Index

A

align_mol_to_positions() (move_class.CBMCSwap method) Angle (class in molecule_class) assignAtomTypes() (simulation_class.Simulation method)

Atom (class in atom_class) atom_class (module) atomsAsGraph() (molecule_class.Molecule method)

B

Bond (class in molecule_class)

C

CBMCRegrowth (class in move_class)

CBMCSwap (class in move_class) constructMolecules() (in module molecule_class)

D

Dihedral (class in molecule_class)

dump_atoms() (simulation_class.Simulation method) dump_group() (simulation_class.Simulation method)

E

evaluate_energies() (move_class.CBMCRegrowth method)

G

get_atom_coords() (simulation_class.Simulation method) get_com() (molecule_class.Molecule method) getAnglesFromAtoms() (in module molecule_class) getAtomByID() (molecule_class.Molecule method) getAtomByMolIndex() (molecule_class.Molecule method) getBondsFromAtoms() (in module molecule_class)

getDihedralAngle() (molecule_class.Molecule method) getDihedralsFromAtoms() (in module molecule_class) getRandomMolecule() (simulation_class.Simulation method) groupAnglesByMol() (in module molecule_class) groupAtomsByMol() (in module molecule_class) groupBondsByMol() (in module molecule_class) groupDihedralsByMol() (in module molecule_class)

I

index2dihedral() (molecule_class.Molecule method) initializeComputes() (simulation_class.Simulation method)

initializeFixes() (simulation_class.Simulation method) initializeGroups() (simulation_class.Simulation method)

L

loadAngles() (in module molecule_class) loadAtoms() (in module atom_class)

loadBonds() (in module molecule_class) loadDihedrals() (in module molecule_class)

M

minimize() (simulation_class.Simulation method) Molecule (class in molecule_class) molecule2graph() (in module molecule_class)

molecule_class (module) Move (class in move_class) move_class (module)

P

parallel_evaluate_energies() (move_class.CBMCRegrowth method)

R

rot_quat() (in module molecule_class)

rotateDihedral() (molecule_class.Molecule method) RotationMove (class in move_class)

S

select_dih_angles() (move_class.CBMCRegrowth method) select_index() (move_class.CBMCRegrowth method) select_random_molecule() (move_class.CBMCRegrowth method) (move_class.TranslationMove method) select_random_molecules() (move_class.CBMCSwap method)

set_anchor_atoms() (in module molecule_class) (move_class.CBMCRegrowth method) setAnchorAtom() (molecule_class.Molecule method) Simulation (class in simulation_class) simulation_class (module) SwapMove (class in move_class)

T

TranslationMove (class in move_class)

turn_off_atoms() (simulation_class.Simulation method)