/* mark the calling thread as done and alert join_all() */
local void reenter(void *dummy)
{
thread *match, **prior;
pthread_t me;
(void)dummy;
/* find this thread in the threads list by matching the thread id */
me = pthread_self();
possess(&(threads_lock));
prior = &(threads);
while ((match = *prior) != NULL) {
if (pthread_equal(match->id, me))
break;
prior = &(match->next);
}
if (match == NULL)
fail(EINVAL);
/* mark this thread as done and move it to the head of the list */
match->done = 1;
if (threads != match) {
*prior = match->next;
match->next = threads;
threads = match;
}
/* update the count of threads to be joined and alert join_all() */
twist(&(threads_lock), BY, +1);
}
void mkptrj(char *prop,int nSel,
int natoms,rvec xav[],int nframes,
int nev,rvec **EV,real **evprj,
int nca,atom_id ca_index[],atom_id bb_index[],
t_atom atom[],matrix box)
{
FILE *out;
char buf[256];
double propje,*pav,*pav2;
int i,j;
rvec *xxx;
snew(pav,nev);
snew(pav2,nev);
snew(xxx,natoms);
sprintf(buf,"%s.trj1",prop);
out=ffopen(buf,"w");
fprintf(out,"Projection of %s on EigenVectors\n",prop);
for(j=0; (j<nframes); j++) {
if ((j % 10) == 0)
fprintf(stderr,"\rFrame %d",j);
for(i=0; (i<nev); i++) {
calc_prj(natoms,xav,xxx,EV[i],evprj[i][j]);
switch (nSel) {
case efhRAD:
propje=radius(NULL,nca,ca_index,xxx);
break;
case efhLEN:
propje=ahx_len(nca,ca_index,xxx,box);
break;
case efhTWIST:
propje=twist(NULL,nca,ca_index,xxx);
break;
case efhCPHI:
propje=ca_phi(nca,ca_index,xxx);
break;
case efhDIP:
propje=dip(natoms,bb_index,xxx,atom);
break;
default:
gmx_fatal(FARGS,"Not implemented");
}
pav[i]+=propje;
pav2[i]+=propje*propje;
fprintf(out,"%8.3f",propje);
}
fprintf(out,"\n");
}
ffclose(out);
fprintf(stderr,"\n");
for(i=0; (i<nev); i++) {
printf("ev %2d, average: %8.3f rms: %8.3f\n",
i+1,pav[i]/nframes,sqrt(pav2[i]/nframes-sqr(pav[i]/nframes)));
}
sfree(pav);
sfree(pav2);
sfree(xxx);
}
void operator()(const float vec[3])
{
geometry_msgs::TwistStamped::Ptr twist(
new geometry_msgs::TwistStamped());
twist->header.stamp=ros::Time();
twist->header.frame_id=frame_id;
//Condition speed mm/s -> m/s
float cond_vec[3];
for (int i=0; i<3;++i) cond_vec[i]=vec[i]/1000;
labust::tools::vectorToPoint(cond_vec,twist->twist.linear);
pub.publish(twist);
}
//! return a random integer in the [0,0xffffffff]-interval
unsigned long nextInt32() const {
if (mti==N)
twist(); /* generate N words at a time */
unsigned long y = mt[mti++];
/* Tempering */
y ^= (y >> 11);
y ^= (y << 7) & 0x9d2c5680UL;
y ^= (y << 15) & 0xefc60000UL;
y ^= (y >> 18);
return y;
}
void Box::transformVertex(QVector3D v, float animationFrame)
{
switch (m_globalDefMode)
{
case Pinch:
pinch(v, 1.0f - animationFrame);
break;
case Mold:
mold(v, 1.0f - animationFrame);
break;
case Twist:
twist(v, animationFrame*360.0f);
break;
case Bend:
bend(v, animationFrame*90.0f);
break;
default:
glVertex3fv(&v[0]);
}
}
void Camera::motion(int x, int y) {
if (!moving) return;
currPos[0] = (float) x / (float) width;
currPos[1] = (float) y / (float) height;
float dx = currPos[0] - prevPos[0];
float dy = currPos[1] - prevPos[1];
float mag = sqrtf(dx * dx + dy * dy);
if (mag < 1.0e-6f) return;
switch (mode) {
case ROTATE: rotate(dx, dy); break;
case ZOOM: zoom(dx, dy); break;
case TWIST: twist(dx, dy); break;
case PAN: pan(dx, dy); break;
}
prevPos[0] = currPos[0];
prevPos[1] = currPos[1];
}
bool ElectronGasOrbitalBuilder::put(xmlNodePtr cur){
int nc=0;
PosType twist(0.0);
OhmmsAttributeSet aAttrib;
aAttrib.add(nc,"shell");
aAttrib.add(twist,"twist");
aAttrib.put(cur);
typedef DiracDeterminant<RealEGOSet> Det_t;
typedef SlaterDeterminant<RealEGOSet> SlaterDeterminant_t;
int nat=targetPtcl.getTotalNum();
int nup=nat/2;
HEGGrid<RealType,OHMMS_DIM> egGrid(targetPtcl.Lattice);
if(nc == 0) nc = egGrid.getShellIndex(nup);
if(nc<0)
{
app_error() << " HEG Invalid Shell." << endl;
APP_ABORT("ElectronGasOrbitalBuilder::put");
}
if(nup!=egGrid.getNumberOfKpoints(nc))
