| active | DrawMolecule | |
| add_angle(int a, int b, int c, int type=-1) | BaseMolecule | |
| add_atoms(int natoms, const char *name, const char *type, int atomicnumber, const char *resname, int resid, const char *chainid, const char *segname, const char *insertion=(char *)"", const char *altloc="") | BaseMolecule | |
| add_bond(int, int, float, int, int=ATOMNORMAL) | BaseMolecule | |
| add_bond_dupcheck(int, int, float, int) | BaseMolecule | |
| add_cent_trans(float, float, float) | Displayable | |
| add_child(Displayable *) | Displayable | |
| add_coor_file(CoorData *) | Molecule | |
| add_cterm(int a, int b, int c, int d, int e, int f, int g, int h) | BaseMolecule | [inline] |
| add_dihedral(int a, int b, int c, int d, int type=-1) | BaseMolecule | |
| add_glob_trans(float, float, float) | Displayable | |
| add_improper(int a, int b, int c, int d, int type=-1) | BaseMolecule | |
| add_instance(Matrix4 &inst) | BaseMolecule | [inline] |
| add_rep(AtomColor *, AtomRep *, AtomSel *, const Material *) | DrawMolecule | |
| add_rot(float x, char axis) | Displayable | |
| add_rot(const Matrix4 &) | Displayable | |
| add_volume_data(const char *name, const float *o, const float *xa, const float *ya, const float *za, int x, int y, int z, float *voldata, float *gradient=NULL, float *variance=NULL) | BaseMolecule | |
| add_volume_data(const char *name, const double *o, const double *xa, const double *ya, const double *za, int x, int y, int z, float *voldata) | BaseMolecule | |
| addForce(int theatom, const float *f) | Molecule | |
| addPersistentForce(int theatom, const float *f) | Molecule | |
| ALTLOC enum value | BaseMolecule | |
| altlocNames | BaseMolecule | |
| analyze(void) | BaseMolecule | |
| ANGLES enum value | BaseMolecule | |
| angles | BaseMolecule | |
| angleTypeNames | BaseMolecule | |
| ANGLETYPES enum value | BaseMolecule | |
| angleTypes | BaseMolecule | |
| app | DrawMolecule | |
| append(int d) | Displayable | [inline, protected] |
| append_frame(Timestep *) | DrawMolecule | |
| atom(int n) | BaseMolecule | [inline] |
| atom_displayed(int) | DrawMolecule | |
| atom_fragment(int) | BaseMolecule | |
| atom_residue(int) | BaseMolecule | |
| ATOMFLAGS enum value | BaseMolecule | |
| ATOMICNUMBER enum value | BaseMolecule | |
| atomNames | BaseMolecule | |
| atomTypes | BaseMolecule | |
| BaseMolecule(int) | BaseMolecule | |
| beta() | BaseMolecule | [inline] |
| BFACTOR enum value | BaseMolecule | |
| BONDORDERS enum value | BaseMolecule | |
| bondorders() | BaseMolecule | [inline] |
| BONDS enum value | BaseMolecule | |
| bondTypeNames | BaseMolecule | |
| BONDTYPES enum value | BaseMolecule | |
| bondtypes() | BaseMolecule | [inline] |
| cacheskip(int onoff) | Displayable | |
| cancel() | Molecule | |
| cent_trans_off(void) | Displayable | [inline] |
| cent_trans_on(void) | Displayable | [inline] |
| cent_translating(void) const | Displayable | [inline] |
| centt | Displayable | |
| chainNames | BaseMolecule | |
| change_center(float x, float y, float z) | Displayable | |
| change_material(const Material *) | Displayable | |
| change_pbc() | DrawMolecule | |
| change_rep(int, AtomColor *, AtomRep *, const char *sel) | DrawMolecule | |
| change_ts() | DrawMolecule | |
| CHARGE enum value | BaseMolecule | |
| charge() | BaseMolecule | [inline] |
| child(int N) const | Displayable | [inline] |
