pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-03 21:44:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
master
rdkit/Code/GraphMol/Fingerprints/MACCS.cpp
Greg Landrum e35f7db009 Cleanup/get atoms and bonds (#9243)
2026-04-18 05:22:09 +02:00

949 lines
33 KiB
C++
Raw Permalink Blame History

// $Id$
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
// Contribution from Roger Sayle
#include <vector>
#include "MACCS.h"
#include <DataStructs/ExplicitBitVect.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/MolOps.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/flyweight.hpp>
#include <boost/flyweight/no_tracking.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace {
struct Patterns {
std::unique_ptr<RDKit::ROMol> bit_8 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]1~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_11 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*1~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_13 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[#7](~[#6])~[#6]"));
std::unique_ptr<RDKit::ROMol> bit_14 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]-[#16]"));
std::unique_ptr<RDKit::ROMol> bit_15 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[#6](~[#8])~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_16 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]1~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_17 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]#[#6]"));
std::unique_ptr<RDKit::ROMol> bit_19 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*1~*~*~*~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_20 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#14]"));
std::unique_ptr<RDKit::ROMol> bit_21 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#6]=[#6](~[!#6!#1])~[!#6!#1]"));
std::unique_ptr<RDKit::ROMol> bit_22 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*1~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_23 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#7]~[#6](~[#8])~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_24 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]-[#8]"));
std::unique_ptr<RDKit::ROMol> bit_25 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#7]~[#6](~[#7])~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_26 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]=@[#6](@*)@*"));
std::unique_ptr<RDKit::ROMol> bit_28 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1]~[CH2]~[!#6!#1]"));
std::unique_ptr<RDKit::ROMol> bit_30 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#6]~[!#6!#1](~[#6])(~[#6])~*"));
std::unique_ptr<RDKit::ROMol> bit_31 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[F,Cl,Br,I]"));
std::unique_ptr<RDKit::ROMol> bit_32 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]~[#16]~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_33 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~[#16]"));
std::unique_ptr<RDKit::ROMol> bit_34 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[CH2]=*"));
std::unique_ptr<RDKit::ROMol> bit_36 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16R]"));
std::unique_ptr<RDKit::ROMol> bit_37 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#7]~[#6](~[#8])~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_38 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#7]~[#6](~[#6])~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_39 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[#16](~[#8])~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_40 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]-[#8]"));
std::unique_ptr<RDKit::ROMol> bit_41 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]#[#7]"));