{
app_error() << " The number of particles does not match to the shell." << endl;
app_error() << " Suggested values for the number of particles " << endl;
app_error() << " " << 2*egGrid.getNumberOfKpoints(nc) << " for shell "<< nc << endl;
app_error() << " " << 2*egGrid.getNumberOfKpoints(nc-1) << " for shell "<< nc-1 << endl;
APP_ABORT("ElectronGasOrbitalBuilder::put");
return false;
}
int nkpts=(nup-1)/2;
//create a E(lectron)G(as)O(rbital)Set
egGrid.createGrid(nc,nkpts);
RealEGOSet* psi=new RealEGOSet(egGrid.kpt,egGrid.mk2);
//create up determinant
Det_t *updet = new Det_t(psi,0);
updet->set(0,nup);
//create down determinant
Det_t *downdet = new Det_t(psi,nup);
downdet->set(nup,nup);
//create a Slater determinant
SlaterDeterminant_t *sdet = new SlaterDeterminant_t;
sdet->add(updet);
sdet->add(downdet);
//add a DummyBasisSet
sdet->setBasisSet(new DummyBasisSet);
//add Slater determinant to targetPsi
targetPsi.addOrbital(sdet,"SlaterDet");
return true;
}
//==== Generate Fuse Component ====//
void PropGeom::generate()
{
int i, j;
//==== Copy Current Section Data into SectVec ====//
sectVec[currSectID].chord = chord();
sectVec[currSectID].twist = twist();
sectVec[currSectID].x_off = loc();
sectVec[currSectID].y_off = offset();
Xsec_surf surf;
surf.set_num_pnts( numPnts.iget() );
surf.set_num_xsecs( sectVec.size()+2 );
//==== Load Up Airfoil ====//
for ( int ip = 0 ; ip < surf.get_num_pnts() ; ip++ )
surf.set_pnt(0, ip, sectVec[0].foil->get_end_cap(ip) );
int numxs = sectVec.size();
for ( i = 0 ; i < numxs ; i++ )
{
for ( j = 0 ; j < surf.get_num_pnts() ; j++ )
{
surf.set_pnt( i+1, j, sectVec[i].foil->get_pnt(j) );
}
}
for ( int ip = 0 ; ip < surf.get_num_pnts() ; ip++ )
surf.set_pnt(numxs+1, ip, sectVec[numxs-1].foil->get_end_cap(ip) );
//==== Build Up One Blade ====//
double rad = diameter()/2.0;
for ( i = 0 ; i < surf.get_num_xsecs() ; i++ )
{
int sid = i;
if ( i > 0 ) sid = i-1;
if ( i > (int)sectVec.size()-1 ) sid = (int)sectVec.size()-1;
Section* sPtr = &(sectVec[sid]);
surf.scale_xsec_x( i, sPtr->chord()*rad );
surf.scale_xsec_z( i, sPtr->chord()*rad );
surf.offset_xsec_x( i, -0.5*(sPtr->chord()*rad) );
surf.rotate_xsec_y( i, 90.0 );
surf.rotate_xsec_y( i, -sPtr->twist() - pitch() );
surf.offset_xsec_y( i, sPtr->x_off()*rad );
surf.offset_xsec_z( i, -sPtr->y_off()*rad );
}
//==== Set Flags So Trailing Edge Remains Sharp ====//
surf.set_pnt_tan_flag( 0, Bezier_curve::SHARP );
surf.set_pnt_tan_flag( 1, Bezier_curve::SHARP );
int num_pnts = surf.get_num_pnts();
surf.set_pnt_tan_flag( num_pnts-1, Bezier_curve::SHARP );
if ( !smoothFlag )
{
for ( i = 0 ; i < surf.get_num_xsecs() ; i++ )
{
surf.set_xsec_tan_flag( i, Bezier_curve::SHARP );
}
}
else // Sharpen End Caps
{
surf.set_xsec_tan_flag( surf.get_num_xsecs()-2, Bezier_curve::SHARP );
}
bezier_surf besurf;
surf.load_bezier_surface( &besurf );
int umax = besurf.get_u_max();
int wmax = besurf.get_w_max();
Xsec_surf smooth_surf;
smooth_surf.set_num_pnts( (surf.get_num_pnts()-1)*numW + 1 );
smooth_surf.set_num_xsecs( (surf.get_num_xsecs()-1)*numU + 1 );
for ( i = 0 ; i < smooth_surf.get_num_xsecs() ; i++ )
{
double fu = (double)i/(double)(smooth_surf.get_num_xsecs()-1);
double u = fu*(double)umax;
for ( j = 0 ; j < smooth_surf.get_num_pnts() ; j++ )
{
double fw = (double)j/(double)(smooth_surf.get_num_pnts()-1);
double w = fw*(double)wmax;
vec3d p = besurf.comp_pnt( u, w );
smooth_surf.set_pnt( i, j, p );
}
}
//==== Load Blades into bladeVec ====//
for ( int nb = 0 ; nb < (int)bladeVec.size() ; nb++ )
{
bladeVec[nb].set_num_pnts( smooth_surf.get_num_pnts() );
bladeVec[nb].set_num_xsecs( smooth_surf.get_num_xsecs() );
//==== Load Points ====//
for ( i = 0 ; i < smooth_surf.get_num_xsecs() ; i++ )
for ( j = 0 ; j < smooth_surf.get_num_pnts() ; j++ )
bladeVec[nb].set_pnt( i, j, smooth_surf.get_pnt( i, j ) );
double xang = 360.0*(double)nb/(double)(bladeVec.size());
