annotate CADDSuite-1.5/data/bond_lengths/BondOrderGAFF.xml @ 7:bfab27640f5e draft

CADDSuite version 1.5

<?xml version="1.0" encoding="ISO-8859-1"?>
<table>
	<!-- 	This file supplies penalty scores for different 
	  		atom types in bond type perception accoring to 
	 								 	
	 				Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and 
	 				bond type perception in molecular mechanical calculations". Journal of 
	 				Molecular Graphics and Modelling , 25, 2006, 247260	

				A penalty score of 0 means that the corresponding valence is optimal.
				Note that the first matching entry is taken as the final atom type.

				Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
				The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
				right rule!

	 			Rev 14.12.2007  Conversion was done by Anna Dehof
 -->	
	<entry id="1">
		<elementstring>H</elementstring>
		<smartstring>SMARTS([#1])</smartstring>
		<penalty valence="0">64</penalty>
		<penalty valence="1">0</penalty>
		<penalty valence="2">64</penalty>
	</entry>
	<entry id="2">
		<elementstring>F</elementstring>
		<smartstring>SMARTS(F)</smartstring>
		<penalty valence="0">64</penalty>
		<penalty valence="1">0</penalty>
		<penalty valence="2">64</penalty>
	</entry>
	<entry id="3">
		<elementstring>Cl</elementstring>
		<smartstring>SMARTS(Cl)</smartstring>
		<penalty valence="0">64</penalty>
		<penalty valence="1">0</penalty>
		<penalty valence="2">64</penalty>
	</entry>
	<entry id="4">
		<elementstring>Br</elementstring>
		<smartstring>SMARTS(Br)</smartstring>
		<penalty valence="0">64</penalty>
		<penalty valence="1">0</penalty>
		<penalty valence="2">64</penalty>
	</entry>
	<entry id="5">
		<elementstring>I</elementstring>
		<smartstring>SMARTS(I)</smartstring>
		<penalty valence="0">64</penalty>
		<penalty valence="1">0</penalty>
		<penalty valence="2">64</penalty>
	</entry>
	<entry id="6">
		<elementstring>C</elementstring>
		<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
		<!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
		<penalty valence="3">0</penalty>
		<penalty valence="4">1</penalty>
		<penalty valence="5">32</penalty>
	</entry>
	<entry id="7">
		<elementstring>C</elementstring>
		<smartstring>SMARTS([#6D1])</smartstring>
		<penalty valence="3">1</penalty>
		<penalty valence="4">0</penalty>
		<penalty valence="5">32</penalty>
	</entry>
	<entry id="8">
		<elementstring>C</elementstring>
		<smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
		<penalty valence="4">32</penalty>
		<penalty valence="5">0</penalty>
		<penalty valence="6">32</penalty>
	</entry>
	<entry id="9">
		<elementstring>C</elementstring>
		<smartstring>SMARTS([#6])</smartstring>
		<penalty valence="2">64</penalty>
		<penalty valence="3">32</penalty>
		<penalty valence="4">0</penalty>
		<penalty valence="5">32</penalty>
		<penalty valence="6">64</penalty>
	</entry>
	<entry id="10">
		<elementstring>Si</elementstring>
		<smartstring>SMARTS([#14])</smartstring>
		<penalty valence="4">0</penalty>
	</entry>
	<entry id="11">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring>
		<penalty valence="2">0</penalty>
		<penalty valence="3">0</penalty>
	</entry>
	<entry id="12">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([#7D1])</smartstring>
		<penalty valence="2">3</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">32</penalty>
	</entry>
	<entry id="13">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring>
		<penalty valence="3">1</penalty>
		<penalty valence="4">0</penalty>
	</entry>
	<entry id="14">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([#7D2])</smartstring>
		<penalty valence="2">4</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">2</penalty>
	</entry>
	<entry id="15">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
		<penalty valence="3">64</penalty>
		<penalty valence="4">32</penalty>
		<penalty valence="5">0</penalty>
		<penalty valence="6">32</penalty>
	</entry>
	<entry id="16">
		<elementstring>N</elementstring>
		<!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->	
		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
		<penalty valence="3">1</penalty>
		<penalty valence="4">0</penalty>
	</entry>
	<entry id="17">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([#7D3])</smartstring>
		<penalty valence="2">32</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">1</penalty>
		<penalty valence="5">2</penalty>
	</entry>
	<entry id="18">
		<elementstring>N</elementstring>
		<smartstring>SMARTS([#7D4])</smartstring>
		<penalty valence="2">64</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">64</penalty>
	</entry>
	<entry id="19">
		<elementstring>O</elementstring>
		<smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
