Index

_

__call__() (neurosnap.protein.Protein method)

__post_init__() (neurosnap.algos.evoef2.Atom method) __sub__() (neurosnap.protein.Protein method)

A

a (neurosnap.algos.evoef2.Bond attribute) aap (neurosnap.algos.evoef2.AAppTable attribute) AAppTable (class in neurosnap.algos.evoef2) AARecord (class in neurosnap.constants) abr (neurosnap.constants.AARecord attribute) align() (neurosnap.protein.Protein method) align_mafft() (in module neurosnap.msa) alignment_coverage() (in module neurosnap.msa) all_residues() (neurosnap.algos.evoef2.Structure method)

animate_frames() (in module neurosnap.rendering) animate_results() (in module neurosnap.algos.clusterprot) Atom (class in neurosnap.algos.evoef2) atom_a (neurosnap.algos.evoef2.CharmmIC attribute) atom_b (neurosnap.algos.evoef2.CharmmIC attribute) atom_c (neurosnap.algos.evoef2.CharmmIC attribute) atom_d (neurosnap.algos.evoef2.CharmmIC attribute) AtomParam (class in neurosnap.algos.evoef2) atoms (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute)

B

b (neurosnap.algos.evoef2.Bond attribute) (neurosnap.log.c attribute) BASE_URL (neurosnap.api.NeurosnapAPI attribute) bins (neurosnap.algos.evoef2.DunbrackLibrary attribute) Bond (class in neurosnap.algos.evoef2)

bond_type (neurosnap.algos.evoef2.Bond attribute) bonds (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute) br (neurosnap.log.c attribute) by_residue (neurosnap.algos.evoef2.DunbrackBin attribute)

C

c (class in neurosnap.log) (neurosnap.log.c attribute) calc_d0() (in module neurosnap.algos.ipsae) calc_d0_array() (in module neurosnap.algos.ipsae) calc_lddt() (in module neurosnap.algos.LDDT) calculate_binding() (in module neurosnap.algos.evoef2) calculate_bsa() (in module neurosnap.protein) calculate_center_of_mass() (neurosnap.protein.Protein method) calculate_distance_matrix() (neurosnap.protein.Protein method) calculate_hydrogen_bonds() (neurosnap.protein.Protein method) calculate_interface_energy() (in module neurosnap.algos.evoef2) calculate_interface_hydrogen_bonding_residues() (neurosnap.protein.Protein method) calculate_ipSAE() (in module neurosnap.algos.ipsae) calculate_pDockQ() (in module neurosnap.algos.pdockq) calculate_protein_volume() (neurosnap.protein.Protein method) calculate_rmsd() (neurosnap.protein.Protein method) calculate_rog() (neurosnap.protein.Protein method) calculate_stability() (in module neurosnap.algos.evoef2) calculate_surface_area() (neurosnap.protein.Protein method)

center() (neurosnap.protein.Protein method) Chain (class in neurosnap.algos.evoef2) chain (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.Residue attribute) chains (neurosnap.algos.evoef2.Structure attribute) chains() (neurosnap.protein.Protein method) charge (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] CharmmIC (class in neurosnap.algos.evoef2) check_alignment_tool() (in module neurosnap.algos.kluster) cluster_projection() (in module neurosnap.algos.kluster) ClusterProt() (in module neurosnap.algos.clusterprot) code (neurosnap.constants.AARecord attribute) compute_distance_matrix() (in module neurosnap.algos.kluster) compute_ec() (in module neurosnap.algos.ec_interface) consensus_sequence() (in module neurosnap.msa) contiguous_ranges() (in module neurosnap.algos.ipsae) create_figure_plotly() (in module neurosnap.algos.clusterprot) CustomLogger (class in neurosnap.log)

D

delete_job_share() (neurosnap.api.NeurosnapAPI method) deletes (neurosnap.algos.evoef2.ResidueTopology attribute) deviations (neurosnap.algos.evoef2.DunbrackRotamer attribute)

distances_from_com() (neurosnap.protein.Protein method) DunbrackBin (class in neurosnap.algos.evoef2) DunbrackLibrary (class in neurosnap.algos.evoef2) DunbrackRotamer (class in neurosnap.algos.evoef2)

E

eef1_free_dg (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] eef1_lambda (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1]

eef1_volume (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] epsilon (neurosnap.algos.evoef2.AtomParam attribute), [1] extract_interchain_metrics() (in module neurosnap.algos.ipsae) extract_non_biopolymers() (in module neurosnap.protein)