for ( i = 0 ; i < bladeVec[nb].get_num_xsecs() ; i++ )
{
bladeVec[nb].rotate_xsec_z( i, cone_angle() );
bladeVec[nb].rotate_xsec_x( i, xang );
}
bladeVec[nb].load_refl_pnts_xsecs();
bladeVec[nb].load_hidden_surf();
bladeVec[nb].load_normals();
bladeVec[nb].load_uw();
}
for ( int i = 0 ; i < (int)sectVec.size() ; i++ )
sectVec[i].SetGeomPtr( this );
update_bbox();
}
void Rubik3D::rotate()
{
for(int x=-isZero(axisX);x<=isZero(axisX);++x)
{
for(int y=-isZero(axisY);y<=isZero(axisY);++y)
{
for(int z=-isZero(axisZ);z<=isZero(axisZ);++z)
{
const int X_from=axisX+x;
const int Y_from=axisY+y;
const int Z_from=axisZ+z;
;
int X_to,Y_to,Z_to;
if(twist(axisX, inverse)==1)
{
X_to = X_from;
Y_to = Z_from;
Z_to = - Y_from;
}
else if(twist(axisY, inverse)==1)
{
X_to = - Z_from;
Y_to = Y_from;
Z_to = X_from;
}
else if(twist(axisZ, inverse)==1)
{
X_to = Y_from;
Y_to = - X_from;
Z_to = Z_from;
}else if(twist(axisX, inverse)==-1)
{
X_to = X_from;
Y_to = - Z_from;
Z_to = Y_from;
}
else if(twist(axisY, inverse)==-1)
{
X_to = Z_from;
Y_to = Y_from;
Z_to = - X_from;
}
else if(twist(axisZ, inverse)==-1)
{
X_to = - Y_from;
Y_to = X_from;
Z_to = Z_from;
}
// swap cube colors
if(axisX)
{
MOVE_TO->left = FROM->Left;
MOVE_TO->right = FROM->Right;
MOVE_TO->up = MOVE_TO->down = FROM->Front + FROM->Back ;
MOVE_TO->front = MOVE_TO->back = FROM->Up + FROM->Down ;
}
else if(axisY)
{
MOVE_TO->down = FROM->Down;
MOVE_TO->up = FROM->Up;
MOVE_TO->left = MOVE_TO->right = FROM->Front + FROM->Back ;
MOVE_TO->back = MOVE_TO->front = FROM->Left + FROM->Right ;
}
else if(axisZ)
{
MOVE_TO->back = FROM->Back;
MOVE_TO->front = FROM->Front;
MOVE_TO->right = MOVE_TO->left = FROM->Up + FROM->Down ;
MOVE_TO->up = MOVE_TO->down = FROM->Right + FROM->Left ;
}
}
}
}
setColors();
}
void nextgalaxy(seedtype *s) /* Apply to base seed; once for galaxy 2 */
{ (*s).w0 = twist((*s).w0); /* twice for galaxy 3, etc. */
(*s).w1 = twist((*s).w1); /* Eighth application gives galaxy 1 again*/
(*s).w2 = twist((*s).w2);
}
int gmx_helix(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes all kinds of helix properties. First, the peptide",
"is checked to find the longest helical part, as determined by",
"hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
"That bit is fitted",
"to an ideal helix around the [IT]z[it]-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file [TT]radius.xvg[tt]). This is merely the",
"RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
"it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file [TT]twist.xvg[tt]). The average helical angle per",
"residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
"for 3-10 helices it will be smaller, and ",
"for 5-helices it will be larger.[BR]",
"[BB]3.[bb] Rise per residue (file [TT]rise.xvg[tt]). The helical rise per",
"residue is plotted as the difference in [IT]z[it]-coordinate between C[GRK]alpha[grk]",
"atoms. For an ideal helix, this is 0.15 nm[BR]",
"[BB]4.[bb] Total helix length (file [TT]len-ahx.xvg[tt]). The total length",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"number of helical residues (see below).[BR]",
"[BB]5.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
"[BB]6.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
"atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
"[BB]7.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
"[BB]8.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
"[BB]9.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
"[PAR]"
};
static gmx_bool bCheck = FALSE, bFit = TRUE, bDBG = FALSE, bEV = FALSE;
static int rStart = 0, rEnd = 0, r0 = 1;
t_pargs pa [] = {
{ "-r0", FALSE, etINT, {&r0},
"The first residue number in the sequence" },
{ "-q", FALSE, etBOOL, {&bCheck},
"Check at every step which part of the sequence is helical" },
{ "-F", FALSE, etBOOL, {&bFit},
"Toggle fit to a perfect helix" },
{ "-db", FALSE, etBOOL, {&bDBG},
"Print debug info" },
{ "-ev", FALSE, etBOOL, {&bEV},
