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colvarmodule::atom_group Member List

This is the complete list of members for colvarmodule::atom_group, including all inherited members.

_get_keyval_scalar_(std::string const &conf, char const *key, TYPE &value, TYPE const &def_value, Parse_Mode const &parse_mode)	colvarparse	[protected]
_get_keyval_scalar_novalue_(std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode)	colvarparse	[protected]
_get_keyval_scalar_novalue_(std::string const &key_str, bool &value, Parse_Mode const &parse_mode)	colvarparse
_get_keyval_scalar_value_(std::string const &key_str, std::string const &data, TYPE &value, TYPE const &def_value)	colvarparse	[protected]
_get_keyval_scalar_value_(std::string const &key_str, std::string const &data, bool &value, bool const &)	colvarparse
_get_keyval_vector_(std::string const &conf, char const *key, std::vector< TYPE > &values, std::vector< TYPE > const &def_values, Parse_Mode const &parse_mode)	colvarparse	[protected]
add_atom(cvm::atom const &a)	colvarmodule::atom_group
add_atom_id(int aid)	colvarmodule::atom_group
add_atom_name_residue_range(std::string const &psf_segid, std::string const &range_conf)	colvarmodule::atom_group
add_atom_numbers(std::string const &numbers_conf)	colvarmodule::atom_group
add_atom_numbers_range(std::string const &range_conf)	colvarmodule::atom_group
add_atoms_of_group(atom_group const *ag)	colvarmodule::atom_group
add_child(colvardeps *child)	colvardeps
add_index_group(std::string const &index_group_name)	colvarmodule::atom_group
add_keyword(char const *key)	colvarparse	[protected]
ag_features	colvarmodule::atom_group	[static]
allowed_keywords	colvarparse	[protected]
apply_colvar_force(cvm::real const &force)	colvarmodule::atom_group
apply_force(cvm::rvector const &force)	colvarmodule::atom_group
apply_translation(cvm::rvector const &t)	colvarmodule::atom_group
atom_group()	colvarmodule::atom_group
atom_group(char const *key)	colvarmodule::atom_group
atom_group(std::vector< cvm::atom > const &atoms_in)	colvarmodule::atom_group
atoms	colvarmodule::atom_group	[protected]
atoms_ids	colvarmodule::atom_group	[protected]
b_dummy	colvarmodule::atom_group
b_user_defined_fit	colvarmodule::atom_group
begin()	colvarmodule::atom_group	[inline]
begin() const	colvarmodule::atom_group	[inline]
calc_apply_roto_translation()	colvarmodule::atom_group
calc_center_of_geometry()	colvarmodule::atom_group
calc_center_of_mass()	colvarmodule::atom_group
calc_dipole(cvm::atom_pos const &dipole_center)	colvarmodule::atom_group
calc_fit_gradients()	colvarmodule::atom_group
calc_required_properties()	colvarmodule::atom_group
center_of_geometry() const	colvarmodule::atom_group	[inline]
center_of_mass() const	colvarmodule::atom_group	[inline]
center_of_mass_scalar_gradient() const	colvarmodule::atom_group	[inline]
center_ref_pos()	colvarmodule::atom_group
check_ascii(std::string const &conf)	colvarparse	[static]
check_braces(std::string const &conf, size_t const start_pos)	colvarparse	[static]
check_enabled(int f, std::string const &reason) const	colvardeps	[inline]
check_keywords(std::string &conf, char const *key)	colvarparse
clear()	colvarparse
clear_keyword_registry()	colvarparse
colvardeps()	colvardeps
colvarparams()	colvarparams	[protected]
colvarparse()	colvarparse
colvarparse(const std::string &conf)	colvarparse
config_string	colvarparse	[protected]
create_sorted_ids()	colvarmodule::atom_group
data_begin_pos	colvarparse	[protected]
data_end_pos	colvarparse	[protected]
decr_ref_count(int f)	colvardeps
delete_features()	colvarmodule::atom_group	[inline, static]
description	colvardeps
dipole() const	colvarmodule::atom_group	[inline]
disable(int f)	colvardeps
do_feature_side_effects(int id)	colvarmodule::atom_group	[virtual]
dummy_atom_pos	colvarmodule::atom_group	[protected]
enable(int f, bool dry_run=false, bool toplevel=true)	colvardeps
end()	colvarmodule::atom_group	[inline]
end() const	colvarmodule::atom_group	[inline]
error_key_required(std::string const &key_str, Parse_Mode const &parse_mode)	colvarparse	[protected]
