Hi, Tim, what are you up to these days?
Please take a look at the code I just checked in for Jmol --
org.jmol.minimize.forcefieldsForceFieldMMFF.java
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java?view=markup
private Integer applyEmpiricalRules(MinObject o, double[] ddata, int
ktype)
I think I simplified that logic considerably. Also, I would appreciate it
if you would take a look at
private static double getRuleBondLength(MinAtom a, MinAtom b, int boAB,
boolean isAromatic)
Seems odd, and there are so few examples that I can't be sure what the
issue is. It validates, but...
Bob
On Sat, May 19, 2012 at 10:29 AM, Tim Vandermeersch <
tim.vandermeer...@gmail.com> wrote:
> Hi,
>
> This is obviously a bug, I'll try to correct this in the following
> week unless you beat me to it.
>
> Tim
>
> On Fri, May 18, 2012 at 5:03 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> > OK, I'm stumped. How does one get to Rule d? Does anyone know if this
> code
> > was ever tested?
> >
> > 03131 if (b->GetBond(c)->IsAromatic()) {
> > 03132 double Ub, Uc, pi_bc, beta;
> > 03133 Ub = GetUParam(b);
> > 03134 Uc = GetUParam(c);
> > 03135
> > 03136 if (!HasPilpSet(type_b) && !HasPilpSet(type_c))
> > 03137 pi_bc = 0.5;
> > 03138 else
> > 03139 pi_bc = 0.3;
> > 03140
> > 03141 if (((GetVal(type_b) == 3) && (GetVal(type_c) == 4)) ||
> > 03142 ((GetVal(type_b) == 4) && (GetVal(type_c) == 3)))
> > 03143 beta = 3.0;
> > 03144 else
> > 03145 beta = 6.0;
> > 03146
> > 03147 torsioncalc.v1 = 0.0;
> > 03148 torsioncalc.v2 = beta * pi_bc * sqrt(Ub * Uc);
> > 03149 torsioncalc.v3 = 0.0;
> > 03150 found_rule = true;
> > 03151 } else {
> > 03152 // rule (c) page 631
> > 03153 double Ub, Uc, pi_bc, beta;
> > 03154 Ub = GetUParam(b);
> > 03155 Uc = GetUParam(c);
> > 03156
> > 03157 if (((GetMltb(type_b) == 2) && (GetMltb(type_c) == 2)) &&
> > a->GetBond(b)->IsDouble())
> > 03158 pi_bc = 1.0;
> > 03159 else
> > 03160 pi_bc = 0.4;
> > 03161
> > 03162 beta = 6.0;
> > 03163 torsioncalc.v1 = 0.0;
> > 03164 torsioncalc.v2 = beta * pi_bc * sqrt(Ub * Uc);
> > 03165 torsioncalc.v3 = 0.0;
> > 03166 found_rule = true;
> > 03167 }
> > 03168
> > 03169 // rule (d) page 632
> > 03170 if (!found_rule)
> > 03171 if (((GetCrd(type_b) == 4) && (GetCrd(type_c) == 4))) {
> > 03172 double Vb, Vc;
> > 03173
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > St. Olaf College
> > 1520 St. Olaf Ave.
> > Northfield, MN 55057
> > http://www.stolaf.edu/people/hansonr
> > phone: 507-786-3107
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> >
> >
> ------------------------------------------------------------------------------
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> >
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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