Mercurial > repos > marcel > caddsuite_linux_x86_64
annotate CADDSuite-1.5/data/bond_lengths/BondOrderGAFF.xml @ 15:ac342506cd4e draft
CADDSuite version 1.5
author | Marcel Schumann <schumann.marcel@gmail.com> |
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date | Tue, 24 Jul 2012 11:08:49 -0400 |
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1 <?xml version="1.0" encoding="ISO-8859-1"?> |
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2 <table> |
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3 <!-- This file supplies penalty scores for different |
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4 atom types in bond type perception accoring to |
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5 |
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6 Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and |
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7 bond type perception in molecular mechanical calculations". Journal of |
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8 Molecular Graphics and Modelling , 25, 2006, 247260 |
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9 |
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10 A penalty score of 0 means that the corresponding valence is optimal. |
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11 Note that the first matching entry is taken as the final atom type. |
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12 |
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13 Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O). |
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14 The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the |
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15 right rule! |
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16 |
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17 Rev 14.12.2007 Conversion was done by Anna Dehof |
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18 --> |
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19 <entry id="1"> |
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20 <elementstring>H</elementstring> |
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21 <smartstring>SMARTS([#1])</smartstring> |
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22 <penalty valence="0">64</penalty> |
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23 <penalty valence="1">0</penalty> |
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24 <penalty valence="2">64</penalty> |
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25 </entry> |
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26 <entry id="2"> |
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27 <elementstring>F</elementstring> |
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28 <smartstring>SMARTS(F)</smartstring> |
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29 <penalty valence="0">64</penalty> |
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30 <penalty valence="1">0</penalty> |
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31 <penalty valence="2">64</penalty> |
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32 </entry> |
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33 <entry id="3"> |
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34 <elementstring>Cl</elementstring> |
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35 <smartstring>SMARTS(Cl)</smartstring> |
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36 <penalty valence="0">64</penalty> |
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37 <penalty valence="1">0</penalty> |
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38 <penalty valence="2">64</penalty> |
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39 </entry> |
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40 <entry id="4"> |
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41 <elementstring>Br</elementstring> |
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42 <smartstring>SMARTS(Br)</smartstring> |
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43 <penalty valence="0">64</penalty> |
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44 <penalty valence="1">0</penalty> |
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45 <penalty valence="2">64</penalty> |
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46 </entry> |
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47 <entry id="5"> |
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48 <elementstring>I</elementstring> |
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49 <smartstring>SMARTS(I)</smartstring> |
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50 <penalty valence="0">64</penalty> |
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51 <penalty valence="1">0</penalty> |
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52 <penalty valence="2">64</penalty> |
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53 </entry> |
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54 <entry id="6"> |
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55 <elementstring>C</elementstring> |
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56 <smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring> |
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57 <!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> --> |
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58 <penalty valence="3">0</penalty> |
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59 <penalty valence="4">1</penalty> |
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60 <penalty valence="5">32</penalty> |
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61 </entry> |
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62 <entry id="7"> |
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63 <elementstring>C</elementstring> |
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64 <smartstring>SMARTS([#6D1])</smartstring> |
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65 <penalty valence="3">1</penalty> |
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66 <penalty valence="4">0</penalty> |
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67 <penalty valence="5">32</penalty> |
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68 </entry> |
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69 <entry id="8"> |
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70 <elementstring>C</elementstring> |
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71 <smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring> |
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72 <penalty valence="4">32</penalty> |
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73 <penalty valence="5">0</penalty> |
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74 <penalty valence="6">32</penalty> |
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75 </entry> |
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76 <entry id="9"> |
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77 <elementstring>C</elementstring> |
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78 <smartstring>SMARTS([#6])</smartstring> |
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79 <penalty valence="2">64</penalty> |
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80 <penalty valence="3">32</penalty> |
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81 <penalty valence="4">0</penalty> |
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82 <penalty valence="5">32</penalty> |
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83 <penalty valence="6">64</penalty> |
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84 </entry> |
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85 <entry id="10"> |
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86 <elementstring>Si</elementstring> |
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87 <smartstring>SMARTS([#14])</smartstring> |
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88 <penalty valence="4">0</penalty> |
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89 </entry> |
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90 <entry id="11"> |
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91 <elementstring>N</elementstring> |
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92 <smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> |
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93 <penalty valence="2">0</penalty> |
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94 <penalty valence="3">0</penalty> |
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95 </entry> |
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96 <entry id="12"> |
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97 <elementstring>N</elementstring> |
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98 <smartstring>SMARTS([#7D1])</smartstring> |
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99 <penalty valence="2">3</penalty> |
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100 <penalty valence="3">0</penalty> |
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101 <penalty valence="4">32</penalty> |
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102 </entry> |
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103 <entry id="13"> |
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104 <elementstring>N</elementstring> |
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105 <smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> |
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106 <penalty valence="3">1</penalty> |
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107 <penalty valence="4">0</penalty> |
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108 </entry> |
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109 <entry id="14"> |
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110 <elementstring>N</elementstring> |
