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colvar::alpha_angles Class Reference

\brief 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...

#include <colvarcomp.h>

Inheritance diagram for colvar::alpha_angles:

colvar::cvc colvarparse colvardeps colvarparams List of all members.

Public Methods

 alpha_angles (std::string const &conf)
 alpha_angles ()
virtual ~alpha_angles ()
void calc_value ()
 \brief Calculate the variable. More...

void calc_gradients ()
 \brief Calculate the atomic gradients, to be reused later in order to apply forces. More...

void collect_gradients (std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)
 Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs. More...

void apply_force (colvarvalue const &force)
 \brief Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) Note: multiple calls to this function within the same simulation step will add the forces altogether
Parameters:
cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object.
 More...

virtual cvm::real dist2 (colvarvalue const &x1, colvarvalue const &x2) const
 \brief Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities) colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the colvarvalue types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the colvarvalue member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar colvarvalue type. More...

virtual colvarvalue dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
 \brief Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). More...

virtual colvarvalue dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
 \brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). More...


Protected Attributes

cvm::real theta_ref
 Reference Calpha-Calpha angle (default: 88 degrees). More...

cvm::real theta_tol
 Tolerance on the Calpha-Calpha angle. More...

std::vector< angle * > theta
 List of Calpha-Calpha angles. More...

std::vector< h_bond * > hb
 List of hydrogen bonds. More...

cvm::real hb_coeff
 Contribution of the hb terms. More...

Detailed Description

\brief 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]).

Definition at line 1132 of file colvarcomp.h.

Constructor & Destructor Documentation

colvar::alpha_angles::alpha_angles (  std::string const &    conf ) 
 

Definition at line 19 of file colvarcomp_protein.C.

References colvarproxy_system::angstrom_to_internal, conf, colvardeps::enable, colvarmodule::error, colvardeps::f_cvc_explicit_gradient, colvarparse::get_keyval, hb, hb_coeff, colvarparse::key_lookup, colvarmodule::log, colvarmodule::main, colvarmodule::proxy, colvar::cvc::register_atom_group, colvar::cvc::set_function_type, theta, theta_ref, theta_tol, colvarvalue::type, colvarvalue::type_scalar, and colvar::cvc::x.

colvar::alpha_angles::alpha_angles (    ) 
 

Definition at line 109 of file colvarcomp_protein.C.

References colvardeps::enable, colvardeps::f_cvc_explicit_gradient, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, and colvar::cvc::x.

colvar::alpha_angles::~alpha_angles (    )  [virtual]
 

Definition at line 118 of file colvarcomp_protein.C.

References colvar::cvc::atom_groups, hb, and theta.

Member Function Documentation

void colvar::alpha_angles::apply_force (  colvarvalue const &    force )  [virtual]
 

\brief Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) Note: multiple calls to this function within the same simulation step will add the forces altogether

Parameters:
cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object.

Implements colvar::cvc.

Definition at line 240 of file colvarcomp_protein.C.

References force, hb, hb_coeff, colvarmodule::real, colvarvalue::real_value, theta, theta_ref, and theta_tol.

void colvar::alpha_angles::calc_gradients (    )  [virtual]
 

\brief Calculate the atomic gradients, to be reused later in order to apply forces.

Reimplemented from colvar::cvc.

Definition at line 177 of file colvarcomp_protein.C.

References hb, and theta.

void colvar::alpha_angles::calc_value (    )  [virtual]
 

\brief Calculate the variable.

Implements colvar::cvc.

Definition at line 133 of file colvarcomp_protein.C.

References colvarmodule::debug, hb, hb_coeff, colvarmodule::log, colvarmodule::real, colvarvalue::real_value, theta, theta_ref, theta_tol, colvarmodule::to_str, and colvar::cvc::x.

void colvar::alpha_angles::collect_gradients (  std::vector< int > const &    atom_ids,
std::vector< cvm::rvector > &    atomic_gradients
)  [virtual]
 

Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs.

Reimplemented from colvar::cvc.

Definition at line 188 of file colvarcomp_protein.C.

References colvar::atom_ids, colvar::atomic_gradients, hb, hb_coeff, colvarmodule::integer_power, colvarmodule::real, colvar::cvc::sup_coeff, colvar::cvc::sup_np, theta, theta_ref, theta_tol, and colvar::cvc::value.

virtual cvm::real colvar::alpha_angles::dist2 (  colvarvalue const &    x1,
colvarvalue const &    x2
)  const [virtual]
 

\brief Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities) colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the colvarvalue types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the colvarvalue member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar colvarvalue type.

Reimplemented from colvar::cvc.

virtual colvarvalue colvar::alpha_angles::dist2_lgrad (  colvarvalue const &    x1,
colvarvalue const &    x2
)  const [virtual]
 

\brief Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::cvc.

virtual colvarvalue colvar::alpha_angles::dist2_rgrad (  colvarvalue const &    x1,
colvarvalue const &    x2
)  const [virtual]
 

\brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::cvc.

Member Data Documentation

std::vector<h_bond *> colvar::alpha_angles::hb [protected]
 

List of hydrogen bonds.

Definition at line 1147 of file colvarcomp.h.

Referenced by alpha_angles, apply_force, calc_gradients, calc_value, collect_gradients, and ~alpha_angles.

cvm::real colvar::alpha_angles::hb_coeff [protected]
 

Contribution of the hb terms.

Definition at line 1150 of file colvarcomp.h.

Referenced by alpha_angles, apply_force, calc_value, and collect_gradients.

std::vector<angle *> colvar::alpha_angles::theta [protected]
 

List of Calpha-Calpha angles.

Definition at line 1144 of file colvarcomp.h.

Referenced by alpha_angles, apply_force, calc_gradients, calc_value, collect_gradients, and ~alpha_angles.

cvm::real colvar::alpha_angles::theta_ref [protected]
 

Reference Calpha-Calpha angle (default: 88 degrees).

Definition at line 1138 of file colvarcomp.h.

Referenced by alpha_angles, apply_force, calc_value, and collect_gradients.

cvm::real colvar::alpha_angles::theta_tol [protected]
 

Tolerance on the Calpha-Calpha angle.

Definition at line 1141 of file colvarcomp.h.

Referenced by alpha_angles, apply_force, calc_value, and collect_gradients.

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