Index

A

add_library() (in module chilife.chilife) add_rotlib_dir() (in module chilife.chilife) alignment_method() (in module chilife.alignment_methods) append_cap() (in module chilife.protein_utils) apply_chain_operators() (MolSysIC method) Atom (class in chilife.MolSys) atom_dict (MolSysIC attribute)

atom_names (dRotamerEnsemble property) (MolSysIC attribute) atom_types (dRotamerEnsemble property) (MolSysIC attribute) atoms (MolSysIC attribute) AtomSelection (class in chilife.MolSys) atype (FreeAtom attribute)

B

backbone_to_site() (RotamerEnsemble method) batch_set_dihedrals() (MolSysIC method) bisect_alignment() (in module chilife.alignment_methods)

bonded_pairs (MolSysIC attribute) bonds (dRotamerEnsemble property) (RotamerEnsemble property)

C

CB (RotamerEnsemble property) centroid (dRotamerEnsemble property) (RotamerEnsemble property) chain (dRotamerEnsemble attribute) chain_operator_idxs (MolSysIC property) chain_operators (MolSysIC property) chains (MolSysIC attribute) chi_idxs() (MolSysIC method) chilife.alignment_methods module chilife.chilife module chilife.io module chilife.MolSys module chilife.MolSysIC module chilife.numba_utils module

chilife.protein_utils module chilife.scoring module clash_ori (dRotamerEnsemble property) (RotamerEnsemble property) compute_bin() (in module chilife.numba_utils) coords (dRotamerEnsemble property) (FreeAtom attribute) (MolecularSystemBase property) (MolSysIC property) (RotamerEnsemble property) copy() (dRotamerEnsemble method) (MolecularSystemBase method) (MolSys method) (MolSysIC method) (RotamerEnsemble method) create_dlibrary() (in module chilife.chilife) create_ensembles() (dRotamerEnsemble method) (dSpinLabel method) create_library() (in module chilife.chilife)

D

dihedral_atoms (dRotamerEnsemble property) dihedral_defs (MolSysIC attribute) dihedrals (dRotamerEnsemble property) (RotamerEnsemble property)

dirichlet() (in module chilife.numba_utils) distance_distribution() (in module chilife.chilife) dRotamerEnsemble (class in chilife) dSpinLabel (class in chilife)

E

evaluate() (dRotamerEnsemble method) (RotamerEnsemble method)

F

fibonacci_points() (in module chilife.numba_utils) fit_alignment() (in module chilife.alignment_methods) fname (MolecularSystemBase property) frame (Trajectory property) FreeAtom (class in chilife.protein_utils) from_arrays() (MolSys class method) from_atoms() (MolSysIC class method) from_atomsel() (MolSys class method)

from_mda() (RotamerEnsemble class method) from_mmm() (SpinLabel class method) from_openMM() (MolSys class method) from_pdb() (MolSys class method) (RotamerEnsemble class method) from_rdkit() (MolSys class method) from_trajectory() (RotamerEnsemble class method) from_wizard() (SpinLabel class method)

G

get_angle() (in module chilife.protein_utils) get_angles() (in module chilife.protein_utils) get_chainbreak_idxs() (in module chilife.MolSysIC) get_delta_r() (in module chilife.numba_utils) get_dihedral() (in module chilife.protein_utils) (MolSysIC method) get_dihedral_rotation_matrix() (in module chilife.protein_utils) get_dihedrals() (in module chilife.protein_utils) get_grid_mx() (in module chilife.protein_utils) get_lib() (dRotamerEnsemble method) (RotamerEnsemble method) get_lj_attr() (in module chilife.scoring)

get_lj_energy() (in module chilife.scoring) get_lj_rep() (in module chilife.scoring) get_lj_scwrl() (in module chilife.scoring) get_missing_residues() (in module chilife.protein_utils) get_sas_res() (in module chilife.protein_utils) get_sasa() (in module chilife.numba_utils) (RotamerEnsemble method) get_site_volume() (in module chilife.protein_utils) get_z_matrix() (in module chilife.MolSysIC) get_z_matrix_idxs() (MolSysIC method) global_mx() (in module chilife.alignment_methods) guess_chain() (dRotamerEnsemble method) guess_mobile_dihedrals() (in module chilife.protein_utils)

H

has_clashes() (MolSysIC method)

histogram() (in module chilife.numba_utils)

I

ic_mx() (in module chilife.MolSysIC) ICS (MolSysIC attribute) ICs_to_site() (RotamerEnsemble method)

increment (dRotamerEnsemble attribute) index (FreeAtom attribute) intra_fit() (RotamerEnsemble method) IntrinsicLabel (class in chilife)

J

jaccard() (in module chilife.numba_utils)

join_arith() (in module chilife.scoring) join_geom() (in module chilife.scoring)

K

kl_divergence() (in module chilife.numba_utils)