std::unique_ptr<RDKit::ROMol> bit_43 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1!H0]~*~[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_44 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol(
"[!#1;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#35;!#53]"));
std::unique_ptr<RDKit::ROMol> bit_45 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]=[#6]~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_47 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]~*~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_48 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[!#6!#1](~[#8])~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_49 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!+0]"));
std::unique_ptr<RDKit::ROMol> bit_50 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#6]=[#6](~[#6])~[#6]"));
std::unique_ptr<RDKit::ROMol> bit_51 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]~[#16]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_52 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_53 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1!H0]~*~*~*~[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_54 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1!H0]~*~*~[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_55 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]~[#16]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_56 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[#7](~[#8])~[#6]"));
std::unique_ptr<RDKit::ROMol> bit_57 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8R]"));
std::unique_ptr<RDKit::ROMol> bit_58 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1]~[#16]~[!#6!#1]"));
std::unique_ptr<RDKit::ROMol> bit_59 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]!:*:*"));
std::unique_ptr<RDKit::ROMol> bit_60 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]=[#8]"));
std::unique_ptr<RDKit::ROMol> bit_61 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~[#16](~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_62 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*@*!@*@*"));
std::unique_ptr<RDKit::ROMol> bit_63 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]=[#8]"));
std::unique_ptr<RDKit::ROMol> bit_64 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*@*!@[#16]"));
std::unique_ptr<RDKit::ROMol> bit_65 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("c:n"));
std::unique_ptr<RDKit::ROMol> bit_66 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#6]~[#6](~[#6])(~[#6])~*"));
std::unique_ptr<RDKit::ROMol> bit_67 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[#16]"));
std::unique_ptr<RDKit::ROMol> bit_68 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1!H0]~[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_69 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_70 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1]~[#7]~[!#6!#1]"));
std::unique_ptr<RDKit::ROMol> bit_71 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_72 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]~*~*~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_73 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]=*"));
std::unique_ptr<RDKit::ROMol> bit_74 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[CH3]~*~[CH3]"));
std::unique_ptr<RDKit::ROMol> bit_75 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*!@[#7]@*"));
std::unique_ptr<RDKit::ROMol> bit_76 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]=[#6](~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_77 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_78 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]=[#7]"));
