| version 1.12 | version 1.13 |
|---|
| |
| x.type(colvarvalue::type_scalar); | x.type(colvarvalue::type_scalar); |
| } | } |
| | |
| | |
| colvar::alpha_angles::~alpha_angles() | colvar::alpha_angles::~alpha_angles() |
| { | { |
| while (theta.size() != 0) { | while (theta.size() != 0) { |
| |
| } | } |
| } | } |
| | |
| | |
| void colvar::alpha_angles::calc_value() | void colvar::alpha_angles::calc_value() |
| { | { |
| x.real_value = 0.0; | x.real_value = 0.0; |
| |
| } | } |
| | |
| | |
| | simple_scalar_dist_functions(alpha_angles) |
| | |
| | |
| | |
| ////////////////////////////////////////////////////////////////////// | ////////////////////////////////////////////////////////////////////// |
| // dihedral principal component | // dihedral principal component |
| ////////////////////////////////////////////////////////////////////// | ////////////////////////////////////////////////////////////////////// |
| |
| cvm::atom(r[i ], "CA", sid), | cvm::atom(r[i ], "CA", sid), |
| cvm::atom(r[i ], "C", sid), | cvm::atom(r[i ], "C", sid), |
| cvm::atom(r[i+1], "N", sid))); | cvm::atom(r[i+1], "N", sid))); |
| | atom_groups.push_back(theta.back()->atom_groups[0]); |
| | atom_groups.push_back(theta.back()->atom_groups[1]); |
| | atom_groups.push_back(theta.back()->atom_groups[2]); |
| | atom_groups.push_back(theta.back()->atom_groups[3]); |
| // Phi (next res) | // Phi (next res) |
| theta.push_back(new colvar::dihedral(cvm::atom(r[i ], "C", sid), | theta.push_back(new colvar::dihedral(cvm::atom(r[i ], "C", sid), |
| cvm::atom(r[i+1], "N", sid), | cvm::atom(r[i+1], "N", sid), |
| cvm::atom(r[i+1], "CA", sid), | cvm::atom(r[i+1], "CA", sid), |
| cvm::atom(r[i+1], "C", sid))); | cvm::atom(r[i+1], "C", sid))); |
| | atom_groups.push_back(theta.back()->atom_groups[0]); |
| | atom_groups.push_back(theta.back()->atom_groups[1]); |
| | atom_groups.push_back(theta.back()->atom_groups[2]); |
| | atom_groups.push_back(theta.back()->atom_groups[3]); |
| } | } |
| | |
| if (cvm::debug()) | if (cvm::debug()) |
| |
| coeffs[2*i+1] * dsindt) * force); | coeffs[2*i+1] * dsindt) * force); |
| } | } |
| } | } |
| | |
| | |
| | simple_scalar_dist_functions(dihedPC) |