F

fetch_accessions() (in module neurosnap.protein) fetch_ccd() (in module neurosnap.chemicals) fetch_uniprot() (in module neurosnap.protein) find_contacts() (in module neurosnap.protein) find_disulfide_bonds() (neurosnap.protein.Protein method) find_hydrophobic_residues() (neurosnap.protein.Protein method) find_interface_contacts() (neurosnap.protein.Protein method)

find_interface_residues() (neurosnap.protein.Protein method) find_LCS() (in module neurosnap.conformers) find_missing_residues() (neurosnap.protein.Protein method) find_non_interface_hydrophobic_patches() (neurosnap.protein.Protein method) find_salt_bridges() (neurosnap.protein.Protein method) foldseek_search() (in module neurosnap.protein) format() (neurosnap.log.CustomLogger method)

G

g (neurosnap.log.c attribute) generate() (in module neurosnap.conformers) generate_df() (neurosnap.protein.Protein method) get_aas() (neurosnap.protein.Protein method) get_atom() (neurosnap.algos.evoef2.Residue method) get_backbone() (neurosnap.protein.Protein method) get_ccds() (in module neurosnap.chemicals) get_job_data() (neurosnap.api.NeurosnapAPI method) get_job_file() (neurosnap.api.NeurosnapAPI method) get_job_status() (neurosnap.api.NeurosnapAPI method)

get_jobs() (neurosnap.api.NeurosnapAPI method) get_mol_center() (in module neurosnap.chemicals) get_pipeline() (neurosnap.api.NeurosnapAPI method) get_reverse_complement() (in module neurosnap.nucleotide) get_services() (neurosnap.api.NeurosnapAPI method) get_team_info() (neurosnap.api.NeurosnapAPI method) get_team_jobs() (neurosnap.api.NeurosnapAPI method) get_weights() (in module neurosnap.algos.evoef2_lib.weights) getAA() (in module neurosnap.protein) grey (neurosnap.log.c attribute)

H

hb_b2 (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] hb_d_or_b (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1]

hb_h_or_a (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] hybrid (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1]

I

ic_param (neurosnap.algos.evoef2.CharmmIC attribute) ics (neurosnap.algos.evoef2.ResidueTopology attribute) init_pairdict_array() (in module neurosnap.algos.ipsae) init_pairdict_scalar() (in module neurosnap.algos.ipsae) init_pairdict_set() (in module neurosnap.algos.ipsae) is_bb (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] is_h (neurosnap.algos.evoef2.Atom attribute) is_hbond_a (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam property)

is_hbond_h (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam property) is_in_hbond (neurosnap.algos.evoef2.Atom attribute), [1] is_nucleic (neurosnap.algos.evoef2.Residue attribute) is_protein (neurosnap.algos.evoef2.Chain attribute) (neurosnap.algos.evoef2.Residue attribute) is_standard (neurosnap.constants.AARecord attribute) is_xyz_valid (neurosnap.algos.evoef2.Atom attribute), [1] isoelectric_point() (in module neurosnap.protein)

L

load_aapropensity() (in module neurosnap.algos.evoef2) load_atom_params() (in module neurosnap.algos.evoef2) load_dunbrack() (in module neurosnap.algos.evoef2)

load_ramachandran() (in module neurosnap.algos.evoef2) load_topology() (in module neurosnap.algos.evoef2) log_format_basic (neurosnap.log.CustomLogger attribute) log_format_detailed (neurosnap.log.CustomLogger attribute)

M

minimize() (in module neurosnap.algos.amber_relax) (in module neurosnap.conformers) models() (neurosnap.protein.Protein method) module neurosnap neurosnap.algos neurosnap.algos.alphafold neurosnap.algos.amber_relax neurosnap.algos.clusterprot neurosnap.algos.ec_interface neurosnap.algos.evoef2 neurosnap.algos.evoef2_lib neurosnap.algos.evoef2_lib.constants neurosnap.algos.evoef2_lib.weights neurosnap.algos.ipsae neurosnap.algos.kluster neurosnap.algos.LDDT neurosnap.algos.pdockq neurosnap.api neurosnap.chemicals neurosnap.conformers neurosnap.constants neurosnap.log neurosnap.msa neurosnap.nucleotide neurosnap.protein neurosnap.rendering

molecular_weight() (in module neurosnap.protein) move_ligand_to_center() (in module neurosnap.chemicals)