std::unique_ptr<RDKit::ROMol> bit_79 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~*~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_80 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~*~*~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_81 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#16]~*(~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_82 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~[CH2]~[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_83 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]1~*~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_84 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[NH2]"));
std::unique_ptr<RDKit::ROMol> bit_85 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#6]~[#7](~[#6])~[#6]"));
std::unique_ptr<RDKit::ROMol> bit_86 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[C;H2,H3][!#6!#1][C;H2,H3]"));
std::unique_ptr<RDKit::ROMol> bit_87 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[F,Cl,Br,I]!@*@*"));
std::unique_ptr<RDKit::ROMol> bit_89 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]~*~*~*~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_90 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[$([!#6!#1!H0]~*~*~[CH2]~*),$([!#6!#1!H0R]1@[R]@[R]@["
"CH2R]1),$([!#6!#1!H0]~[R]1@[R]@[CH2R]1)]"));
std::unique_ptr<RDKit::ROMol> bit_91 = std::unique_ptr<
RDKit::ROMol>(RDKit::SmartsToMol(
"[$([!#6!#1!H0]~*~*~*~[CH2]~*),$([!#6!#1!H0R]1@[R]@[R]@[R]@[CH2R]1),$([!#"
"6!#1!H0]~[R]1@[R]@[R]@[CH2R]1),$([!#6!#1!H0]~*~[R]1@[R]@[CH2R]1)]"));
std::unique_ptr<RDKit::ROMol> bit_92 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[#6](~[#7])~[#6]"));
std::unique_ptr<RDKit::ROMol> bit_93 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[CH3]"));
std::unique_ptr<RDKit::ROMol> bit_94 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_95 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~*~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_96 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*1~*~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_97 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~*~*~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_98 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1]1~*~*~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_99 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]=[#6]"));
std::unique_ptr<RDKit::ROMol> bit_100 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~[CH2]~[#7]"));
std::unique_ptr<RDKit::ROMol> bit_101 = std::unique_ptr<
RDKit::ROMol>(RDKit::SmartsToMol(
"[$([R]1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@1),$([R]1@[R]@[R]@[R]@[R]@[R]@[R]@["
"R]@[R]@1),$([R]1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@1),$([R]1@[R]@[R]@["
"R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@1),$([R]1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]"
"@[R]@[R]@[R]@1),$([R]1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@"
"1),$([R]1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@1)]"));
std::unique_ptr<RDKit::ROMol> bit_102 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_104 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1!H0]~*~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_105 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*@*(@*)@*"));
std::unique_ptr<RDKit::ROMol> bit_106 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[!#6!#1]~*(~[!#6!#1])~[!#6!#1]"));
std::unique_ptr<RDKit::ROMol> bit_107 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[F,Cl,Br,I]~*(~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_108 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[CH3]~*~*~*~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_109 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~[CH2]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_110 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~[#6]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_111 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_112 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~*(~*)(~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_113 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]!:*:*"));
