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1 ##############################################################################
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2 # #
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3 # Open Babel file: atomtyp.txt #
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4 # #
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5 # #
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6 # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
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7 # Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison #
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8 # Part of the Open Babel package, under the GNU General Public License (GPL)#
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9 # #
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10 # SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) #
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11 # #
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12 # INTHYB: used to assign the internal hybridization values for atoms #
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13 # IMPVAL: used to assign the implicit valence of an atom #
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14 # EXTTYP: used to assign the external type of an atom for translation to #
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15 # package specific types (i.e. Sybyl Mol2) #
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16 # (these should correspond to INT type names in types.txt too.) #
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17 # #
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18 # The LAST PATTERN MATCHED is used to assign values with the corresponding #
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19 # INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
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20 # in the EXTRA DEFINITIONS section (to separate from original patterns.) #
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21 # #
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22 ##############################################################################
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23
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24 INTHYB [D4] 3 #any 4-valent atom -- tetrahedral
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25 INTHYB [D5] 5 #any 5-valent atom -- trigbipy
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26 INTHYB [D6] 6 #any 6-valent atom -- oct
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27 INTHYB [C] 3 #sp3 carbon
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28 INTHYB [c,$(C=*)] 2 #sp2 carbon
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29 # INTHYB [$([#6]([#8D1])[#8D1])] 2 # Commented out after PR#3089597
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30 INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon
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31
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32 INTHYB [N] 3 #sp3 nitrogen
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33 INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
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34 INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen
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35 INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen
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36
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37 INTHYB [O] 3 #sp3 oxygen
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38 INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen
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39 INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen
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40 INTHYB [$(O#*)] 1 #sp oxygen
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41
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42 INTHYB [P] 3 #sp3 phosphorus
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43 INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus
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44 INTHYB [PD5] 5 #sp3d phosphorus, as in PF5
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45 INTHYB [Pv5] 5 #sp3d phosphorus, as in H3PO4
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46 INTHYB [S] 3 #sp3 sulfur
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47 INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur
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48 INTHYB [SD6] 6 #sp3d2 sulfur, as in SF6
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49 INTHYB [B] 2 #sp2 boron
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50 INTHYB [BD4] 3 #sp3 boron
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51
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52 INTHYB [Al] 2 # typical sp2 Al (and family)
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53 INTHYB [Ga] 2
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54 INTHYB [In] 2
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55 INTHYB [Tl] 2
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56 INTHYB [AlD4] 3 # sp3 Al
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57 INTHYB [Si] 3 # sp3 Si (and family)
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58 INTHYB [Pb] 3
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59 INTHYB [Ge;!D5] 3
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60 INTHYB [Sn;!D5] 3
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61 INTHYB [AsD3] 3 # AsCl3 (AsCl5 handled by D5 above)
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62 INTHYB [SbD3] 3 #
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63 # SbD5, AsD5 are all trigbpy so are handled by D5 above
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64 INTHYB [BiD3] 3 #
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65 INTHYB [BiD5] 6 # BiF5 is square-pyr, not trigbpy
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66
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67 INTHYB [se] 2 # aromatic sp2 Se
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68 INTHYB [Se] 3 # sp3 hybridization Se (and family)
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69 INTHYB [Te] 3
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70 INTHYB [Po] 3
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71
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72 INTHYB [Be] 1 # Alkaline earth, like sp hybrids
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73 INTHYB [Mg] 1
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74 INTHYB [Ca] 1
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75 INTHYB [Sr] 1
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76 INTHYB [Ba] 1
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77 INTHYB [Ra] 1
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78
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79 #INTHYB [Pt] 4 # normally square planar
