float ShakerDoDist(float target, float *v0, float *v1, float *d0to1, float *d1to0,
float wt)
{
float d[3], push[3];
float len, dev, dev_2, sc, result;
subtract3f(v0, v1, d);
len = (float) length3f(d);
dev = target - len;
if((result = fabs(dev)) > R_SMALL8) {
dev_2 = wt * dev * 0.5F;
if(len > R_SMALL8) { /* nonoverlapping */
sc = dev_2 / len;
scale3f(d, sc, push);
add3f(push, d0to1, d0to1);
subtract3f(d1to0, push, d1to0);
} else { /* overlapping, so just push in a random direction */
float rd[3];
get_random3f(rd);
d0to1[0] -= rd[0] * dev_2;
d1to0[0] += rd[0] * dev_2;
d0to1[1] -= rd[1] * dev_2;
d1to0[1] += rd[1] * dev_2;
d0to1[2] -= rd[2] * dev_2;
d1to0[2] += rd[2] * dev_2;
}
} else
result = 0.0;
return result;
}
float ShakerDoPyra(float targ1, float targ2,
float *v0, float *v1, float *v2, float *v3,
float *p0, float *p1, float *p2, float *p3, float wt, float inv_wt)
{
float d0[3], cp[3], d2[3], d3[3];
float av[3], t0[3], push[3];
float cur, dev, sc, result1, result2 = 0.0F;
add3f(v1, v2, av);
subtract3f(v2, v1, d2);
add3f(v3, av, av);
subtract3f(v3, v1, d3);
subtract3f(av, v0, t0);
cross_product3f(d2, d3, cp);
scale3f(av, 0.33333333F, av);
normalize3f(cp);
subtract3f(av, v0, d0);
cur = dot_product3f(d0, cp);
dev = cur - targ1;
result1 = (float) fabs(dev);
if(result1 > R_SMALL8) {
sc = wt * dev;
if((cur * targ1) < 0.0) /* inverted */
sc = sc * inv_wt; /* inversion fixing weight */
scale3f(cp, sc, push);
add3f(push, p0, p0);
scale3f(push, 0.333333F, push);
subtract3f(p1, push, p1);
subtract3f(p2, push, p2);
subtract3f(p3, push, p3);
}
if((targ2 >= 0.0F) && ((cur * targ1 > 0.0) || (fabs(targ1) < 0.1))) {
/* so long as we're not inverted...
also make sure v0 is the right distance from the average point */
cur = length3f(d0);
normalize3f(d0);
dev = cur - targ2;
result2 = (float) fabs(dev);
if(result2 > R_SMALL4) {
sc = wt * dev * 2.0F;
scale3f(d0, sc, push);
add3f(push, p0, p0);
scale3f(push, 0.333333F, push);
subtract3f(p1, push, p1);
subtract3f(p2, push, p2);
subtract3f(p3, push, p3);
}
}
return result1 + result2;
}
float ShakerGetPyra(float *targ2, float *v0, float *v1, float *v2, float *v3)
{
float d0[3], cp[3], d2[3], d3[3];
float av[3], t0[3];
add3f(v1, v2, av);
subtract3f(v2, v1, d2);
add3f(v3, av, av);
subtract3f(v3, v1, d3);
subtract3f(av, v0, t0);
cross_product3f(d2, d3, cp);
scale3f(av, 0.33333333F, av);
normalize3f(cp);
subtract3f(av, v0, d0);
(*targ2) = length3f(d0);
return (dot_product3f(d0, cp));
}
float ShakerDoLine(float *v0, float *v1, float *v2,
float *p0, float *p1, float *p2, float wt)
{
/* v0-v1-v2 */
float d0[3], d1[3], cp[3], d2[3], d3[3], d4[3], push[3];
float dev, sc, lcp, result;
subtract3f(v2, v1, d2);
subtract3f(v0, v1, d1);
normalize3f(d2);
normalize23f(d1, d0);
cross_product3f(d2, d0, cp);
lcp = (float) length3f(cp);
if(lcp > R_SMALL4) {
lcp = 1.0F / lcp;
scale3f(cp, lcp, cp); /* axis 0 */
subtract3f(v2, v0, d3);
normalize3f(d3); /* axis 1 */
cross_product3f(cp, d3, d4);
normalize3f(d4); /* displacement direction */
dev = dot_product3f(d1, d4); /* current deviation */
if((result = (float) fabs(dev)) > R_SMALL8) {
sc = wt * dev;
scale3f(d4, sc, push);
add3f(push, p1, p1);
scale3f(push, 0.5F, push);
subtract3f(p0, push, p0);