"Write a new 'trajectory' file for ED" },
{ "-ahxstart", FALSE, etINT, {&rStart},
"First residue in helix" },
{ "-ahxend", FALSE, etINT, {&rEnd},
"Last residue in helix" }
};
typedef struct {
FILE *fp, *fp2;
gmx_bool bfp2;
const char *filenm;
const char *title;
const char *xaxis;
const char *yaxis;
real val;
} t_xvgrfile;
t_xvgrfile xf[efhNR] = {
{ NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)", 0.0 },
{ NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 },
{ NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 },
{ NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 },
{ NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 },
{ NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "rmsa-ahx", "Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg", 0.0 },
{ NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 },
{ NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg", 0.0 },
{ NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg", 0.0 },
{ NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm", 0.0 },
{ NULL, NULL, FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz", 0.0 },
{ NULL, NULL, FALSE, "helicity", "Helicity per Residue", "Residue", "% of time", 0.0 }
};
output_env_t oenv;
char buf[54];
t_trxstatus *status;
int natoms, nre, nres;
t_bb *bb;
int i, j, m, nall, nbb, nca, teller, nSel = 0;
atom_id *bbindex, *caindex, *allindex;
t_topology *top;
int ePBC;
rvec *x, *xref;
real t;
real rms;
matrix box;
gmx_rmpbc_t gpbc = NULL;
gmx_bool bRange;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efSTO, "-cz", "zconf", ffWRITE },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
opt2parg_bSet("-ahxend", asize(pa), pa));
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
natoms = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
if (natoms != top->atoms.nr)
{
gmx_fatal(FARGS, "Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
top->atoms.nr, natoms);
}
bb = mkbbind(ftp2fn(efNDX, NFILE, fnm), &nres, &nbb, r0, &nall, &allindex,
top->atoms.atomname, top->atoms.atom, top->atoms.resinfo);
snew(bbindex, natoms);
snew(caindex, nres);
fprintf(stderr, "nall=%d\n", nall);
/* Open output files, default x-axis is time */
for (i = 0; (i < efhNR); i++)
{
sprintf(buf, "%s.xvg", xf[i].filenm);
remove(buf);
xf[i].fp = xvgropen(buf, xf[i].title,
xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
xf[i].yaxis, oenv);
if (xf[i].bfp2)
{
sprintf(buf, "%s.out", xf[i].filenm);
remove(buf);
xf[i].fp2 = gmx_ffopen(buf, "w");
}
}
/* Read reference frame from tpx file to compute helix length */
snew(xref, top->atoms.nr);
read_tpx(ftp2fn(efTPX, NFILE, fnm),
NULL, NULL, &natoms, xref, NULL, NULL, NULL);
calc_hxprops(nres, bb, xref);
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
sfree(xref);
if (bDBG)
{
fprintf(stderr, "nca=%d, nbb=%d\n", nca, nbb);
pr_bb(stdout, nres, bb);
}
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
teller = 0;
do
{
if ((teller++ % 10) == 0)
{
fprintf(stderr, "\rt=%.2f", t);
}
gmx_rmpbc(gpbc, natoms, box, x);
calc_hxprops(nres, bb, x);
if (bCheck)
{
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, FALSE, 0, 0);
}
if (nca >= 5)
{
rms = fit_ahx(nres, bb, natoms, nall, allindex, x, nca, caindex, bFit);
if (teller == 1)
{
write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis",
&(top->atoms), x, NULL, ePBC, box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2, nca, caindex, x);
xf[efhTWIST].val = twist(nca, caindex, x);
xf[efhRISE].val = rise(nca, caindex, x);
xf[efhLEN].val = ahx_len(nca, caindex, x);
xf[efhCD222].val = ellipticity(nres, bb);
xf[efhDIP].val = dip(nbb, bbindex, x, top->atoms.atom);
xf[efhRMS].val = rms;
xf[efhCPHI].val = ca_phi(nca, caindex, x);
xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2, nres, bb);
for (j = 0; (j <= efhCPHI); j++)
{
fprintf(xf[j].fp, "%10g %10g\n", t, xf[j].val);
}
av_phipsi(xf[efhPHI].fp, xf[efhPSI].fp, xf[efhPHI].fp2, xf[efhPSI].fp2,
