|
unpacked
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aspirin.class,
aspirin.java,
aterm.class,
aterm.java,
atom.class,
atom.java,
buckybal.class,
buckybal.java,
carbon.class,
carbon.java,
diamond.class,
diamond.java,
dl_atom.class,
dl_atom.java,
dl_bond.class,
dl_bond.java,
dlentry.class,
dlentry.java,
dlforce.class,
dlforce.java,
group.class,
group.java,
hydrogen.class,
hydrogen.java,
lrterm.class,
lrterm.java,
lterm.class,
lterm.java,
nanocad.class,
nanocad.java,
ncad.html,
nitrogen.class,
nitrogen.java,
oxygen.class,
oxygen.java,
propane.class,
propane.java,
term.class,
term.java,
tterm.class,
tterm.java,
tworings.class,
tworings.java,
view.class,
view.java,
water.class,
water.java,
wrapper.class,
wrapper.java
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/**
* aterm.java - MM2-style angle energy term
* Copyright (c) 1997 Will Ware, all rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and other materials provided with the distribution.
* 3. All advertising materials mentioning features or use of this software
* or its derived works must display the following acknowledgement:
* This product includes software developed by Will Ware.
*
* This software is provided "as is" and any express or implied warranties,
* including, but not limited to, the implied warranties of merchantability
* or fitness for any particular purpose are disclaimed. In no event shall
* Will Ware be liable for any direct, indirect, incidental, special,
* exemplary, or consequential damages (including, but not limited to,
* procurement of substitute goods or services; loss of use, data, or
* profits; or business interruption) however caused and on any theory of
* liability, whether in contract, strict liability, or tort (including
* negligence or otherwise) arising in any way out of the use of this
* software, even if advised of the possibility of such damage.
*/
import java.lang.Math;
import java.util.Vector;
import atom;
public class aterm extends term
{
public static final String rcsid =
"$Id: aterm.java,v 1.9 1997/09/09 03:38:49 wware Exp $";
private static final double convert = 3.1415926 / 180; // degrees to radians
private double kth, th0;
public aterm (atom a1, atom a2, atom a3)
{
int i;
boolean found;
myAtoms = new atom[3];
myAtoms[0] = a1;
myAtoms[1] = a2;
myAtoms[2] = a3;
for (i = 0, found = false; i < angleCoeffs.length && !found; i++)
if ((a1.atomicNumber () == angleCoeffs[i][0] &&
a1.hybridization == angleCoeffs[i][1] &&
a2.atomicNumber () == angleCoeffs[i][2] &&
a2.hybridization == angleCoeffs[i][3] &&
a3.atomicNumber () == angleCoeffs[i][4] &&
a3.hybridization == angleCoeffs[i][5]) ||
(a1.atomicNumber () == angleCoeffs[i][4] &&
a1.hybridization == angleCoeffs[i][5] &&
a2.atomicNumber () == angleCoeffs[i][2] &&
a2.hybridization == angleCoeffs[i][3] &&
a3.atomicNumber () == angleCoeffs[i][0] &&
a3.hybridization == angleCoeffs[i][1]))
{
found = true;
