Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite-1.6/data/bond_lengths/BondOrderGAFF.xml @ 10:eda78e0f5df6 draft default tip
Deleted selected files
| author | marcel |
|---|---|
| date | Sun, 30 Nov 2014 03:46:08 -0500 |
| parents | 488032d372e1 |
| children |
line wrap: on
line diff
--- a/CADDSuite-1.6/data/bond_lengths/BondOrderGAFF.xml Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,306 +0,0 @@ -<?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)&$(*aR)&n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> --> - <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#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&!#16,!D1])(~[!#8&!#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([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])</smartstring> - <penalty valence="5">32</penalty> - <penalty valence="6">0</penalty> - <penalty valence="7">32</penalty> - </entry> - <entry id="26"> - <elementstring>P</elementstring> - <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#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&!#16,!D1])(~[!#8&!#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([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring> - <penalty valence="6">0</penalty> - <penalty valence="7">32</penalty> - </entry> - <entry id="33"> - <elementstring>S</elementstring> - <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#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>