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80 #INTHYB [Pd] 4
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81 #INTHYB [Cu] 4
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82 #INTHYB [Ag] 4
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83 #INTHYB [Au] 4
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84
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85 #
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86 #IMPLICIT VALENCE RULES
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87 #
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88 #IMPVAL [#3,#11,#19,#37,#55,#87] 1 # Alkali metals
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89 #IMPVAL [#4,#12,#20,#38,#56,#88] 2 # Alkaline earth
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90
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91 IMPVAL [#5+] 2
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92 IMPVAL [#5-] 4
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93 IMPVAL [#5] 3 # Generic boron
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94 IMPVAL [$([#6+]=*)] 2
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95 IMPVAL [$([#6+]#*)] 1 # just for InChI C2
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96
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97 IMPVAL [#6^3] 4
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98 IMPVAL [#6^2] 3
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99 IMPVAL [#6^1] 2
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100 IMPVAL [#6^3+] 3
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101 IMPVAL [#6^2+] 2
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102 IMPVAL [#6^1+] 1
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103
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104 IMPVAL [#6^3-] 3
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105 IMPVAL [#6^2-] 2
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106 IMPVAL [#6^1-] 1 # isocyanides, CO (valence=1, bond order=3)
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107 IMPVAL [c+] 2
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108
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109 IMPVAL [N^3] 3
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110 IMPVAL [N^3+] 4
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111 IMPVAL [N^2] 3
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112 #IMPVAL [N^2-,N^3-] 2
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113 IMPVAL [ND1^1] 1
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114 IMPVAL [ND2^1] 2
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115 IMPVAL [$(N([OD1])*)] 3
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116 IMPVAL [$(NC=O)] 3
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117 #IMPVAL [$(n(c=O)c=O)] 3 # aromatic diimide
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118 IMPVAL [$(N(~[OD1])~[OD1])] 3
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119 IMPVAL [$([Nr0]C=[Nr0])] 3
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120 IMPVAL [$(N=*)] 2
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121 #IMPVAL [$([Nr0]=C[Nr0])] 3
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122 IMPVAL [$([Nr0]=C[Nr0])] 2
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123 IMPVAL [$([N+r0]=C[Nr0])] 3 # patch from Steve Constable
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124 IMPVAL [$([#7D1-]=*)] 1
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125 IMPVAL [N^1-] 1 # N2O [N-]=[N+]=O (valence=1, bondorder=2)
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126 IMPVAL [N-] 2
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127 IMPVAL [n] 2
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128 IMPVAL [n-] 2
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129 IMPVAL [n+] 3
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130 IMPVAL [$([#7-]=*)] 1
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131 IMPVAL [$([#7+]#*)] 2
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132 IMPVAL [$([#7+]=*)] 3
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133 IMPVAL [$([#7+](=*)=*)] 2
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134
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135 IMPVAL [$([#8+]#*)] 1
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136
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137 IMPVAL [#8] 2 # Generic O
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138 IMPVAL [#8-] 1
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139 IMPVAL [#8-2] 0
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140 IMPVAL [#8+] 3
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141 IMPVAL [$([#8]=*)] 1
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142 IMPVAL [#8^1+] 1 # carbon monoxide
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143
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144 IMPVAL [#9D0] 1
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145 IMPVAL [#9D0-] 0 #[F-]
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146
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147 IMPVAL [#13] 3 # generic Al
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148
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149 IMPVAL [#14] 4 # regular sp3 Si
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150 IMPVAL [#14^2] 2 # silylenes
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151 IMPVAL [$([#14]=*)] 3 # e.g., Si=O
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152 IMPVAL [$([#14](=*)=*)] 0 # e.g., Si(=O)=O
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153 IMPVAL [$([#14+]#*)] 1 # just for InChI Si2
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154 IMPVAL [$([#14-]#*)] 1 # just for InChI Si2
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155
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156 IMPVAL [#15D4] 4
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157 IMPVAL [#15D3] 3
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158 IMPVAL [#15D2] 3
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159 IMPVAL [#15D1^3] 3
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160 IMPVAL [#15D1^2] 3
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161 IMPVAL [#15D0] 3
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162 IMPVAL [$([#15]=[#6])] 2
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163 IMPVAL [pD2] 2
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164 IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence)
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165 IMPVAL [$([#15](=[#8])=[#8])] 3 # metaphosphate (double bond = one valence)
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166 IMPVAL [$([#15+](=[#8])([#8]))] 0 # R-P+O2
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167
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168 IMPVAL [#16] 2 #revised CM April 2008
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169 IMPVAL [$([#16D1]=*)] 1
