Particles _give_particles_copy(Model *m) {
Particles ret;
while (ret.size() < 10) {
ret.push_back(new Particle(m));
}
return ret;
}
const Particles &_give_particles(Model *m) {
static Particles ret;
while (ret.size() < 10) {
ret.push_back(new Particle(m));
}
return ret;
}
void add_NuisanceMover(Particle *p, double dp, core::MonteCarloMovers &mvs) {
// put particle in a list
Particles ps;
ps.push_back(p);
// put nuisance floatkey in a list
FloatKeys fks;
fks.push_back(FloatKey("nuisance"));
IMP_NEW(core::NormalMover, mv, (ps, fks, dp));
mvs.push_back(mv);
}
SecondaryStructureResidues read_psipred(TextInput inf, Model* mdl) {
Strings ss = parse_psipred_file(inf);
int nres = ss[0].size();
Particles ps;
for (int nr = 0; nr < nres; nr++) {
IMP_NEW(Particle, p, (mdl));
ps.push_back(p);
}
return create_sses_from_strings(ss, ps);
}
inline explicit Simulation(const size_t np,
const size_t nw,
const double delta_lambda) :
delta_lam(delta_lambda),
delta_tau(delta_lam*delta_lam),
workers(nw,as_capacity),
running(),
waiting(),
ran( )
{
ran.reseed( Randomized::Bits::Simple() );
for(size_t i=np;i>0;--i) { running.push_back( new Particle() ); }
for(size_t i=nw;i>0;--i) { const Worker::Pointer pW( new Worker() ); workers.push_back(pW); }
}
Hierarchy create_protein(Model *m,
std::string name,
double resolution,
int number_of_residues,
int first_residue_index,
double volume,
bool ismol) {
double mass= atom::get_mass_from_number_of_residues(number_of_residues)/1000;
if (volume < 0) {
volume= atom::get_volume_from_mass(mass*1000);
}
// assume a 20% overlap in the beads to make the protein not too bumpy
double overlap_frac=.2;
std::pair<int, double> nr= compute_n(volume, resolution, overlap_frac);
Hierarchy pd=Hierarchy::setup_particle(new Particle(m));
if (ismol) Molecule::setup_particle(pd);
pd->set_name(name);
Particles ps;
for (int i=0; i< nr.first; ++i) {
Particle *pc= new Particle(m);
std::ostringstream oss;
oss << name << "-" << i;
pc->set_name(oss.str());
atom::Fragment pcd
=atom::Fragment::setup_particle(pc);
pd.add_child(pcd);
core::XYZR xyzd=core::XYZR::setup_particle(pc);
xyzd.set_radius(nr.second);
xyzd.set_coordinates_are_optimized(true);
ps.push_back(pc);
Ints indexes;
for (int j= i*(number_of_residues/nr.first)
+ first_residue_index; j <(i+1)*(number_of_residues/nr.first)
+ first_residue_index; ++j) {
indexes.push_back(j);
}
pcd.set_residue_indexes(indexes);
atom::Mass::setup_particle(pc, mass/nr.first);
}
IMP_INTERNAL_CHECK(pd.get_is_valid(true),
"Invalid hierarchy produced " << pd);
return pd;
}
void CHARMMParameters::add_angle(Particle *p1, Particle *p2, Particle *p3,
Particles &ps) const
{
IMP_OBJECT_LOG;
Angle ad = Angle::setup_particle(new Particle(p1->get_model()),
core::XYZ(p1), core::XYZ(p2),
core::XYZ(p3));
try {
const CHARMMBondParameters &p
= get_angle_parameters(CHARMMAtom(p1).get_charmm_type(),
CHARMMAtom(p2).get_charmm_type(),
CHARMMAtom(p3).get_charmm_type());
ad.set_ideal(p.ideal / 180.0 * PI);
ad.set_stiffness(std::sqrt(p.force_constant * 2.0));
} catch (const IndexException &e) {
// If no parameters, warn only
IMP_WARN(e.what());
}
ps.push_back(ad);
}
void detectImpact(const double delta_lam,
IRandom &ran) throw()
{
count = 0;
Particles tmp;
while(running.size>0)
{
Particle *p = running.pop_back();
const int ans = p->moveAndDetectImpact(delta_lam,ran);
if(ans!=0)
{
count += ans;
waiting.push_back(p);
}
else
{
tmp.push_front(p);
}
}
tmp.swap_with(running);
}
void remove(Particle *p)
{
removeList.push_back(p);
}
void add(Particle *p)
{
particles.push_back(p);
}
int main(int argc, char ** argv)
{
invalid_argument er(
"Bond angle correlation function\n"
#ifdef use_periodic
"Syntax : periodic_g6 [path]filename NbOfBins Nb dx dy dz [mode=0 [l=6]]\n"
#else
"Syntax : g6 [path]filename radius NbOfBins range [mode=0 [l=6 [zmin zmax]]]\n"
" range is in diameter unit\n"
#endif
" mode\t0 raw boo\n"
" \t1 coarse grained boo\n"
);
try
{
if(argc<3) throw er;
const string filename(argv[1]);
const string inputPath = filename.substr(0,filename.find_last_of("."));
vector<size_t> inside;
//construct the particle container out of the datafile
#ifdef use_periodic
if(argc<7) throw er;
const size_t Nbins = atoi(argv[2]);
const size_t Nb = atoi(argv[3]);
double nbDiameterCutOff =atof(argv[4]);