kth = angleCoeffs[i][6];
th0 = angleCoeffs[i][7] * convert;
}
if (!found)
{
kth = 0.3;
th0 = 120.0 * convert;
}
}
// need these routines to make sure a bond doesn't already exist
public boolean redundant (aterm t)
{
if ((t.myAtoms[0] == myAtoms[0] &&
t.myAtoms[1] == myAtoms[1] &&
t.myAtoms[2] == myAtoms[2]) ||
(t.myAtoms[2] == myAtoms[0] &&
t.myAtoms[1] == myAtoms[1] &&
t.myAtoms[0] == myAtoms[2]))
return true;
return false;
}
public void enumerate (Vector atomList, Vector termList)
{
int i, j, k;
for (i = 0; i < atomList.size (); i++)
{
atom a1 = (atom) atomList.elementAt (i);
for (j = 0; j < a1.bonds.size (); j++)
{
atom a2 = (atom) a1.bonds.elementAt (j);
for (k = 0; k < a2.bonds.size (); k++)
{
atom a3 = (atom) a2.bonds.elementAt (k);
if (a1 != a2 && a1 != a3 && a2 != a3)
{
aterm t = new aterm (a1, a2, a3);
if (!t.redundant (termList))
{
termList.addElement (t);
}
}
}
}
}
}
public void computeForces ()
{
if (kth == 0.0) return;
int i;
// compute forces on each atom, add it to the atom's force vector
double[] adiff = new double[3];
double[] bdiff = new double[3];
double aa = 0.0, ab = 0.0, bb = 0.0, th, tdif, duDth;
for (i = 0; i < 3; i++)
{
adiff[i] = myAtoms[0].x[i] - myAtoms[1].x[i];
bdiff[i] = myAtoms[2].x[i] - myAtoms[1].x[i];
aa += adiff[i] * adiff[i];
ab += adiff[i] * bdiff[i];
bb += bdiff[i] * bdiff[i];
}
if (aa > 3.0 || bb > 3.0)
return;
th = acos (ab / sqrt (aa * bb));
tdif = th - th0;
duDth = kth * (tdif * (1.0 + 1.508 * tdif * tdif));
double[] f0 = new double[3];
double[] f2 = new double[3];
double ff0 = 0.0, ff2 = 0.0;
for (i = 0; i < 3; i++)
{
f0[i] = aa * bdiff[i] - ab * adiff[i];
ff0 += f0[i] * f0[i];
f2[i] = bb * adiff[i] - ab * adiff[i];
ff2 += f2[i] * f2[i];
}
double m0 = duDth / sqrt (ff0 * aa);
double m2 = duDth / sqrt (ff2 * bb);
for (i = 0; i < 3; i++)
{
f0[i] *= m0;
f2[i] *= m2;
myAtoms[0].f[i] += f0[i];
myAtoms[1].f[i] -= f0[i] + f2[i];
myAtoms[2].f[i] += f2[i];
}
}
private final static double[][] angleCoeffs =
{
{ C, atom.SP3, C, atom.SP3, C, atom.SP3, 0.450, 109.470 },
{ C, atom.SP3, C, atom.SP3, C, atom.SP2, 0.450, 109.470 },
{ C, atom.SP3, C, atom.SP3, C, atom.SP, 0.450, 109.470 },
{ C, atom.SP3, C, atom.SP3, H, atom.NONE, 0.360, 109.390 },
{ C, atom.SP3, C, atom.SP3, O, atom.SP3, 0.700, 107.500 },
{ C, atom.SP3, C, atom.SP3, N, atom.SP3, 0.570, 109.470 },
{ C, atom.SP3, C, atom.SP3, N, atom.SP2, 0.500, 109.280 },
{ C, atom.SP3, C, atom.SP3, N, atom.SP3, 0.570, 103.500 },
{ C, atom.SP3, C, atom.SP3, O, atom.SP2, 0.700, 107.500 },
{ C, atom.SP2, C, atom.SP3, C, atom.SP2, 0.450, 109.470 },
{ C, atom.SP2, C, atom.SP3, C, atom.SP, 0.470, 109.470 },
{ C, atom.SP2, C, atom.SP3, H, atom.NONE, 0.360, 109.390 },
{ C, atom.SP2, C, atom.SP3, O, atom.SP3, 0.700, 109.500 },
{ C, atom.SP2, C, atom.SP3, N, atom.SP3, 1.045, 110.740 },
{ C, atom.SP2, C, atom.SP3, N, atom.SP2, 0.500, 109.800 },
{ C, atom.SP2, C, atom.SP3, N, atom.SP3, 1.045, 110.740 },
