#include <fstream>#include <cmath>#include "colvarmodule.h"#include "colvar.h"#include "colvaratoms.h"Go to the source code of this file.
Classes | |
| class | colvar::cvc |
| Colvar component (base class); most implementations of utilize one or more or objects to access atoms. More... | |
| class | colvar::distance |
| Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)). More... | |
| class | colvar::distance_vec |
| class | colvar::distance_dir |
| Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unitvector type, range [-1:1]x[-1:1]x[-1:1]). More... | |
| class | colvar::distance_z |
| Colvar component: projection of the distance vector along an axis (colvarvalue::type_scalar type, range (-*:*)). More... | |
| class | colvar::distance_xy |
| Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)). More... | |
| class | colvar::min_distance |
| Colvar component: projection of the distance vector along a fixed axis (colvarvalue::type_scalar type, range (-*:*)). More... | |
| class | colvar::gyration |
| Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)). More... | |
| class | colvar::eigenvector |
| Colvar component: projection of 3N coordinates onto an eigenvector (colvarvalue::type_scalar type, range (-*:*)). More... | |
| class | colvar::angle |
| Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]). More... | |
| class | colvar::dihedral |
| Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]). More... | |
| class | colvar::coordnum |
| Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]). More... | |
| class | colvar::selfcoordnum |
| Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]). More... | |
| class | colvar::h_bond |
| Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]). More... | |
| class | colvar::alpha_angles |
| Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of phi/psi dihedral angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1]) Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1]). More... | |
| class | colvar::dihedPC |
| Colvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs. More... | |
| class | colvar::orientation |
| Colvar component: orientation in space of an atom group, with respect to a set of reference coordinates (colvarvalue::type_quaternion type, range [-1:1]x[-1:1]x[-1:1]x[-1:1]). More... | |
| class | colvar::orientation_angle |
| Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI)). More... | |
| class | colvar::tilt |
| Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1]). More... | |
| class | colvar::spin_angle |
| Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]). More... | |
| class | colvar::rmsd |
| Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)). More... | |
| class | colvar::logmsd |
| Colvar component: mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)). More... | |
Defines | |
| #define | simple_scalar_dist_functions(TYPE) |
Functions | |
| simple_scalar_dist_functions (distance) simple_scalar_dist_functions(distance_xy) simple_scalar_dist_functions(min_distance) simple_scalar_dist_functions(angle) simple_scalar_dist_functions(coordnum) simple_scalar_dist_functions(selfcoordnum) simple_scalar_dist_functions(h_bond) simple_scalar_dist_functions(gyration) simple_scalar_dist_functions(rmsd) simple_scalar_dist_functions(logmsd) simple_scalar_dist_functions(orientation_angle) simple_scalar_dist_functions(tilt) simple_scalar_dist_functions(eigenvector) simple_scalar_dist_functions(alpha_angles) simple_scalar_dist_functions(dihedPC) inline cvm | |
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Value: \ inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return std::pow (x1.real_value - x2.real_value, int (2)); \ } \ \ inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return 2.0 * (x1.real_value - x2.real_value); \ } \ \ inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return this->dist2_lgrad (x2, x1); \ } \ \ inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \ colvarvalue const &x2) const \ { \ return this->dist2_lgrad (x1, x2); \ } \ \ Definition at line 1221 of file colvarcomp.h. |
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Definition at line 1248 of file colvarcomp.h. References cvm, and colvarvalue::real_value. 01249 : distance_z has explicit functions, see below 01250 simple_scalar_dist_functions (distance_xy) 01251 simple_scalar_dist_functions (min_distance) 01252 simple_scalar_dist_functions (angle) 01253 simple_scalar_dist_functions (coordnum) 01254 simple_scalar_dist_functions (selfcoordnum) 01255 simple_scalar_dist_functions (h_bond) 01256 simple_scalar_dist_functions (gyration) 01257 simple_scalar_dist_functions (rmsd) 01258 simple_scalar_dist_functions (logmsd) 01259 simple_scalar_dist_functions (orientation_angle) 01260 simple_scalar_dist_functions (tilt) 01261 simple_scalar_dist_functions (eigenvector) 01262 // simple_scalar_dist_functions (alpha_dihedrals) 01263 simple_scalar_dist_functions (alpha_angles) 01264 simple_scalar_dist_functions (dihedPC) 01265 01266 01267 // Projected distance 01268 // Differences should always be wrapped around 0 (ignoring wrap_center) 01269 inline cvm::real colvar::distance_z::dist2 (colvarvalue const &x1, 01270 colvarvalue const &x2) const 01271 { 01272 cvm::real diff = x1.real_value - x2.real_value; 01273 if (period != 0.0) { 01274 cvm::real shift = std::floor (diff/period + 0.5); 01275 diff -= shift * period; 01276 } 01277 return diff * diff; 01278 }
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1.3.9.1