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170 IMPVAL [$([#16D3](=O)(=O)-O)] 4 #e.g. O[S](=O)=O
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171 IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O
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172 IMPVAL [#16D1-] 1
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173
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174 IMPVAL [#17D0] 1
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175 IMPVAL [#17D0-] 0 #[Cl-]
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176
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177 IMPVAL [#31] 3
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178 IMPVAL [#32] 4
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179
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180 IMPVAL [#33] 3
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181 IMPVAL [as] 3
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182
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183 IMPVAL [#34] 2
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184
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185 IMPVAL [#35D0] 1
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186 IMPVAL [#35D0-] 0 #[Br-]
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187
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188 #IMPVAL [#49,#81] 3 # In, Tl, like Ga
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189 #IMPVAL [#50,#82] 4 # Sn, Pb, like Ge
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190 #IMPVAL [#51,#83] 3 # Sb, Bi, like As
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191
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192 IMPVAL [#52] 2
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193 IMPVAL [#53D0] 1
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194 IMPVAL [#53D0-] 0 #[I-]
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195
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196 #
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197 #EXTERNAL TYPE RULES
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198 #
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199
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200 # Tinker OH hydrogens for MM2
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201 # Fixes PR# 1839274
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202 EXTTYP [#1][#8] HO
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203
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204 EXTTYP [#7^3] N3
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205 EXTTYP [#7X4] N3+
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206 EXTTYP [#7^2] Npl
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207 EXTTYP [#7^1] N1
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208 EXTTYP [$(N=*)] N2
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209 EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+
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210 EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+
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211 EXTTYP [$([ND1]=C[ND1])] Ng+
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212 EXTTYP [$([ND1]C=[ND1])] Ng+
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213 EXTTYP [$(N(O)*)] Nox
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214 EXTTYP [$(NC=[O,S])] Nam
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215 EXTTYP [$(N(~[OD1])~[OD1])] Ntr
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216 EXTTYP [n] Nar
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217
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218 EXTTYP [#6^3] C3
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219 EXTTYP [#6^2] C2
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220 EXTTYP [$(C(=O)[OD1])] Cac
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221 EXTTYP [c] Car
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222 EXTTYP [#6^1] C1
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223 EXTTYP [#6+] C+
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224 EXTTYP [#6-] C-
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225
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226 EXTTYP [#8^3] O3
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227 EXTTYP [#8^2] O2
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228 EXTTYP [$(Oa)] O2
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229 #The following 2 lines used for correct Sybyl atom typing
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230 EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen
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231 EXTTYP [$(Oa)] O3 #aromatic ether
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232 EXTTYP [#8-] O-
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233 EXTTYP [$([#8D1]~[#6^2]~[#8D1])] O.co2
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234
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235 EXTTYP [#15] P
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236 EXTTYP [#15X4+] P3+
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237 EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac
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238 EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac
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239
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240 EXTTYP [#16] S3
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241 EXTTYP [#16D3+,#16X3+] S3+
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242 EXTTYP [#16;s,$([SD1]=*)] S2
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243 EXTTYP [#16D4;$(S(=O)(=O))] So2
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244 EXTTYP [#16D3;$(S(=O))] Sox
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245 EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac
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246 EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac
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247
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248 EXTTYP [#5] B2
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249 EXTTYP [#5D4] B3
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250
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251 ######################## Add Extra Definitions Here ##########################
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252
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253 #INTHYB [U] 3
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254 #INTHYB [W] 3
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255 #INTHYB [Mo] 6 # for development
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256 #INTHYB [Cr] 5 # for development
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257
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258 ############################# End Extra Definitions ##########################
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259
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