		<penalty valence="1">0</penalty>
		<penalty valence="2">1</penalty>
	</entry>
	<entry id="20">
		<elementstring>O</elementstring>
		<smartstring>SMARTS([#8D1])</smartstring>
		<penalty valence="1">1</penalty>
		<penalty valence="2">0</penalty>
		<penalty valence="3">64</penalty>
	</entry>
	<entry id="21">
		<elementstring>O</elementstring>
		<smartstring>SMARTS([#8D2])</smartstring>
		<penalty valence="1">32</penalty>
		<penalty valence="2">0</penalty>
		<penalty valence="3">64</penalty>
	</entry>
	<entry id="22">
		<elementstring>P</elementstring>
		<smartstring>SMARTS(#15D1)</smartstring>
		<penalty valence="2">2</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">32</penalty>
	</entry>
	<entry id="23">
		<elementstring>P</elementstring>
		<smartstring>SMARTS(#15D2)</smartstring>
		<penalty valence="2">4</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">2</penalty>
	</entry>
	<entry id="24">
		<elementstring>P</elementstring>
		<smartstring>SMARTS(#15D3)</smartstring>
		<penalty valence="2">32</penalty>
		<penalty valence="3">0</penalty>
		<penalty valence="4">1</penalty>
		<penalty valence="5">2</penalty>
	</entry>
	<entry id="25">
		<elementstring>P</elementstring>
		<!-- Note: this is _SLOW_ -->
		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
		<penalty valence="5">32</penalty>
		<penalty valence="6">0</penalty>
		<penalty valence="7">32</penalty>
	</entry>
	<entry id="26">
		<elementstring>P</elementstring>
		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
		<penalty valence="6">32</penalty>
		<penalty valence="7">0</penalty>
	</entry>
	<entry id="27">
		<elementstring>P</elementstring>
		<!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
		<smartstring>SMARTS(#15D4)</smartstring>
		<penalty valence="3">64</penalty>
		<penalty valence="4">1</penalty>
		<penalty valence="5">0</penalty>
		<penalty valence="6">32</penalty>
	</entry>
	<entry id="28">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(S)</smartstring>
		<penalty valence="1">0</penalty>
		<penalty valence="2">1</penalty>
	</entry>
	<entry id="29">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([#16D1])</smartstring>
		<penalty valence="1">2</penalty>
		<penalty valence="2">0</penalty>
		<penalty valence="3">64</penalty>
	</entry>
	<entry id="30">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([#16D2])</smartstring>
		<!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different!		
		<penalty valence="1">32</penalty>
		<penalty valence="2">0</penalty>
		<penalty valence="3">32</penalty>
		<penalty valence="4">1</penalty> -->
		<penalty valence="1">2</penalty>
		<penalty valence="2">0</penalty>
		<penalty valence="3">64</penalty>
	</entry>
	<entry id="31">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([#16D3])</smartstring>
		<penalty valence="3">1</penalty>
		<penalty valence="4">0</penalty>
		<penalty valence="5">2</penalty>
		<penalty valence="6">2</penalty>
	</entry>
	<entry id="32">
		<elementstring>S</elementstring>
		<smartstring>	SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
		<penalty valence="6">0</penalty>
		<penalty valence="7">32</penalty>
	</entry>
	<entry id="33">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>		
		<penalty valence="6">32</penalty>
		<penalty valence="7">0</penalty>
	</entry>
	<entry id="34">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
		<penalty valence="6">32</penalty>
		<penalty valence="7">0</penalty>
	</entry>
	<entry id="35">
		<elementstring>S</elementstring>
		<smartstring>SMARTS([#16D4])</smartstring>
		<penalty valence="4">4</penalty>
		<penalty valence="5">2</penalty>
		<penalty valence="6">0</penalty>
	</entry>
	<!-- The following rules are added to cope with ions -->
	<entry id="40">
		<elementstring>Li</elementstring>
		<smartstring>SMARTS([#3])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>
	<entry id="41">
		<elementstring>Na</elementstring>
		<smartstring>SMARTS([#11])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>
	<entry id="42">
		<elementstring>Mg</elementstring>
		<smartstring>SMARTS([#12])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>
	<entry id="43">
		<elementstring>K</elementstring>
		<smartstring>SMARTS([#19])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>
	<entry id="44">
		<elementstring>Ca</elementstring>
		<smartstring>SMARTS([#20])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>
	<entry id="45">
		<elementstring>Cu</elementstring>
		<smartstring>SMARTS([#29])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>
	<entry id="46">
		<elementstring>Zn</elementstring>
		<smartstring>SMARTS([#30])</smartstring>
		<penalty valence="0">0</penalty>
	</entry>

</table>