version 1.12 | version 1.13 |
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x.type(colvarvalue::type_scalar); | x.type(colvarvalue::type_scalar); |
} | } |
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colvar::alpha_angles::~alpha_angles() | colvar::alpha_angles::~alpha_angles() |
{ | { |
while (theta.size() != 0) { | while (theta.size() != 0) { |
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} | } |
} | } |
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void colvar::alpha_angles::calc_value() | void colvar::alpha_angles::calc_value() |
{ | { |
x.real_value = 0.0; | x.real_value = 0.0; |
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} | } |
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| simple_scalar_dist_functions(alpha_angles) |
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////////////////////////////////////////////////////////////////////// | ////////////////////////////////////////////////////////////////////// |
// dihedral principal component | // dihedral principal component |
////////////////////////////////////////////////////////////////////// | ////////////////////////////////////////////////////////////////////// |
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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]); |
} | } |
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if (cvm::debug()) | if (cvm::debug()) |
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coeffs[2*i+1] * dsindt) * force); | coeffs[2*i+1] * dsindt) * force); |
} | } |
} | } |
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| simple_scalar_dist_functions(dihedPC) |