void Molecule::addPersistentForce(int theatom, const float *f) {
// reset the force on this atom if any are stored
// remove it completely if <f> is (0,0,0)
float mag2 = f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
int ind = persistent_force_indices.find(theatom);
if (ind < 0) {
if (mag2 > 0) {
// only set if non-zero
reset_disp_list();
persistent_force_indices.append(theatom);
for (int i=0; i<3; i++) persistent_force_vectors.append(f[i]);
}
} else {
if (mag2 > 0) {
reset_disp_list();
for (int i=0; i<3; i++) persistent_force_vectors[3*ind+i] = f[i];
} else {
// remove the persistent force (a zero will be sent automatically!)
persistent_force_indices.remove(ind);
// remove same index three times since this is a ResizeArray
// and it will shift elements down as they are removed...
persistent_force_vectors.remove(3*ind);
persistent_force_vectors.remove(3*ind);
persistent_force_vectors.remove(3*ind);
}
}
}
void FPS::prepare() {
if (!displayed()) return;
++loop_count;
double curtime = time_of_day();
// force a redraw....
need_matrix_recalc();
// but don't redraw indicator more than twice per second
if (curtime - last_update < 0.5) return;
double rate = loop_count / (curtime - last_update);
last_update = curtime;
loop_count = 0;
reset_disp_list();
append(DMATERIALOFF);
float asp = disp->aspect();
float poscale = 1.2f;
float pos[3];
pos[0] = asp * poscale;
pos[1] = poscale;
pos[2] = 0;
DispCmdColorIndex cmdColor;
cmdColor.putdata(usecolor, cmdList);
DispCmdText cmdText;
char buf[20];
sprintf(buf, "%5.2f", rate);
cmdText.putdata(pos, buf, 1.0f, cmdList);
}
// draw the geometry marker in the given Displayable's drawing list
void GeometryBond::create_cmd_list() {
char valbuf[32];
// get the transformed positions, and draw a line between them
float pos1[3], pos2[3];
reset_disp_list();
if(!transformed_atom_coord(0, pos1))
return;
if(!transformed_atom_coord(1, pos2))
return;
append(DMATERIALOFF);
DispCmdColorIndex cmdColor;
cmdColor.putdata(my_color, cmdList);
DispCmdLineType cmdLineType;
DispCmdLineWidth cmdLineWidth;
cmdLineType.putdata(DASHEDLINE, cmdList);
cmdLineWidth.putdata(4, cmdList);
// print value of distance at midpoint
midpoint(valuePos, pos1, pos2);
// left-align the value so that it doesn't appear to shift its position
// when the label text size changes. Shift it to the right by a constant
// amount so that it doesn't intersect the line.
valuePos[0] += 0.05f;
sprintf(valbuf, "%-7.2f", geomValue);
display_string(valbuf, cmdList);
// draw a line into the given Displayable
display_line(pos1, pos2, cmdList);
}
// draw the geometry marker in the given Displayable's drawing list
void GeometryAtom::create_cmd_list() {
reset_disp_list();
// get the molecule pointer and atom position
Molecule *mol = transformed_atom_coord(0, valuePos);
// do not draw if illegal molecule, or atom is not on
if(!mol)
return;
append(DMATERIALOFF);
