/usr/share/openbabel/2.3.2/SMARTS_InteLigand.txt is in libopenbabel4v5 2.3.2+dfsg-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 | #
# SMARTS Patterns for Functional Group Classification
#
# written by Christian Laggner
# Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH
#
# Released under the Lesser General Public License (LGPL license)
# see http://www.gnu.org/copyleft/lesser.html
# Modified from Version 221105
#####################################################################################################
# General Stuff:
# These patters were written in an attempt to represent the classification of organic compounds
# from the viewpoint of an organic chemist.
# They are often very restrictive. This may be generally a good thing, but it also takes some time
# for filtering/indexing large compound sets.
# For filtering undesired groups (in druglike compounds) one will want to have more general patterns
# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...).
#
# Part I: Carbon
# ==============
# I.1: Carbon-Carbon Bonds
# ------------------------
# I.1.1 Alkanes:
Primary_carbon: [CX4H3][#6]
Secondary_carbon: [CX4H2]([#6])[#6]
Tertiary_carbon: [CX4H1]([#6])([#6])[#6]
Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]
# I.1.2 C-C double and Triple Bonds
Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]
# sp2 C may be substituted only by C or H -
# does not hit ketenes and allenes, nor enamines, enols and the like
Alkyne: [CX2]#[CX2]
# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination
Allene: [CX3]=[CX2]=[CX3]
# I.2: One Carbon-Hetero Bond
# ---------------------------
# I.2.1 Alkyl Halogenides
Alkylchloride: [ClX1][CX4]
# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats
# a more restrictive version can be obtained by modifying the Alcohol string.
Alkylfluoride: [FX1][CX4]
Alkylbromide: [BrX1][CX4]
Alkyliodide: [IX1][CX4]
# I.2.2 Alcohols and Ethers
Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
# nonspecific definition, no acetals, aminals, and the like
Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
# no acetals and the like; no enolethers
Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
# no acetals and the like; no enolethers
Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
# no acetals and the like; no enolethers
Diarylether: [c][OX2][c]
Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
Diarylthioether: [c][SX2][c]
Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
# can't be aromatic, thus O and not #8
# I.2.3 Amines
Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...
# the following amines include also the protonated forms
Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
Primary_arom_amine: [NX3H2+0,NX4H3+]c
Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]
# only C and H substituents allowed. Quaternary or protonated amines
# NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present
# I.2.4 Others
Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
Disulfide: [SX2D2][SX2D2]
1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
# does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc.
1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
# does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc.
1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
Hydroperoxide: [OX2H][OX2]
#does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides
Peroxo: [OX2D2][OX2D2]
Organolithium_compounds: [LiX1][#6,#14]
Organomagnesium_compounds: [MgX2][#6,#14]
# not restricted to Grignard compounds, also dialkyl Mg
Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
# very general, includes all metals covalently bound to carbon
# I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives)
# ----------------------------
# I.3.1 Double Bond to Hetero
Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1]
# hits aldehydes including formaldehyde
Ketone: [#6][CX3](=[OX1])[#6]
# does not include oxo-groups connected to a (hetero-) aromatic ring
Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1]
Thioketone: [#6][CX3](=[SX1])[#6]
# does not include thioxo-groups connected to a (hetero-) aromatic ring
Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
# nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar
Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
# ether, not ester or amide; does not hit isoxazole
# I.3.2. Two Single Bonds to Hetero
Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
# does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc.
Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]
# Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups
Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
# hits chloromethylenethers and other reactive alkylating agents
Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
# includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar
Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
# also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed
NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
# Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side
Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
# Combination of the last two patterns
Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
# I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar)
Chloroalkene: [ClX1][CX3]=[CX3]
Fluoroalkene: [FX1][CX3]=[CX3]
Bromoalkene: [BrX1][CX3]=[CX3]
Iodoalkene: [IX1][CX3]=[CX3]
Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
# no phenols
Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
# no 1,2-diphenols, ketenacetals, ...
Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
# finds also endiodiethers, but not enolesters, no aromats
Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
# does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic
Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
# I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives)
# ------------------------------
Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]
Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]
Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]
Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
# all of the above
# The following contains all simple carboxylic combinations of O, N, S, & Hal -
# - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...)
# Cyclic structures (including aromats) like lactones, lactames, ... got their own
# definitions. Structures where both heteroatoms are part of an aromatic ring
# (oxazoles, imidazoles, ...) were excluded.
Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
# includes carboxylate anions
Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
# does not hit anhydrides or lactones
Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
# may also be aromatic
Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
# anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic
Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
# includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole
Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
# hits both tautomeric forms, as well as anions
Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
# may also be aromatic
Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
# does not hit lactames
Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
# cyclic amides, may also be aromatic
Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
# may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide
N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
# everything else than H or C at central N
Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
# can be deprotonated
Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
# does not hit thiolactames
Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
# cyclic thioamides, may also be aromatic
Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
# may also be part of a ring / aromatic
Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
# only basic amidines, not as part of aromatic ring (e.g. imidazole)
Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
# does not hit anhydrides of carboxylic acids withs hydroxamic acids
Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
# not cyclic
Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
# the enamide-form of lactames. may be aromatic like 2-hydroxypyridine
Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
# esters of the above structures. no anhydrides.
Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
# no oxazoles and similar
Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
# not cyclic
Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
# the enamide-form of thiolactames. may be aromatic like 2-thiopyridine
Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
# thioesters of the above structures. no anhydrides.
Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
# no thioxazoles and similar
Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
# only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring
Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]
# one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole
Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
# not cyclic
Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
# may also be aromatic
# may be ring, aromatic, substituted with carbonyls, hetero, ...
# (everything else would get too complicated)
Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
# hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ...
Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
# N may be alkylated, but not part of an amide (as in peptides), ionic forms are included
# includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C
# N may not be aromatic as in 1H-pyrrole-2-carboxylic acid
Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-]
Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
# finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides
Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
# finds C-terminal amino acids
Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
# finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond.
Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]
# hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues)
Ketene: [CX3]=[CX2]=[OX1]
Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]
# includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be
Nitrile: [NX1]#[CX2]
# includes cyanhydrines
Isonitrile: [CX1-]#[NX2+]
Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
# may be part of a ring, even aromatic
Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
# I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives)
# -----------------------------
Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
# may be part of a ring, even aromatic
Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
# unstable
Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6]
Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
# may be part of a ring, even aromatic
Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
# no check whether part of imide, biuret, etc. Aromatic structures are only hit if
# both N share no double bonds, like in the dioxo-form of uracil
Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
# O may be substituted. no check whether further amide-like bonds are present. Aromatic
# structures are only hit if single bonded N shares no additional double bond, like in
# the 1-hydroxy-3-oxo form of uracil
Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
# also hits guanidinium salts. v3 and v4 to avoid nitroamidines
Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-]
# quite unstable, unlikely to be found. Also hits salts
Urethan: [#7X3][#6](=[OX1])[#8X2][#6]
# also hits when part of a ring, no check whether the last C is part of carbonyl
Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
Isocyanate: [NX2]=[CX2]=[OX1]
Cyanate: [OX2][CX2]#[NX1]
Isothiocyanate: [NX2]=[CX2]=[SX1]
Thiocyanate: [SX2][CX2]#[NX1]
Carbodiimide: [NX2]=[CX2]=[NX2]
Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
# halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more
# stable as for example C(OCH3)4)
# I.6 Aromatics
# -------------
# I know that this classification is not very logical, arylamines are found under I.2 ...
Phenol: [OX2H][c]
1,2-Diphenol: [OX2H][c][c][OX2H]
Arylchloride: [Cl][c]
Arylfluoride: [F][c]
Arylbromide: [Br][c]
Aryliodide: [I][c]
Arylthiol: [SX2H][c]
Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
# N may be substituted with H or C, but not carbonyl or similar
# aromatic atom is always C, not S or P (these are not planar when substituted)
Oxoarene: [c]=[OX1]
Thioarene: [c]=[SX1]
Hetero_N_basic_H: [nX3H1+0]
# as in pyrole. uncharged to exclude pyridinium ions
Hetero_N_basic_no_H: [nX3H0+0]
# as in N-methylpyrole. uncharged to exclude pyridinium ions
Hetero_N_nonbasic: [nX2,nX3+]
# as in pyridine, pyridinium
Hetero_O: [o]
Hetero_S: [sX2]
# X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic
# (is not planar because of lonepair at S)
Heteroaromatic: [a;!c]
# Part II: N, S, P, Si, B
# =======================
# II.1 Nitrogen
# -------------
Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])]
# hits nitrous acid, its anion, esters, and other O-substituted derivatives
Thionitrite: [SX2][NX2]=[OX1]
Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]
# hits nitric acid, its anion, esters, and other O-substituted derivatives
Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
# hits nitro groups attached to C,N, ... but not nitrates
Nitroso: [NX2](=[OX1])[!#7;!#8]
# no nitrites, no nitrosamines
Azide: [NX1]~[NX2]~[NX2,NX1]
# hits both mesomeric forms, also anion
Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1]
Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]
Diazonium: [#6][NX2+]#[NX1]
Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1]
Nitrosamide: [NX2](=[OX1])N-*=O
# includes nitrososulfonamides
N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]
# Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate.
Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
# no hydrazides
Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
# no discrimination between O-, N-, and O,N-substitution
# II.2 Sulfur
# -----------
Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
# can't be aromatic, thus S and not #16
Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
# can't be aromatic, thus S and not #16
Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
# includes anions
Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
# everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative
# than sulfur, but this should be very very rare, anyway)
#### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
# includes all of the above and many more
# for comparison: this is what "all sulfonic derivatives but not the ones above" would look like:
# [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])]
Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6]
# II.3 Phosphorous
# ----------------
Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
# similar to amine, but less restrictive: includes also amide- and aminal-analogues
Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
# similar to Ammonium
Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
# conventions for the following acids and derivatives:
# acids find protonated and deprotonated acids
# esters do not find mixed anhydrides ( ...P-O-C(=O))
# derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O,
# thus including acids and esters)
Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
# includes anions
Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
# all of the above and much more
Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
# includes anions
Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6]
Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
# II.4 Silicon
# ------------
Quart_silane: [SiX4]([#6])([#6])([#6])[#6]
# four C-substituents. non-reactive, non-toxic, in experimental phase for drug development
Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
# has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to
# the free positions at Si, thus Hs had to be added implicitly
Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
# reagents for inserting protection groups
Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6]
# mostly acid-labile protection groups such as trimethylsilyl-ethers
Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6]
Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6]
Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6]
# four substituent which are neither C nor H
# II.5 Boron
# ----------
Trialkylborane: [BX3]([#6])([#6])[#6]
# also carbonyls allowed
Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6]
# includes acids, esters, amides, ... H-substituent at B is very rare.
Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6]
# # includes acids, esters, amides, ...
Borohydride: [BH1,BH2,BH3,BH4]
# at least one H attached to B
Quaternary_boron: [BX4]
# mostly borates (negative charge), in complex with Lewis-base
# Part III: Some Special Patterns
# ===============================
# III.1 Chains
# ------------
# some simple chains
# III.2 Rings
# -----------
Aromatic: a
Heterocyclic: [!#6;!R0]
# may be aromatic or not
Epoxide: [OX2r3]1[#6r3][#6r3]1
# toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione)
NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1
# toxic/reactive according to Maybridge's garbage filter
Spiro: [D4R;$(*(@*)(@*)(@*)@*)]
# at least two different rings can be found which are sharing just one atom.
# these two rings can be connected by a third ring, so it matches also some
# bridged systems, like morphine
Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]
# two different rings sharing exactly two atoms
Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]
# part of two or more rings, not spiro, not annelated -> finds bridgehead atoms,
# but only if they are not annelated at the same time - otherwise impossible (?)
# to distinguish from non-bridgehead annelated atoms
# some basic ring-patterns (just size, no other information):
# III.3 Sugars and Nucleosides/Nucleotides, Steroids
# --------------------------------------------------
# because of the large variety of sugar derivatives, different patterns can be applied.
# The choice of patterns and their combinations will depend on the contents of the database
# e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the
# desired restriction
Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
# 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents.
Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
# 5 or 6-membered ring containing one O and an acetal-like bond at postion 2.
Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
# combination of the two above
Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
# 5 or 6-membered cyclic hemi-acetal
Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
# 5 or 6-membered cyclic hemi-acetal
Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
# 5 or 6-membered cyclic hemi-acetal
##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)])
# pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!)
##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)])
# pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!)
# III.4 Everything else...
# ------------------------
Conjugated_double_bond: *=*[*]=,#,:[*]
Conjugated_tripple_bond: *#*[*]=,#,:[*]
Cis_double_bond: */[D2]=[D2]\*
# only one single-bonded substituent on each DB-atom. no aromats.
# only found when character of DB is explicitely stated.
Trans_double_bond: */[D2]=[D2]/*
# analog
Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
# should hits all combinations of two acids
Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]
Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]
# Halogen which is not mono-substituted nor an anion, e.g. chlorate.
# Most of these cases should be also filtered by Halogen_on_hetero.
Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
# C with three F attached, connected to anything which is not another halogen
C_ONS_bond: [#6]~[#7,#8,#16]
# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter
## Mixture: (*).(*)
# two or more seperate parts, may also be salt
# component-level grouping is not yet supported in Open Babel Version 2.0
Charged: [!+0]
Anion: [-1,-2,-3,-4,-5,-6,-7]
Kation: [+1,+2,+3,+4,+5,+6,+7]
Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
# two or more seperate components with opposite charges
##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])
# both negative and positive charges somewhere within the same molecule.
1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]
# 1,3 migration of H allowed. Includes keto/enol and amide/enamide.
# Aromatic rings must stay aromatic - no keto form of phenol
1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]
Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
# taken from http://www.daylight.com/support/contrib/smarts/content.html
Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
# the classical case: C=C near carbonyl, nitrile, nitro, or similar
# Oxo-heteroaromats and similar are not included.
Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
# Michael-like acceptor, see Mitsunobu reaction
# H-Bond_donor:
# H-Bond_acceptor:
# Pos_ionizable:
# Neg_ionizable:
# Unlikely_ions:
# O+,N-,C+,C-, ...
CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed.
# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded.
# hits also CH-acidic_strong
CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]
# same as above (without pentadiene), but carbonyl or similar on two or three sides
Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string
# depictmach does not find oxonium, sulfonium, or sulfoxides!
# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)]
# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string
# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0
|