bool FormatTopology::save(string topfile, Space &spc) {
std::set<string> done;
std::ofstream f(topfile.c_str());
if (f) {
f << "[ defaults ]\n"
<< ";nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ\n"
<< " 1 2 yes 1.0000 1.0000\n";
f << writeAtomTypes(spc);
for (auto g : spc.groupList() ) {
if ( done.find(g->name)==done.end() ) {
f << writeMoleculeType(*g, spc);
done.insert(g->name);
}
}
f << "[ system ]\n" << "something" << endl;
f << "[ molecules ]\n" << "prot " << spc.groupList().size() << endl;
return true;
}
return false;
}
bool FormatGRO::save(string file, Space &spc) {
assert( abs(len*len*len-spc.geo->getVolume())<1e-6 && "Did you forget to pass box size to FormatGRO?" );
string name;
int nres=1, natom=1;
char buf[79];
double halflen=len/2;
std::ostringstream o;
o << "Generated by Faunus -- http://faunus.sourceforge.net"
<< std::endl << spc.p.size() << std::endl;
for (auto g : spc.groupList()) {
for (auto i : *g) {
name=atom[ spc.p[i].id ].name;
sprintf(buf, "%5d%5s%5s%5d%8.3f%8.3f%8.3f\n",
nres,name.c_str(),name.c_str(),natom++,
spc.p[i].x()/10+halflen, spc.p[i].y()/10+halflen, spc.p[i].z()/10+halflen );
o << buf;
}
nres++;
}
if (len>0)
o << len << " " << len << " " << len << std::endl;
return IO::writeFile(file, o.str());
}