L

list_available_rotlibs() (in module chilife.chilife) load_new() (MolSys method) (MolSysIC method) (Trajectory method)

local_mx() (in module chilife.alignment_methods) logic_keywords (MolecularSystemBase property)

M

make_mda_uni() (in module chilife.protein_utils) make_peptide() (in module chilife.protein_utils) minimize() (dRotamerEnsemble method) (RotamerEnsemble method) mmm_alignment() (in module chilife.alignment_methods) module chilife.alignment_methods chilife.chilife chilife.io chilife.MolSys chilife.MolSysIC chilife.numba_utils chilife.protein_utils chilife.scoring

MolecularSystemBase (class in chilife.MolSys) MolSys (class in chilife.MolSys) molsys_keywords (MolecularSystemBase property) MolSysIC (class in chilife.MolSysIC) mutate() (in module chilife.protein_utils) mx (RotamerEnsemble property)

N

n_atoms (MolecularSystemBase property) n_chains (MolecularSystemBase property) n_residues (MolecularSystemBase property) name (dRotamerEnsemble attribute) (FreeAtom attribute)

non_bonded (dRotamerEnsemble property) (RotamerEnsemble property) nonbonded (MolSysIC property) normdist() (in module chilife.numba_utils) np_all_axis1() (in module chilife.numba_utils)

O

omega_idxs() (MolSysIC method)

origin (RotamerEnsemble property)

P

pairwise_dist() (in module chilife.numba_utils) parse_backbone() (in module chilife.alignment_methods) parse_sequence() (in module chilife.protein_utils) perturbed (MolSysIC attribute) phi_idxs() (MolSysIC method)

phi_selection() (Residue method) pose2mda() (in module chilife.protein_utils) positions (MolecularSystemBase property) protein (dRotamerEnsemble attribute) psi_idxs() (MolSysIC method) psi_selection() (Residue method)

R

randomize_rotamers() (in module chilife.protein_utils) RE1 (dRotamerEnsemble attribute) RE2 (dRotamerEnsemble attribute) read_distance_distribution() (in module chilife.io) read_library() (in module chilife.io) reconfigure_cap() (in module chilife.MolSysIC) remove_library() (in module chilife.chilife) remove_rotlib_dir() (in module chilife.chilife) repack() (in module chilife.chilife) res (dRotamerEnsemble attribute)

resi (FreeAtom attribute) Residue (class in chilife.MolSys) residues (MolecularSystemBase property) ResidueSelection (class in chilife.MolSys) resis (MolSysIC attribute) resn (FreeAtom attribute) resnames (MolSysIC attribute) reweight_rotamers() (in module chilife.scoring) rosetta_alignment() (in module chilife.alignment_methods) RotamerEnsemble (class in chilife)

S

sample() (RotamerEnsemble method) save() (in module chilife.io) save_ensemble() (in module chilife.protein_utils) save_pdb() (dRotamerEnsemble method) (in module chilife.protein_utils) (RotamerEnsemble method) Segment (class in chilife.MolSys) segments (MolecularSystemBase property) SegmentSelection (class in chilife.MolSys) select_atoms() (MolecularSystemBase method) set_cartesian_coords() (MolSysIC method) set_dihedral() (in module chilife.protein_utils) (MolSysIC method) set_dihedral_sampling_sigmas() (RotamerEnsemble method) set_site() (RotamerEnsemble method) shift_resnum() (MolSysIC method) side_chain_idx (dRotamerEnsemble property) site1 (dRotamerEnsemble attribute)

site2 (dRotamerEnsemble attribute) SL1 (dSpinLabel attribute) SL2 (dSpinLabel attribute) smiles2residue() (in module chilife.protein_utils) spin_atoms (dSpinLabel property) spin_centers (dSpinLabel property) (IntrinsicLabel property) (SpinLabel property) spin_centroid (dSpinLabel property) (IntrinsicLabel property) (SpinLabel property) spin_coords (dSpinLabel property) (IntrinsicLabel property) (SpinLabel property) spin_idx (dSpinLabel property) spin_weights (dSpinLabel property) SpinLabel (class in chilife) store_cap() (in module chilife.protein_utils)

T

template_ICs() (in module chilife.protein_utils) to_cartesian() (MolSysIC method) to_rotlib() (RotamerEnsemble method)

to_site() (RotamerEnsemble method) Trajectory (class in chilife.MolSys) trim_rotamers() (dRotamerEnsemble method) (RotamerEnsemble method)

U

universe (MolecularSystemBase property)

update_weight() (RotamerEnsemble method) use_frames() (MolSysIC method)

W

weights (dRotamerEnsemble property)

write_atoms() (in module chilife.io) write_grid() (in module chilife.protein_utils)

X

xplor2mda() (in module chilife.protein_utils)

Z

z_matrix (MolSysIC property) z_matrix_idxs (MolSysIC attribute)

zmatrix_idxs_to_local() (in module chilife.MolSysIC) zmats (MolSysIC attribute)