int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
opts::BasicOptions* bopts = new opts::BasicOptions;
opts::ModelWithCoords* mopts = new opts::ModelWithCoords;
ToolOptions* topts = new ToolOptions;
opts::AggregateOptions options;
options.add(bopts).add(mopts).add(topts);
if (!options.parse(argc, argv))
exit(-1);
AtomicGroup model = mopts->model;
if (topts->reimage) {
if (!model.isPeriodic()) {
cerr << "WARNING- Reimaging requested, but the model has no periodic box information\n";
} else {
if (!topts->bonds_name.empty()) {
AtomicGroup bonds = createSystem(topts->bonds_name);
copyBonds(model, bonds);
}
if (!model.hasBonds()) {
cerr << "WARNING- The model has no connectivity. Assigning bonds based on distance.\n";
model.findBonds();
}
}
}
AtomicGroup center_mol = selectAtoms(model, topts->center_sel);
GCoord center = center_mol.centroid();
AtomicGroup apply_mol = selectAtoms(model, topts->apply_sel);
GCoord offset = topts->translate - center;
if (topts->center_xy)
offset.z() = 0.0;
for (AtomicGroup::iterator atom = apply_mol.begin(); atom != apply_mol.end(); ++atom)
(*atom)->coords() += offset;
if (topts->reimage && model.isPeriodic()) {
vGroup molecules = model.splitByMolecule();
vGroup segments = model.splitByUniqueSegid();
for (vGroup::iterator seg = segments.begin(); seg != segments.end(); ++seg)
seg->reimage();
for (vGroup::iterator mol =molecules.begin(); mol != molecules.end(); ++mol)
mol->reimage();
}
AtomicGroup write_mol = selectAtoms(model, topts->write_sel);
PDB pdb = PDB::fromAtomicGroup(write_mol);
pdb.remarks().add(hdr);
cout << pdb;
}
int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
opts::BasicOptions* bopts = new opts::BasicOptions(fullHelpMessage());
ToolOptions* topts = new ToolOptions;
opts::RequiredArguments* ropts = new opts::RequiredArguments;
ropts->addArgument("matrix", "matrix-file");
opts::AggregateOptions options;
options.add(bopts).add(topts).add(ropts);
if (!options.parse(argc, argv))
exit(-1);
string matrix_name = ropts->value("matrix");
RealMatrix A;
readAsciiMatrix(matrix_name, A);
uint m = A.rows();
if (rows.empty())
for (uint i=0; i<m; ++i)
rows.push_back(i);
uint resid = 1;
uint total_chunks = rows.size() / (chunksize ? chunksize : rows.size());
uint chunk = 1;
AtomicGroup model;
// Warn about pymol...
if (rows.size() >= 100000 && bonds)
cerr << "Warning- PyMol may not correctly handle the CONECT records generated by this tool.\n";
for (uint atomid = 0; atomid < rows.size(); ++atomid, ++resid) {
if (chunksize && resid > chunksize) {
if (bonds) {
for (uint i=atomid - chunksize; i<atomid-1; ++i)
model[i]->addBond(model[i+1]);
}
resid = 1;
++chunk;
}
GCoord c(scales[0] * A(rows[atomid], columns[0]),
scales[1] * A(rows[atomid], columns[1]),
scales[2] * A(rows[atomid], columns[2]));
pAtom pa(new Atom(atomid+1, atom_name, c));
pa->resid(resid);
pa->resname(residue_name);
ostringstream segstream;
segstream << boost::format(segid_fmt) % chunk;
pa->segid(segstream.str());
double b;
double q = 0.0;
if (chunksize) {
b = (100.0 * (resid-1)) / chunksize;
q = static_cast<double>(chunk-1) / total_chunks;
} else
b = 100.0 * atomid / rows.size();
pa->bfactor(b);
pa->occupancy(q);
model.append(pa);
}
if (bonds) {
if (chunksize && resid > 1)
for (uint i=rows.size() - chunksize; i<rows.size()-1; ++i)
model[i]->addBond(model[i+1]);
else if (!chunksize)
for (uint i=0; i<rows.size()-1; ++i)
model[i]->addBond(model[i+1]);
}
PDB pdb = PDB::fromAtomicGroup(model);
pdb.remarks().add(hdr);
cout << pdb;
}
int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
cout << "# " << hdr << endl;
parseArgs(argc, argv);
DoubleMatrix eigvals;
readAsciiMatrix(eigvals_name, eigvals);
DoubleMatrix eigvecs;
readAsciiMatrix(eigvecs_name, eigvecs);
if (modes.empty())
for (uint i=0; i<eigvals.rows(); ++i)
modes.push_back(i);
uint n = modes.size();
uint m = eigvecs.rows();
// V = m x n matrix of eigenvectors
DoubleMatrix V(m, n);
for (uint i=0; i<n; ++i)
for (uint j=0; j<m; ++j)
V(j, i) = eigvecs(j, modes[i]);
// Make a copy and scale by the appropriate eigenvalue,
// remembering that eigenvalues are inverted for ENM,
// or squaring and not inverting in the case of PCA
DoubleMatrix VS = V.copy();
for (uint i=0; i<n; ++i) {
double e = eigvals[modes[i]];
double s = (pca_input) ? (scale * e * e): (scale / e);
for (uint j=0; j<m; ++j)
VS(j, i) *= s;
}
// U = Covariance matrix
DoubleMatrix U = loos::Math::MMMultiply(VS,V,false,true);
// B-factors come from trace of diagonal 3x3 superblocks
vector<double> B;
double prefactor = 8.0 * M_PI * M_PI / 3.0;
for (uint i=0; i<m; i += 3) {
double b = prefactor * (U(i,i) + U(i+1, i+1) + U(i+2, i+2));
B.push_back(b);
cout << boost::format("%-8d %g\n") % (i/3) % b;
}
if (!pdb_name.empty()) {
AtomicGroup model = createSystem(pdb_name);
AtomicGroup subset = selectAtoms(model, selection);
if ((unsigned int)subset.size() != B.size()) {
cerr << boost::format("Error- selection has %d atoms, but %d were expected.\n") % subset.size() % B.size();
exit(-10);
}
for (uint i=0; i<B.size(); ++i)
subset[i]->bfactor(B[i]);
PDB pdb = PDB::fromAtomicGroup(model);
pdb.remarks().add(hdr);
ofstream ofs(out_name.c_str());
ofs << pdb;
}
}