model Member List

This is the complete list of members for model, including all inherited members.

about() const	model
append(const model &m)	model
appender_info	model	friend
assign_bonds(const distance_type_matrix &mobility)	model	private
assign_types()	model	private
atom_coords(const atom_index &i) const	model
atom_exists_between(const distance_type_matrix &mobility, const atom_index &a, const atom_index &b, const szv &relevant_atoms) const	model
atom_typing_used() const	model	inline
atoms	model	private
bonded_to(sz a, sz n, szv &out) const	model	private
bonded_to(sz a, sz n) const	model	private
bonded_to_HD(const atom &a) const	model	private
bonded_to_heteroatom(const atom &a) const	model	private
cache	model	friend
check_internal_pairs() const	model
clash_penalty() const	model
clash_penalty_aux(const interacting_pairs &pairs) const	model	private
conf_independent_inputs	model	friend
coords	model	private
distance_sqr_between(const atom_index &a, const atom_index &b) const	model
distance_type_between(const distance_type_matrix &mobility, const atom_index &i, const atom_index &j) const	model
eval(const precalculate &p, const igrid &ig, const vec &v, const conf &c)	model
eval_adjusted(const scoring_function &sf, const precalculate &p, const igrid &ig, const vec &v, const conf &c, fl intramolecular_energy)	model
eval_deriv(const precalculate &p, const igrid &ig, const vec &v, const conf &c, change &g)	model
eval_intramolecular(const precalculate &p, const vec &v, const conf &c)	model
evale(const precalculate &p, const igrid &ig, const vec &v) const	model
evali(const precalculate &p, const vec &v) const	model
find_ligand(sz a) const	model	private
flex	model	private
flex_context	model	private
get_atom(const atom_index &i) const	model	inlineprivate
get_atom(const atom_index &i)	model	inlineprivate
get_heavy_atom_movable_coords() const	model	inline
get_initial_conf() const	model
get_ligand_coords() const	model	inline
get_ligand_internal_coords() const	model	inline
get_movable_atom_types(atom_type::t atom_typing_used_) const	model
get_size() const	model
grid_atoms	model	private
gyration_radius(sz ligand_number) const	model
initialize(const distance_type_matrix &mobility)	model	private
initialize_pairs(const distance_type_matrix &mobility)	model	private
internal_coords	model	private
ligand_degrees_of_freedom(sz ligand_number) const	model	inline
ligand_length(sz ligand_number) const	model
ligand_longest_branch(sz ligand_number) const	model
ligands	model	private
m_atom_typing_used	model	private
m_num_movable_atoms	model	private
minus_forces	model	private
model()	model	inlineprivate
model_test	model	friend
movable_atom(sz i) const	model	inline
movable_atoms_box(fl add_to_each_dimension, fl granularity=0.375) const	model
movable_coords(sz i) const	model	inline
naive_non_cache	model	friend
non_cache	model	friend
num_flex() const	model	inline
num_internal_pairs() const	model
num_ligands() const	model	inline
num_movable_atoms() const	model	inline
num_other_pairs() const	model	inline
other_pairs	model	private
pdbqt_initializer	model	friend
print_stuff() const	model
rmsd_ligands_upper_bound(const model &m) const	model
rmsd_lower_bound(const model &m) const	model
rmsd_lower_bound_asymmetric(const model &x, const model &y) const	model	private
rmsd_upper_bound(const model &m) const	model
set(const conf &c)	model
sete(const conf &c)	model
seti(const conf &c)	model
sz_to_atom_index(sz i) const	model	private
szv_grid	model	friend
terms	model	friend
verify_bond_lengths() const	model
write_context(const context &c, std::stringstream &out) const	model	private
write_context(const context &c, ofile &out) const	model	private
write_context(const context &c, ofile &out, const std::string &remark) const	model	inlineprivate
write_context(const context &c, const path &name) const	model	inlineprivate
write_context(const context &c, const path &name, const std::string &remark) const	model	inlineprivate
write_flex(const path &name, const std::string &remark) const	model	inline
write_ligand(sz ligand_number, const path &name, const std::string &remark) const	model	inline
write_model(std::stringstream &out, sz model_number, const std::string &remark) const	model	inline
write_model(ofile &out, sz model_number, const std::string &remark) const	model	inline
write_structure(std::stringstream &out) const	model	inline
write_structure(ofile &out) const	model	inline
write_structure(std::stringstream &out, const std::string &remark) const	model	inline
write_structure(ofile &out, const std::string &remark) const	model	inline
write_structure(const path &name) const	model	inline