std::unique_ptr<RDKit::ROMol> bit_114 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[CH3]~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_115 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[CH3]~*~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_116 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[$([CH3]~*~*~[CH2]~*),$([CH3]~*1~*~[CH2]1)]"));
std::unique_ptr<RDKit::ROMol> bit_117 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_118 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[$(*~[CH2]~[CH2]~*),$(*1~[CH2]~[CH2]1)]"));
std::unique_ptr<RDKit::ROMol> bit_119 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]=*"));
std::unique_ptr<RDKit::ROMol> bit_120 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6R]"));
std::unique_ptr<RDKit::ROMol> bit_121 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7R]"));
std::unique_ptr<RDKit::ROMol> bit_122 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~[#7](~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_123 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]~[#6]~[#8]"));
std::unique_ptr<RDKit::ROMol> bit_124 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[!#6!#1]"));
std::unique_ptr<RDKit::ROMol> bit_126 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*!@[#8]!@*"));
std::unique_ptr<RDKit::ROMol> bit_127 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*@*!@[#8]"));
std::unique_ptr<RDKit::ROMol> bit_128 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol(
"[$(*~[CH2]~*~*~*~[CH2]~*),$([R]1@[CH2R]@[R]@[R]@[R]@[CH2R]1),$(*~["
"CH2]~[R]1@[R]@[R]@[CH2R]1),$(*~[CH2]~*~[R]1@[R]@[CH2R]1)]"));
std::unique_ptr<RDKit::ROMol> bit_129 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[$(*~[CH2]~*~*~[CH2]~*),$([R]1@[CH2]@[R]@[R]@[CH2R]1)"
",$(*~[CH2]~[R]1@[R]@[CH2R]1)]"));
std::unique_ptr<RDKit::ROMol> bit_131 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1!H0]"));
std::unique_ptr<RDKit::ROMol> bit_132 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]~*~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_133 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*@*!@[#7]"));
std::unique_ptr<RDKit::ROMol> bit_135 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]!:*:*"));
std::unique_ptr<RDKit::ROMol> bit_136 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]=*"));
std::unique_ptr<RDKit::ROMol> bit_137 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!C!cR]"));
std::unique_ptr<RDKit::ROMol> bit_138 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[!#6!#1]~[CH2]~*"));
std::unique_ptr<RDKit::ROMol> bit_139 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[O!H0]"));
std::unique_ptr<RDKit::ROMol> bit_140 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#8]"));
std::unique_ptr<RDKit::ROMol> bit_141 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[CH3]"));
std::unique_ptr<RDKit::ROMol> bit_142 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]"));
std::unique_ptr<RDKit::ROMol> bit_144 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*!:*:*!:*"));
std::unique_ptr<RDKit::ROMol> bit_145 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*1~*~*~*~*~*~1"));
std::unique_ptr<RDKit::ROMol> bit_147 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[$(*~[CH2]~[CH2]~*),$([R]1@[CH2R]@[CH2R]1)]"));
std::unique_ptr<RDKit::ROMol> bit_148 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*~[!#6!#1](~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_149 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[C;H3,H4]"));
