Index

A

add_bond() (MolecularSystemBase method) add_bonds() (MolecularSystemBase method) add_library() (in module chilife.chilife) add_rotlib_dir() (in module chilife.chilife) align_points() (in module chilife.alignment_methods) alignment_method() (in module chilife.alignment_methods) angles (Atom property) append_cap() (in module chilife.protein_utils) apply_chain_operators() (MolSysIC method)

assign_atom_names() (in module chilife.ligand_utils) 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_ic2cart() (in module chilife.numba_utils) batch_set_dihedrals() (MolSysIC method) bisect_alignment() (in module chilife.alignment_methods) bond_atom_names (MolecularSystemBase property) bond_chiral (MolecularSystemBase property) bond_types (MolecularSystemBase property)

bonded_atoms (Atom property) bonded_pairs (MolSysIC attribute) bonds (Atom property) (dRotamerEnsemble property) (LigandEnsemble property) (MolecularSystemBase property) (RotamerEnsemble property)

C

CB (RotamerEnsemble property) centroid (dRotamerEnsemble property) (LigandEnsemble 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.ligand_utils module chilife.MolSys module chilife.MolSysIC module chilife.numba_utils module chilife.protein_utils module

chilife.scoring module clash_ori (dRotamerEnsemble property) (LigandEnsemble property) (RotamerEnsemble property) compute_bin() (in module chilife.numba_utils) coords (dRotamerEnsemble property) (FreeAtom attribute) (LigandEnsemble property) (MolecularSystemBase property) (MolSysIC property) (RotamerEnsemble property) copy() (dRotamerEnsemble method) (LigandEnsemble method) (MolecularSystemBase method) (MolSys method) (MolSysIC method) (RotamerEnsemble method) create_ccd_dicts() (in module chilife.io) 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 (Atom property) (dRotamerEnsemble property) (LigandEnsemble 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) (LigandEnsemble 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_cif() (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_sdf() (LigandEnsemble class method) (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) (LigandEnsemble 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) (in module chilife.protein_utils) 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() (LigandEnsemble method) (RotamerEnsemble method)

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

J

jaccard() (in module chilife.numba_utils) join_arith() (in module chilife.scoring)

join_ccd_info() (in module chilife.io) join_geom() (in module chilife.scoring)

K

kl_divergence() (in module chilife.numba_utils)

L

ligand_alignment_method() (in module chilife.alignment_methods) LigandEnsemble (class in chilife) linear_alignment() (in module chilife.alignment_methods) 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.ligand_utils 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 (LigandEnsemble property) (RotamerEnsemble property)

N

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

new_chain() (in module chilife.protein_utils) non_bonded (dRotamerEnsemble property) (LigandEnsemble 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 (LigandEnsemble property) (RotamerEnsemble property)

P

pairwise_dist() (in module chilife.numba_utils) param_from_rotlibs() (in module chilife.protein_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) position (Atom property) positions (MolecularSystemBase property) protein (dRotamerEnsemble attribute) protein_setup() (LigandEnsemble method) psi_idxs() (MolSysIC method) psi_selection() (Residue method)

R

randomize_rotamers() (in module chilife.protein_utils) RE1 (dRotamerEnsemble attribute) RE2 (dRotamerEnsemble attribute) read_cif() (in module chilife.io) read_distance_distribution() (in module chilife.io) read_library() (in module chilife.io) read_pdb() (in module chilife.io) read_sdf() (in module chilife.io) reconfigure_cap() (in module chilife.MolSysIC) remap_sdf() (in module chilife.ligand_utils) remove_bond() (MolecularSystemBase method) remove_bonds() (MolecularSystemBase method) 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() (LigandEnsemble method) (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() (LigandEnsemble method) (RotamerEnsemble method) set_site() (LigandEnsemble method) (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 (IntrinsicLabel property) (SpinLabel property) spin_centroid (IntrinsicLabel property) (SpinLabel property) spin_coords (IntrinsicLabel property) (SpinLabel property) spin_idx (dSpinLabel property) spin_weights (dSpinLabel property) SpinLabel (class in chilife) SpinLigand (class in chilife) store_cap() (in module chilife.protein_utils) svd_alignment() (in module chilife.alignment_methods)

T

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

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

U

universe (MolecularSystemBase property)

update() (LigandEnsemble method) use_frames() (MolSysIC method)

W

weights (dRotamerEnsemble property) write_atoms() (in module chilife.io) write_cif() (in module chilife.io) (MolecularSystemBase method)

write_grid() (in module chilife.protein_utils) write_sdf() (in module chilife.io) (MolecularSystemBase method)

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)