| child_index(Displayable *d) | Displayable | [inline] |
| children | Displayable | [protected] |
| clear_angles(void) | BaseMolecule | [inline] |
| clear_bonds(void) | BaseMolecule | |
| clear_cterms() | BaseMolecule | [inline] |
| clear_dihedrals(void) | BaseMolecule | [inline] |
| clear_impropers(void) | BaseMolecule | [inline] |
| clear_instances(void) | BaseMolecule | [inline] |
| clipplane(int i) | Displayable | [inline] |
| close_coor_file(CoorData *) | Molecule | |
| cmdList | Displayable | [protected] |
| color_changed(int cat) | Displayable | |
| color_rgb_changed(int color) | Displayable | |
| color_scale_changed() | Displayable | |
| component(int) | DrawMolecule | |
| component_from_pickable(const Pickable *) | DrawMolecule | |
| components(void) | DrawMolecule | [inline] |
| compute_volume_gradient(VolumetricData *) | BaseMolecule | |
| count_bonds(void) | BaseMolecule | |
| cov(float &, float &, float &) | DrawMolecule | |
| cpu_threadpool(void) | DrawMolecule | |
| CTERMS enum value | BaseMolecule | |
| cterms | BaseMolecule | |
| cuda_devpool(void) | DrawMolecule | |
| curr_material() const | Displayable | |
| current() | DrawMolecule | [inline] |
| dataset_flag enum name | BaseMolecule | |
| datasetflags | BaseMolecule | |
| default_beta(void) | BaseMolecule | [inline] |
| default_charge(const char *) | BaseMolecule | |
| default_mass(const char *) | BaseMolecule | |
| default_occup(void) | BaseMolecule | [inline] |
| default_radius(const char *) | BaseMolecule | |
| del_rep(int) | DrawMolecule | |
| delete_frame(int n) | DrawMolecule | |
| delete_material(int n, const MaterialList *) | Displayable | |
| dihedrals | BaseMolecule | |
| dihedralTypeNames | BaseMolecule | |
| dihedralTypes | BaseMolecule | |
| Displayable(Displayable *) | Displayable | |
| Displayable(Scene *) | Displayable | |
| displayed(void) const | Displayable | [inline] |
| do_color_changed(int cat) | Displayable | [inline, protected, virtual] |
| do_color_rgb_changed(int color) | Displayable | [inline, protected, virtual] |
| do_color_scale_changed() | Displayable | [inline, protected, virtual] |
| doCent | Displayable | [protected] |
| doGlob | Displayable | [protected] |
| doRot | Displayable | [protected] |
| doScale | Displayable | [protected] |
| draw(DisplayDevice *) const | Displayable | |
| draw_prepare() | Displayable | |
| DrawMolecule(VMDApp *, Displayable *) | DrawMolecule | |
| duplicate_frame(const Timestep *) | DrawMolecule | |
| extraflg | BaseMolecule | |
| extraflt | BaseMolecule | |
| extraint | BaseMolecule | |
| file_in_progress() | Molecule | [inline] |
| find_atom_in_residue(int atomnameindex, int residue) | BaseMolecule | [inline] |
| find_atom_in_residue(const char *atomname, int residue) | BaseMolecule | |
| find_bonds_from_timestep() | BaseMolecule | [inline] |
| find_unique_bonds_from_timestep() | BaseMolecule | [inline] |
| fix(void) | Displayable | [inline] |
| fixed(void) const | Displayable | [inline] |
| flags() | BaseMolecule | [inline] |
| force_recalc(int) | DrawMolecule | |
| fragList | BaseMolecule | |
| fragment(int) | BaseMolecule | |
| frame() const | DrawMolecule | [inline] |
| get_accession(int i) const | Molecule | [inline] |
| get_angletype(int a) | BaseMolecule | |
| get_component_by_name(const char *) | DrawMolecule | |