std::unique_ptr<RDKit::ROMol> bit_150 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*!@*@*!@*"));
std::unique_ptr<RDKit::ROMol> bit_151 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7!H0]"));
std::unique_ptr<RDKit::ROMol> bit_152 = std::unique_ptr<RDKit::ROMol>(
RDKit::SmartsToMol("[#8]~[#6](~[#6])~[#6]"));
std::unique_ptr<RDKit::ROMol> bit_154 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]=[#8]"));
std::unique_ptr<RDKit::ROMol> bit_155 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("*!@[CH2]!@*"));
std::unique_ptr<RDKit::ROMol> bit_156 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#7]~*(~*)~*"));
std::unique_ptr<RDKit::ROMol> bit_157 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]-[#8]"));
std::unique_ptr<RDKit::ROMol> bit_158 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[#6]-[#7]"));
std::unique_ptr<RDKit::ROMol> bit_162 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("a"));
std::unique_ptr<RDKit::ROMol> bit_165 =
std::unique_ptr<RDKit::ROMol>(RDKit::SmartsToMol("[R]"));
};
boost::flyweight<std::unique_ptr<Patterns>, boost::flyweights::no_tracking>
gpats;
void GenerateFP(const RDKit::ROMol &mol, ExplicitBitVect &fp) {
if (!gpats.get()) {
gpats = std::unique_ptr<Patterns>(new Patterns());
}
const Patterns &pats = *(gpats.get());
PRECONDITION(fp.size() == 167, "bad fingerprint");
fp.clearBits();
if (!mol.getNumAtoms()) {
return;
}
std::vector<RDKit::MatchVectType> matches;
RDKit::RWMol::ConstAtomIterator atom;
RDKit::MatchVectType match;
unsigned int count;
for (const auto atom : mol.atoms()) {
switch (atom->getAtomicNum()) {
case 3:
case 11:
case 19:
case 37:
case 55:
case 87:
fp.setBit(35);
break;
case 4:
case 12:
case 20:
case 38:
case 56:
case 88:
fp.setBit(10);
break;
case 5:
case 13:
case 31:
case 49:
case 81:
fp.setBit(18);
break;
case 9:
fp.setBit(42);
fp.setBit(134);
break;
case 15:
fp.setBit(29);
break;
case 16:
fp.setBit(88);
break;
case 17:
fp.setBit(103);
fp.setBit(134);
break;
case 21:
case 22:
case 39:
case 40:
case 72:
fp.setBit(5);
break;
case 23:
case 24:
case 25:
case 41:
case 42:
case 43:
case 73:
case 74:
case 75:
fp.setBit(7);
break;
case 26:
case 27:
case 28:
case 44:
case 45:
case 46:
case 76:
case 77:
case 78:
fp.setBit(9);
break;
case 29:
case 30:
case 47:
case 48:
case 79:
case 80:
fp.setBit(12);
break;
case 32:
case 33:
case 34:
case 50:
case 51:
case 52:
case 82:
case 83:
case 84:
fp.setBit(3);
break;
case 35:
fp.setBit(46);
fp.setBit(134);
break;
case 53:
fp.setBit(27);
fp.setBit(134);
break;
case 57:
case 58:
case 59:
case 60:
case 61:
case 62:
case 63:
case 64:
case 65:
case 66:
case 67:
case 68:
case 69:
case 70:
case 71:
fp.setBit(6);
break;
case 89:
case 90:
case 91:
case 92:
case 93:
case 94:
case 95:
case 96:
case 97:
case 98:
case 99:
case 100:
case 101:
case 102:
case 103:
fp.setBit(4);
break;
case 104:
fp.setBit(2);
break;
}
}
if (RDKit::SubstructMatch(mol, *pats.bit_8, match, true)) {
fp.setBit(8);
}
if (RDKit::SubstructMatch(mol, *pats.bit_11, match, true)) {
fp.setBit(11);
}
if (RDKit::SubstructMatch(mol, *pats.bit_13, match, true)) {
fp.setBit(13);
}
if (RDKit::SubstructMatch(mol, *pats.bit_14, match, true)) {
fp.setBit(14);
}
if (RDKit::SubstructMatch(mol, *pats.bit_15, match, true)) {
fp.setBit(15);
}
if (RDKit::SubstructMatch(mol, *pats.bit_16, match, true)) {
fp.setBit(16);
}
if (RDKit::SubstructMatch(mol, *pats.bit_17, match, true)) {
fp.setBit(17);
}
if (RDKit::SubstructMatch(mol, *pats.bit_19, match, true)) {
fp.setBit(19);
}
if (RDKit::SubstructMatch(mol, *pats.bit_20, match, true)) {
fp.setBit(20);
}
if (RDKit::SubstructMatch(mol, *pats.bit_21, match, true)) {
fp.setBit(21);
}
if (RDKit::SubstructMatch(mol, *pats.bit_22, match, true)) {
fp.setBit(22);
}