BoundingBox b;
for(size_t d=0;d<3;++d)
{
b.edges[d].first=0.0;
b.edges[d].second = atof(argv[4+d]);
if(nbDiameterCutOff>b.edges[d].second)
nbDiameterCutOff=b.edges[d].second;
}
nbDiameterCutOff /=4.0;
const bool mode = (argc<8)?0:atoi(argv[7]);
const size_t l = (argc<9)?6:atoi(argv[8]);
PeriodicParticles Centers(Nb,b,filename,1.0);
cout << "With periodic boundary conditions"<<endl;
#else
const double radius = atof(argv[2]),
nbDiameterCutOff = atof(argv[4]);
const size_t Nbins = atoi(argv[3]);
const bool mode = (argc<6)?0:atoi(argv[5]);
const size_t l = (argc<7)?6:atoi(argv[6]);
Particles Centers(filename,radius);
#endif
cout << Centers.size() << " particles ... ";
//read q6m
vector<BooData> rawBoo, allBoo;
Centers.load_qlm(inputPath+".qlm", rawBoo);
if(mode)
{
Centers.makeNgbList(loadBonds(inputPath+".bonds"));
//select all particles who's all neighbours' qlms are not null
vector<size_t> second_inside;
second_inside.reserve(Centers.size());
for(size_t p=0; p<Centers.getNgbList().size(); ++p)
{
bool hasNullNgb = false;
for(size_t n=0; n<Centers.getNgbList()[p].size(); ++n)
hasNullNgb = (hasNullNgb || rawBoo[Centers.getNgbList()[p][n]].isnull());
if(!hasNullNgb)
second_inside.push_back(p);
}
cout<< second_inside.size()<< " have coarse grained qlms ... ";
Centers.getCgBOOs(second_inside, rawBoo, allBoo);
}
else
allBoo=rawBoo;
#ifndef use_periodic
vector<size_t> slab;
slab.reserve(Centers.size());
//Case where we ask to discard all points out of the interval [zmin, zmax]
if(argc>8)
{
const double zmin = atof(argv[7]),
zmax = atof(argv[8]);
//look for the particles that are in the slab and have non null qlm
for(size_t p=0; p<Centers.size(); ++p)
if(Centers[p][2]>zmin && Centers[p][2]<zmax && !allBoo[p].isnull())
slab.push_back(p);
}
else
for(size_t p=0; p<Centers.size(); ++p)
if(!allBoo[p].isnull())
slab.push_back(p);
//reduce the centers list
Particles cen;
cen.radius = Centers.radius;
cen.reserve(slab.size());
for(size_t p=0; p<slab.size(); ++p)
cen.push_back(Centers[slab[p]]);
Centers.swap(cen);
Centers.delNgbList();
//reduce the qlm
vector<BooData> boo(slab.size());
for(size_t p=0; p<slab.size(); ++p)
boo[p] = allBoo[slab[p]];
allBoo.swap(boo);
#endif
vector<size_t> nb(Nbins, 0);
vector<double> gl(Nbins, 0.0);
const double maxdistsq = pow(2.0*nbDiameterCutOff, 2);
for(size_t p=0; p<Centers.size(); ++p)
for(size_t q=p+1; q<Centers.size(); ++q)
{
Coord diff = Centers.getDiff(p, q);
const double distsq = (diff*diff).sum();
if(distsq<maxdistsq)
{
const size_t r = sqrt(distsq) / (2.0*nbDiameterCutOff) * Nbins;
nb[r]++;
gl[r] += allBoo[p].innerProduct(allBoo[q], l);
}
}
cout << " done !" << endl;
ostringstream rdffilename;
rdffilename << inputPath << (mode?".cg":".g") << l;
ofstream rdfFile(rdffilename.str().c_str(), ios::out | ios::trunc);
rdfFile << "#r\tg"<<l<<"(r)\tg(r)"<<endl;
for(size_t r=0; r<Nbins; ++r)
rdfFile<< r/(double)Nbins*nbDiameterCutOff <<"\t"<< gl[r] <<"\t"<< nb[r] <<"\n";
//all particles are "inside"
/*inside.reserve(Centers.size());
for(size_t p=0; p<Centers.size(); ++p)
inside[p] = p;
cout << Centers.size() << " inside ... ";
Centers.makeRTreeIndex();*/
//create binner
//Particles::GlBinner binner(Centers, Nbins, nbDiameterCutOff, allBoo, l);
//select particles and bin them
//vector<size_t> inside = Centers.selectInside(2.0*radius*(nbDiameterCutOff+(1+mode)*1.3/2));
//Case where we ask to discard all points out of the interval [zmin, zmax]
/*if(argc>8)
{
const double zmin = atof(argv[7]),
zmax = atof(argv[8]);
//cout<<"\tl="<<l<<"\tzmin="<<zmin<<"\tzmax="<<zmax;
vector<size_t> in;
in.reserve(inside.size());
for(vector<size_t>::const_iterator p=inside.begin(); p!=inside.end(); ++p)
if(Centers[*p][2]>=zmin && Centers[*p][2]<=zmax)
in.push_back(*p);
in.swap(inside);
}*/
/*binner << inside;
//binner.normalize(inside.size());
cout << " done !" << endl;
ostringstream rdffilename;
rdffilename << inputPath << (mode?".cg":".g") << l;
ofstream rdfFile(rdffilename.str().c_str(), ios::out | ios::trunc);
rdfFile << "#r\tg"<<l<<"(r)\tg(r)"<<endl;
for(size_t r=0; r<Nbins; ++r)
rdfFile<< r/(double)Nbins*nbDiameterCutOff <<"\t"<< binner.gl[r] <<"\t"<< binner.g[r] <<"\n";*/
}
catch(const std::exception &e)
{
cerr<<e.what() << endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}