Index

_

__eq__() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) __getitem__() (neurosnap.structure.Chain method) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Chain method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __hash__() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) __init__() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __iter__() (neurosnap.structure.Chain method) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Chain method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method)

__len__() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __post_init__() (neurosnap.algos.evoef2.Atom method) __repr__() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack 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) (class in neurosnap.constants.sequence) abr (neurosnap.constants.AARecord attribute) (neurosnap.constants.sequence.AARecord attribute) add_annotation() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) align() (in module neurosnap.structure) (in module neurosnap.structure.compare) align_mafft() (in module neurosnap.sequence.align) align_molecule_to_reference() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) alignment_coverage() (in module neurosnap.sequence.align) all_residues() (neurosnap.algos.evoef2.Structure method) animate_frames() (in module neurosnap.structure) (in module neurosnap.structure.rendering) animate_results() (in module neurosnap.algos.clusterprot) annotations (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute)

append() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) Atom (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) atom_a (neurosnap.algos.evoef2.CharmmIC attribute) atom_b (neurosnap.algos.evoef2.CharmmIC attribute) atom_c (neurosnap.algos.evoef2.CharmmIC attribute) atom_count (neurosnap.structure.structure.StructureStack property) (neurosnap.structure.StructureStack property) atom_d (neurosnap.algos.evoef2.CharmmIC attribute) atom_indices() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) atom_name (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute) AtomParam (class in neurosnap.algos.evoef2) atoms (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute) atoms() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method)

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) ca_distance_matrix() (in module neurosnap.structure) (in module neurosnap.structure.analysis) 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.structure) (in module neurosnap.structure.interface) calculate_center_of_mass() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) calculate_distance_matrix() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) (in module neurosnap.structure) (in module neurosnap.structure.analysis) calculate_geometric_center() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) calculate_hydrogen_bonds() (in module neurosnap.structure) (in module neurosnap.structure.interactions) calculate_interface_energy() (in module neurosnap.algos.evoef2) calculate_interface_hydrogen_bonding_residues() (in module neurosnap.structure) (in module neurosnap.structure.interactions) calculate_ipSAE() (in module neurosnap.algos.ipsae) calculate_pDockQ() (in module neurosnap.algos.pdockq) calculate_protein_volume() (in module neurosnap.structure) (in module neurosnap.structure.analysis) calculate_rmsd() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) (in module neurosnap.structure) (in module neurosnap.structure.compare) calculate_rog() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) calculate_stability() (in module neurosnap.algos.evoef2) calculate_surface_area() (in module neurosnap.structure) (in module neurosnap.structure.analysis) canonicalize_smiles() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles)

CCD (class in neurosnap.database) (class in neurosnap.database.ccd) center_at() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) Chain (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) chain (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.Residue attribute) chain_id (neurosnap.structure.Atom attribute) (neurosnap.structure.Chain attribute), [1] (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Chain attribute), [1] (neurosnap.structure.structure.Residue attribute), [1] chain_ids() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) chains (neurosnap.algos.evoef2.Structure attribute) chains() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure 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) (neurosnap.constants.sequence.AARecord attribute) (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1] compute_distance_matrix() (in module neurosnap.algos.kluster) compute_ec() (in module neurosnap.algos.ec_interface) consensus_sequence() (in module neurosnap.sequence.align) contiguous_ranges() (in module neurosnap.algos.ipsae) coord (neurosnap.structure.Atom property) (neurosnap.structure.structure.Atom property) 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() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure 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]

element (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute) epsilon (neurosnap.algos.evoef2.AtomParam attribute), [1] extract_interchain_metrics() (in module neurosnap.algos.ipsae) extract_non_biopolymers() (in module neurosnap.structure) (in module neurosnap.structure.analysis)