if (RDKit::SubstructMatch(mol, *pats.bit_23, match, true)) {
fp.setBit(23);
}
if (RDKit::SubstructMatch(mol, *pats.bit_24, match, true)) {
fp.setBit(24);
}
if (RDKit::SubstructMatch(mol, *pats.bit_25, match, true)) {
fp.setBit(25);
}
if (RDKit::SubstructMatch(mol, *pats.bit_26, match, true)) {
fp.setBit(26);
}
if (RDKit::SubstructMatch(mol, *pats.bit_28, match, true)) {
fp.setBit(28);
}
if (RDKit::SubstructMatch(mol, *pats.bit_30, match, true)) {
fp.setBit(30);
}
if (RDKit::SubstructMatch(mol, *pats.bit_31, match, true)) {
fp.setBit(31);
}
if (RDKit::SubstructMatch(mol, *pats.bit_32, match, true)) {
fp.setBit(32);
}
if (RDKit::SubstructMatch(mol, *pats.bit_33, match, true)) {
fp.setBit(33);
}
if (RDKit::SubstructMatch(mol, *pats.bit_34, match, true)) {
fp.setBit(34);
}
if (RDKit::SubstructMatch(mol, *pats.bit_36, match, true)) {
fp.setBit(36);
}
if (RDKit::SubstructMatch(mol, *pats.bit_37, match, true)) {
fp.setBit(37);
}
if (RDKit::SubstructMatch(mol, *pats.bit_38, match, true)) {
fp.setBit(38);
}
if (RDKit::SubstructMatch(mol, *pats.bit_39, match, true)) {
fp.setBit(39);
}
if (RDKit::SubstructMatch(mol, *pats.bit_40, match, true)) {
fp.setBit(40);
}
if (RDKit::SubstructMatch(mol, *pats.bit_41, match, true)) {
fp.setBit(41);
}
if (RDKit::SubstructMatch(mol, *pats.bit_43, match, true)) {
fp.setBit(43);
}
if (RDKit::SubstructMatch(mol, *pats.bit_44, match, true)) {
fp.setBit(44);
}
if (RDKit::SubstructMatch(mol, *pats.bit_45, match, true)) {
fp.setBit(45);
}
if (RDKit::SubstructMatch(mol, *pats.bit_47, match, true)) {
fp.setBit(47);
}
if (RDKit::SubstructMatch(mol, *pats.bit_48, match, true)) {
fp.setBit(48);
}
if (RDKit::SubstructMatch(mol, *pats.bit_49, match, true)) {
fp.setBit(49);
}
if (RDKit::SubstructMatch(mol, *pats.bit_50, match, true)) {
fp.setBit(50);
}
if (RDKit::SubstructMatch(mol, *pats.bit_51, match, true)) {
fp.setBit(51);
}
if (RDKit::SubstructMatch(mol, *pats.bit_52, match, true)) {
fp.setBit(52);
}
if (RDKit::SubstructMatch(mol, *pats.bit_53, match, true)) {
fp.setBit(53);
}
if (RDKit::SubstructMatch(mol, *pats.bit_54, match, true)) {
fp.setBit(54);
}
if (RDKit::SubstructMatch(mol, *pats.bit_55, match, true)) {
fp.setBit(55);
}
if (RDKit::SubstructMatch(mol, *pats.bit_56, match, true)) {
fp.setBit(56);
}
if (RDKit::SubstructMatch(mol, *pats.bit_57, match, true)) {
fp.setBit(57);
}
if (RDKit::SubstructMatch(mol, *pats.bit_58, match, true)) {
fp.setBit(58);
}
if (RDKit::SubstructMatch(mol, *pats.bit_59, match, true)) {
fp.setBit(59);
}
if (RDKit::SubstructMatch(mol, *pats.bit_60, match, true)) {
fp.setBit(60);
}
if (RDKit::SubstructMatch(mol, *pats.bit_61, match, true)) {
fp.setBit(61);
}
if (RDKit::SubstructMatch(mol, *pats.bit_62, match, true)) {
fp.setBit(62);
}
if (RDKit::SubstructMatch(mol, *pats.bit_63, match, true)) {
fp.setBit(63);
}
if (RDKit::SubstructMatch(mol, *pats.bit_64, match, true)) {
fp.setBit(64);
}
if (RDKit::SubstructMatch(mol, *pats.bit_65, match, true)) {
fp.setBit(65);
}
if (RDKit::SubstructMatch(mol, *pats.bit_66, match, true)) {
fp.setBit(66);
}
if (RDKit::SubstructMatch(mol, *pats.bit_67, match, true)) {
fp.setBit(67);
}
if (RDKit::SubstructMatch(mol, *pats.bit_68, match, true)) {
fp.setBit(68);
}
if (RDKit::SubstructMatch(mol, *pats.bit_69, match, true)) {
fp.setBit(69);
}
if (RDKit::SubstructMatch(mol, *pats.bit_70, match, true)) {
fp.setBit(70);
}
if (RDKit::SubstructMatch(mol, *pats.bit_71, match, true)) {
fp.setBit(71);
}
if (RDKit::SubstructMatch(mol, *pats.bit_72, match, true)) {
fp.setBit(72);
}
if (RDKit::SubstructMatch(mol, *pats.bit_73, match, true)) {
fp.setBit(73);
}
if (RDKit::SubstructMatch(mol, *pats.bit_74, match, true)) {
fp.setBit(74);
}
if (RDKit::SubstructMatch(mol, *pats.bit_75, match, true)) {
fp.setBit(75);
}
if (RDKit::SubstructMatch(mol, *pats.bit_76, match, true)) {