exclude_feature_self(int f, int g)	colvardeps
f_ag_active enum value	colvardeps
f_ag_atom_forces enum value	colvardeps
f_ag_center enum value	colvardeps
f_ag_center_origin enum value	colvardeps
f_ag_collect_atom_ids enum value	colvardeps
f_ag_explicit_gradient enum value	colvardeps
f_ag_fit_gradients enum value	colvardeps
f_ag_fitting_group enum value	colvardeps
f_ag_ntot enum value	colvardeps
f_ag_rotate enum value	colvardeps
f_ag_scalable enum value	colvardeps
f_ag_scalable_com enum value	colvardeps
f_cv_active enum value	colvardeps
f_cv_awake enum value	colvardeps
f_cv_collect_atom_ids enum value	colvardeps
f_cv_collect_gradient enum value	colvardeps
f_cv_corrfunc enum value	colvardeps
f_cv_custom_function enum value	colvardeps
f_cv_extended_Lagrangian enum value	colvardeps
f_cv_external enum value	colvardeps
f_cv_fdiff_velocity enum value	colvardeps
f_cv_gradient enum value	colvardeps
f_cv_grid enum value	colvardeps
f_cv_hard_lower_boundary enum value	colvardeps
f_cv_hard_upper_boundary enum value	colvardeps
f_cv_hide_Jacobian enum value	colvardeps
f_cv_homogeneous enum value	colvardeps
f_cv_Jacobian enum value	colvardeps
f_cv_Langevin enum value	colvardeps
f_cv_linear enum value	colvardeps
f_cv_lower_boundary enum value	colvardeps
f_cv_multiple_ts enum value	colvardeps
f_cv_ntot enum value	colvardeps
f_cv_output_applied_force enum value	colvardeps
f_cv_output_energy enum value	colvardeps
f_cv_output_total_force enum value	colvardeps
f_cv_output_value enum value	colvardeps
f_cv_output_velocity enum value	colvardeps
f_cv_periodic enum value	colvardeps
f_cv_reflecting_lower_boundary enum value	colvardeps
f_cv_reflecting_upper_boundary enum value	colvardeps
f_cv_runave enum value	colvardeps
f_cv_scalar enum value	colvardeps
f_cv_scripted enum value	colvardeps
f_cv_single_cvc enum value	colvardeps
f_cv_subtract_applied_force enum value	colvardeps
f_cv_total_force enum value	colvardeps
f_cv_total_force_calc enum value	colvardeps
f_cv_upper_boundary enum value	colvardeps
f_cvb_active enum value	colvardeps
f_cvb_apply_force enum value	colvardeps
f_cvb_awake enum value	colvardeps
f_cvb_bypass_ext_lagrangian enum value	colvardeps
f_cvb_calc_pmf enum value	colvardeps
f_cvb_calc_ti_samples enum value	colvardeps
f_cvb_get_total_force enum value	colvardeps
f_cvb_history_dependent enum value	colvardeps
f_cvb_ntot enum value	colvardeps
f_cvb_output_acc_work enum value	colvardeps
f_cvb_scalar_variables enum value	colvardeps
f_cvb_scale_biasing_force enum value	colvardeps
f_cvb_step_zero_data enum value	colvardeps
f_cvb_time_dependent enum value	colvardeps
f_cvb_write_ti_pmf enum value	colvardeps
f_cvb_write_ti_samples enum value	colvardeps
f_cvc_active enum value	colvardeps
f_cvc_collect_atom_ids enum value	colvardeps
f_cvc_com_based enum value	colvardeps
f_cvc_debug_gradient enum value	colvardeps
f_cvc_explicit_gradient enum value	colvardeps
f_cvc_gradient enum value	colvardeps
f_cvc_inv_gradient enum value	colvardeps
f_cvc_Jacobian enum value	colvardeps
f_cvc_lower_boundary enum value	colvardeps
f_cvc_ntot enum value	colvardeps
f_cvc_one_site_total_force enum value	colvardeps
f_cvc_pbc_minimum_image enum value	colvardeps
f_cvc_periodic enum value	colvardeps
f_cvc_scalable enum value	colvardeps
f_cvc_scalable_com enum value	colvardeps
f_cvc_scalar enum value	colvardeps
f_cvc_upper_boundary enum value	colvardeps
f_cvc_width enum value	colvardeps
f_type_dynamic enum value	colvardeps	[protected]
f_type_not_set enum value	colvardeps	[protected]
f_type_static enum value	colvardeps	[protected]
f_type_user enum value	colvardeps	[protected]
feature_states	colvardeps	[protected]
feature_type enum name	colvardeps	[protected]
features() const	colvarmodule::atom_group	[inline, virtual]
features_atomgroup enum name	colvardeps
features_biases enum name	colvardeps
features_colvar enum name	colvardeps
features_cvc enum name	colvardeps
fit_gradients	colvarmodule::atom_group
fitting_group	colvarmodule::atom_group
free_children_deps()	colvardeps
get_config() const	colvarparse	[inline]
get_key_string_multi_value(std::string const &conf, char const *key, std::vector< std::string > &data)	colvarparse	[protected]