| get_component_name(int) | DrawMolecule | |
| get_database(int i) const | Molecule | [inline] |
| get_dihedraltype(int d) | BaseMolecule | |
| get_file(int i) const | Molecule | [inline] |
| get_file_specs(int i) const | Molecule | [inline] |
| get_frame(int n) | DrawMolecule | [inline] |
| get_impropertype(int i) | BaseMolecule | |
| get_last_frame() | DrawMolecule | [inline] |
| get_new_frames() | Molecule | |
| get_radii_minmax(float &min, float &max) | BaseMolecule | [inline] |
| get_remarks(int i) const | Molecule | [inline] |
| get_type(int i) const | Molecule | [inline] |
| get_volume_data(int) | BaseMolecule | |
| getbondorder(int atom, int bond) | BaseMolecule | |
| getbondtype(int atom, int bond) | BaseMolecule | |
| glob_trans_off(void) | Displayable | [inline] |
| glob_trans_on(void) | Displayable | [inline] |
| glob_translating(void) const | Displayable | [inline] |
| globt | Displayable | |
| has_structure() const | BaseMolecule | [inline] |
| highlighted_rep() const | DrawMolecule | |
| id(void) const | BaseMolecule | [inline] |
| impropers | BaseMolecule | |
| improperTypeNames | BaseMolecule | |
| improperTypes | BaseMolecule | |
| init_atoms(int n) | BaseMolecule | |
| INSERTION enum value | BaseMolecule | |
| instances | BaseMolecule | |
| invalidate_ss() | DrawMolecule | |
| isFixed | Displayable | [protected] |
| isOn | Displayable | [protected] |
| MASS enum value | BaseMolecule | |
| mass() | BaseMolecule | [inline] |
| max_children | Displayable | [protected] |
| modify_volume_data(int) | BaseMolecule | |
| Molecule(const char *, VMDApp *, Displayable *) | Molecule | |
| moleculeGraphics() const | DrawMolecule | [inline] |
| moleculename | BaseMolecule | [protected] |
| molname() const | BaseMolecule | [inline] |
| mult_scale(float s) | Displayable | |
| nAtoms | BaseMolecule | |
| need_find_bonds | BaseMolecule | [protected] |
| need_matrix_recalc(void) | Displayable | [inline] |
| need_secondary_structure(int) | DrawMolecule | |
| needUpdate(void) | Displayable | [inline] |
| next_frame() | Molecule | |
| nfragCyclic | BaseMolecule | |
| nfragList | BaseMolecule | |
| nFragments | BaseMolecule | |
| nNucleicFragments | BaseMolecule | |
| NODATA enum value | BaseMolecule | |
| notify() | DrawMolecule | |
| nProteinFragments | BaseMolecule | |
| nResidues | BaseMolecule | |
| nSegments | BaseMolecule | |
| num_angles() | BaseMolecule | [inline] |
| num_children | Displayable | [protected] |
| num_cterms() | BaseMolecule | [inline] |
| num_dihedrals() | BaseMolecule | [inline] |
| num_files() const | Molecule | [inline] |
| num_impropers() | BaseMolecule | [inline] |
| num_instances(void) | BaseMolecule | [inline] |
| num_volume_data() | BaseMolecule | |
| numframes() const | DrawMolecule | [inline] |
| nWaters | BaseMolecule | |
| occupancy() | BaseMolecule | [inline] |
| OCCUPANCY enum value | BaseMolecule | |
| off(void) | Displayable | |
| on(void) | Displayable | |
| operator delete(void *, size_t) | Displayable | |
| operator new(size_t) | Displayable | |
| override_current_frame(int frame) | DrawMolecule | |
| parent | Displayable | [protected] |
| pfragCyclic | BaseMolecule | |
| pfragList | BaseMolecule | |
| pick_cmd_list(void) | Displayable | [virtual] |
| pick_end(PickMode *, DisplayDevice *) | Pickable | [inline, virtual] |