DispCmdColorIndex cmdColor;
cmdColor.putdata(my_color,cmdList);
// everything is OK, draw text at atom position
JString str;
atom_formatted_name(str, mol, comIndex[0]);
display_string((const char *)str, cmdList);
}
// create the drawing command list
void Stage::create_cmdlist(void) {
int i, j, k, odd;
float c[4][3], mycorner1[3];
mycorner1[0] = mycorner1[2] = -1.0; mycorner1[1] = 0.0;
c[0][1] = c[1][1] = c[2][1] = c[3][1] = 0.0;
// do reset first
reset_disp_list();
// turn off material characteristics
append(DMATERIALOFF);
// draw odd/even squares separately
for(k=0; k < 2; k++) {
odd = (k == 1);
// set color in checkerboard
if (odd)
cmdColor.putdata(usecolors[0],cmdList);
else
cmdColor.putdata(usecolors[1],cmdList);
// start in lower-left corner
c[0][0] = c[3][0] = mycorner1[0];
c[1][0] = c[2][0] = mycorner1[0] + inc;
for(i=0; i < Panels; i++) {
c[0][2] = c[1][2] = mycorner1[2];
c[2][2] = c[3][2] = mycorner1[2] + inc;
for(j=0; j < Panels; j++) {
if(!odd)
cmdSquare.putdata(c[2], c[1], c[0], cmdList);
odd = !odd;
c[0][2] += inc; c[1][2] += inc; c[2][2] += inc; c[3][2] += inc;
}
c[0][0] += inc; c[1][0] += inc; c[2][0] += inc; c[3][0] += inc;
if(Panels % 2 == 0)
odd = !odd;
}
}
}
void VMDTitle::redraw_list(void) {
reset_disp_list();
float x; // offset to center VMD
x = letter_V_width() + STROKE_WIDTH/2.0f +
letter_M_width() + STROKE_WIDTH/2.0f +
letter_V_width(); // same width as 'V'
x=x/2; // center on the screen
append(DMATERIALON);
color.putdata(REGRED, cmdList);
draw_letter_V(-x, -0.4f, cmdList);
color.putdata(REGGREEN, cmdList);
draw_letter_M(-x + STROKE_WIDTH/2.0f + letter_V_width(), -0.4f, cmdList);
color.putdata(REGBLUE, cmdList);
draw_letter_D(-x + STROKE_WIDTH/2.0f + letter_V_width() +
STROKE_WIDTH/2.0f + letter_M_width(), -0.4f, cmdList);
append(DMATERIALOFF);
if (letterson) {
color.putdata(REGWHITE, cmdList);
float pos[3];
pos[0] = -x;
pos[1] = -0.6f;
pos[2] = 0.0f;
DispCmdText txt;
txt.putdata(pos, "Theoretical and Computational Biophysics Group", cmdList);
pos[1] -= 0.1f;
txt.putdata(pos, "NIH Resource for Macromolecular Modeling and Bioinformatics", cmdList);
pos[1] -= 0.1f;
txt.putdata(pos, "University of Illinois at Urbana-Champaign", cmdList);
pos[1] -= 0.1f;
txt.putdata(pos, VMD_AUTHORS_LINE1, cmdList);
pos[1] -= 0.1f;
txt.putdata(pos, VMD_AUTHORS_LINE2, cmdList);
pos[1] -= 0.1f;
txt.putdata(pos, VMD_AUTHORS_LINE3, cmdList);
}
}
// create the drawing command list
void Axes::create_cmdlist(void) {
char commentBuffer[128];
reset_disp_list(); // regenerate both data block and display commands
sprintf(commentBuffer, "VMD: Starting axes output.");
cmdCommentX.putdata(commentBuffer, cmdList);
cmdBeginRepGeomGroup.putdata("vmd_axes", cmdList);
#if defined(USELINEAXES)
DispCmdLine cmdline;
float arrow1[3], arrow2[3];
// turn on material characteristics
append(DMATERIALOFF);
// Draw axes as lines of width 2, faster for wimpy machines...