subtract3f(p2, push, p2);
} else {
result = 0.0;
}
} else
result = 0.0;
return result;
}
float ShakerDoDistLimit(float target, float *v0, float *v1, float *d0to1, float *d1to0,
float wt)
{
float d[3], push[3];
float len, dev, dev_2, sc;
if(wt == 0.0F)
return 0.0F;
subtract3f(v0, v1, d);
len = (float) length3f(d);
dev = target - len;
if(dev < 0.0F) { /* assuming len is non-zero since it is above target */
dev_2 = wt * dev * 0.5F;
sc = dev_2 / len;
scale3f(d, sc, push);
add3f(push, d0to1, d0to1);
subtract3f(d1to0, push, d1to0);
return -dev;
} else
return 0.0F;
}
static void RepValence(CGO *cgo, bool s1, bool s2, bool isRamped, float *v1, float *v2, int *other,
int a1, int a2, float *coord, float *color1, float *color2, int ord,
float tube_size, int fancy, unsigned int b1, unsigned int b2, int a, bool b1masked, bool b2masked)
{
float d[3], t[3], p0[3], p1[3], p2[3];
int a3;
const float indent = tube_size;
/* direction vector */
subtract3f(v2, v1, p0);
copy3f(p0, d);
normalize3f(p0);
/* need a prioritized third atom to get planarity */
a3 = ObjectMoleculeGetPrioritizedOther(other, a1, a2, NULL);
if(a3 < 0) {
t[0] = p0[0];
t[1] = p0[1];
t[2] = -p0[2];
} else {
subtract3f(coord + 3 * a3, v1, t);
normalize3f(t);
}
cross_product3f(d, t, p1);
normalize3f(p1);
if(length3f(p1) == 0.0) {
p1[0] = p0[1];
p1[1] = p0[2];
p1[2] = p0[0];
cross_product3f(p0, p1, p2);
normalize3f(p2);
} else {
cross_product3f(d, p1, p2);
normalize3f(p2);
}
/* now we have a coordinate system */
mult3f(p2, tube_size, t);
bool ord3 = (ord == 3);
if (ord3)
mult3f(t, 2.f, t);
if (fancy || ord3){
RepLine(cgo, s1, s2, isRamped, v1, v2, color1, b1, b2, a, color2, b1masked, b2masked);
}
if(fancy) {
float f[] = { indent, 1.f - indent };
float f_1[] = { 1.f - f[0], 1.f - f[1] };
float vv1[] = { (f_1[0] * v1[0] + f[0] * v2[0]) - 2 * t[0],
(f_1[0] * v1[1] + f[0] * v2[1]) - 2 * t[1],
(f_1[0] * v1[2] + f[0] * v2[2]) - 2 * t[2] };
float vv2[] = { (f_1[1] * v1[0] + f[1] * v2[0]) - 2 * t[0],
(f_1[1] * v1[1] + f[1] * v2[1]) - 2 * t[1],
(f_1[1] * v1[2] + f[1] * v2[2]) - 2 * t[2] };
RepLine(cgo, s1, s2, isRamped, vv1, vv2, color1, b1, b2, a, color2, b1masked, b2masked);
} else {
float vv1[][3] = { { v1[0] - t[0], v1[1] - t[1], v1[2] - t[2] },
{ v1[0] + t[0], v1[1] + t[1], v1[2] + t[2] } };
float vv2[][3] = { { v2[0] - t[0], v2[1] - t[1], v2[2] - t[2] },
{ v2[0] + t[0], v2[1] + t[1], v2[2] + t[2] } };
RepLine(cgo, s1, s2, isRamped, vv1[0], vv2[0], color1, b1, b2, a, color2, b1masked, b2masked);
RepLine(cgo, s1, s2, isRamped, vv1[1], vv2[1], color1, b1, b2, a, color2, b1masked, b2masked);
}
}
static int RepWireZeroOrderBond(CGO *cgo, bool s1, bool s2, float *v1, float *v2, float *rgb1, float *rgb2,
unsigned int b1, unsigned int b2, int a, float dash_gap, float dash_length, bool b1masked, bool b2masked)
{
int ok = true;
float axis[3], naxis[3];
subtract3f(v2, v1, axis);
copy3f(axis, naxis);
normalize3f(naxis);
float blen = length3f(axis);
float dash_tot = dash_gap + dash_length;
int ndashes = blen / dash_tot;
// only do even number of dashes
if (ndashes < 2) {
ndashes = 2;
} else if (ndashes % 2) {
--ndashes;
}
float remspace = blen - (ndashes * dash_length); // remaining space for first gaps
