Index

A

Atom (class in spindry) atom_ids (spindry.Bond attribute)

atoms (spindry.Molecule attribute) (spindry.SupraMolecule attribute)

B

Bond (class in spindry)

bonds (spindry.Molecule attribute) (spindry.SupraMolecule attribute)

C

calculate_centroid_distance() (in module spindry) calculate_min_atom_distance() (in module spindry) charge (spindry.Atom attribute) cid (spindry.SupraMolecule attribute)

compute_potential() (spindry.Potential method) (spindry.SpdPotential method) (spindry.Spinner method) (spindry.VaryingEpsilonPotential method)

E

element_string (spindry.Atom attribute)

epsilon (spindry.Atom attribute)

G

get_atom1_id() (spindry.Bond method) get_atom2_id() (spindry.Bond method) get_atom_distance() (in module spindry) get_atoms() (spindry.Molecule method) (spindry.SupraMolecule method) get_bonds() (spindry.Molecule method) (spindry.SupraMolecule method) get_centroid() (spindry.Molecule method) (spindry.SupraMolecule method) get_cid() (spindry.SupraMolecule method) get_components() (spindry.SupraMolecule method) get_conformers() (spindry.Spinner method)

get_element_string() (spindry.Atom method) get_final_conformer() (spindry.Spinner method) get_id() (spindry.Atom method) (spindry.Bond method) get_num_atoms() (spindry.Molecule method) (spindry.SupraMolecule method) get_position_matrix() (spindry.Molecule method) (spindry.SupraMolecule method) get_potential() (spindry.SupraMolecule method) get_radius() (spindry.Atom method) get_subunits() (spindry.Molecule method) (spindry.SupraMolecule method)

I

id (spindry.Atom attribute) (spindry.Bond attribute)

init_from_components() (spindry.SupraMolecule class method)

M

module spindry

Molecule (class in spindry)

P

position_matrix (spindry.Molecule attribute) (spindry.SupraMolecule attribute)

Potential (class in spindry) potential (spindry.SupraMolecule attribute)

R

radius (spindry.Atom attribute)

S

sigma (spindry.Atom attribute) SpdPotential (class in spindry) spindry module

Spinner (class in spindry) SupraMolecule (class in spindry)

V

VaryingEpsilonPotential (class in spindry)

W

with_displacement() (spindry.Molecule method) (spindry.SupraMolecule method) with_position_matrix() (spindry.Molecule method) (spindry.SupraMolecule method) write_pdb_file() (spindry.Molecule method) (spindry.SupraMolecule method)

write_xyz_content() (spindry.Molecule method) (spindry.SupraMolecule method) write_xyz_file() (spindry.Molecule method) (spindry.SupraMolecule method)