add_angle(const CHARMMAngle &bond) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
add_atom(const CHARMMAtomTopology &atom) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
add_bond(const CHARMMBond &bond) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
add_dihedral(const CHARMMDihedral &bond) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
add_improper(const CHARMMDihedral &bond) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
add_internal_coordinate(const CHARMMInternalCoordinate &ic) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
add_removed_atom(std::string name) (defined in IMP::atom::CHARMMPatch) | IMP::atom::CHARMMPatch | |
angles_ (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
apply(CHARMMResidueTopology *res) const | IMP::atom::CHARMMPatch | |
apply(CHARMMResidueTopology *res1, CHARMMResidueTopology *res2) const | IMP::atom::CHARMMPatch | |
atoms_ (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
bonds_ (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
CHARMMPatch(std::string type) | IMP::atom::CHARMMPatch | |
CHARMMResidueTopologyBase(std::string type) (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
clear_caches() | IMP::Object | virtual |
dihedrals_ (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
do_destroy() | IMP::Object | protectedvirtual |
get_angle(unsigned int index) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_atom(unsigned int i) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_atom(AtomType type) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_atom(std::string name) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_bond(unsigned int index) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_check_level() const (defined in IMP::Object) | IMP::Object | |
get_dihedral(unsigned int index) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_improper(unsigned int index) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_internal_coordinate(unsigned int index) const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_log_level() const (defined in IMP::Object) | IMP::Object | |
get_name() const (defined in IMP::Object) | IMP::Object | |
get_number_of_angles() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_number_of_atoms() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_number_of_bonds() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_number_of_dihedrals() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_number_of_impropers() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_number_of_internal_coordinates() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_number_of_removed_atoms() const (defined in IMP::atom::CHARMMPatch) | IMP::atom::CHARMMPatch | |
get_removed_atom(unsigned int i) const (defined in IMP::atom::CHARMMPatch) | IMP::atom::CHARMMPatch | |
get_type() const (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | |
get_type_name() const (defined in IMP::atom::CHARMMPatch) | IMP::atom::CHARMMPatch | virtual |
get_version_info() const | IMP::atom::CHARMMPatch | virtual |
impropers_ (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
internal_coordinates_ (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protected |
NonCopyable() (defined in IMP::NonCopyable) | IMP::NonCopyable | protected |
Object(std::string name) | IMP::Object | protected |
set_check_level(CheckLevel l) | IMP::Object | |
set_log_level(LogLevel l) | IMP::Object | |
set_name(std::string name) (defined in IMP::Object) | IMP::Object | |
set_was_used(bool tf) const | IMP::Object | |
show(std::ostream &out=std::cout) const (defined in IMP::Object) | IMP::Object | |
~CHARMMPatch() (defined in IMP::atom::CHARMMPatch) | IMP::atom::CHARMMPatch | protectedvirtual |
~CHARMMResidueTopologyBase() (defined in IMP::atom::CHARMMResidueTopologyBase) | IMP::atom::CHARMMResidueTopologyBase | protectedvirtual |
~Object() (defined in IMP::Object) | IMP::Object | virtual |