{ C, atom.SP, C, atom.SP3, C, atom.SP, 0.470, 109.470 },
{ C, atom.SP, C, atom.SP3, H, atom.NONE, 0.360, 109.390 },
{ H, atom.NONE, C, atom.SP3, H, atom.NONE, 0.320, 109.400 },
{ H, atom.NONE, C, atom.SP3, O, atom.SP3, 0.540, 106.700 },
{ H, atom.NONE, C, atom.SP3, N, atom.SP3, 0.500, 108.800 },
{ H, atom.NONE, C, atom.SP3, N, atom.SP2, 0.420, 109.000 },
{ H, atom.NONE, C, atom.SP3, N, atom.SP3, 0.500, 108.800 },
{ H, atom.NONE, C, atom.SP3, O, atom.SP2, 0.540, 106.700 },
{ O, atom.SP3, C, atom.SP3, O, atom.SP3, 0.460, 99.900 },
{ N, atom.SP3, C, atom.SP3, N, atom.SP3, 1.045, 110.740 },
{ N, atom.SP3, C, atom.SP3, N, atom.SP3, 1.045, 110.740 },
{ C, atom.SP3, C, atom.SP2, C, atom.SP3, 0.450, 117.200 },
{ C, atom.SP3, C, atom.SP2, C, atom.SP2, 0.550, 121.400 },
{ C, atom.SP3, C, atom.SP2, C, atom.SP, 0.470, 122.000 },
{ C, atom.SP3, C, atom.SP2, H, atom.NONE, 0.360, 118.200 },
{ C, atom.SP3, C, atom.SP2, O, atom.SP3, 0.500, 120.000 },
{ C, atom.SP2, C, atom.SP2, C, atom.SP2, 0.430, 120.000 },
{ C, atom.SP2, C, atom.SP2, H, atom.NONE, 0.360, 120.000 },
{ C, atom.SP2, C, atom.SP2, O, atom.SP3, 0.700, 124.300 },
{ C, atom.SP2, C, atom.SP2, N, atom.SP3, 0.616, 123.000 },
{ C, atom.SP2, C, atom.SP2, N, atom.SP2, 0.500, 118.000 },
{ C, atom.SP2, C, atom.SP2, O, atom.SP2, 0.600, 120.000 },
{ C, atom.SP, C, atom.SP2, H, atom.NONE, 0.360, 121.100 },
{ H, atom.NONE, C, atom.SP2, H, atom.NONE, 0.320, 119.000 },
{ H, atom.NONE, C, atom.SP2, O, atom.SP3, 0.540, 116.400 },
{ H, atom.NONE, C, atom.SP2, N, atom.SP3, 0.540, 119.000 },
{ H, atom.NONE, C, atom.SP2, N, atom.SP2, 0.300, 109.000 },
{ H, atom.NONE, C, atom.SP2, O, atom.SP2, 0.450, 108.000 },
{ N, atom.SP2, C, atom.SP2, N, atom.SP2, 0.400, 120.000 },
{ C, atom.SP3, C, atom.SP, C, atom.SP, 0.200, 180.000 },
{ C, atom.SP3, C, atom.SP, N, atom.SP, 0.325, 180.000 },
{ C, atom.SP2, C, atom.SP, C, atom.SP2, 0.400, 180.000 },
{ C, atom.SP2, C, atom.SP, C, atom.SP, 0.470, 180.000 },
{ C, atom.SP, C, atom.SP, H, atom.NONE, 0.360, 180.000 },
{ C, atom.SP3, O, atom.SP3, C, atom.SP3, 0.770, 106.800 },
{ C, atom.SP3, O, atom.SP3, C, atom.SP2, 0.770, 110.800 },
{ C, atom.SP3, O, atom.SP3, O, atom.SP3, 0.635, 98.700 },
{ C, atom.SP3, N, atom.SP3, C, atom.SP3, 0.630, 107.700 },
{ C, atom.SP3, N, atom.SP3, C, atom.SP2, 0.698, 107.000 },
{ C, atom.SP3, N, atom.SP3, N, atom.SP3, 0.740, 105.500 },
{ C, atom.SP3, N, atom.SP2, C, atom.SP3, 0.760, 126.000 },
{ C, atom.SP3, N, atom.SP2, C, atom.SP2, 0.630, 119.900 },
{ C, atom.SP2, N, atom.SP2, C, atom.SP2, 0.400, 107.000 },
{ C, atom.SP3, N, atom.SP3, C, atom.SP3, 0.630, 108.600 },
{ C, atom.SP3, N, atom.SP3, H, atom.NONE, 0.500, 109.470 },
{ H, atom.NONE, N, atom.SP3, H, atom.NONE, 0.500, 104.500 },
{ C, atom.SP3, O, atom.SP2, C, atom.SP2, 0.770, 113.600 },
{ C, atom.SP2, O, atom.SP2, C, atom.SP2, 0.870, 113.950 }
};
}
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