| pick_move(PickMode *, DisplayDevice *, int, int, const float *) | Pickable | [inline, virtual] |
| pick_start(PickMode *, DisplayDevice *, int, int, const int *cell, int, const float *) | Pickable | [inline, virtual] |
| Pickable() | Pickable | [inline] |
| pickable_on(void) | Displayable | [virtual] |
| prepare() | Molecule | [virtual] |
| qm_data | BaseMolecule | |
| radii_max | BaseMolecule | |
| radii_min | BaseMolecule | |
| radii_minmax_need_update | BaseMolecule | |
| RADIUS enum value | BaseMolecule | |
| radius() | BaseMolecule | [inline] |
| recalc_bonds(void) | DrawMolecule | |
| recalc_mat(void) | Displayable | [protected] |
| recalc_ss() | DrawMolecule | |
| record_database(const char *dbname, const char *dbcode) | Molecule | [inline] |
| record_file(const char *filename, const char *filetype, const char *filespecs) | Molecule | [inline] |
| record_remarks(const char *remarks) | Molecule | [inline] |
| register_monitor(DrawMoleculeMonitor *) | DrawMolecule | |
| remove_child(Displayable *) | Displayable | |
| remove_child(int N) | Displayable | [inline] |
| remove_volume_data(int idx) | BaseMolecule | |
| rename(const char *newname) | Molecule | |
| repList | DrawMolecule | |
| reset_disp_list(void) | Displayable | |
| reset_transformation(void) | Displayable | [virtual] |
| residue(int) | BaseMolecule | |
| residueList | BaseMolecule | |
| resNames | BaseMolecule | |
| rot_off(void) | Displayable | [inline] |
| rot_on(void) | Displayable | [inline] |
| rotating(void) const | Displayable | [inline] |
| rotm | Displayable | |
| scale | Displayable | |
| scale_factor() | DrawMolecule | |
| scale_off(void) | Displayable | [inline] |
| scale_on(void) | Displayable | [inline] |
| scaling(void) const | Displayable | [inline] |
| scene | Displayable | [protected] |
| segNames | BaseMolecule | |
| set_angletype(int a, int type) | BaseMolecule | |
| set_cent_trans(float, float, float) | Displayable | |
| set_clip_center(int i, const float *center) | Displayable | [inline] |
| set_clip_color(int i, const float *color) | Displayable | [inline] |
| set_clip_normal(int i, const float *normal) | Displayable | [inline] |
| set_clip_status(int i, int mode) | Displayable | [inline] |
| set_dataset_flag(int flag) | BaseMolecule | [inline] |
| set_dihedraltype(int d, int type) | BaseMolecule | |
| set_glob_trans(float, float, float) | Displayable | |
| set_impropertype(int i, int type) | BaseMolecule | |
| set_radii_changed() | BaseMolecule | [inline] |
| set_rot(float x, char axis) | Displayable | |
| set_rot(const Matrix4 &) | Displayable | |
| set_scale(float s) | Displayable | |
| setbondorder(int atom, int bond, float order) | BaseMolecule | |
| setbondtype(int atom, int bond, int type) | BaseMolecule | |
| show_rep(int repid, int onoff) | DrawMolecule | |
| test_dataset_flag(int flag) | BaseMolecule | [inline] |
| tm | Displayable | |
| unfix(void) | Displayable | [inline] |
| unregister_monitor(DrawMoleculeMonitor *) | DrawMolecule | |
| unset_dataset_flag(int flag) | BaseMolecule | [inline] |
| update_material(const Material *mat) | Displayable | |
| volumeList | BaseMolecule | [protected] |
| ~BaseMolecule(void) | BaseMolecule | [virtual] |
| ~Displayable(void) | Displayable | [virtual] |
| ~DrawMolecule() | DrawMolecule | [virtual] |
| ~Molecule(void) | Molecule | [virtual] |
| ~Pickable() | Pickable | [inline, virtual] |
