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; */ }