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