| 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_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_improper(int a, int b, int c, int d, int type=-1) | BaseMolecule | |
| add_instance(Matrix4 &inst) | BaseMolecule | [inline] |
| 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 | |
| ALTLOC enum value | BaseMolecule | |
| altlocNames | BaseMolecule | |
| analyze(void) | BaseMolecule | |
| angles | BaseMolecule | |
| ANGLES enum value | BaseMolecule | |
| angleTypeNames | BaseMolecule | |
| angleTypes | BaseMolecule | |
| ANGLETYPES enum value | BaseMolecule | |
| atom(int n) | BaseMolecule | [inline] |
| 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() | BaseMolecule | [inline] |
| BONDORDERS enum value | BaseMolecule | |
| BONDS enum value | BaseMolecule | |
| bondTypeNames | BaseMolecule | |
| bondtypes() | BaseMolecule | [inline] |
| BONDTYPES enum value | BaseMolecule | |
| chainNames | BaseMolecule | |
| charge() | BaseMolecule | [inline] |
| CHARGE enum value | BaseMolecule | |
| 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] |
| compute_volume_gradient(VolumetricData *) | BaseMolecule | |
| count_bonds(void) | BaseMolecule | |
| cterms | BaseMolecule | |
| CTERMS enum value | BaseMolecule | |
| 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 | |
| dihedrals | BaseMolecule | |
| dihedralTypeNames | BaseMolecule | |
| dihedralTypes | BaseMolecule | |
| extraflg | BaseMolecule | |
| extraflt | BaseMolecule | |
| extraint | BaseMolecule | |
| 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] |
| flags() | BaseMolecule | [inline] |
| fragList | BaseMolecule | |
| fragment(int) | BaseMolecule | |
| get_angletype(int a) | BaseMolecule | |
| get_dihedraltype(int d) | BaseMolecule | |
| get_impropertype(int i) | BaseMolecule | |
| get_radii_minmax(float &min, float &max) | BaseMolecule | [inline] |
| get_volume_data(int) | BaseMolecule | |
| getbondorder(int atom, int bond) | BaseMolecule | |
| getbondtype(int atom, int bond) | BaseMolecule | |
| has_structure() const | BaseMolecule | [inline] |
| id(void) const | BaseMolecule | [inline] |
| impropers | BaseMolecule | |
| improperTypeNames | BaseMolecule | |
| improperTypes | BaseMolecule | |
| init_atoms(int n) | BaseMolecule | |
| INSERTION enum value | BaseMolecule | |
| instances | BaseMolecule | |
| mass() | BaseMolecule | [inline] |
| MASS enum value | BaseMolecule | |
| modify_volume_data(int) | BaseMolecule | |
| moleculename | BaseMolecule | [protected] |
| molname() const | BaseMolecule | [inline] |
| nAtoms | BaseMolecule | |
| need_find_bonds | BaseMolecule | [protected] |
| nfragCyclic | BaseMolecule | |
| nfragList | BaseMolecule | |
| nFragments | BaseMolecule | |
| nNucleicFragments | BaseMolecule | |
| NODATA enum value | BaseMolecule | |
| nProteinFragments | BaseMolecule | |
| nResidues | BaseMolecule | |
| nSegments | BaseMolecule | |
| num_angles() | BaseMolecule | [inline] |
| num_cterms() | BaseMolecule | [inline] |
| num_dihedrals() | BaseMolecule | [inline] |
| num_impropers() | BaseMolecule | [inline] |
| num_instances(void) | BaseMolecule | [inline] |
| num_volume_data() | BaseMolecule | |
| nWaters | BaseMolecule | |
| OCCUPANCY enum value | BaseMolecule | |
| occupancy() | BaseMolecule | [inline] |
| pfragCyclic | BaseMolecule | |
| pfragList | BaseMolecule | |
| qm_data | BaseMolecule | |
| radii_max | BaseMolecule | |
| radii_min | BaseMolecule | |
| radii_minmax_need_update | BaseMolecule | |
| RADIUS enum value | BaseMolecule | |
| radius() | BaseMolecule | [inline] |
| remove_volume_data(int idx) | BaseMolecule | |
| residue(int) | BaseMolecule | |
| residueList | BaseMolecule | |
| resNames | BaseMolecule | |
| segNames | BaseMolecule | |
| set_angletype(int a, int type) | BaseMolecule | |
| set_dataset_flag(int flag) | BaseMolecule | [inline] |
| set_dihedraltype(int d, int type) | BaseMolecule | |
| set_impropertype(int i, int type) | BaseMolecule | |
| set_radii_changed() | BaseMolecule | [inline] |
| setbondorder(int atom, int bond, float order) | BaseMolecule | |
| setbondtype(int atom, int bond, int type) | BaseMolecule | |
| test_dataset_flag(int flag) | BaseMolecule | [inline] |
| unset_dataset_flag(int flag) | BaseMolecule | [inline] |
| volumeList | BaseMolecule | [protected] |
| ~BaseMolecule(void) | BaseMolecule | [virtual] |