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111 <smartstring>SMARTS([#7D2])</smartstring> |
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112 <penalty valence="2">4</penalty> |
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113 <penalty valence="3">0</penalty> |
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114 <penalty valence="4">2</penalty> |
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115 </entry> |
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116 <entry id="15"> |
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117 <elementstring>N</elementstring> |
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118 <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring> |
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119 <penalty valence="3">64</penalty> |
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120 <penalty valence="4">32</penalty> |
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123 </entry> |
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124 <entry id="16"> |
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145 </entry> |
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151 </entry> |
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153 <elementstring>O</elementstring> |
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154 <smartstring>SMARTS([#8D1])</smartstring> |
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158 </entry> |
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160 <elementstring>O</elementstring> |
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161 <smartstring>SMARTS([#8D2])</smartstring> |
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165 </entry> |
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167 <elementstring>P</elementstring> |
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168 <smartstring>SMARTS(#15D1)</smartstring> |
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172 </entry> |
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174 <elementstring>P</elementstring> |
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175 <smartstring>SMARTS(#15D2)</smartstring> |
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179 </entry> |
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180 <entry id="24"> |
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181 <elementstring>P</elementstring> |
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182 <smartstring>SMARTS(#15D3)</smartstring> |
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184 <penalty valence="3">0</penalty> |
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185 <penalty valence="4">1</penalty> |
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187 </entry> |
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188 <entry id="25"> |
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189 <elementstring>P</elementstring> |
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190 <!-- Note: this is _SLOW_ --> |
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191 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])</smartstring> |
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195 </entry> |
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198 <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> |
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201 </entry> |
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204 <!-- This rule should be the last PD4 rule because it should only match when the other rules fail! --> |
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205 <smartstring>SMARTS(#15D4)</smartstring> |
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210 </entry> |
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211 <entry id="28"> |
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212 <elementstring>S</elementstring> |
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213 <smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)</smartstring> |
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216 </entry> |
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217 <entry id="29"> |
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218 <elementstring>S</elementstring> |
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219 <smartstring>SMARTS([#16D1])</smartstring> |
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223 </entry> |
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224 <entry id="30"> |
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225 <elementstring>S</elementstring> |
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226 <smartstring>SMARTS([#16D2])</smartstring> |
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227 <!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different! |
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235 </entry> |
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236 <entry id="31"> |
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237 <elementstring>S</elementstring> |
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238 <smartstring>SMARTS([#16D3])</smartstring> |
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239 <penalty valence="3">1</penalty> |
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243 </entry> |
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244 <entry id="32"> |
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245 <elementstring>S</elementstring> |
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246 <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring> |
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249 </entry> |
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250 <entry id="33"> |
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251 <elementstring>S</elementstring> |
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252 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> |
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254 <penalty valence="7">0</penalty> |
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255 </entry> |
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256 <entry id="34"> |
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257 <elementstring>S</elementstring> |
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258 <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring> |
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261 </entry> |
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262 <entry id="35"> |
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263 <elementstring>S</elementstring> |
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264 <smartstring>SMARTS([#16D4])</smartstring> |
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267 <penalty valence="6">0</penalty> |
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268 </entry> |
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269 <!-- The following rules are added to cope with ions --> |
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270 <entry id="40"> |
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271 <elementstring>Li</elementstring> |
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272 <smartstring>SMARTS([#3])</smartstring> |
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273 <penalty valence="0">0</penalty> |
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274 </entry> |
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275 <entry id="41"> |
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276 <elementstring>Na</elementstring> |
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277 <smartstring>SMARTS([#11])</smartstring> |
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278 <penalty valence="0">0</penalty> |
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279 </entry> |
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280 <entry id="42"> |
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281 <elementstring>Mg</elementstring> |
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282 <smartstring>SMARTS([#12])</smartstring> |
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283 <penalty valence="0">0</penalty> |
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284 </entry> |
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285 <entry id="43"> |
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286 <elementstring>K</elementstring> |
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287 <smartstring>SMARTS([#19])</smartstring> |
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288 <penalty valence="0">0</penalty> |
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289 </entry> |
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290 <entry id="44"> |
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291 <elementstring>Ca</elementstring> |
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292 <smartstring>SMARTS([#20])</smartstring> |
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293 <penalty valence="0">0</penalty> |
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294 </entry> |
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295 <entry id="45"> |
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296 <elementstring>Cu</elementstring> |
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297 <smartstring>SMARTS([#29])</smartstring> |
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298 <penalty valence="0">0</penalty> |
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299 </entry> |
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300 <entry id="46"> |
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301 <elementstring>Zn</elementstring> |
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302 <smartstring>SMARTS([#30])</smartstring> |
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303 <penalty valence="0">0</penalty> |
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304 </entry> |
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305 |
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306 </table> |