Module: Chem

Defined in:
lib/chem.rb,
lib/chem/db.rb,
lib/chem/db/gd.rb,
lib/chem/model.rb,
lib/chem/utils.rb,
lib/chem/db/cdx.rb,
lib/chem/db/cml.rb,
lib/chem/db/eps.rb,
lib/chem/db/g98.rb,
lib/chem/db/kcf.rb,
lib/chem/db/mdl.rb,
lib/chem/db/msi.rb,
lib/chem/db/pdb.rb,
lib/chem/db/pdf.rb,
lib/chem/db/sdf.rb,
lib/chem/db/swf.rb,
lib/chem/db/xyz.rb,
lib/chem/db/kegg.rb,
lib/chem/db/smbl.rb,
lib/chem/db/gspan.rb,
lib/chem/db/mopac.rb,
lib/chem/db/opsin.rb,
lib/chem/db/sybyl.rb,
lib/chem/db/cansmi.rb,
lib/chem/db/tinker.rb,
lib/chem/db/vector.rb,
lib/chem/utils/cdk.rb,
lib/chem/utils/net.rb,
lib/chem/utils/sub.rb,
lib/chem/db/pdb_dic.rb,
lib/chem/db/pubchem.rb,
lib/chem/db/rmagick.rb,
lib/chem/utils/prop.rb,
lib/chem/utils/sssr.rb,
lib/chem/db/kcf_rpair.rb,
lib/chem/db/kcf_glycan.rb,
lib/chem/utils/ullmann.rb,
lib/chem/model/skeleton.rb,
lib/chem/utils/geometry.rb,
lib/chem/utils/traverse.rb,
lib/chem/utils/openbabel.rb,
lib/chem/utils/transform.rb,
lib/chem/db/types/type_gd.rb,
lib/chem/db/types/type_cdx.rb,
lib/chem/db/types/type_kcf.rb,
lib/chem/db/types/type_mdl.rb,
lib/chem/db/types/type_pdf.rb,
lib/chem/db/types/type_png.rb,
lib/chem/db/types/type_rdf.rb,
lib/chem/db/types/type_rxn.rb,
lib/chem/db/types/type_sdf.rb,
lib/chem/db/types/type_xyz.rb,
lib/chem/utils/fingerprint.rb,
lib/chem/data/atomic_weight.rb,
lib/chem/db/types/type_kegg.rb,
lib/chem/appl/tinker/nucleic.rb,
lib/chem/data/periodic_table.rb,
lib/chem/db/smiles/smiparser.rb,
lib/chem/db/types/type_gspan.rb,
lib/chem/db/types/type_sybyl.rb,
lib/chem/db/types/type_cansmi.rb,
lib/chem/db/types/type_kcf_glycan.rb,
ext/subcomp.c

Overview

Table of atomic weight extracted from www.chem.qmul.ac.uk/iupac/AtWt/index.html

Defined Under Namespace

Modules: Atom, Bond, CDK, CDX, Db, G98, KCF, KCFRPairType, KEGG, MDL, MSI, Molecule, Mopac7, NetUtils, OpenBabel, PDB, Reaction, SMBL, Sybyl, TINKER, Transform, Type, Writer, XYZ Classes: BitMatrix, CMLAtom, CMLBond, CMLMolecule, CompoundDB, GDWriter, GSpan, GSpanAtom, GSpanBond, GSpanMolecule, KEGGException, NCBI, OpsinMolecule, PDFWriter, PdbDic, RMagickWriter, ReactionSkeleton, Ring, SWFWriter, SkeletonAtom, SmilesAtom, SmilesBond, SmilesMol, TinkerNucleic

Constant Summary collapse

DefaultDataDir = 
File.join(ENV["HOME"], "data")
ChemTypeRegistry = 
[]
HierarchicElementCounts =

Section 1.

{
  :H => [
    [4, 0],
    [8, 1],
    [16, 2],
    [32, 3]],
  :Li => [
    [ 1, 4],
    [ 2, 5]],
  :B => [
    [ 1, 6],
    [ 2, 7],
    [ 4, 8]],
  :C => [
    [ 2, 9],
    [ 4, 10],
    [ 8, 11],
    [ 16, 12],
    [ 32, 13]],
  :N => [
    [ 1, 14],
    [ 2, 15],
    [ 4, 16],
    [ 8, 17]],
  :O => [
    [ 1, 18],
    [ 2, 19],
    [ 4, 20],
    [ 8, 21],
    [ 16, 22]],
  :F => [
    [ 1, 23],
    [ 2, 24],
    [ 4, 25]],
  :Na => [
    [ 1, 26],
    [ 2, 27]],
  :Si => [
    [ 1, 28],
    [ 2, 29]],
  :P => [
    [ 1, 30],
    [ 2, 31],
    [ 4, 32]],
  :S => [
    [ 1, 33],
    [ 2, 34],
    [ 4, 35],
    [ 8, 36]],
  :Cl => [
    [ 1, 37],
    [ 2, 38],
    [ 4, 39],
    [ 8, 40]],
  :K => [
    [ 1, 41],
    [ 2, 42]],
  :Br => [
    [ 1, 43],
    [ 2, 44],
    [ 4, 45]],
  :I => [
    [ 1, 46],
    [ 2, 47],
    [ 4, 48]],
  :Be => [[ 1, 49 ]],
  :Mg => [[ 1, 50]],
  :Al => [[ 1, 51]],
  :Ca => [[ 1, 52]],
  :Sc => [[ 1, 53]],
  :Ti => [[ 1, 54]],
  :V => [[ 1, 55]],
  :Cr => [[ 1, 56]],
  :Mn => [[ 1, 57]],
  :Fe => [[ 1, 58]],
  :Co => [[ 1, 59]],
  :Ni => [[ 1, 60]],
  :Cu => [[ 1, 61]],
  :Zn => [[ 1, 62]],
  :Ga => [[ 1, 63]],
  :Ge => [[ 1, 64]],
  :As => [[ 1, 65]],
  :Se => [[ 1, 66]],
  :Kr => [[ 1, 67]],
  :Rb => [[ 1, 68]],
  :Sr => [[ 1, 69]],
  :Y => [[ 1, 70]],
  :Zr => [[ 1, 71]],
  :Nb => [[ 1, 72]],
  :Mo => [[ 1, 73]],
  :Ru => [[ 1, 74]],
  :Rh => [[ 1, 75]],
  :Pd => [[ 1, 76]],
  :Ag => [[ 1, 77]],
  :Cd => [[ 1, 78]],
  :In => [[ 1, 79]],
  :Sn => [[ 1, 80]],
  :Sb => [[ 1, 81]],
  :Te => [[ 1, 82]],
  :Xe => [[ 1, 83]],
  :Cs => [[ 1, 84]],
  :Ba => [[ 1, 85]],
  :Lu => [[ 1, 86]],
  :Hf => [[ 1, 87]],
  :Ta => [[ 1, 88]],
  :W => [[ 1, 89]],
  :Re => [[ 1, 90]],
  :Os => [[ 1, 91]],
  :Ir => [[ 1, 92]],
  :Pt => [[ 1, 93]],
  :Au => [[ 1, 94]],
  :Hg => [[ 1, 95]],
  :Tl => [[ 1, 96]],
  :Pb => [[ 1, 97]],
  :Bi => [[ 1, 98]],
  :La => [[ 1, 99]],
  :Ce => [[ 1, 100]],
  :Pr => [[ 1, 101]],
  :Nd => [[ 1, 102]],
  :Pm => [[ 1, 103]],
  :Sm => [[ 1, 104]],
  :Eu => [[ 1, 105]],
  :Gd => [[ 1, 106]],
  :Tb => [[ 1, 107]],
  :Dy => [[ 1, 108]],
  :Ho => [[ 1, 109]],
  :Er => [[ 1, 110]],
  :Tm => [[ 1, 111]],
  :Yb => [[ 1, 112]],
  :Tc => [[ 1, 113]],
  :U => [[ 1, 114]],
}
Section3 =