N

n_cb_in_8a (neurosnap.algos.evoef2.Residue attribute) na_torsions (neurosnap.algos.evoef2.Residue attribute) name (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.AtomParam attribute), [1] (neurosnap.algos.evoef2.Chain attribute) (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute) (neurosnap.constants.AARecord attribute) net_charge() (in module neurosnap.protein) neurosnap module neurosnap.algos module neurosnap.algos.alphafold module neurosnap.algos.amber_relax module neurosnap.algos.clusterprot module neurosnap.algos.ec_interface module neurosnap.algos.evoef2 module neurosnap.algos.evoef2_lib module neurosnap.algos.evoef2_lib.constants module neurosnap.algos.evoef2_lib.weights module

neurosnap.algos.ipsae module neurosnap.algos.kluster module neurosnap.algos.LDDT module neurosnap.algos.pdockq module neurosnap.api module neurosnap.chemicals module neurosnap.conformers module neurosnap.constants module neurosnap.log module neurosnap.msa module neurosnap.nucleotide module neurosnap.protein module neurosnap.rendering module NeurosnapAPI (class in neurosnap.api)

O

o (neurosnap.log.c attribute)

P

p (neurosnap.log.c attribute) pad_seqs() (in module neurosnap.msa) param (neurosnap.algos.evoef2.Atom attribute), [1] parse_chain_pairs() (in module neurosnap.algos.ec_interface) patches (neurosnap.algos.evoef2.Residue attribute) phipsi (neurosnap.algos.evoef2.Residue attribute)

polarity (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] pos (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.Residue attribute) probability (neurosnap.algos.evoef2.DunbrackRotamer attribute) Protein (class in neurosnap.protein) ptm_func() (in module neurosnap.algos.ipsae)

R

r (neurosnap.log.c attribute) radius (neurosnap.algos.evoef2.AtomParam attribute), [1] rama (neurosnap.algos.evoef2.RamaTable attribute) RamaTable (class in neurosnap.algos.evoef2) read_msa() (in module neurosnap.msa) rebuild_missing_atoms() (in module neurosnap.algos.evoef2) reduce_dimensions() (in module neurosnap.algos.kluster) remove() (neurosnap.protein.Protein method) remove_non_biopolymers() (neurosnap.protein.Protein method) remove_nucleotides() (neurosnap.protein.Protein method) remove_waters() (neurosnap.protein.Protein method) render_protein_pseudo3D() (in module neurosnap.rendering)

render_pseudo3D() (in module neurosnap.rendering) renumber() (neurosnap.protein.Protein method) res (neurosnap.algos.evoef2.Atom attribute), [1] Residue (class in neurosnap.algos.evoef2) residues (neurosnap.algos.evoef2.Chain attribute) ResidueTopology (class in neurosnap.algos.evoef2) run_alignment() (in module neurosnap.algos.kluster) run_blast() (in module neurosnap.protein) run_mmseqs2() (in module neurosnap.msa) run_mmseqs2_modes() (in module neurosnap.msa) run_phmmer() (in module neurosnap.msa) run_phmmer_mafft() (in module neurosnap.msa)

S

sanitize_aa_seq() (in module neurosnap.protein) save() (neurosnap.protein.Protein method) score_af2m_binding() (in module neurosnap.algos.alphafold) sdf_to_smiles() (in module neurosnap.chemicals) select_residues() (neurosnap.protein.Protein method) seqid() (in module neurosnap.msa)

set_job_note() (neurosnap.api.NeurosnapAPI method) set_job_share() (neurosnap.api.NeurosnapAPI method) smiles_to_sdf() (in module neurosnap.chemicals) split_interleaved_fastq() (in module neurosnap.nucleotide) standard_equiv_abr (neurosnap.constants.AARecord attribute) Structure (class in neurosnap.algos.evoef2) submit_job() (neurosnap.api.NeurosnapAPI method)

T

to_sdf() (neurosnap.protein.Protein method) torsion_proper (neurosnap.algos.evoef2.CharmmIC attribute)

torsions (neurosnap.algos.evoef2.DunbrackRotamer attribute) type (neurosnap.algos.evoef2.AtomParam attribute), [1]

V

validate_smiles() (in module neurosnap.chemicals) vdw_epsilon (neurosnap.algos.evoef2.Atom attribute)

vdw_radius (neurosnap.algos.evoef2.Atom attribute) visualize_projection() (in module neurosnap.algos.kluster) visualize_projection_interactive() (in module neurosnap.algos.kluster)

W

wait_job_status() (neurosnap.api.NeurosnapAPI method)

write_msa() (in module neurosnap.msa) write_single_chain_pdb() (in module neurosnap.algos.ec_interface)

X

xtorsions (neurosnap.algos.evoef2.Residue attribute)

xyz (neurosnap.algos.evoef2.Atom attribute), [1]

Y

y (neurosnap.log.c attribute)