fp.setBit(76);
}
if (RDKit::SubstructMatch(mol, *pats.bit_77, match, true)) {
fp.setBit(77);
}
if (RDKit::SubstructMatch(mol, *pats.bit_78, match, true)) {
fp.setBit(78);
}
if (RDKit::SubstructMatch(mol, *pats.bit_79, match, true)) {
fp.setBit(79);
}
if (RDKit::SubstructMatch(mol, *pats.bit_80, match, true)) {
fp.setBit(80);
}
if (RDKit::SubstructMatch(mol, *pats.bit_81, match, true)) {
fp.setBit(81);
}
if (RDKit::SubstructMatch(mol, *pats.bit_82, match, true)) {
fp.setBit(82);
}
if (RDKit::SubstructMatch(mol, *pats.bit_83, match, true)) {
fp.setBit(83);
}
if (RDKit::SubstructMatch(mol, *pats.bit_84, match, true)) {
fp.setBit(84);
}
if (RDKit::SubstructMatch(mol, *pats.bit_85, match, true)) {
fp.setBit(85);
}
if (RDKit::SubstructMatch(mol, *pats.bit_86, match, true)) {
fp.setBit(86);
}
if (RDKit::SubstructMatch(mol, *pats.bit_87, match, true)) {
fp.setBit(87);
}
if (RDKit::SubstructMatch(mol, *pats.bit_89, match, true)) {
fp.setBit(89);
}
if (RDKit::SubstructMatch(mol, *pats.bit_90, match, true)) {
fp.setBit(90);
}
if (RDKit::SubstructMatch(mol, *pats.bit_91, match, true)) {
fp.setBit(91);
}
if (RDKit::SubstructMatch(mol, *pats.bit_92, match, true)) {
fp.setBit(92);
}
if (RDKit::SubstructMatch(mol, *pats.bit_93, match, true)) {
fp.setBit(93);
}
if (RDKit::SubstructMatch(mol, *pats.bit_94, match, true)) {
fp.setBit(94);
}
if (RDKit::SubstructMatch(mol, *pats.bit_95, match, true)) {
fp.setBit(95);
}
if (RDKit::SubstructMatch(mol, *pats.bit_96, match, true)) {
fp.setBit(96);
}
if (RDKit::SubstructMatch(mol, *pats.bit_97, match, true)) {
fp.setBit(97);
}
if (RDKit::SubstructMatch(mol, *pats.bit_98, match, true)) {
fp.setBit(98);
}
if (RDKit::SubstructMatch(mol, *pats.bit_99, match, true)) {
fp.setBit(99);
}
if (RDKit::SubstructMatch(mol, *pats.bit_100, match, true)) {
fp.setBit(100);
}
if (RDKit::SubstructMatch(mol, *pats.bit_101, match, true)) {
fp.setBit(101);
}
if (RDKit::SubstructMatch(mol, *pats.bit_102, match, true)) {
fp.setBit(102);
}
if (RDKit::SubstructMatch(mol, *pats.bit_104, match, true)) {
fp.setBit(104);
}
if (RDKit::SubstructMatch(mol, *pats.bit_105, match, true)) {
fp.setBit(105);
}
if (RDKit::SubstructMatch(mol, *pats.bit_106, match, true)) {
fp.setBit(106);
}
if (RDKit::SubstructMatch(mol, *pats.bit_107, match, true)) {
fp.setBit(107);
}
if (RDKit::SubstructMatch(mol, *pats.bit_108, match, true)) {
fp.setBit(108);
}
if (RDKit::SubstructMatch(mol, *pats.bit_109, match, true)) {
fp.setBit(109);
}
if (RDKit::SubstructMatch(mol, *pats.bit_110, match, true)) {
fp.setBit(110);
}
if (RDKit::SubstructMatch(mol, *pats.bit_111, match, true)) {
fp.setBit(111);
}
if (RDKit::SubstructMatch(mol, *pats.bit_112, match, true)) {
fp.setBit(112);
}
if (RDKit::SubstructMatch(mol, *pats.bit_113, match, true)) {
fp.setBit(113);
}
if (RDKit::SubstructMatch(mol, *pats.bit_114, match, true)) {
fp.setBit(114);
}
if (RDKit::SubstructMatch(mol, *pats.bit_115, match, true)) {
fp.setBit(115);
}
if (RDKit::SubstructMatch(mol, *pats.bit_116, match, true)) {
fp.setBit(116);
}
if (RDKit::SubstructMatch(mol, *pats.bit_117, match, true)) {
fp.setBit(117);
}
if (RDKit::SubstructMatch(mol, *pats.bit_118, matches, true, true) > 1) {
fp.setBit(118);
}
if (RDKit::SubstructMatch(mol, *pats.bit_119, match, true)) {
fp.setBit(119);
}
if (RDKit::SubstructMatch(mol, *pats.bit_120, matches, true, true) > 1) {
fp.setBit(120);
}
if (RDKit::SubstructMatch(mol, *pats.bit_121, match, true)) {
fp.setBit(121);
}
if (RDKit::SubstructMatch(mol, *pats.bit_122, match, true)) {
fp.setBit(122);
}
if (RDKit::SubstructMatch(mol, *pats.bit_123, match, true)) {
fp.setBit(123);
}
count = RDKit::SubstructMatch(mol, *pats.bit_124, matches, true, true);
if (count > 0) {
fp.setBit(124);
}
if (count > 1) {
fp.setBit(130);
}
if (RDKit::SubstructMatch(mol, *pats.bit_126, match, true)) {