Section 3

{
  'H-Li'  => 263,
  'Li-Li' => 264,
  'B-Li'  => 265,
  'C-Li'  => 266,
  'Li-O'  => 267,
  'F-Li'  => 268,
  'Li-P'  => 269,
  'Li-S'  => 270,
  'Cl-Li' => 271,
  'B-H'   => 272,
  'B-B'   => 273,
  'B-C'   => 274,
  'B-N'   => 275,
  'B-O'   => 276,
  'B-F'   => 277,
  'B-Si'  => 278,
  'B-P'   => 279,
  'B-S'   => 280,
  'B-Cl'  => 281,
  'B-Br'  => 282,
  'C-H'   => 283,
  'C-C'   => 284,
  'C-N'   => 285,
  'C-O'   => 286,
  'C-F'   => 287,
  'C-Na'  => 288,
  'C-Mg'  => 289,
  'Al-C'  => 290,
  'C-Si'  => 291,
  'C-P'   => 292,
  'C-S'   => 293,
  'C-Cl'  => 294,
  'As-C'  => 295,
  'C-Se'  => 296,
  'Br-C'  => 297,
  'C-I'   => 298,
  'H-N'   => 299,
  'N-N'   => 300,
  'N-O'   => 301,
  'F-N'   => 302,
  'N-Si'  => 303,
  'N-P'   => 304,
  'N-S'   => 305,
  'Cl-N'  => 306,
  'Br-N'  => 307,
  'H-O'   => 308,
  'O-O'   => 309,
  'Mg-O'  => 310,
  'Na-O'  => 311,
  'Al-O'  => 312,
  'O-Si'  => 313,
  'O-P'   => 314,
  'K-O'   => 315,
  'F-P'   => 316,
  'F-S'   => 317,
  'Al-H'  => 318,
  'Al-Cl' => 319,
  'H-Si'  => 320,
  'Si-Si' => 321,
  'Cl-Si' => 322,
  'H-P'   => 323,
  'P-P'   => 324,
  'As-H'  => 325,
  'As-As' => 326,
}
Section4 =

Section 4 Simple atom nearest neighbors

{
  :C => [
    ["-Br", "-C", 327],
    ["-Br", "-C", "-C", 328],
    ["-Br", "-H", 329],
    ["-Br", "~C", 330],
    ["-Br", "~N", 331],
    ["-C", "-C", 332],
    ["-C", "-C", "-C", 333],
    ["-C", "-C", "-C", "-C", 334],
    ["-C", "-C", "-C", "-H", 335],
    ["-C", "-C", "-C", "-N", 336],
    ["-C", "-C", "-C", "-O", 337],
    ["-C", "-C", "-H", "-N", 338],
    ["-C", "-C", "-H", "-O", 339],
    ["-C", "-C", "-N", 340],
    ["-C", "-C", "-O", 341],
    ["-C", "-Cl", 342],
    ["-C", "-Cl", "-H", 343],
    ["-C", "-H", 344],
    ["-C", "-H", "-N", 345],
    ["-C", "-H", "-O", 346],
    ["-C", "-H", "-O", "-O", 347],
    ["-C", "-H", "-P", 348],
    ["-C", "-H", "-S", 349],
    ["-C", "-I", 350],
    ["-C", "-N", 351],
    ["-C", "-O", 352],
    ["-C", "-S", 353],
    ["-C", "-Si", 354],
    ["-C", "~C", 355],
    ["-C", "~C", "~C", 356],
    ["-C", "~C", "~N", 357],
    ["-C", "~N", 358],
    ["-C", "~N", "~N", 359],
    ["-Cl", "-Cl", 360],
    ["-Cl", "-H", 361],
    ["-Cl", "~C", 362],
    ["-F", "-F", 363],
    ["-F", "~C", 364],
    ["-H", "-N", 365],
    ["-H", "-O", 366],
    ["-H", "-O", "-O", 367],
    ["-H", "-S", 368],
    ["-H", "-Si", 369],
    ["-H", "~C", 370],
    ["-H", "~C", "~C", 371],
    ["-H", "~C", "~N", 372],
    ["-H", "~N", 373],
    ["-H", "-H", "-H", 374],
    ["-N", "-N", 375],
    ["-N", "~C", 376],
    ["-N", "~C", "~C", 377],
    ["-N", "~C", "~N", 378],
    ["-N", "~N", 379],
    ["-O", "-O", 380],
    ["-O", "~C", 381],
    ["-O", "~C", "~C", 382],
    ["-S", "~C", 383],
    ["~C", "~C", 384],
    ["~C", "~C", "~C", 385],
    ["~C", "~C", "~N", 386],
    ["~C", "~N", 387],
    ["~C", "~N", "~N", 388],
    ["~N", "~N", 389]],
  :N => [
    ["-C", "-C", 390],
    ["-C", "-C", "-C", 391],
    ["-C", "-C", "-H", 392],
    ["-C", "-H", 393],
    ["-C", "-H", "-N", 394],
    ["-C", "-O", 395],
    ["-C", "~C", 396],
    ["-C", "~C", "~C", 397],
    ["-H", "-N", 398],
    ["-H", "~C", 399],
    ["-H", "~C", "~C", 400],
    ["-O", "-O", 401],
    ["-O", "~O", 402],
    ["~C", "~C", 403],
    ["~C", "~C", "~C", 404]],
  :O => [
    ["-C", "-C", 405],
    ["-C", "-H", 406],
    ["-C", "-P", 407],
    ["-H", "-S", 408],
    ["~C", "~C", 409]],
  :P => [
    ["-C", "-C", 410],
    ["-O", "-O", 411]],
  :S => [
    ["-C", "-C", 412],
    ["-C", "-H", 413],
    ["-C", "-O", 414]],
  :Si => [
    ["-C", "-C", 415]
  ]
}
Section6 =

