";"Ir";"Pt";"Au";"Hg";"Tl";"Pb";"Bi";"Po";"At";"Rn";"Fr";"Ra";"Ac";"Th";
    "Pa";"U";"Np";"Pu";"Am";"Cm";"Bk";"Cf";"Es";"Fm";"Md";"No";"Lr";"Rf";"Db";
    "Sg";"Bh";"Hs";"Mt";"Ds";"Rg";"Cn";"Nh";"Fl";"Mc";"Lv";"Ts";"Og"|]

let symbol_of_anum a =
  if a = 0 || a > max_atomic_number then
    (Log.fatal "Ptable.symbol_of_anum: no such anum: %d" a;
     exit 1)
  else
    symbols.(a)

let symbol2anum =
  Ht.of_list [("H",1);
              ("He",2);
              ("Li",3);
              ("Be",4);
              ("B",5);
              ("C",6);
              ("N",7);
              ("O",8);
              ("F",9);
              ("Ne",10);
              ("Na",11);
              ("Mg",12);
              ("Al",13);
              ("Si",14);
              ("P",15);
              ("S",16);
              ("Cl",17);
              ("Ar",18);
              ("K",19);
              ("Ca",20);
              ("Sc",21);
              ("Ti",22);
              ("V",23);
              ("Cr",24);
              ("Mn",25);
              ("Fe",26);
              ("Co",27);
              ("Ni",28);
              ("Cu",29);
              ("Zn",30);
              ("Ga",31);
              ("Ge",32);
              ("As",33);
              ("Se",34);
              ("Br",35);
              ("Kr",36);
              ("Rb",37);
              ("Sr",38);
              ("Y",39);
              ("Zr",40);
              ("Nb",41);
              ("Mo",42);
              ("Tc",43);
              ("Ru",44);
              ("Rh",45);
              ("Pd",46);
              ("Ag",47);
              ("Cd",48);
              ("In",49);
              ("Sn",50);
              ("Sb",51);
              ("Te",52);
              ("I",53);
              ("Xe",54);
              ("Cs",55);
              ("Ba",56);
              ("La",57);
              ("Ce",58);
              ("Pr",59);
              ("Nd",60);
              ("Pm",61);
              ("Sm",62);
              ("Eu",63);
              ("Gd",64);
              ("Tb",65);
              ("Dy",66);
              ("Ho",67);
              ("Er",68);
              ("Tm",69);
              ("Yb",70);
              ("Lu",71);
              ("Hf",72);
              ("Ta",73);
              ("W",74);
              ("Re",75);
              ("Os",76);
              ("Ir",77);
              ("Pt",78);
              ("Au",79);
              ("Hg",80);
              ("Tl",81);
              ("Pb",82);
              ("Bi",83);
              ("Po",84);
              ("At",85);
              ("Rn",86);
              ("Fr",87);
              ("Ra",88);
              ("Ac",89);
              ("Th",90);
              ("Pa",91);
              ("U",92);
              ("Np",93);
              ("Pu",94);
              ("Am",95);
              ("Cm",96);
              ("Bk",97);
              ("Cf",98);
              ("Es",99);
              ("Fm",100);
              ("Md",101);
              ("No",102);
              ("Lr",103);
              ("Rf",104);
              ("Db",105);
              ("Sg",106);
              ("Bh",107);
              ("Hs",108);
              ("Mt",109);
              ("Ds",110);
              ("Rg",111);
              ("Cn",112);
              ("Nh",113);
              ("Fl",114);
              ("Mc",115);
              ("Lv",116);
              ("Ts",117);
              ("Og",118)]

let anum_of_symbol s =
  try Ht.find symbol2anum s
  with Not_found ->
    (Log.fatal "Ptable.anum_of_symbol: no such chemical element: %s" s;
     exit 1)

let prime_for_anum a =
  prime_for_symbol (symbol_of_anum a)