get_key_string_value(std::string const &conf, char const *key, std::string &data)	colvarparse	[protected]
get_keyval(std::string const &conf, char const *key, int &value, int const &def_value=(int) 0, Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, size_t &value, size_t const &def_value=(size_t) 0, Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, cvm::step_number &value, cvm::step_number const &def_value=0, Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::string &value, std::string const &def_value=std::string(""), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, cvm::real &value, cvm::real const &def_value=(cvm::real) 0.0, Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, cvm::rvector &value, cvm::rvector const &def_value=cvm::rvector(), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, cvm::quaternion &value, cvm::quaternion const &def_value=cvm::quaternion(), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, colvarvalue &value, colvarvalue const &def_value=colvarvalue(colvarvalue::type_notset), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< int > &values, std::vector< int > const &def_values=std::vector< int >(0,(int) 0), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< size_t > &values, std::vector< size_t > const &def_values=std::vector< size_t >(0,(size_t) 0), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< long > &values, std::vector< long > const &def_values=std::vector< long >(0,(long) 0), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< std::string > &values, std::vector< std::string > const &def_values=std::vector< std::string >(0, std::string("")), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< cvm::real > &values, std::vector< cvm::real > const &def_values=std::vector< cvm::real >(0,(cvm::real) 0.0), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< cvm::rvector > &values, std::vector< cvm::rvector > const &def_values=std::vector< cvm::rvector >(0, cvm::rvector()), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< cvm::quaternion > &values, std::vector< cvm::quaternion > const &def_values=std::vector< cvm::quaternion >(0, cvm::quaternion()), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval(std::string const &conf, char const *key, std::vector< colvarvalue > &values, std::vector< colvarvalue > const &def_values=std::vector< colvarvalue >(0, colvarvalue(colvarvalue::type_notset)), Parse_Mode const parse_mode=parse_normal)	colvarparse
get_keyval_feature(colvarparse *cvp, std::string const &conf, char const *key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)	colvardeps	[protected]
get_param(std::string const &param_name)	colvarparams	[virtual]
get_param_grad_names()	colvarparams	[virtual]
get_param_grad_ptr(std::string const &param_name)	colvarparams	[virtual]
get_param_names()	colvarparams	[virtual]
get_param_ptr(std::string const &param_name)	colvarparams	[virtual]
get_time_step_factor() const	colvardeps	[inline]
getline_nocomments(std::istream &is, std::string &s)	colvarparse	[static]
ids() const	colvarmodule::atom_group	[inline]
index	colvarmodule::atom_group	[protected]
init()	colvarmodule::atom_group
init_dependencies()	colvarmodule::atom_group	[virtual]
init_feature(int feature_id, const char *description, feature_type type)	colvardeps
is_available(int f=f_cv_active) const	colvardeps	[inline]
is_dynamic(int id)	colvardeps	[inline]
is_enabled(int f=f_cv_active) const	colvardeps	[inline]
is_not_set(int id)	colvardeps	[inline]
is_static(int id)	colvardeps	[inline]
is_user(int id)	colvardeps	[inline]
key	colvarmodule::atom_group
key_already_set(std::string const &key_str)	colvarparse	[protected]
key_lookup(std::string const &conf, char const *key, std::string *data=NULL, size_t *save_pos=NULL)	colvarparse
key_not_set enum value	colvarparse	[protected]
key_set_default enum value	colvarparse	[protected]
key_set_mode enum name	colvarparse	[protected]
key_set_modes	colvarparse	[protected]
key_set_user enum value	colvarparse	[protected]
keyword_delimiters_left	colvarparse	[protected]