Section 6 Simple SMARTS patterns

{
  "C-C-C#C" => 460,
  "O-C-C=N" => 461,
  "O-C-C=O" => 462,
  "N:C-S-[#1]" => 463,
  "N-C-C=C" => 464,
  "O=S-C-C" => 465,
  "N#C-C=C" => 466,
  "C=N-N-C" => 467,
  "O=S-C-N" => 468,
  "S-S-C:C" => 469,
  "C:C-C=C" => 470,
  "S:C:C:C" => 471,
  "C:N:C-C" => 472,
  "S-C:N:C" => 473,
  "S:C:C:N" => 474,
  "S-C=N-C" => 475,
  "C-O-C=C" => 476,
  "N-N-C:C" => 477,
  "S-C=N-[#1]" => 478,
  "S-C-S-C" => 479,
  "C:S:C-C" => 480,
  "O-S-C:C" => 481,
  "C:N-C:C" => 482,
  "N-S-C:C" => 483,
  "N-C:N:C" => 484,
  "N:C:C:N" => 485,
  "N-C:N:N" => 486,
  "N-C=N-C" => 487,
  "N-C=N-[#1]" => 488,
  "N-C-S-C" => 489,
  "C-C-C=C" => 490,
  "C-N:C-[#1]" => 491,
  "N-C:O:C" => 492,
  "O=C-C:C" => 493,
  "O=C-C:N" => 494,
  "C-N-C:C" => 495,
  "N:N-C-[#1]" => 496,
  "O-C:C:N" => 497,
  "O-C=C-C" => 498,
  "N-C:C:N" => 499,
  "C-S-C:C" => 500,
  "Cl-C:C-C" => 501,
  "N-C=C-[#1]" => 502,
  "Cl-C:C-[#1]" => 503,
  "N:C:N-C" => 504,
  "Cl-C:C-O" => 505,
  "C-C:N:C" => 506,
  "C-C-S-C" => 507,
  "S=C-N-C" => 508,
  "Br-C:C-C" => 509,
  "[#1]-N-N-[#1]" => 510,
  "S=C-N-[#1]" => 511,
  "C-[As]-O-[#1]" => 512,
  "S:C:C-[#1]" => 513,
  "O-N-C-C" => 514,
  "N-N-C-C" => 515,
  "[#1]-C=C-[#1]" => 516,
  "N-N-C-N" => 517,
  "O=C-N-N" => 518,
  "N=C-N-C" => 519,
  "C=C-C:C" => 520,
  "C:N-C-[#1]" => 521,
  "C-N-N-[#1]" => 522,
  "N:C:C-C" => 523,
  "C-C=C-C" => 524,
  "[As]-C:C-[#1]" => 525,
  "Cl-C:C-Cl" => 526,
  "C:C:N-[#1]" => 527,
  "[#1]-N-C-[#1]" => 528,
  "Cl-C-C-Cl" => 529,
  "N:C-C:C" => 530,
  "S-C:C-C" => 531,
  "S-C:C-[#1]" => 532,
  "S-C:C-N" => 533,
  "S-C:C-O" => 534,
  "O=C-C-C" => 535,
  "O=C-C-N" => 536,
  "O=C-C-O" => 537,
  "N=C-C-C" => 538,
  "N=C-C-[#1]" => 539,
  "C-N-C-[#1]" => 540,
  "O-C:C-C" => 541,
  "O-C:C-[#1]" => 542,
  "O-C:C-N" => 543,
  "O-C:C-O" => 544,
  "N-C:C-C" => 545,
  "N-C:C-[#1]" => 546,
  "N-C:C-N" => 547,
  "O-C-C:C" => 548,
  "N-C-C:C" => 549,
  "Cl-C-C-C" => 550,
  "Cl-C-C-O" => 551,
  "C:C-C:C" => 552,
  "O=C-C=C" => 553,
  "Br-C-C-C" => 554,
  "N=C-C=C" => 555,
  "C=C-C-C" => 556,
  "N:C-O-[#1]" => 557,
  "O=N-C:C" => 558,
  "O-C-N-[#1]" => 559,
  "N-C-N-C" => 560,
  "Cl-C-C=O" => 561,
  "Br-C-C=O" => 562,
  "O-C-O-C" => 563,
  "C=C-C=C" => 564,
  "C:C-O-C" => 565,
  "O-C-C-N" => 566,
  "O-C-C-O" => 567,
  "N#C-C-C" => 568,
  "N-C-C-N" => 569,
  "C:C-C-C" => 570,
  "[#1]-C-O-[#1]" => 571,
  "N:C:N:C" => 572,
  "O-C-C=C" => 573,
  "O-C-C:C-C" => 574,
  "O-C-C:C-O" => 575,
  "N=C-C:C-[#1]" => 576,
  "C:C-N-C:C" => 577,
  "C-C:C-C:C" => 578,
  "O=C-C-C-C" => 579,
  "O=C-C-C-N" => 580,
  "O=C-C-C-O" => 581,
  "C-C-C-C-C" => 582,
  "Cl-C:C-O-C" => 583,
  "C:C-C=C-C" => 584,
  "C-C:C-N-C" => 585,
  "C-S-C-C-C" => 586,
  "N-C:C-O-[#1]" => 587,
  "O=C-C-C=O" => 588,
  "C-C:C-O-C" => 589,
  "C-C:C-O-[#1]" => 590,
  "Cl-C-C-C-C" => 591,
  "N-C-C-C-C" => 592,
  "N-C-C-C-N" => 593,
  "C-O-C-C=C" => 594,
  "C:C-C-C-C" => 595,
  "N=C-N-C-C" => 596,
  "O=C-C-C:C" => 597,
  "Cl-C:C:C-C" => 598,
  "[#1]-C-C=C-[#1]" => 599,
  "N-C:C:C-C" => 600,
  "N-C:C:C-N" => 601,
  "O=C-C-N-C" => 602,
  "C-C:C:C-C" => 603,
  "C-O-C-C:C" => 604,
  "O=C-C-O-C" => 605,
  "O-C:C-C-C" => 606,
  "N-C-C-C:C" => 607,
  "C-C-C-C:C" => 608,
  "Cl-C-C-N-C" => 609,
  "C-O-C-O-C" => 610,
  "N-C-C-N-C" => 611,
  "N-C-O-C-C" => 612,
  "C-N-C-C-C" => 613,
  "C-C-O-C-C" => 614,
  "N-C-C-O-C" => 615,
  "C:C:N:N:C" => 616,
  "C-C-C-O-[#1]" => 617,
  "C:C-C-C:C" => 618,
  "O-C-C=C-C" => 619,
  "C:C-O-C-C" => 620,
  "N-C:C:C:N" => 621,
  "O=C-O-C:C" => 622,
  "O=C-C:C-C" => 623,
  "O=C-C:C-N" => 624,
  "O=C-C:C-O" => 625,
  "C-O-C:C-C" => 626,
  "O=[As]-C:C:C" => 627,
  "C-N-C-C:C" => 628,
  "S-C:C:C-N" => 629,
  "O-C:C-O-C" => 630,
  "O-C:C-O-[#1]" => 631,
  "C-C-O-C:C" => 632,
  "N-C-C:C-C" => 633,
  "C-C-C:C-C" => 634,
  "N-N-C-N-[#1]" => 635,
  "C-N-C-N-C" => 636,
  "O-C-C-C-C" => 637,
  "O-C-C-C-N" => 638,
  "O-C-C-C-O" => 639,
  "C=C-C-C-C" => 640,
  "O-C-C-C=C" => 641,
  "O-C-C-C=O" => 642,
  "[#1]-C-C-N-[#1]" => 643,
  "C-C=N-N-C" => 644,
  "O=C-N-C-C" => 645,
  "O=C-N-C-[#1]" => 646,
  "O=C-N-C-N" => 647,
  "O=N-C:C-N" => 648,
  "O=N-C:C-O" => 649,
  "O=C-N-C=O" => 650,
  "O-C:C:C-C" => 651,
  "O-C:C:C-N" => 652,
  "O-C:C:C-O" => 653,
  "N-C-N-C-C" => 654,
  "O-C-C-C:C" => 655,
  "C-C-N-C-C" => 656,
  "C-N-C:C-C" => 657,
  "C-C-S-C-C" => 658,
  "O-C-C-N-C" => 659,
  "C-C=C-C-C" => 660,
  "O-C-O-C-C" => 661,
  "O-C-C-O-C" => 662,
  "O-C-C-O-[#1]" => 663,
  "C-C=C-C=C" => 664,
  "N-C:C-C-C" => 665,
  "C=C-C-O-C" => 666,
  "C=C-C-O-[#1]" => 667,
  "C-C:C-C-C" => 668,
  "Cl-C:C-C=O" => 669,
  "Br-C:C:C-C" => 670,
  "O=C-C=C-C" => 671,
  "O=C-C=C-[#1]" => 672,
  "O=C-C=C-N" => 673,
  "N-C-N-C:C" => 674,
  "Br-C-C-C:C" => 675,
  "N#C-C-C-C" => 676,
  "C-C=C-C:C" => 677,
  "C-C-C=C-C" => 678,
  "C-C-C-C-C-C" => 679,
  "O-C-C-C-C-C" => 680,
  "O-C-C-C-C-O" => 681,
  "O-C-C-C-C-N" => 682,
  "N-C-C-C-C-C" => 683,
  "O=C-C-C-C-C" => 684,
  "O=C-C-C-C-N" => 685,
  "O=C-C-C-C-O" => 686,
  "O=C-C-C-C=O" => 687,
  "C-C-C-C-C-C-C" => 688,
  "O-C-C-C-C-C-C" => 689,
  "O-C-C-C-C-C-O" => 690,
  "O-C-C-C-C-C-N" => 691,
  "O=C-C-C-C-C-C" => 692,
  "O=C-C-C-C-C-O" => 693,
  "O=C-C-C-C-C=O" => 694,
  "O=C-C-C-C-C-N" => 695,
  "C-C-C-C-C-C-C-C" => 696,
  "C-C-C-C-C-C(C)-C" => 697,
  "O-C-C-C-C-C-C-C" => 698,
  "O-C-C-C-C-C(C)-C" => 699,
  "O-C-C-C-C-C-O-C" => 700,
  "O-C-C-C-C-C(O)-C" => 701,
  "O-C-C-C-C-C-N-C" => 702,
  "O-C-C-C-C-C(N)-C" => 703,
  "O=C-C-C-C-C-C-C" => 704,
  "O=C-C-C-C-C(O)-C" => 705,
  "O=C-C-C-C-C(=O)-C" => 706,
  "O=C-C-C-C-C(N)-C" => 707,
  "C-C(C)-C-C" => 708,
  "C-C(C)-C-C-C" => 709,
  "C-C-C(C)-C-C" => 710,
  "C-C(C)(C)-C-C" => 711,
  "C-C(C)-C(C)-C" => 712,
}
Section7 =