t, nres, bb);
av_hblen(xf[efhHB3].fp, xf[efhHB3].fp2,
xf[efhHB4].fp, xf[efhHB4].fp2,
xf[efhHB5].fp, xf[efhHB5].fp2,
t, nres, bb);
}
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
gmx_rmpbc_done(gpbc);
close_trj(status);
for (i = 0; (i < nres); i++)
{
if (bb[i].nrms > 0)
{
fprintf(xf[efhRMSA].fp, "%10d %10g\n", r0+i, bb[i].rmsa/bb[i].nrms);
}
fprintf(xf[efhAHX].fp, "%10d %10g\n", r0+i, (bb[i].nhx*100.0)/(real )teller);
fprintf(xf[efhJCA].fp, "%10d %10g\n",
r0+i, 140.3+(bb[i].jcaha/(double)teller));
}
for (i = 0; (i < efhNR); i++)
{
gmx_ffclose(xf[i].fp);
if (xf[i].bfp2)
{
gmx_ffclose(xf[i].fp2);
}
do_view(oenv, xf[i].filenm, "-nxy");
}
return 0;
}
PxU32 RevoluteJointSolverPrep(Px1DConstraint* constraints,
PxVec3& body0WorldOffset,
PxU32 /*maxConstraints*/,
PxConstraintInvMassScale &invMassScale,
const void* constantBlock,
const PxTransform& bA2w,
const PxTransform& bB2w)
{
const RevoluteJointData& data = *reinterpret_cast<const RevoluteJointData*>(constantBlock);
invMassScale = data.invMassScale;
const PxJointAngularLimitPair& limit = data.limit;
bool limitEnabled = data.jointFlags & PxRevoluteJointFlag::eLIMIT_ENABLED;
bool limitIsLocked = limitEnabled && limit.lower >= limit.upper;
PxTransform cA2w = bA2w * data.c2b[0];
PxTransform cB2w = bB2w * data.c2b[1];
if(cB2w.q.dot(cA2w.q)<0.f)
cB2w.q = -cB2w.q;
body0WorldOffset = cB2w.p-bA2w.p;
Ext::joint::ConstraintHelper ch(constraints, cB2w.p - bA2w.p, cB2w.p - bB2w.p);
ch.prepareLockedAxes(cA2w.q, cB2w.q, cA2w.transformInv(cB2w.p), 7, PxU32(limitIsLocked ? 7 : 6));
if(limitIsLocked)
return ch.getCount();
PxVec3 axis = cA2w.rotate(PxVec3(1.f,0,0));
if(data.jointFlags & PxRevoluteJointFlag::eDRIVE_ENABLED)
{
Px1DConstraint *c = ch.getConstraintRow();
c->solveHint = PxConstraintSolveHint::eNONE;
c->linear0 = PxVec3(0);
c->angular0 = -axis;
c->linear1 = PxVec3(0);
c->angular1 = -axis * data.driveGearRatio;
c->velocityTarget = data.driveVelocity;
c->minImpulse = -data.driveForceLimit;
c->maxImpulse = data.driveForceLimit;
if(data.jointFlags & PxRevoluteJointFlag::eDRIVE_FREESPIN)
{
if(data.driveVelocity > 0)
c->minImpulse = 0;
if(data.driveVelocity < 0)
c->maxImpulse = 0;
}
c->flags |= Px1DConstraintFlag::eHAS_DRIVE_LIMIT;
}
if(limitEnabled)
{
PxQuat cB2cAq = cA2w.q.getConjugate() * cB2w.q;
PxQuat twist(cB2cAq.x,0,0,cB2cAq.w);
PxReal magnitude = twist.normalize();
PxReal tqPhi = physx::intrinsics::fsel(magnitude - 1e-6f, twist.x / (1.0f + twist.w), 0.f);
ch.quarterAnglePair(tqPhi, data.tqLow, data.tqHigh, data.tqPad, axis, limit);
}
return ch.getCount();
}
int gmx_helix(int argc,char *argv[])
{
const char *desc[] = {
"g_helix computes all kind of helix properties. First, the peptide",
"is checked to find the longest helical part. This is determined by",
"Hydrogen bonds and Phi/Psi angles.",
"That bit is fitted",
"to an ideal helix around the Z-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file radius.xvg). This is merely the",
"RMS deviation in two dimensions for all Calpha atoms.",
"it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file twist.xvg). The average helical angle per",
"residue is calculated. For alpha helix it is 100 degrees,",
"for 3-10 helices it will be smaller,",
"for 5-helices it will be larger.[BR]",
"[BB]3.[bb] Rise per residue (file rise.xvg). The helical rise per",
"residue is plotted as the difference in Z-coordinate between Ca",
"atoms. For an ideal helix this is 0.15 nm[BR]",
"[BB]4.[bb] Total helix length (file len-ahx.xvg). The total length",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"number of helical residues (see below).[BR]",
"[BB]5.[bb] Number of helical residues (file n-ahx.xvg). The title says",
"it all.[BR]",
"[BB]6.[bb] Helix Dipole, backbone only (file dip-ahx.xvg).[BR]",
"[BB]7.[bb] RMS deviation from ideal helix, calculated for the Calpha",
"atoms only (file rms-ahx.xvg).[BR]",