DispCmdLineWidth cmdwidth;
cmdwidth.putdata(2, cmdList);
// x-axis
xcol.putdata(usecolors[0], cmdList);
cmdline.putdata(origin, xLineCap, cmdList);
arrow1[0] = xLine[0];
arrow1[1] = xLine[1] - AXESCAPRAD/sqrt(2.0f);
arrow1[2] = xLine[2] + AXESCAPRAD/sqrt(2.0f);
arrow2[0] = xLine[0];
arrow2[1] = xLine[1] + AXESCAPRAD/sqrt(2.0f);
arrow2[2] = xLine[2] - AXESCAPRAD/sqrt(2.0f);
cmdline.putdata(xLineCap, arrow1, cmdList);
cmdline.putdata(xLineCap, arrow2, cmdList);
// y-axis
xcol.putdata(usecolors[1], cmdList);
cmdline.putdata(origin, yLineCap, cmdList);
arrow1[0] = yLine[0] + AXESCAPRAD/sqrt(2.0f);
arrow1[1] = yLine[1];
arrow1[2] = yLine[2] - AXESCAPRAD/sqrt(2.0f);
arrow2[0] = yLine[0] - AXESCAPRAD/sqrt(2.0f);
arrow2[1] = yLine[1];
arrow2[2] = yLine[2] + AXESCAPRAD/sqrt(2.0f);
cmdline.putdata(yLineCap, arrow1, cmdList);
cmdline.putdata(yLineCap, arrow2, cmdList);
// z-axis
xcol.putdata(usecolors[2], cmdList);
cmdline.putdata(origin, zLineCap, cmdList);
arrow1[0] = zLine[0] - AXESCAPRAD/sqrt(2.0f);
arrow1[1] = zLine[1] + AXESCAPRAD/sqrt(2.0f);
arrow1[2] = zLine[2];
arrow2[0] = zLine[0] + AXESCAPRAD/sqrt(2.0f);
arrow2[1] = zLine[1] - AXESCAPRAD/sqrt(2.0f);
arrow2[2] = zLine[2];
cmdline.putdata(zLineCap, arrow1, cmdList);
cmdline.putdata(zLineCap, arrow2, cmdList);
#else
// Draw axes as solid cylinders/cones, for faster machines...
// turn on material characteristics
append(DMATERIALON);
// set sphere type and resolution
sphres.putdata(AXESSPHRES, cmdList);
sphtype.putdata(SOLIDSPHERE, cmdList);
// put in commands to draw lines
// x-axis
xcol.putdata(usecolors[0], cmdList);
xcyl.putdata(origin, xLine, AXESRAD, AXESRES, 0, cmdList);
xcap.putdata(xLine, xLineCap, AXESCAPRAD, 0, AXESRES, cmdList);
// y-axis
xcol.putdata(usecolors[1], cmdList);
xcyl.putdata(origin, yLine, AXESRAD, AXESRES, 0, cmdList);
xcap.putdata(yLine, yLineCap, AXESCAPRAD, 0, AXESRES, cmdList);
// z-axis
xcol.putdata(usecolors[2], cmdList);
xcyl.putdata(origin, zLine, AXESRAD, AXESRES, 0, cmdList);
xcap.putdata(zLine, zLineCap, AXESCAPRAD, 0, AXESRES, cmdList);
// put in commands to draw sphere at origin
xcol.putdata(usecolors[3], cmdList);
sph.putdata(origin, AXESRAD, cmdList);
// turn off material characteristics
append(DMATERIALOFF);
#endif
// put in commands to label the axes
xcol.putdata(usecolors[4], cmdList);
txt.putdata(xText, "x", 1.0f, cmdList);
txt.putdata(yText, "y", 1.0f, cmdList);
txt.putdata(zText, "z", 1.0f, cmdList);
// put in commands to draw pickpoints at axes endpoints
pickPoint.putdata(origin, 0, cmdList);
pickPoint.putdata(xLine, 1, cmdList);
pickPoint.putdata(xLineCap, 2, cmdList);
pickPoint.putdata(yLine, 3, cmdList);
pickPoint.putdata(yLineCap, 4, cmdList);
pickPoint.putdata(zLine, 5, cmdList);
pickPoint.putdata(zLineCap, 6, cmdList);
// done drawing axes
sprintf(commentBuffer, "VMD: Done with axes.");
cmdCommentX.putdata(commentBuffer, cmdList);
need_create_cmdlist = FALSE;
}
void MoleculeGraphics::create_cmdlist(void) {
reset_disp_list();
// set the default values
DispCmdTriangle triangle;
DispCmdCylinder cylinder;
DispCmdPoint point;
DispCmdLine line;
DispCmdCone cone;
DispCmdColorIndex color;
DispCmdLineType linetype;
DispCmdLineWidth linewidth;
DispCmdSphere sphere;
DispCmdSphereRes sph_res;
//DispCmdComment comment;