Section 7: Complex SMARTS patterns

{
  "Cc1ccc(C)cc1" => 713,
  "Cc1ccc(O)cc1" => 714,
  "Cc1ccc(S)cc1" => 715,
  "Cc1ccc(N)cc1" => 716,
  "Cc1ccc(Cl)cc1" => 717,
  "Cc1ccc(Br)cc1" => 718,
  "Oc1ccc(O)cc1" => 719,
  "Oc1ccc(S)cc1" => 720,
  "Oc1ccc(N)cc1" => 721,
  "Oc1ccc(Cl)cc1" => 722,
  "Oc1ccc(Br)cc1" => 723,
  "Sc1ccc(S)cc1" => 724,
  "Sc1ccc(N)cc1" => 725,
  "Sc1ccc(Cl)cc1" => 726,
  "Sc1ccc(Br)cc1" => 727,
  "Nc1ccc(N)cc1" => 728,
  "Nc1ccc(Cl)cc1" => 729,
  "Nc1ccc(Br)cc1" => 730,
  "Clc1ccc(Cl)cc1" => 731,
  "Clc1ccc(Br)cc1" => 732,
  "Brc1ccc(Br)cc1" => 733,
  "Cc1cc(C)ccc1" => 734,
  "Cc1cc(O)ccc1" => 735,
  "Cc1cc(S)ccc1" => 736,
  "Cc1cc(N)ccc1" => 737,
  "Cc1cc(Cl)ccc1" => 738,
  "Cc1cc(Br)ccc1" => 739,
  "Oc1cc(O)ccc1" => 740,
  "Oc1cc(S)ccc1" => 741,
  "Oc1cc(N)ccc1" => 742,
  "Oc1cc(Cl)ccc1" => 743,
  "Oc1cc(Br)ccc1" => 744,
  "Sc1cc(S)ccc1" => 745,
  "Sc1cc(N)ccc1" => 746,
  "Sc1cc(Cl)ccc1" => 747,
  "Sc1cc(Br)ccc1" => 748,
  "Nc1cc(N)ccc1" => 749,
  "Nc1cc(Cl)ccc1" => 750,
  "Nc1cc(Br)ccc1" => 751,
  "Clc1cc(Cl)ccc1" => 752,
  "Clc1cc(Br)ccc1" => 753,
  "Brc1cc(Br)ccc1" => 754,
  "Cc1c(C)cccc1" => 755,
  "Cc1c(O)cccc1" => 756,
  "Cc1c(S)cccc1" => 757,
  "Cc1c(N)cccc1" => 758,
  "Cc1c(Cl)cccc1" => 759,
  "Cc1c(Br)cccc1" => 760,
  "Oc1c(O)cccc1" => 761,
  "Oc1c(S)cccc1" => 762,
  "Oc1c(N)cccc1" => 763,
  "Oc1c(Cl)cccc1" => 764,
  "Oc1c(Br)cccc1" => 765,
  "Sc1c(S)cccc1" => 766,
  "Sc1c(N)cccc1" => 767,
  "Sc1c(Cl)cccc1" => 768,
  "Sc1c(Br)cccc1" => 769,
  "Nc1c(N)cccc1" => 770,
  "Nc1c(Cl)cccc1" => 771,
  "Nc1c(Br)cccc1" => 772,
  "Clc1c(Cl)cccc1" => 773,
  "Clc1c(Br)cccc1" => 774,
  "Brc1c(Br)cccc1" => 775,
  "CC1CCC(C)CC1" => 776,
  "CC1CCC(O)CC1" => 777,
  "CC1CCC(S)CC1" => 778,
  "CC1CCC(N)CC1" => 779,
  "CC1CCC(Cl)CC1" => 780,
  "CC1CCC(Br)CC1" => 781,
  "OC1CCC(O)CC1" => 782,
  "OC1CCC(S)CC1" => 783,
  "OC1CCC(N)CC1" => 784,
  "OC1CCC(Cl)CC1" => 785,
  "OC1CCC(Br)CC1" => 786,
  "SC1CCC(S)CC1" => 787,
  "SC1CCC(N)CC1" => 788,
  "SC1CCC(Cl)CC1" => 789,
  "SC1CCC(Br)CC1" => 790,
  "NC1CCC(N)CC1" => 791,
  "NC1CCC(Cl)CC1" => 792,
  "NC1CCC(Br)CC1" => 793,
  "ClC1CCC(Cl)CC1" => 794,
  "ClC1CCC(Br)CC1" => 795,
  "BrC1CCC(Br)CC1" => 796,
  "CC1CC(C)CCC1" => 797,
  "CC1CC(O)CCC1" => 798,
  "CC1CC(S)CCC1" => 799,
  "CC1CC(N)CCC1" => 800,
  "CC1CC(Cl)CCC1" => 801,
  "CC1CC(Br)CCC1" => 802,
  "OC1CC(O)CCC1" => 803,
  "OC1CC(S)CCC1" => 804,
  "OC1CC(N)CCC1" => 805,
  "OC1CC(Cl)CCC1" => 806,
  "OC1CC(Br)CCC1" => 807,
  "SC1CC(S)CCC1" => 808,
  "SC1CC(N)CCC1" => 809,
  "SC1CC(Cl)CCC1" => 810,
  "SC1CC(Br)CCC1" => 811,
  "NC1CC(N)CCC1" => 812,
  "NC1CC(Cl)CCC1" => 813,
  "NC1CC(Br)CCC1" => 814,
  "ClC1CC(Cl)CCC1" => 815,
  "ClC1CC(Br)CCC1" => 816,
  "BrC1CC(Br)CCC1" => 817,
  "CC1C(C)CCCC1" => 818,
  "CC1C(O)CCCC1" => 819,
  "CC1C(S)CCCC1" => 820,
  "CC1C(N)CCCC1" => 821,
  "CC1C(Cl)CCCC1" => 822,
  "CC1C(Br)CCCC1" => 823,
  "OC1C(O)CCCC1" => 824,
  "OC1C(S)CCCC1" => 825,
  "OC1C(N)CCCC1" => 826,
  "OC1C(Cl)CCCC1" => 827,
  "OC1C(Br)CCCC1" => 828,
  "SC1C(S)CCCC1" => 829,
  "SC1C(N)CCCC1" => 830,
  "SC1C(Cl)CCCC1" => 831,
  "SC1C(Br)CCCC1" => 832,
  "NC1C(N)CCCC1" => 833,
  "NC1C(Cl)CCCC1" => 834,
  "NC1C(Br)CCCC1" => 835,
  "ClC1C(Cl)CCCC1" => 836,
  "ClC1C(Br)CCCC1" => 837,
  "BrC1C(Br)CCCC1" => 838,
  "CC1CC(C)CC1" => 839,
  "CC1CC(O)CC1" => 840,
  "CC1CC(S)CC1" => 841,
  "CC1CC(N)CC1" => 842,
  "CC1CC(Cl)CC1" => 843,
  "CC1CC(Br)CC1" => 844,
  "OC1CC(O)CC1" => 845,
  "OC1CC(S)CC1" => 846,
  "OC1CC(N)CC1" => 847,
  "OC1CC(Cl)CC1" => 848,
  "OC1CC(Br)CC1" => 849,
  "SC1CC(S)CC1" => 850,
  "SC1CC(N)CC1" => 851,
  "SC1CC(Cl)CC1" => 852,
  "SC1CC(Br)CC1" => 853,
  "NC1CC(N)CC1" => 854,
  "NC1CC(Cl)CC1" => 855,
  "NC1CC(Br)CC1" => 856,
  "ClC1CC(Cl)CC1" => 857,
  "ClC1CC(Br)CC1" => 858,
  "BrC1CC(Br)CC1" => 859,
  "CC1C(C)CCC1" => 860,
  "CC1C(O)CCC1" => 861,
  "CC1C(S)CCC1" => 862,
  "CC1C(N)CCC1" => 863,
  "CC1C(Cl)CCC1" => 864,
  "CC1C(Br)CCC1" => 865,
  "OC1C(O)CCC1" => 866,
  "OC1C(S)CCC1" => 867,
  "OC1C(N)CCC1" => 868,
  "OC1C(Cl)CCC1" => 869,
  "OC1C(Br)CCC1" => 870,
  "SC1C(S)CCC1" => 871,
  "SC1C(N)CCC1" => 872,
  "SC1C(Cl)CCC1" => 873,
