Right, the XYZ format doesn't have atom names. It's main advantage is that
you can have an unlimited number of atoms. How about another format? Maybe
CML? The format is just about as simple as XYZ; a bit more verbose. "id"
should be atom name. You could then add "bonds" if you want.
<?xml version="1.0" encoding="ISO-8859-1"?>
<molecule id="METHANOL" xmlns="http://www.xml-cml.org/schema/cml2/core";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core cmlAll.xsd">
<atomArray>
<atom id="a1" elementType="C" x3="-0.748" y3="-0.015" z3="0.024"/>
<atom id="a2" elementType="O" x3="0.558" y3="0.420" z3="-0.278"/>
<atom id="a3" elementType="H" x3="-1.263" y3="0.202" z3="-0.901"/>
<atom id="a4" elementType="H" x3="-0.699" y3="-0.934" z3="0.609"/>
<atom id="a5" elementType="H" x3="0.716" y3="1.404" z3="0.137"/>
<atom id="a6" elementType="H" x3="-1.263" y3="0.754" z3="0.600"/>
</atomArray>
</molecule>
Actually, SmilesParser isn't it. That's something different.
On Tue, Feb 15, 2011 at 4:37 PM, J. Lamar Barnett <j.lamar.barn...@gmail.com
> wrote:
> Hello,
>
> My apologies on the first mail that was sent. I'm a trying to adapt
> Jmol for usage as a viewer for antigenic cartography data. As of
> current with a slightly tweaked menu and using xyz input files we are
> able to show a 3D model of antigen relations with Jmol however, Jmol
> does not like the atoms in the xyz input file having their antigen
> names. I have found where the input is parsed ( SmilesParser.java:
> parseAtom ) but am slight at a loss of how to "bypass" the throwing of
> an invalid atom symbol and inserting our own data.
>
> Thank you,
>
> Lamar Barnett
>
> j.lamar.barn...@gmail.com
>
>
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it is better to take what answer we get.
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------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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