1. What are the default values and typical values for:
bondTolerance
public final static float DEFAULT_BOND_TOLERANCE = 0.45f;
minBondDistance
//minimum acceptable bonding distance ... from OpenBabel ... mth 2003 05
26
public final static float DEFAULT_MIN_BOND_DISTANCE = 0.4f;
All specified distance units in Jmol are Angstroms.
2. Have later versions of Java possibly caused a change in how these
parameters are initially set? We've been running with a frozen version of
Jmol on our website and just noticed problems with methyl groups. Since our
code and data have not changed, Java update seem like the only source of
changes.
I don't recall anything changing in that regard any time recently. But
perhaps years ago. How old is that version? Send me a file or two so I can
take a look at what you have. Certainly this is very unusual.
Bob Hanson
On Fri, Aug 29, 2008 at 8:59 PM, Andrew M. Simms
[EMAIL PROTECTED]wrote:
Has something changed recently with defaults related to autobond. Ball
and stick structures that were fine in the past seem to end up with nearly
every adjacent atom being bonded to each other (i.e. hydrogens bond to their
carbon as well as to each other) .
Questions:
1. What are the default values and typical values for:
bondTolerance
minBondDistance
and most importantly, what are the units for these (I was surprised the
docs described these as decimal as opposed to decimal in angstroms or
something else)?
2. Have later versions of Java possibly caused a change in how these
parameters are initially set? We've been running with a frozen version of
Jmol on our website and just noticed problems with methyl groups. Since our
code and data have not changed, Java update seem like the only source of
changes.
--Andrew
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
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