  "SC1C(Br)CCC1" => 874,
  "NC1C(N)CCC1" => 875,
  "NC1C(Cl)CC1" => 876,
  "NC1C(Br)CCC1" => 877,
  "ClC1C(Cl)CCC1" => 878,
  "ClC1C(Br)CCC1" => 879,
  "BrC1C(Br)CCC1" => 880,
}
PubChemSubsKey = 
[
  ">= 4 H",
  ">= 8 H",
  ">= 16 H",
  ">= 32 H",
  ">= 1 Li",
  ">= 2 Li",
  ">= 1 B",
  ">= 2 B",
  ">= 4 B",
  ">= 2 C",
  ">= 4 C",
  ">= 8 C",
  ">= 16 C",
  ">= 32 C",
  ">= 1 N",
  ">= 2 N",
  ">= 4 N",
  ">= 8 N",
  ">= 1 O",
  ">= 2 O",
  ">= 4 O",
  ">= 8 O",
  ">= 16 O",
  ">= 1 F",
  ">= 2 F",
  ">= 4 F",
  ">= 1 Na",
  ">= 2 Na",
  ">= 1 Si",
  ">= 2 Si",
  ">= 1 P",
  ">= 2 P",
  ">= 4 P",
  ">= 1 S",
  ">= 2 S",
  ">= 4 S",
  ">= 8 S",
  ">= 1 Cl",
  ">= 2 Cl",
  ">= 4 Cl",
  ">= 8 Cl",
  ">= 1 K",
  ">= 2 K",
  ">= 1 Br",
  ">= 2 Br",
  ">= 4 Br",
  ">= 1 I",
  ">= 2 I",
  ">= 4 I",
  ">= 1 Be",
  ">= 1 Mg",
  ">= 1 Al",
  ">= 1 Ca",
  ">= 1 Sc",
  ">= 1 Ti",
  ">= 1 V",
  ">= 1 Cr",
  ">= 1 Mn",
  ">= 1 Fe",
  ">= 1 Co",
  ">= 1 Ni",
  ">= 1 Cu",
  ">= 1 Zn",
  ">= 1 Ga",
  ">= 1 Ge",
  ">= 1 As",
  ">= 1 Se",
  ">= 1 Kr",
  ">= 1 Rb",
  ">= 1 Sr",
  ">= 1 Y",
  ">= 1 Zr",
  ">= 1 Nb",
  ">= 1 Mo",
  ">= 1 Ru",
  ">= 1 Rh",
  ">= 1 Pd",
  ">= 1 Ag",
  ">= 1 Cd",
  ">= 1 In",
  ">= 1 Sn",
  ">= 1 Sb",
  ">= 1 Te",
  ">= 1 Xe",
  ">= 1 Cs",
  ">= 1 Ba",
  ">= 1 Lu",
  ">= 1 Hf",
  ">= 1 Ta",
  ">= 1 W",
  ">= 1 Re",
  ">= 1 Os",
  ">= 1 Ir",
  ">= 1 Pt",
  ">= 1 Au",
  ">= 1 Hg",
  ">= 1 Tl",
  ">= 1 Pb",
  ">= 1 Bi",
  ">= 1 La",
  ">= 1 Ce",
  ">= 1 Pr",
  ">= 1 Nd",
  ">= 1 Pm",
  ">= 1 Sm",
  ">= 1 Eu",
  ">= 1 Gd",
  ">= 1 Tb",
  ">= 1 Dy",
  ">= 1 Ho",
  ">= 1 Er",
  ">= 1 Tm",
  ">= 1 Yb",
  ">= 1 Tc",
  ">= 1 U",
  ">= 1 any ring size 3",
  ">= 1 saturated carbon-only ring size 3",
  ">= 1 saturated nitrogen-containing ring size 3",
  ">= 1 saturated heteroatom-containing ring size 3",
  ">= 1 unsaturated or aromatic carbon-only ring size 3",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 3",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 3",
  ">= 2 any ring size 3",
  ">= 2 saturated carbon-only ring size 3",
  ">= 2 saturated nitrogen-containing ring size 3",
  ">= 2 saturated heteroatom-containing ring size 3",
  ">= 2 unsaturated or aromatic carbon-only ring size 3",
  ">= 2 unsaturated or aromatic nitrogen-containing ring size 3",
  ">= 2 unsaturated or aromatic heteroatom-containing ring size 3",
  ">= 1 any ring size 4",
  ">= 1 saturated carbon-only ring size 4",
  ">= 1 saturated nitrogen-containing ring size 4",
  ">= 1 saturated heteroatom-containing ring size 4",
  ">= 1 unsaturated or aromatic carbon-only ring size 4",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 4",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 4",
  ">= 2 any ring size 4",
  ">= 2 saturated carbon-only ring size 4",
  ">= 2 saturated nitrogen-containing ring size 4",
  ">= 2 saturated heteroatom-containing ring size 4",
  ">= 2 unsaturated or aromatic carbon-only ring size 4",
  ">= 2 unsaturated or aromatic nitrogen-containing ring size 4",
  ">= 2 unsaturated or aromatic heteroatom-containing ring size 4",
  ">= 1 any ring size 5",
  ">= 1 saturated carbon-only ring size 5",
  ">= 1 saturated nitrogen-containing ring size 5",
  ">= 1 saturated heteroatom-containing ring size 5",
  ">= 1 unsaturated or aromatic carbon-only ring size 5",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 5",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 5",
  ">= 2 any ring size 5",
  ">= 2 saturated carbon-only ring size 5",
  ">= 2 saturated nitrogen-containing ring size 5",
  ">= 2 saturated heteroatom-containing ring size 5",
  ">= 2 unsaturated or aromatic carbon-only ring size 5",
  ">= 2 unsaturated or aromatic nitrogen-containing ring size 5",
  ">= 2 unsaturated or aromatic heteroatom-containing ring size 5",
  ">= 3 any ring size 5",
  ">= 3 saturated carbon-only ring size 5",
  ">= 3 saturated nitrogen-containing ring size 5",
  ">= 3 saturated heteroatom-containing ring size 5",
  ">= 3 unsaturated or aromatic carbon-only ring size 5",
  ">= 3 unsaturated or aromatic nitrogen-containing ring size 5",