"[BB]8.[bb] Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).[BR]",
"[BB]9.[bb] Average Phi and Psi angles (file phipsi.xvg).[BR]",
"[BB]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]",
"[PAR]"
};
static const char *ppp[efhNR+2] = {
NULL, "RAD", "TWIST", "RISE", "LEN", "NHX", "DIP", "RMS", "CPHI",
"RMSA", "PHI", "PSI", "HB3", "HB4", "HB5", "CD222", NULL
};
static gmx_bool bCheck=FALSE,bFit=TRUE,bDBG=FALSE,bEV=FALSE;
static int rStart=0,rEnd=0,r0=1;
t_pargs pa [] = {
{ "-r0", FALSE, etINT, {&r0},
"The first residue number in the sequence" },
{ "-q", FALSE, etBOOL,{&bCheck},
"Check at every step which part of the sequence is helical" },
{ "-F", FALSE, etBOOL,{&bFit},
"Toggle fit to a perfect helix" },
{ "-db", FALSE, etBOOL,{&bDBG},
"Print debug info" },
{ "-prop", FALSE, etENUM, {ppp},
"Select property to weight eigenvectors with. WARNING experimental stuff" },
{ "-ev", FALSE, etBOOL,{&bEV},
"Write a new 'trajectory' file for ED" },
{ "-ahxstart", FALSE, etINT, {&rStart},
"First residue in helix" },
{ "-ahxend", FALSE, etINT, {&rEnd},
"Last residue in helix" }
};
typedef struct {
FILE *fp,*fp2;
gmx_bool bfp2;
const char *filenm;
const char *title;
const char *xaxis;
const char *yaxis;
real val;
} t_xvgrfile;
t_xvgrfile xf[efhNR] = {
{ NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)" , 0.0 },
{ NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 },
{ NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 },
{ NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 },
{ NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 },
{ NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "rmsa-ahx","Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
{ NULL, NULL,FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 },
{ NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL,FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz" , 0.0 },
{ NULL, NULL,FALSE, "helicity","Helicity per Residue", "Residue", "% of time" , 0.0 }
};
output_env_t oenv;
FILE *otrj;
char buf[54],prop[256];
t_trxstatus *status;
int natoms,nre,nres;
t_bb *bb;
int i,j,ai,m,nall,nbb,nca,teller,nSel=0;
atom_id *bbindex,*caindex,*allindex;
t_topology *top;
int ePBC;
rvec *x,*xref,*xav;
real t;
real rms,fac;
matrix box;
gmx_rmpbc_t gpbc=NULL;
gmx_bool bRange;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efG87, "-to", NULL, ffOPTWR },
{ efSTO, "-cz", "zconf",ffWRITE },
{ efSTO, "-co", "waver",ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
bRange=(opt2parg_bSet("-ahxstart",asize(pa),pa) &&
opt2parg_bSet("-ahxend",asize(pa),pa));
top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
natoms=read_first_x(oenv,&status,opt2fn("-f",NFILE,fnm),&t,&x,box);
if (opt2bSet("-to",NFILE,fnm)) {
otrj=opt2FILE("-to",NFILE,fnm,"w");
strcpy(prop,ppp[0]);
fprintf(otrj,"%s Weighted Trajectory: %d atoms, NO box\n",prop,natoms);
}
else
otrj=NULL;
if (natoms != top->atoms.nr)
gmx_fatal(FARGS,"Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
top->atoms.nr,natoms);
bb=mkbbind(ftp2fn(efNDX,NFILE,fnm),&nres,&nbb,r0,&nall,&allindex,
top->atoms.atomname,top->atoms.atom,top->atoms.resinfo);
snew(bbindex,natoms);
snew(caindex,nres);
fprintf(stderr,"nall=%d\n",nall);
/* Open output files, default x-axis is time */
for(i=0; (i<efhNR); i++) {
sprintf(buf,"%s.xvg",xf[i].filenm);
remove(buf);
xf[i].fp=xvgropen(buf,xf[i].title,
xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
xf[i].yaxis,oenv);
if (xf[i].bfp2) {
sprintf(buf,"%s.out",xf[i].filenm);
remove(buf);
xf[i].fp2=ffopen(buf,"w");
}
}
/* Read reference frame from tpx file to compute helix length */
snew(xref,top->atoms.nr);
read_tpx(ftp2fn(efTPX,NFILE,fnm),
NULL,NULL,&natoms,xref,NULL,NULL,NULL);
calc_hxprops(nres,bb,xref,box);
do_start_end(nres,bb,xref,&nbb,bbindex,&nca,caindex,bRange,rStart,rEnd);
sfree(xref);
if (bDBG) {
fprintf(stderr,"nca=%d, nbb=%d\n",nca,nbb);
pr_bb(stdout,nres,bb);
}
gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box);