F

fetch_accessions() (in module neurosnap.database) (in module neurosnap.database.uniprot) fetch_uniprot() (in module neurosnap.database) (in module neurosnap.database.uniprot) find_contacts() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_disulfide_bonds() (in module neurosnap.structure) (in module neurosnap.structure.interactions) find_hydrophobic_residues() (in module neurosnap.structure) (in module neurosnap.structure.interactions) find_interface_contacts() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_interface_residues() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_LCS() (in module neurosnap.chemistry) (in module neurosnap.chemistry.conformers)

find_non_interface_hydrophobic_patches() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_salt_bridges() (in module neurosnap.structure) (in module neurosnap.structure.interactions) first() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) fix_nucleic_termini() (in module neurosnap.structure) (in module neurosnap.structure.filters) foldseek_search() (in module neurosnap.database) (in module neurosnap.database.foldseek) format() (neurosnap.log.CustomLogger method) from_ensemble() (neurosnap.structure.structure.StructureStack class method) (neurosnap.structure.StructureStack class method)

G

g (neurosnap.log.c attribute) generate() (in module neurosnap.chemistry) (in module neurosnap.chemistry.conformers) get_atom() (neurosnap.algos.evoef2.Residue method) get_backbone() (in module neurosnap.structure) (in module neurosnap.structure.analysis) get_ccd() (in module neurosnap.database) (in module neurosnap.database.ccd) get_ccd_entries() (in module neurosnap.database) (in module neurosnap.database.ccd) 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.chemistry) (in module neurosnap.chemistry.geometry) get_pipeline() (neurosnap.api.NeurosnapAPI method) get_reverse_complement() (in module neurosnap.sequence.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.sequence.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]

hetero (neurosnap.structure.Atom attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue 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) ins_code (neurosnap.structure.Atom attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] 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) (neurosnap.constants.sequence.AARecord attribute) is_xyz_valid (neurosnap.algos.evoef2.Atom attribute), [1] isoelectric_point() (in module neurosnap.sequence.protein)

K

key() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method)

L

largest_fragment() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) 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.chemistry) (in module neurosnap.chemistry.conformers) missing_residue_ids() (neurosnap.structure.Chain method) (neurosnap.structure.structure.Chain method) models() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack 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.chemistry neurosnap.chemistry.conformers neurosnap.chemistry.geometry neurosnap.chemistry.smiles neurosnap.constants neurosnap.constants.api neurosnap.constants.chemistry neurosnap.constants.sequence neurosnap.constants.structure neurosnap.database neurosnap.database.blast neurosnap.database.ccd neurosnap.database.foldseek neurosnap.database.uniprot neurosnap.io neurosnap.io.mmcif neurosnap.io.pdb neurosnap.io.sdf neurosnap.log neurosnap.sequence neurosnap.sequence.align neurosnap.sequence.nucleotide neurosnap.sequence.protein neurosnap.structure neurosnap.structure.analysis neurosnap.structure.compare neurosnap.structure.filters neurosnap.structure.interactions neurosnap.structure.interface neurosnap.structure.rendering neurosnap.structure.selectors neurosnap.structure.structure

molecular_weight() (in module neurosnap.sequence.protein) move_ligand_to_center() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry)

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) (neurosnap.constants.sequence.AARecord attribute) (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1] net_charge() (in module neurosnap.sequence.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.chemistry module neurosnap.chemistry.conformers module neurosnap.chemistry.geometry module neurosnap.chemistry.smiles module neurosnap.constants module neurosnap.constants.api module

neurosnap.constants.chemistry module neurosnap.constants.sequence module neurosnap.constants.structure module neurosnap.database module neurosnap.database.blast module neurosnap.database.ccd module neurosnap.database.foldseek module neurosnap.database.uniprot module neurosnap.io module neurosnap.io.mmcif module neurosnap.io.pdb module neurosnap.io.sdf module neurosnap.log module neurosnap.sequence module neurosnap.sequence.align module neurosnap.sequence.nucleotide module neurosnap.sequence.protein module neurosnap.structure module neurosnap.structure.analysis module neurosnap.structure.compare module neurosnap.structure.filters module neurosnap.structure.interactions module neurosnap.structure.interface module neurosnap.structure.rendering module neurosnap.structure.selectors module neurosnap.structure.structure module NeurosnapAPI (class in neurosnap.api) neutralize_molecule() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles)