  ">= 3 unsaturated or aromatic heteroatom-containing ring size 5",
  ">= 4 any ring size 5",
  ">= 4 saturated carbon-only ring size 5",
  ">= 4 saturated nitrogen-containing ring size 5",
  ">= 4 saturated heteroatom-containing ring size 5",
  ">= 4 unsaturated or aromatic carbon-only ring size 5",
  ">= 4 unsaturated or aromatic nitrogen-containing ring size 5",
  ">= 4 unsaturated or aromatic heteroatom-containing ring size 5",
  ">= 5 any ring size 5",
  ">= 5 saturated carbon-only ring size 5",
  ">= 5 saturated nitrogen-containing ring size 5",
  ">= 5 saturated heteroatom-containing ring size 5",
  ">= 5 unsaturated or aromatic carbon-only ring size 5",
  ">= 5 unsaturated or aromatic nitrogen-containing ring size 5",
  ">= 5 unsaturated or aromatic heteroatom-containing ring size 5",
  ">= 1 any ring size 6",
  ">= 1 saturated carbon-only ring size 6",
  ">= 1 saturated nitrogen-containing ring size 6",
  ">= 1 saturated heteroatom-containing ring size 6",
  ">= 1 unsaturated or aromatic carbon-only ring size 6",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 6",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 6",
  ">= 2 any ring size 6",
  ">= 2 saturated carbon-only ring size 6",
  ">= 2 saturated nitrogen-containing ring size 6",
  ">= 2 saturated heteroatom-containing ring size 6",
  ">= 2 unsaturated or aromatic carbon-only ring size 6",
  ">= 2 unsaturated or aromatic nitrogen-containing ring size 6",
  ">= 2 unsaturated or aromatic heteroatom-containing ring size 6",
  ">= 3 any ring size 6",
  ">= 3 saturated carbon-only ring size 6",
  ">= 3 saturated nitrogen-containing ring size 6",
  ">= 3 saturated heteroatom-containing ring size 6",
  ">= 3 unsaturated or aromatic carbon-only ring size 6",
  ">= 3 unsaturated or aromatic nitrogen-containing ring size 6",
  ">= 3 unsaturated or aromatic heteroatom-containing ring size 6",
  ">= 4 any ring size 6",
  ">= 4 saturated carbon-only ring size 6",
  ">= 4 saturated nitrogen-containing ring size 6",
  ">= 4 saturated heteroatom-containing ring size 6",
  ">= 4 unsaturated or aromatic carbon-only ring size 6",
  ">= 4 unsaturated or aromatic nitrogen-containing ring size 6",
  ">= 4 unsaturated or aromatic heteroatom-containing ring size 6",
  ">= 5 any ring size 6",
  ">= 5 saturated carbon-only ring size 6",
  ">= 5 saturated nitrogen-containing ring size 6",
  ">= 5 saturated heteroatom-containing ring size 6",
  ">= 5 unsaturated or aromatic carbon-only ring size 6",
  ">= 5 unsaturated or aromatic nitrogen-containing ring size 6",
  ">= 5 unsaturated or aromatic heteroatom-containing ring size 6",
  ">= 1 any ring size 7",
  ">= 1 saturated carbon-only ring size 7",
  ">= 1 saturated nitrogen-containing ring size 7",
  ">= 1 saturated heteroatom-containing ring size 7",
  ">= 1 unsaturated or aromatic carbon-only ring size 7",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 7",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 7",
  ">= 2 any ring size 7",
  ">= 2 saturated carbon-only ring size 7",
  ">= 2 saturated nitrogen-containing ring size 7",
  ">= 2 saturated heteroatom-containing ring size 7",
  ">= 2 unsaturated or aromatic carbon-only ring size 7",
  ">= 2 unsaturated or aromatic nitrogen-containing ring size 7",
  ">= 2 unsaturated or aromatic heteroatom-containing ring size 7",
  ">= 1 any ring size 8",
  ">= 1 saturated carbon-only ring size 8",
  ">= 1 saturated nitrogen-containing ring size 8",
  ">= 1 saturated heteroatom-containing ring size 8",
  ">= 1 unsaturated or aromatic carbon-only ring size 8",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 8",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 8",
  ">= 2 any ring size 8",
  ">= 2 saturated carbon-only ring size 8",
  ">= 2 saturated nitrogen-containing ring size 8",
  ">= 2 saturated heteroatom-containing ring size 8",
  ">= 2 unsaturated or aromatic carbon-only ring size 8",
  ">= 2 unsaturated or aromatic nitrogen-containing ring size 8",
  ">= 2 unsaturated or aromatic heteroatom-containing ring size 8",
  ">= 1 any ring size 9",
  ">= 1 saturated carbon-only ring size 9",