float dgap = remspace / (ndashes - 1.f); // endpoints at each vertex, therefore only account for ndashes-1 spaces
float placep[3], placep2[3], adddlen[3], adddtot[3];
float dplace;
int ndashes_drawn = 0;
bool color2_set = false;
mult3f(naxis, dash_length, adddlen); // adddlen - length of dash as x/y/z vector
mult3f(naxis, dash_length + dgap, adddtot); // adddtot - length of dash plus gap as x/y/z vector
copy3f(v1, placep);
if (s1){
ok &= CGOColorv(cgo, rgb1);
ok &= CGOPickColor(cgo, b1, b1masked ? cPickableNoPick : a);
for (dplace = 0.f; (dplace+dash_length) < blen / 2.f; ){
add3f(placep, adddlen, placep2);
cgo->add<cgo::draw::line>(placep, placep2);
add3f(placep, adddtot, placep);
dplace += dash_length + dgap;
++ndashes_drawn;
}
if (!s2){
if (dplace < blen / 2.f){
// if we are behind the mid-point, only s1, so draw a half-bond
add3f(placep, adddlen, placep2);
cgo->add<cgo::draw::line>(placep, placep2);
add3f(placep, adddtot, placep);
dplace += dash_length + dgap;
++ndashes_drawn;
}
}
} else {
float tmpp[3];
dplace = (ndashes/2) * (dash_length + dgap);
mult3f(naxis, dplace, tmpp);
add3f(v1, tmpp, placep);
ndashes_drawn = ndashes/2;
// if !s1, then definitely s2, so draw half-bond
if (dplace <= blen / 2.f){
// if no s1, and we are behind the mid-point, draw half-bond with only s2
add3f(placep, adddlen, placep2);
ok &= CGOColorv(cgo, rgb2);
ok &= CGOPickColor(cgo, b2, b2masked ? cPickableNoPick : a);
color2_set = true;
cgo->add<cgo::draw::line>(placep, placep2);
add3f(placep, adddtot, placep);
dplace += dash_length + dgap;
++ndashes_drawn;
}
}
if (s2){
if (dplace < blen / 2.f){
// if we are behind the mid-point, draw a split cylinder with both colors
float tmpp[3];
mult3f(axis, .5f, tmpp);
add3f(v1, tmpp, tmpp);
cgo->add<cgo::draw::line>(placep, tmpp);
add3f(placep, adddlen, placep2);
if (!color2_set){
ok &= CGOColorv(cgo, rgb2);
ok &= CGOPickColor(cgo, b2, b2masked ? cPickableNoPick : a);
}
cgo->add<cgo::draw::line>(tmpp, placep2);
add3f(placep, adddtot, placep);
dplace += dash_length + dgap;
++ndashes_drawn;
} else if (!color2_set){
ok &= CGOColorv(cgo, rgb2);
ok &= CGOPickColor(cgo, b2, b2masked ? cPickableNoPick : a);
}
while (ndashes_drawn < ndashes){
add3f(placep, adddlen, placep2);
cgo->add<cgo::draw::line>(placep, placep2);
add3f(placep, adddtot, placep);
dplace += dash_length + dgap;
++ndashes_drawn;
}
}
return ok;
}
static void RepAromatic(CGO *cgo, bool s1, bool s2, bool isRamped, float *v1, float *v2, int *other,
int a1, int a2, float *coord, float *color1, float *color2,
float tube_size, int half_state, unsigned int b1, unsigned int b2, int a, bool b1masked, bool b2masked)
{
float d[3], t[3], p0[3], p1[3], p2[3], *vv;
int a3;
int double_sided;
/* direction vector */
p0[0] = (v2[0] - v1[0]);
p0[1] = (v2[1] - v1[1]);
p0[2] = (v2[2] - v1[2]);
copy3f(p0, d);
normalize3f(p0);
/* need a prioritized third atom to get planarity */
a3 = ObjectMoleculeGetPrioritizedOther(other, a1, a2, &double_sided);
if(a3 < 0) {
t[0] = p0[0];
t[1] = p0[1];
t[2] = -p0[2];
} else {
vv = coord + 3 * a3;
t[0] = *(vv++) - v1[0];
t[1] = *(vv++) - v1[1];
t[2] = *(vv++) - v1[2];
normalize3f(t);
}
cross_product3f(d, t, p1);
normalize3f(p1);
if(length3f(p1) == 0.0) {
p1[0] = p0[1];
p1[1] = p0[2];
p1[2] = p0[0];