fp.setBit(126);
}
count = RDKit::SubstructMatch(mol, *pats.bit_127, matches, true, true);
if (count > 1) {
fp.setBit(127);
}
if (count > 0) {
fp.setBit(143);
}
if (RDKit::SubstructMatch(mol, *pats.bit_128, match, true)) {
fp.setBit(128);
}
if (RDKit::SubstructMatch(mol, *pats.bit_129, match, true)) {
fp.setBit(129);
}
if (RDKit::SubstructMatch(mol, *pats.bit_131, matches, true, true) > 1) {
fp.setBit(131);
}
if (RDKit::SubstructMatch(mol, *pats.bit_132, match, true)) {
fp.setBit(132);
}
if (RDKit::SubstructMatch(mol, *pats.bit_133, match, true)) {
fp.setBit(133);
}
if (RDKit::SubstructMatch(mol, *pats.bit_135, match, true)) {
fp.setBit(135);
}
if (RDKit::SubstructMatch(mol, *pats.bit_136, matches, true, true) > 1) {
fp.setBit(136);
}
if (RDKit::SubstructMatch(mol, *pats.bit_137, match, true)) {
fp.setBit(137);
}
count = RDKit::SubstructMatch(mol, *pats.bit_138, matches, true, true);
if (count > 1) {
fp.setBit(138);
}
if (count > 0) {
fp.setBit(153);
}
if (RDKit::SubstructMatch(mol, *pats.bit_139, match, true)) {
fp.setBit(139);
}
count = RDKit::SubstructMatch(mol, *pats.bit_140, matches, true, true);
if (count > 3) {
fp.setBit(140);
}
if (count > 2) {
fp.setBit(146);
}
if (count > 1) {
fp.setBit(159);
}
if (count > 0) {
fp.setBit(164);
}
if (RDKit::SubstructMatch(mol, *pats.bit_141, matches, true, true) > 2) {
fp.setBit(141);
}
count = RDKit::SubstructMatch(mol, *pats.bit_142, matches, true, true);
if (count > 1) {
fp.setBit(142);
}
if (count > 0) {
fp.setBit(161);
}
if (RDKit::SubstructMatch(mol, *pats.bit_144, match, true)) {
fp.setBit(144);
}
count = RDKit::SubstructMatch(mol, *pats.bit_145, matches, true, true);
if (count > 1) {
fp.setBit(145);
}
if (count > 0) {
fp.setBit(163);
}
if (RDKit::SubstructMatch(mol, *pats.bit_147, match, true)) {
fp.setBit(147);
}
if (RDKit::SubstructMatch(mol, *pats.bit_148, match, true)) {
fp.setBit(148);
}
count = RDKit::SubstructMatch(mol, *pats.bit_149, matches, true, true);
if (count > 1) {
fp.setBit(149);
}
if (count > 0) {
fp.setBit(160);
}
if (RDKit::SubstructMatch(mol, *pats.bit_150, match, true)) {
fp.setBit(150);
}
if (RDKit::SubstructMatch(mol, *pats.bit_151, match, true)) {
fp.setBit(151);
}
if (RDKit::SubstructMatch(mol, *pats.bit_152, match, true)) {
fp.setBit(152);
}
if (RDKit::SubstructMatch(mol, *pats.bit_154, match, true)) {
fp.setBit(154);
}
if (RDKit::SubstructMatch(mol, *pats.bit_155, match, true)) {
fp.setBit(155);
}
if (RDKit::SubstructMatch(mol, *pats.bit_156, match, true)) {
fp.setBit(156);
}
if (RDKit::SubstructMatch(mol, *pats.bit_157, match, true)) {
fp.setBit(157);
}
if (RDKit::SubstructMatch(mol, *pats.bit_158, match, true)) {
fp.setBit(158);
}
if (RDKit::SubstructMatch(mol, *pats.bit_162, match, true)) {
fp.setBit(162);
}
if (RDKit::SubstructMatch(mol, *pats.bit_165, match, true)) {
fp.setBit(165);
}
/* BIT 125 */
RDKit::RingInfo *info = mol.getRingInfo();
unsigned int ringcount = info->numRings();
unsigned int nArom = 0;
for (unsigned int i = 0; i < ringcount; i++) {
bool isArom = true;
const std::vector<int> *ring = &info->bondRings()[i];
std::vector<int>::const_iterator iter;
for (iter = ring->begin(); iter != ring->end(); ++iter) {
if (!mol.getBondWithIdx(*iter)->getIsAromatic()) {
isArom = false;
break;
}
}
if (isArom) {
if (nArom) {
fp.setBit(125);
break;
} else {
nArom++;
}
}
}
/* BIT 166 */
std::vector<int> mapping;
if (RDKit::MolOps::getMolFrags(mol, mapping) > 1) {
fp.setBit(166);
}
}
} // namespace
namespace RDKit {
namespace MACCSFingerprints {
ExplicitBitVect *getFingerprintAsBitVect(const ROMol &mol) {
std::unique_ptr<ExplicitBitVect> fp(new ExplicitBitVect(167));
GenerateFP(mol, *fp);
return fp.release();
}
} // namespace MACCSFingerprints
} // namespace RDKit
Reference in New Issue View Git Blame Copy Permalink