  ">= 1 saturated nitrogen-containing ring size 9",
  ">= 1 saturated heteroatom-containing ring size 9",
  ">= 1 unsaturated or aromatic carbon-only ring size 9",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 9",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 9",
  ">= 1 any ring size 10",
  ">= 1 saturated carbon-only ring size 10",
  ">= 1 saturated nitrogen-containing ring size 10",
  ">= 1 saturated heteroatom-containing ring size 10",
  ">= 1 unsaturated or aromatic carbon-only ring size 10",
  ">= 1 unsaturated or aromatic nitrogen-containing ring size 10",
  ">= 1 unsaturated or aromatic heteroatom-containing ring size 10",
  ">= 1 aromatic ring",
  ">= 1 hetero-aromatic ring",
  ">= 2 aromatic rings",
  ">= 2 hetero-aromatic rings",
  ">= 3 aromatic rings",
  ">= 3 hetero-aromatic rings",
  ">= 4 aromatic rings",
  ">= 4 hetero-aromatic rings",
]
RingSizeBaseNum = 
{
  3 =>  115,
  4 =>  129,
  5 =>  143,
  6 =>  178,
  7 =>  213,
  8 =>  227,
  9 =>  241,
  10 => 248,
}
AtomicWeight = 
{
  :H => 1.00794,
  :He => 4.002602,
  :Li => 6.941,
  :Be => 9.012182,
  :B  => 10.811,
  :C  => 12.0107,
  :N  => 14.0067,
  :O  => 15.9994,
  :F  => 18.9984032,
  :Ne => 20.1797,
  :Na => 22.989770,
  :Mg => 24.3050,
  :Al => 26.981538,
  :Si => 28.0855,
  :P  => 30.973761,
  :S  => 32.065,
  :Cl => 35.453,
  :Ar => 39.948,
  :K  => 39.0983,
  :Ca => 40.078,
  :Sc => 44.955910,
  :Ti => 47.867,
  :V  => 50.9415,
  :Cr => 51.9961,
  :Mn => 54.938049,
  :Fe => 55.845,
  :Co => 58.933200,
  :Ni => 58.6934,
  :Cu => 63.546,
  :Zn => 65.409,
  :Ga => 69.723,
  :Ge => 72.64,
  :As => 74.92160,
  :Se => 78.96,
  :Br => 79.904,
  :Kr => 83.798,
  :Rb => 85.4678,
  :Sr => 87.62,
  :Y  => 88.90585,
  :Zr => 91.224,
  :Nb => 92.90638,
  :Mo => 95.94,
  :Tc => 98,
  :Ru => 101.07,
  :Rh => 102.90550,
  :Pd => 106.42,
  :Ag => 107.8682,
  :Cd => 112.411,
  :In => 114.818,
  :Sn => 118.710,
  :Sb => 121.760,
  :Te => 127.60,
  :I  => 126.90447,
  :Xe => 131.293,
  :Cs => 132.90545,
  :Ba => 137.327,
  :La => 138.9055,
  :Ce => 140.116,
  :Pr => 140.90765,
  :Nd => 144.24,
  :Pm => 145,
  :Sm => 150.36,
  :Eu => 151.964,
  :Gd => 157.25,
  :Tb => 158.92534,
  :Dy => 162.500,
  :Ho => 164.93032,
  :Er => 167.259,
  :Tm => 168.93421,
  :Yb => 173.04,
  :Lu => 174.967,
  :Hf => 178.49,
  :Ta => 180.9479,
  :W  => 183.84,
  :Re => 186.207,
  :Os => 190.23,
  :Ir => 192.217,
  :Pt => 195.078,
  :Au => 196.96655,
  :Hg => 200.59,
  :Tl => 204.3833,
  :Pb => 207.2,
  :Bi => 208.98038,
  :Po => 209,
  :At => 210,
  :Rn => 222,
  :Fr => 223,
  :Ra => 226,
  :Ac => 227,
  :Th => 232.0381,
  :Pa => 231.03588,
  :U  => 238.02891,
  :Np => 237,
  :Pu => 244,
  :Am => 243,
  :Cm => 247,
  :Bk => 247,
  :Cf => 251,
  :Es => 252,
  :Fm => 257,
  :Md => 258,
  :No => 259,
  :Lr => 262,
  :Rf => 261,
  :Db => 262,
  :Sg => 266,
  :Bh => 264,
  :Hs => 277,
  :Mt => 268,
  :Ds => 281,
  :Rg => 272,
  :Uub=> 285,
  :Uut=> 284,
  :Uuq=> 289,
  :Uup=> 288,
  #116   Uuh    Ununhexium                  see Note above 
  #118   Uuo    Ununoctium                  see Note above 
}
Element2Number = 
{:Bk=>97, :Si=>14, :In=>49, :Fr=>87, :V=>23, :Na=>11, :Tb=>65, :Po=>84, :Pd=>46, :Al=>13, :Ho=>67, :Ba=>56, :As=>33, :Rn=>86, :Nb=>41, :Hg=>80, :P=>15, :Bi=>83, :Be=>4, :Ru=>44, :S=>16, :O=>8, :Ra=>88, :Es=>99, :Xe=>54, :He=>2, :N=>7, :Am=>95, :Pr=>59, :Er=>68, :Au=>79, :Rh=>45, :Ce=>58, :Tm=>69, :Gd=>64, :Ir=>77, :Sr=>38, :La=>57, :Cm=>96, :Ca=>20, :C=>6, :Sm=>62, :Hf=>72, :Ag=>47, :At=>85, :F=>9, :Tc=>43, :Zn=>30, :Lu=>71, :B=>5, :Np=>93, :Ga=>31, :XX=>101, :Sn=>50, :Os=>76, :Eu=>63, :Dy=>66, :Yb=>70, :K=>19, :Tl=>81, :I=>53, :Ar=>18, :Th=>90, :Zr=>40, :Pt=>78, :Fe=>26, :Ge=>32, :Cr=>24, :Cf=>98, :Kr=>36, :Rb=>37, :ZZ=>103, :Ta=>73, :W=>74, :Sc=>21, :Mn=>25, :Pu=>94, :Mg=>12, :Se=>34, :Ti=>22, :Cd=>48, :Sb=>51, :Fm=>100, :Cs=>55, :Nd=>60, :Co=>27, :Pb=>82, :Cl=>17, :Cu=>29, :Y=>39, :Re=>75, :U=>92, :Pa=>91, :Mo=>42, :H=>1, :D=>0, :Te=>52, :Li=>3, :Br=>35, :YY=>102, :Pm=>61, :Ac=>89, :Ni=>28, :Ne=>10}
Number2Element = 
[:D, :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, :XX, :YY, :ZZ]