keyword_delimiters_right	colvarparse	[protected]
mark_key_set_default(std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode)	colvarparse	[protected]
mark_key_set_user(std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode)	colvarparse	[protected]
modify_features()	colvarmodule::atom_group	[inline, virtual]
name	colvarmodule::atom_group
noforce	colvarmodule::atom_group
operator[](size_t const i)	colvarmodule::atom_group	[inline]
operator[](size_t const i) const	colvarmodule::atom_group	[inline]
overlap(const atom_group &g1, const atom_group &g2)	colvarmodule::atom_group	[static]
param_exists(std::string const &param_name)	colvarparams
param_grad_map	colvarparams	[protected]
param_map	colvarparams	[protected]
parse(std::string const &conf)	colvarmodule::atom_group
parse_deprecated enum value	colvarparse
parse_deprecation_warning enum value	colvarparse
parse_echo enum value	colvarparse
parse_echo_default enum value	colvarparse
parse_fitting_options(std::string const &group_conf)	colvarmodule::atom_group
Parse_Mode enum name	colvarparse
parse_normal enum value	colvarparse
parse_null enum value	colvarparse
parse_override enum value	colvarparse
parse_required enum value	colvarparse
parse_restart enum value	colvarparse
parse_silent enum value	colvarparse
positions() const	colvarmodule::atom_group
positions_shifted(cvm::rvector const &shift) const	colvarmodule::atom_group
print_atom_ids() const	colvarmodule::atom_group
print_properties(std::string const &colvar_name, int i, int j)	colvarmodule::atom_group
print_state()	colvardeps
provide(int feature_id, bool truefalse=true)	colvardeps
read_config_line(std::istream &is, std::string &line)	colvarparse
read_positions()	colvarmodule::atom_group
read_total_forces()	colvarmodule::atom_group
read_velocities()	colvarmodule::atom_group
ref_pos	colvarmodule::atom_group
ref_pos_cog	colvarmodule::atom_group
register_param(std::string const &param_name, void *param_ptr)	colvarparams	[protected]
register_param_grad(std::string const &param_name, colvarvalue *param_grad_ptr)	colvarparams	[protected]
remove_all_children()	colvardeps
remove_atom(cvm::atom_iter ai)	colvarmodule::atom_group
remove_child(colvardeps *child)	colvardeps
require_feature_alt(int f, int g, int h)	colvardeps
require_feature_alt(int f, int g, int h, int i)	colvardeps
require_feature_alt(int f, int g, int h, int i, int j)	colvardeps
require_feature_children(int f, int g)	colvardeps
require_feature_self(int f, int g)	colvardeps
reset_atoms_data()	colvarmodule::atom_group	[inline]
restore_children_deps()	colvardeps
rot	colvarmodule::atom_group
set_dummy()	colvarmodule::atom_group
set_dummy_pos(cvm::atom_pos const &pos)	colvarmodule::atom_group
set_enabled(int feature_id, bool truefalse=true)	colvardeps
set_param(std::string const &param_name, void const *new_value)	colvarparams	[virtual]
set_string(std::string const &conf)	colvarparse
set_weighted_gradient(cvm::rvector const &grad)	colvarmodule::atom_group
setup()	colvarmodule::atom_group
size() const	colvarmodule::atom_group	[inline]
sorted_atoms_ids	colvarmodule::atom_group	[protected]
sorted_atoms_ids_map	colvarmodule::atom_group	[protected]
sorted_ids() const	colvarmodule::atom_group	[inline]
sorted_ids_map() const	colvarmodule::atom_group	[inline]
split_string(const std::string &data, const std::string &delim, std::vector< std::string > &dest)	colvarparse	[static]
strip_values(std::string &conf)	colvarparse	[protected]
time_step_factor	colvardeps	[protected]
to_lower_cppstr(std::string const &in)	colvarparse	[inline, static]
total_charge	colvarmodule::atom_group
total_force() const	colvarmodule::atom_group
total_forces() const	colvarmodule::atom_group
total_mass	colvarmodule::atom_group
update_total_charge()	colvarmodule::atom_group
update_total_mass()	colvarmodule::atom_group
velocities() const	colvarmodule::atom_group
white_space	colvarparse	[static]
~atom_group()	colvarmodule::atom_group
~colvardeps()	colvardeps	[virtual]
~colvarparams()	colvarparams	[protected, virtual]
~colvarparse()	colvarparse	[virtual]

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