DispCmdPickPoint cmdPickPoint;
append(DMATERIALON);
color.putdata(0, cmdList); // use the first color by default (blue)
int last_res = -1; // default sphere resolution
int last_line = ::SOLIDLINE; // default for lines
linetype.putdata(last_line, cmdList); // solid and
int last_width = 1;
linewidth.putdata(last_width, cmdList); // of width 1
// go down the list and draw things
int num = num_elements();
ShapeClass *shape;
for (int i=0; i<num; i++) {
shape = &(shapes[i]);
switch (shape->shape) {
case NONE: {
break;
}
case POINT: {
append(DMATERIALOFF);
point.putdata(shape->data+0, cmdList);
append(DMATERIALON);
break;
}
case PICKPOINT:
cmdPickPoint.putdata(shape->data, (int)shape->data[3], cmdList);
break;
case LINE: {
append(DMATERIALOFF);
int style = int(shape->data[6]);
int width = int(shape->data[7]);
if (style != last_line) {
linetype.putdata(style, cmdList);
last_line = style;
}
if (width != last_width) {
linewidth.putdata(width, cmdList);
last_width = width;
}
line.putdata(shape->data+0, shape->data+3, cmdList);
append(DMATERIALON);
break;
}
case TRIANGLE: {
triangle.putdata(shape->data+0, shape->data+3, shape->data+6, cmdList);
break;
}
case TRINORM: {
triangle.putdata(shape->data+0, shape->data+3 , shape->data+6,
shape->data+9, shape->data+12, shape->data+15, cmdList);
break;
}
case TRICOLOR:
{
// compute rgb colors from indices
float colors[9];
for (int i=0; i<3; i++) {
int c = (int)shape->data[18+i];
c = clamp_int(c, 0, MAXCOLORS-1);
vec_copy(colors+3*i, scene->color_value(c));
}
const float *verts = shape->data+0;
const float *norms = shape->data+9;
int facets[3] = { 0,1,2 };
DispCmdTriMesh::putdata(verts, norms, colors, 3, facets, 1, 0, cmdList);
}
break;
case CYLINDER: {
cylinder.putdata(shape->data+0, shape->data+3, shape->data[6],
int(shape->data[7]),
(int (shape->data[8])) ?
CYLINDER_TRAILINGCAP | CYLINDER_LEADINGCAP : 0,
cmdList);
break;
}
case CONE: {
cone.putdata(shape->data+0, shape->data+3, shape->data[6],
shape->data[8], int(shape->data[7]), cmdList);
break;
}
case TEXT: {
append(DMATERIALOFF);
DispCmdText text;
DispCmdTextSize textSize;
textSize.putdata(shape->data[3], cmdList);
text.putdata(shape->data, shapetext[(int)shape->data[5]], shape->data[4], cmdList);
append(DMATERIALON);
break;
}
#if 0
// these aren't supported yet
case DBEGINREPGEOMGROUP: {
char *s = (char *) (shape);
beginrepgeomgroup.putdata(s,cmdList);
break;
}
case DCOMMENT: {
char *s = (char *) (shape);
comment.putdata(s,cmdList);
break;
}
#endif
case SPHERE: {
int res = int (shape->data[4]);
if (res != last_res) {
sph_res.putdata(res, cmdList);
last_res = res;
}
sphere.putdata(shape->data+0, shape->data[3], cmdList);
break;
}
case MATERIALS: {
if (shape->data[0] == 0) append(DMATERIALOFF);
else append(DMATERIALON);
break;
}
case MATERIAL: {
const float *data = shape->data;
cmdList->ambient = data[0];
cmdList->specular = data[1];
cmdList->diffuse = data[2];
cmdList->shininess = data[3];
cmdList->mirror = data[4];
cmdList->opacity = data[5];
cmdList->outline = data[6];
cmdList->outlinewidth = data[7];
cmdList->transmode = data[8];
cmdList->materialtag = (int)data[9];
break;
}
case COLOR: {
color.putdata(int(shape->data[0]), cmdList);
break;
}
default:
msgErr << "Sorry, can't draw that" << sendmsg;
}
}
needRegenerate = 0;
}