Class Method Summary collapse

Class Method Details

.autodetect(file) ⇒ Object

format_class = Chem.autodetect(“file.mol”)

Automatically detect file type and returns appropriate class to parse it



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# File 'lib/chem.rb', line 56

def self.autodetect file
  ChemTypeRegistry.find{|format| format.detect_file file}
end

.data_dir ⇒ Object 



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# File 'lib/chem.rb', line 41

def self.data_dir
  DefaultDataDir
end

.db_search(database_name, q_mol, block) ⇒ Object 



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# File 'ext/subcomp.c', line 456

static VALUE
db_search(VALUE self, VALUE database_name, VALUE q_mol, VALUE block)
{
  char * filename;
  struct CompoundDB db;
  struct Query query;

  filename = StringValuePtr(database_name);

  if(strlen(filename) > 40){
    rb_raise(rb_eException, "length of database name must less than 40!");
  }

  query_setup(q_mol, & query);

  db.mat = db_file_open(filename, ".mat");
  db.idx = db_file_open(filename, ".idx");
  db.typ = db_file_open(filename, ".typ");

  db_load(& db, & query);

  query_free(& query);

  fclose(db.mat);
  fclose(db.idx);
  fclose(db.typ);
}

.match_by_ullmann(q_mol, t_mol) ⇒ Object 



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# File 'ext/subcomp.c', line 517

static VALUE
mol_by_mol(VALUE self, VALUE q_mol, VALUE t_mol)
{
  struct Query  query;
  struct Target target;
  struct State  state;
  VALUE result;

  target.max_length = 0;
  state.max_length = 0;

  query_setup(  q_mol, & query  );
  target_setup( t_mol, & target );

  state_allocate(& state, & query, & target);

  if(rb_block_given_p() == Qtrue){
    state_setup_block(& state);
  }
  else{
    state_setup(& state, & query, & target);
  }

  search_by_ullmann(& state, & query, & target);
  result = state_get_result(& state);

  query_free(& query);
  target_free(& target);
  state_free(& state);

  return result;
}

.open_kegg(dir) ⇒ Object 



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# File 'lib/chem.rb', line 95

def open_kegg dir
  require 'chem/db/kegg'
  Chem::KEGG::KeggDirectory.new(dir)
end

.open_mol(file, format_type = nil) ⇒ Object Also known as: parse_file, load

Makes possible to open chemical files. Guesses the file type based on the extension of the file name.

Examples : So if the file name is “benzene.mol”,

mol = Chem.open_mol(“benzene.mol”) # returns MDLMolecule object

Raises:

  • (NotImplementedError) 


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# File 'lib/chem.rb', line 67

def open_mol file, format_type = nil
  format = nil
  if format_type == nil
    format = Chem.autodetect(file)
  else
    format = ChemTypeRegistry.find{|format| format.detect_type format_type}
  end
  raise NotImplementedError unless format
  return format.parse(file) if format
end

.opsin_parse(iupac_name) ⇒ Object 



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# File 'lib/chem/db/opsin.rb', line 4

def self.opsin_parse(iupac_name)
  OpsinMolecule.new(iupac_name)
end

.parse_gspan(file) ⇒ Object 



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# File 'lib/chem/db/gspan.rb', line 103

def self.parse_gspan file
  t = "t"[0]
  v = "v"[0]
  e = "e"[0]

  mols = []
  mol = GSpanMolecule.new

  open(file).each do |line|
    case line[0]
    when t
      mol = GSpanMolecule.new
      mols.push(mol)
    when v
      mol.nodes.push(GSpanAtom.parse_line(line))
    when e
      ary = line.split
      node1 = mol.nodes[ary[1].to_i]
      node2 = mol.nodes[ary[2].to_i]
      mol.edges.push([GSpanBond.new(ary[3].to_i), node1, node2])
    else
    end
  end
  mols
end

.parse_smiles(smiles) ⇒ Object 



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# File 'lib/chem.rb', line 89

def parse_smiles smiles
  require 'chem/db/smiles'
  require 'chem/db/smiles/smiparser'
  ::SmilesParser.parse_smiles(smiles)
end

.save(array, filename, params = {}) ⇒ Object 



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# File 'lib/chem.rb', line 84

def self.save(array, filename, params = {})
  format = autodetect filename
  format.save(array, filename, params)
end

.search_net(term, options) ⇒ Object 



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# File 'lib/chem/utils/net.rb', line 21

def self.search_net(term, options)
  case options[:db]
  when :pubmed
    Chem::NCBI::ESearch.query(term, options)
  when :pubchem
    Chem::NCBI::ESearch.query(term, options)
  end
end