Index

A

add_step_result() (mchammer.Result method) Atom (class in mchammer)

atom_ids (mchammer.Bond attribute) atoms (mchammer.Molecule attribute)

B

Bond (class in mchammer)

bonds (mchammer.Molecule attribute)

C

charge (mchammer.Atom attribute)

Collapser (class in mchammer) compute_potential() (mchammer.Optimizer method)

E

element_string (mchammer.Atom attribute)

epsilon (mchammer.Atom attribute)

G

get_atom1_id() (mchammer.Bond method) get_atom2_id() (mchammer.Bond method) get_atom_distance() (in module mchammer) get_atoms() (mchammer.Molecule method) get_bond_vector() (in module mchammer) get_bonds() (mchammer.Molecule method) get_centroid() (mchammer.Molecule method) get_element_string() (mchammer.Atom method) get_final_position_matrix() (mchammer.Result method) get_id() (mchammer.Atom method) (mchammer.Bond method) get_log() (mchammer.Result method) get_num_atoms() (mchammer.Molecule method) get_number_passed() (mchammer.Result method)

get_position_matrix() (mchammer.Molecule method) get_properties() (mchammer.MCStepResult method) (mchammer.StepResult method) get_radius() (in module mchammer) (mchammer.Atom method) get_result() (mchammer.Collapser method) (mchammer.Optimizer method) get_step_count() (mchammer.Result method) get_steps_properties() (mchammer.Result method) get_subunits() (mchammer.Molecule method) get_timing() (mchammer.Result method) get_trajectory() (mchammer.Collapser method) (mchammer.Optimizer method) (mchammer.Result method)

I

id (mchammer.Atom attribute) (mchammer.Bond attribute)

L

log (mchammer.MCStepResult attribute) (mchammer.StepResult attribute)

M

max_bond_distance (mchammer.MCStepResult attribute) (mchammer.StepResult attribute) mchammer module

MCStepResult (class in mchammer) module mchammer Molecule (class in mchammer)

N

nonbonded_potential (mchammer.MCStepResult attribute)

O

Optimizer (class in mchammer)

P

passed (mchammer.MCStepResult attribute) position_matrix (mchammer.MCStepResult attribute) (mchammer.Molecule attribute) (mchammer.StepResult attribute)

R

radius (mchammer.Atom attribute) Result (class in mchammer)

rotate_molecule_by_angle() (in module mchammer) rotation_matrix_arbitrary_axis() (in module mchammer)

S

sigma (mchammer.Atom attribute) step (mchammer.MCStepResult attribute) (mchammer.StepResult attribute)

StepResult (class in mchammer) system_potential (mchammer.MCStepResult attribute)

T

test_move() (in module mchammer)

translate_atoms_along_vector() (in module mchammer) translate_molecule_along_vector() (in module mchammer)

U

update_log() (mchammer.Result method)

W

with_displacement() (mchammer.Molecule method) with_position_matrix() (mchammer.Molecule method)

write_pdb_file() (mchammer.Molecule method) write_xyz_content() (mchammer.Molecule method) write_xyz_file() (mchammer.Molecule method)