snew(xav,natoms);
teller=0;
do {
if ((teller++ % 10) == 0)
fprintf(stderr,"\rt=%.2f",t);
gmx_rmpbc(gpbc,natoms,box,x);
calc_hxprops(nres,bb,x,box);
if (bCheck)
do_start_end(nres,bb,x,&nbb,bbindex,&nca,caindex,FALSE,0,0);
if (nca >= 5) {
rms=fit_ahx(nres,bb,natoms,nall,allindex,x,nca,caindex,box,bFit);
if (teller == 1) {
write_sto_conf(opt2fn("-cz",NFILE,fnm),"Helix fitted to Z-Axis",
&(top->atoms),x,NULL,ePBC,box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2,nca,caindex,x);
xf[efhTWIST].val = twist(xf[efhTWIST].fp2,nca,caindex,x);
xf[efhRISE].val = rise(nca,caindex,x);
xf[efhLEN].val = ahx_len(nca,caindex,x,box);
xf[efhCD222].val = ellipticity(nres,bb);
xf[efhDIP].val = dip(nbb,bbindex,x,top->atoms.atom);
xf[efhRMS].val = rms;
xf[efhCPHI].val = ca_phi(nca,caindex,x,box);
xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2,nres,bb);
for(j=0; (j<=efhCPHI); j++)
fprintf(xf[j].fp, "%10g %10g\n",t,xf[j].val);
av_phipsi(xf[efhPHI].fp,xf[efhPSI].fp,xf[efhPHI].fp2,xf[efhPSI].fp2,
t,nres,bb);
av_hblen(xf[efhHB3].fp,xf[efhHB3].fp2,
xf[efhHB4].fp,xf[efhHB4].fp2,
xf[efhHB5].fp,xf[efhHB5].fp2,
t,nres,bb);
if (otrj)
dump_otrj(otrj,nall,allindex,x,xf[nSel].val,xav);
}
} while (read_next_x(oenv,status,&t,natoms,x,box));
fprintf(stderr,"\n");
gmx_rmpbc_done(gpbc);
close_trj(status);
if (otrj) {
ffclose(otrj);
fac=1.0/teller;
for(i=0; (i<nall); i++) {
ai=allindex[i];
for(m=0; (m<DIM); m++)
xav[ai][m]*=fac;
}
write_sto_conf_indexed(opt2fn("-co",NFILE,fnm),
"Weighted and Averaged conformation",
&(top->atoms),xav,NULL,ePBC,box,nall,allindex);
}
for(i=0; (i<nres); i++) {
if (bb[i].nrms > 0) {
fprintf(xf[efhRMSA].fp,"%10d %10g\n",r0+i,bb[i].rmsa/bb[i].nrms);
}
fprintf(xf[efhAHX].fp,"%10d %10g\n",r0+i,(bb[i].nhx*100.0)/(real )teller);
fprintf(xf[efhJCA].fp,"%10d %10g\n",
r0+i,140.3+(bb[i].jcaha/(double)teller));
}
for(i=0; (i<efhNR); i++) {
ffclose(xf[i].fp);
if (xf[i].bfp2)
ffclose(xf[i].fp2);
do_view(oenv,xf[i].filenm,"-nxy");
}
thanx(stderr);
return 0;
}
virtual void MySendCommands() {
ScopedLock lock(mutex);
double dt = t - last_t;
//advance limbs
if(robotState.leftLimb.sendCommand) {
if(robotState.leftLimb.controlMode == LimbState::POSITION || robotState.leftLimb.controlMode == LimbState::RAW_POSITION)
robotState.leftLimb.sendCommand = false;
else if(robotState.leftLimb.controlMode == LimbState::VELOCITY)
robotState.leftLimb.commandedConfig.madd(robotState.leftLimb.commandedVelocity,dt);
else //effort mode not supported
robotState.leftLimb.sendCommand = false;
//handle joint limits
if(robotModel) {
for(size_t i=0;i<leftKlamptIndices.size();i++) {
if(robotState.leftLimb.commandedConfig[i] < robotModel->qMin[leftKlamptIndices[i]] ||
robotState.leftLimb.commandedConfig[i] > robotModel->qMax[leftKlamptIndices[i]]) {
robotState.leftLimb.commandedConfig[i] = Clamp(robotState.leftLimb.commandedConfig[i],robotModel->qMin[leftKlamptIndices[i]],robotModel->qMax[leftKlamptIndices[i]]);
robotState.leftLimb.commandedVelocity[i] = 0;
}
}
}
}
if(robotState.rightLimb.sendCommand) {
if(robotState.rightLimb.controlMode == LimbState::POSITION || robotState.rightLimb.controlMode == LimbState::RAW_POSITION)
robotState.rightLimb.sendCommand = false;
else if(robotState.rightLimb.controlMode == LimbState::VELOCITY)
robotState.rightLimb.commandedConfig.madd(robotState.rightLimb.commandedVelocity,dt);
else //effort mode not supported
robotState.rightLimb.sendCommand = false;
//handle joint limits
if(robotModel) {
for(size_t i=0;i<rightKlamptIndices.size();i++) {
if(robotState.rightLimb.commandedConfig[i] < robotModel->qMin[rightKlamptIndices[i]] ||
robotState.rightLimb.commandedConfig[i] > robotModel->qMax[rightKlamptIndices[i]]) {
robotState.rightLimb.commandedConfig[i] = Clamp(robotState.rightLimb.commandedConfig[i],robotModel->qMin[rightKlamptIndices[i]],robotModel->qMax[rightKlamptIndices[i]]);
robotState.rightLimb.commandedVelocity[i] = 0;
}
}