cross_product3f(p0, p1, p2);
normalize3f(p2);
} else {
cross_product3f(d, p1, p2);
normalize3f(p2);
}
t[0] = p2[0] * tube_size * 2;
t[1] = p2[1] * tube_size * 2;
t[2] = p2[2] * tube_size * 2;
RepLine(cgo, s1, s2, isRamped, v1, v2, color1, b1, b2, a, color2, b1masked, b2masked);
if (s1){
CGOColorv(cgo, color1);
CGOPickColor(cgo, b1, b1masked ? cPickableNoPick : a);
float f[] = { 0.14F, 0.4F } ;
float f_1[] = { 1.0F - f[0], 1.0F - f[1] };
float pt1[] = { (f_1[0] * v1[0] + f[0] * v2[0]),
(f_1[0] * v1[1] + f[0] * v2[1]),
(f_1[0] * v1[2] + f[0] * v2[2]) };
float pt2[] = { (f_1[1] * v1[0] + f[1] * v2[0]),
(f_1[1] * v1[1] + f[1] * v2[1]),
(f_1[1] * v1[2] + f[1] * v2[2]) };
float p1[3], p2[3];
subtract3f(pt1, t, p1);
subtract3f(pt2, t, p2);
cgo->add<cgo::draw::line>(p1, p2);
if(double_sided) {
add3f(pt1, t, p1);
add3f(pt2, t, p2);
cgo->add<cgo::draw::line>(p1, p2);
}
}
if (s2){
CGOColorv(cgo, color2);
CGOPickColor(cgo, b2, b2masked ? cPickableNoPick : a);
float f[] = { 0.6F, 0.86F } ;
float f_1[] = { 1.0F - f[0], 1.0F - f[1] };
float pt1[] = { (f_1[0] * v1[0] + f[0] * v2[0]),
(f_1[0] * v1[1] + f[0] * v2[1]),
(f_1[0] * v1[2] + f[0] * v2[2]) };
float pt2[] = { (f_1[1] * v1[0] + f[1] * v2[0]),
(f_1[1] * v1[1] + f[1] * v2[1]),
(f_1[1] * v1[2] + f[1] * v2[2]) };
float p1[3], p2[3];
subtract3f(pt1, t, p1);
subtract3f(pt2, t, p2);
cgo->add<cgo::draw::line>(p1, p2);
if(double_sided) {
add3f(pt1, t, p1);
add3f(pt2, t, p2);
cgo->add<cgo::draw::line>(p1, p2);
}
}
}
float ShakerDoPlan(float *v0, float *v1, float *v2, float *v3,
float *p0, float *p1, float *p2, float *p3,
float target, int fixed, float wt)
{
float result;
float d01[3], d12[3], d23[3], d03[3], cp0[3], cp1[3], dp, sc, dev, d0[3], push[3];
double s01, s12, s23, s03;
subtract3f(v0, v1, d01);
subtract3f(v1, v2, d12);
subtract3f(v2, v3, d23);
subtract3f(v0, v3, d03);
s03 = lengthsq3f(d03);
s01 = lengthsq3f(d01);
s12 = lengthsq3f(d12);
s23 = lengthsq3f(d23);
if((s03 < s01) || (s03 < s12) || (s03 < s23))
return 0.0F;
cross_product3f(d01, d12, cp0);
cross_product3f(d12, d23, cp1);
normalize3f(cp0);
normalize3f(cp1);
dp = dot_product3f(cp0, cp1);
result = (dev = 1.0F - (float) fabs(dp));
if(dev > R_SMALL4) {
/*
add3f(cp0,cp1,d0);
normalize3f(d0);
cross_product3f(cp0,d12,pos);
dp2 = dot_product3f(cp1,pos);
*/
if(fixed && (dp * target < 0.0F)) {
/* fixed & backwards... */
if(dp < 0.0F) {
sc = -wt * dev * 0.5F;
} else {
sc = wt * dev * 0.5F;
}
sc *= 0.02F; /* weaken considerably to allow resolution of
inconsistencies (folded rings, etc.) */
} else if(dp > 0) {
sc = -wt * dev * 0.5F;
} else {
sc = wt * dev * 0.5F;
}
if(fixed && (fixed < 7)) {
/* in small rings, ramp up the planarity factor */
sc *= 8;
} else {
sc *= 0.2F;
}
/* pair-wise nudges */
subtract3f(v0, v3, d0);
normalize3f(d0);
scale3f(d0, sc, push);
add3f(push, p0, p0);
subtract3f(p3, push, p3);
subtract3f(v1, v2, d0);
normalize3f(d0);
scale3f(d0, sc, push);
add3f(push, p1, p1);
subtract3f(p2, push, p2);
sc = -sc;
subtract3f(v0, v2, d0);
normalize3f(d0);
scale3f(d0, sc, push);
add3f(push, p0, p0);
subtract3f(p2, push, p2);
subtract3f(v1, v3, d0);
normalize3f(d0);
scale3f(d0, sc, push);
add3f(push, p1, p1);
subtract3f(p3, push, p3);
} else {
result = 0.0;
}
return result;
}