void AmberNetcdf::updateGroupCoordsImpl(AtomicGroup& g) {
for (AtomicGroup::iterator i = g.begin(); i != g.end(); ++i) {
uint idx = (*i)->index();
if (idx >= _natoms)
throw(LOOSError(**i, "Atom index into trajectory frame is out of bounds"));
idx *= 3;
(*i)->coords(GCoord(_coord_data[idx], _coord_data[idx+1], _coord_data[idx+2]));
}
if (_periodic)
g.periodicBox(GCoord(_box_data[0], _box_data[1], _box_data[2]));
}
GRGlue::GRGlue(GRStaff * grstf, int _isstart) // (JB) Something obscur: sometimes, GRGlue is
// created with _isstart = -1, why is that ?
// I'd like to replace it by a bool, but I can't...
{
mGrStaff = grstf;
mIsStart = _isstart;
mNeedsSpring = 1;
float curLSPACE = LSPACE;
if (mGrStaff)
curLSPACE = mGrStaff->getStaffLSPACE();
if (mIsStart == 1)
{
mSConst = SCONST_GLUESTART;
// this does not work?
mRightSpace = GCoord(curLSPACE);
}
else
{
mSConst = 100; // SCONST_GLUENOSTART;
mRightSpace = GCoord(curLSPACE);
// leftSpace = 5*LSPACE;
}
mPartner = NULL;
// this is the left and right margin that need
// to be maintained in all cases ...
mBoundingBox.right = 0;
mBoundingBox.left = 0;
/* if (isstart)
mBoundingBox.right = LSPACE;
else
mBoundingBox.left = -LSPACE;
*/
}