}
}
//advance grippers
if(robotState.leftGripper.sendCommand)
robotState.leftGripper.sendCommand = false;
robotState.leftGripper.moving = false;
for(int i=0;i<robotState.leftGripper.position.n;i++) {
double pdes = Clamp(robotState.leftGripper.positionCommand[i],0.0,1.0);
double v = Clamp(robotState.leftGripper.speedCommand[i],0.0,1.0);
double old = robotState.leftGripper.position[i];
robotState.leftGripper.position[i] += dt*Sign(pdes-robotState.leftGripper.position[i])*v;
if(Sign(old-pdes) != Sign(robotState.leftGripper.position[i]-pdes))
//stop
robotState.leftGripper.position[i] = pdes;
if(robotState.leftGripper.position[i] != pdes)
robotState.leftGripper.moving=true;
}
if(robotState.rightGripper.sendCommand)
robotState.rightGripper.sendCommand = false;
robotState.rightGripper.moving = false;
for(int i=0;i<robotState.leftGripper.position.n;i++) {
double pdes = Clamp(robotState.rightGripper.positionCommand[i],0.0,1.0);
double v = Clamp(robotState.leftGripper.speedCommand[i],0.0,1.0);
double old = robotState.rightGripper.position[i];
robotState.rightGripper.position[i] += dt*Sign(pdes-robotState.rightGripper.position[i])*v;
if(Sign(old-pdes) != Sign(robotState.rightGripper.position[i]-pdes))
//stop
robotState.rightGripper.position[i] = pdes;
if(robotState.rightGripper.position[i] != pdes)
robotState.rightGripper.moving = true;
}
//process base commands
if(robotState.base.sendCommand) {
Assert(robotState.base.command.size()==3);
if(robotState.base.controlMode == BaseState::NONE) {
robotState.base.sendCommand = false;
robotState.base.moving = false;
robotState.base.velocity.set(0.0);
}
else if(robotState.base.controlMode == BaseState::RELATIVE_POSITION || robotState.base.controlMode == BaseState::ODOMETRY_POSITION) {
if(robotState.base.controlMode == BaseState::RELATIVE_POSITION) {
//first transform to global odometry
robotState.base.controlMode = BaseState::ODOMETRY_POSITION;
Vector newCommand(3);
robotState.base.ToOdometry(robotState.base.command,newCommand);
robotState.base.command = newCommand;
}
}
else if(robotState.base.controlMode == BaseState::RELATIVE_VELOCITY) {
//physical mode latches the command ... kinematic mode doesnt
//robotState.base.sendCommand = false;
if(robotState.base.command.norm() < 1e-3) { //done!
robotState.base.sendCommand = false;
robotState.base.moving = false;
robotState.base.velocity.set(0.0);
}
}
robotState.base.IntegrateCommand(baseCalibration,dt);
//cout<<"Desired twist "<<robotState.base.commandedVelocity<<endl;
if(robotState.base.controlMode == BaseState::RELATIVE_POSITION || robotState.base.controlMode == BaseState::ODOMETRY_POSITION) {
if(robotState.base.commandedPosition.distance(robotState.base.command)<1e-3 && robotState.base.commandedVelocity.norm() < 1e-3) {
printf("Arrived, setting sendCommand/moving = false\n");
robotState.base.sendCommand = false;
robotState.base.moving = false;
robotState.base.velocity.set(0.0);
}
}
}
//simulate base
if(robotState.base.enabled && robotState.base.sendCommand) {
//simulate friction
Vector twist(3,0.0);
robotState.base.DesiredToLowLevelCommand(baseCalibration,dt,twist);
cout<<"Commanded twist "<<twist<<", dt "<<endl;
if(Abs(twist(0)) < baseCalibration.xFriction)
twist(0) = 0;
else
twist(0) -= Sign(twist(0))*baseCalibration.xFriction;
if(Abs(twist(1)) < baseCalibration.yFriction)
twist(1) = 0;
else
twist(1) -= Sign(twist(1))*baseCalibration.yFriction;
if(Abs(twist(2)) < baseCalibration.angFriction)
twist(2) = 0;
else
twist(2) -= Sign(twist(2))*baseCalibration.angFriction;
cout<<"Friction changed twist to "<<twist<<endl;
robotState.base.velocity = twist;
Matrix2 R; R.setRotate(robotState.base.odometry(2));
Vector2 vworld = R*Vector2(twist(0),twist(1));
robotState.base.odometry(0) += vworld.x*dt;
robotState.base.odometry(1) += vworld.y*dt;
robotState.base.odometry(2) += twist(2)*dt;
robotState.base.senseUpdateTime = t;
assert(robotState.base.sendCommand == true);
}
}