1 #include "PAR.h" 2 3 #include "mathutilities.h" 4 5 //using namespace ProtoMol::Report; 6 7 namespace ProtoMol { 8 9 //_________________________________________________________________ PAR 10 const Real PAR::Nonbonded::SIGMA_CHARMM19_TO_CHARMM28(pow(2.0,-5.0/6.0)); 11 const Real PAR::Nonbonded::SIGMA_CHARMM28_TO_CHARMM19(pow(2.0, 5.0/6.0)); 12 clear()13 void PAR::clear(){ 14 bonds.clear(); 15 angles.clear(); 16 dihedrals.clear(); 17 impropers.clear(); 18 nonbondeds.clear(); 19 nbfixs.clear(); 20 hbonds.clear(); 21 } 22 23 24 //_________________________________________________________________globals 25 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Bond & p) { 26 // OS <<p.number<<","<<p.atom1<<","<<p.atom2<<","<<p.forceConstant<<","<<p.distance; 27 // return OS; 28 // } 29 30 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Angle & p) { 31 // OS <<p.number<<","<<p.atom1<<","<<p.atom2<<","<<p.atom3<<","<<p.forceConstant<<","<<p.angleval<<","<<p.ub_flag<<","<<p.k_ub<<","<<p.r_ub; 32 // return OS; 33 // } 34 35 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Dihedral & p) { 36 // OS <<p.number<<","<<p.atom1<<","<<p.atom2<<","<<p.atom3<<","<<p.atom4<<","<<p.multiplicity; 37 // for(unsigned int i=0;i<p.forceConstant.size();++i) 38 // OS << ","<<p.forceConstant[i]; 39 // for(unsigned int i=0;i<p.periodicity.size();++i) 40 // OS << ","<<p.forceConstant[i]; 41 // for(unsigned int i=0;i<p.phaseShift.size();++i) 42 // OS << ","<<p.forceConstant[i]; 43 // return OS; 44 // } 45 46 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Improper & p) { 47 // OS <<p.number<<","<<p.atom1<<","<<p.atom2<<","<<p.atom3<<","<<p.atom4<<","<<p.forceConstant<< ","<<p.periodicity<<","<<p.phaseShift; 48 // return OS; 49 // } 50 51 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Nonbonded & p) { 52 // OS <<p.number<<","<<p.atom<<","<<p.polarizability<<","<<p.epsilon<<","<<p.sigma<<","<<p.negative<< "," 53 // <<p.vdw<<","<<p.polarizability2<<","<<p.epsilon14<<","<<p.sigma14<<","<<p.negative2; 54 // return OS; 55 // } 56 57 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Nbfix & p) { 58 // OS <<p.number<<","<<p.atom1<<","<<p.atom2<<","<<p.a<<","<<p.b<<","<<p.a14<< ","<<p.b14; 59 // return OS; 60 // } 61 62 // MyStreamer& operator<< (MyStreamer& OS, const PAR::Hbond & p) { 63 // OS <<p.number<<","<<p.atom1<<","<<p.atom2<<","<<p.emin<<","<<p.rmin; 64 // return OS; 65 // } 66 } 67