O

o (neurosnap.log.c attribute)

P

p (neurosnap.log.c attribute) pad_seqs() (in module neurosnap.sequence.align) param (neurosnap.algos.evoef2.Atom attribute), [1] parse_chain_pairs() (in module neurosnap.algos.ec_interface) parse_mmcif() (in module neurosnap.io.mmcif) parse_pdb() (in module neurosnap.io.pdb) parse_sdf() (in module neurosnap.io.sdf)

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) 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.sequence.align) rebuild_missing_atoms() (in module neurosnap.algos.evoef2) reduce_dimensions() (in module neurosnap.algos.kluster) remove_annotation() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) remove_atoms() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_chains() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_model() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) remove_non_biopolymers() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_nucleotides() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_residues() (in module neurosnap.structure.filters) remove_salts() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) remove_waters() (in module neurosnap.structure) (in module neurosnap.structure.filters) render_pseudo3D() (in module neurosnap.structure) (in module neurosnap.structure.rendering) render_structure_pseudo3D() (in module neurosnap.structure) (in module neurosnap.structure.rendering)

renumber() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) res (neurosnap.algos.evoef2.Atom attribute), [1] res_id (neurosnap.structure.Atom attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] res_name (neurosnap.structure.Atom attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] Residue (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) residues (neurosnap.algos.evoef2.Chain attribute) residues() (neurosnap.structure.Chain method) (neurosnap.structure.structure.Chain method) ResidueTopology (class in neurosnap.algos.evoef2) run_alignment() (in module neurosnap.algos.kluster) run_blast() (in module neurosnap.database) (in module neurosnap.database.blast) run_mmseqs2() (in module neurosnap.sequence.align) run_mmseqs2_modes() (in module neurosnap.sequence.align) run_phmmer() (in module neurosnap.sequence.align) run_phmmer_mafft() (in module neurosnap.sequence.align)

S

sanitize_aa_seq() (in module neurosnap.sequence.protein) save_cif() (in module neurosnap.io.mmcif) save_pdb() (in module neurosnap.io.pdb) save_sdf() (in module neurosnap.io.sdf) score_af2m_binding() (in module neurosnap.algos.alphafold) sdf_to_smiles() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) select_residues() (in module neurosnap.structure) (in module neurosnap.structure.selectors) seqid() (in module neurosnap.sequence.align) sequence() (neurosnap.structure.Chain method) (neurosnap.structure.structure.Chain method) set_job_note() (neurosnap.api.NeurosnapAPI method) set_job_share() (neurosnap.api.NeurosnapAPI method) smiles (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1]

smiles_canonical() (neurosnap.database.CCD method) (neurosnap.database.ccd.CCD method) smiles_to_sdf() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) split_interleaved_fastq() (in module neurosnap.sequence.nucleotide) standard_equiv_abr (neurosnap.constants.AARecord attribute) (neurosnap.constants.sequence.AARecord attribute) standardize_molecule() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) Structure (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) StructureEnsemble (class in neurosnap.structure) (class in neurosnap.structure.structure) StructureStack (class in neurosnap.structure) (class in neurosnap.structure.structure) submit_job() (neurosnap.api.NeurosnapAPI method)

T

to_dataframe() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) to_ensemble() (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureStack method) to_mol() (neurosnap.database.CCD method) (neurosnap.database.ccd.CCD method)

to_stack() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.StructureEnsemble method) torsion_proper (neurosnap.algos.evoef2.CharmmIC attribute) torsions (neurosnap.algos.evoef2.DunbrackRotamer attribute) translate() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) translate_molecule() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) type (neurosnap.algos.evoef2.AtomParam attribute), [1]

V

validate_smiles() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) 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.sequence.align) write_single_chain_pdb() (in module neurosnap.algos.ec_interface)

X

x (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute)

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

Y

y (neurosnap.log.c attribute) (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute)

Z

z (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute)