Index

_

__init__() (ocelot.curator.Contribution.Contribution method) (ocelot.curator.DataSchema.DataAccess method) (ocelot.curator.DataSchema.DataEntry method) (ocelot.curator.DataSchema.DataProvider method) (ocelot.routines.conformerparser.ACParser method) (ocelot.routines.disparser.AsymmUnit method) (ocelot.routines.disparser.AtomLabel method) (ocelot.routines.disparser.DisorderUnit method) (ocelot.routines.disparser.DisParser method) (ocelot.routines.loop.Loopsearcher method) (ocelot.routines.mopac.MopacInput method) (ocelot.routines.mopac.MopacOutput method) (ocelot.schema.configuration.Config method) (ocelot.schema.conformer.BasicConformer method) (ocelot.schema.conformer.BondConformer method) (ocelot.schema.conformer.BoneConformer method) (ocelot.schema.conformer.ConformerDimer method) (ocelot.schema.conformer.DimerCollection method) (ocelot.schema.conformer.FragConformer method) (ocelot.schema.conformer.MolConformer method) (ocelot.schema.conformer.RingConformer method) (ocelot.schema.conformer.SidechainConformer method) (ocelot.schema.conformer.SiteidOperation method) (ocelot.schema.graph.BackboneGraph method) (ocelot.schema.graph.BasicGraph method) (ocelot.schema.graph.FragmentGraph method) (ocelot.schema.graph.MolGraph method) (ocelot.schema.graph.SidechainGraph method) (ocelot.task.bzcal.DispersionRelationLine method) (ocelot.task.bzcal.LineSegment method) (ocelot.task.calec.ElectronicCoupling method) (ocelot.task.confgen.ConfGen method) (ocelot.task.dbwrite.DBChromophore method) (ocelot.task.dbwrite.DBChromophoreConformer method) (ocelot.task.dbwrite.DBConfiguration method) (ocelot.task.dbwrite.DBCrystal method) (ocelot.task.dbwrite.DBMolConformer method) (ocelot.task.dftd3.DFTD3 method) (ocelot.task.emtensor.EmTensor method) (ocelot.task.hop.Hop method) (ocelot.task.hop.IJK method) (ocelot.task.idchg.IdChg method) (ocelot.task.nics.NICSjob method) (ocelot.task.pkid.PackingIdentifier method) (ocelot.task.readcif.ReadCif method) (ocelot.task.reorg.Reorganization method) (ocelot.task.wtuning.WtuningJob method) (ocelot.task.zindo.ZindoJob method)

A

abcabg2pbc() (in module ocelot.routines.geometry) ACParser (class in ocelot.routines.conformerparser) add_bqlines() (ocelot.task.nics.NICSjob static method) addBO2mol() (ocelot.routines.conformerparser.ACParser method) alex_method() (ocelot.routines.loop.Loopsearcher method) alpha_atune() (ocelot.task.wtuning.WtuningJob method) alpha_format() (ocelot.task.wtuning.WtuningJob method) alpha_iopstr() (ocelot.task.wtuning.WtuningJob property) alpha_shape() (in module ocelot.routines.geometry) alpha_tune() (ocelot.task.wtuning.WtuningJob method) angle_btw() (in module ocelot.routines.geometry) apply_symmop() (in module ocelot.routines.disparser_functions) applysym_to_coupling_data() (ocelot.task.hop.Hop static method) arbitrary_noraml() (in module ocelot.routines.geometry) are_collinear() (in module ocelot.routines.geometry)

as_dict() (ocelot.curator.DataSchema.DataAccess method) (ocelot.schema.configuration.Config method) (ocelot.schema.conformer.BasicConformer method) (ocelot.schema.conformer.ConformerDimer method) (ocelot.schema.conformer.FragConformer method) (ocelot.schema.conformer.MolConformer method) (ocelot.schema.conformer.RingConformer method) (ocelot.schema.graph.BasicGraph method) (ocelot.schema.graph.FragmentGraph method) (ocelot.schema.graph.SidechainGraph method) assign_siteid() (ocelot.schema.conformer.SiteidOperation method) AsymmUnit (class in ocelot.routines.disparser) atomic_numbers() (ocelot.schema.conformer.BasicConformer property) AtomicRadius() (in module ocelot.routines.pbc) AtomLabel (class in ocelot.routines.disparser) atuning_cycle() (ocelot.task.wtuning.WtuningJob method)

B

BackboneGraph (class in ocelot.schema.graph) BasicConformer (class in ocelot.schema.conformer) BasicGraph (class in ocelot.schema.graph) beta_iopstr() (ocelot.task.wtuning.WtuningJob property) block_fill() (ocelot.task.calec.ElectronicCoupling static method) BO_is_OK() (ocelot.routines.conformerparser.ACParser method)

BondConformer (class in ocelot.schema.conformer) bondmat() (ocelot.schema.conformer.BasicConformer property) bonds_in_ring() (ocelot.schema.conformer.RingConformer property) bone_overlap() (ocelot.schema.conformer.ConformerDimer method) BoneConformer (class in ocelot.schema.conformer) braket2float() (in module ocelot.routines.disparser_functions) build_supercell_full_disorder() (ocelot.routines.disparser.ConfigConstructor static method)

C

cal_emtensor() (ocelot.task.emtensor.EmTensor method) cal_energy() (ocelot.task.confgen.ConfGen static method) calculate_conformer_properties() (ocelot.schema.conformer.BoneConformer method) (ocelot.schema.conformer.FragConformer method) (ocelot.schema.conformer.MolConformer method) calculate_coupling_gauss() (ocelot.task.calec.ElectronicCoupling static method) can_rdmol() (ocelot.schema.conformer.BasicConformer property) cart2frac() (in module ocelot.routines.geometry) cart2polar() (in module ocelot.routines.geometry) cart_coords() (ocelot.schema.conformer.BasicConformer property) check_allgausslog() (in module ocelot.routines.fileop) check_gausslog() (in module ocelot.routines.fileop) check_outcar() (in module ocelot.routines.fileop) check_path() (in module ocelot.routines.fileop) checkstatus() (ocelot.schema.conformer.SiteidOperation method) chiral_stereo_check() (in module ocelot.routines.conformerparser) chrom_partition() (ocelot.schema.conformer.MolConformer static method) CifFileError classify() (ocelot.routines.disparser.DisParser method) clean_charges() (in module ocelot.routines.conformerparser) clear_cif_from_crystalmaker() (in module ocelot.curator.Contribution) cluster_by_rmsd() (ocelot.task.confgen.ConfGen static method) cmd_option_string() (ocelot.task.dftd3.DFTD3 property) collect_rawdata() (ocelot.curator.Contribution.Contribution method)

collect_with_log() (ocelot.curator.Contribution.Contribution method) compare() (ocelot.schema.conformer.BasicConformer method) composition() (ocelot.schema.conformer.BasicConformer property) conf2xyz() (ocelot.schema.rdfunc.RdFunc static method) ConfGen (class in ocelot.task.confgen) ConfGenError Config (class in ocelot.schema.configuration) ConfigConstructor (class in ocelot.routines.disparser) conformer_addh() (in module ocelot.schema.conformer) conformer_addhmol() (in module ocelot.schema.conformer) ConformerDimer (class in ocelot.schema.conformer) ConformerError Contribution (class in ocelot.curator.Contribution) conver2zindo() (in module ocelot.task.zindo) coord_reverse() (in module ocelot.routines.geometry) coord_transform() (in module ocelot.routines.geometry) copyfile() (in module ocelot.routines.fileop) create_matrix() (ocelot.task.calec.ElectronicCoupling static method) createdir() (in module ocelot.routines.fileop) curate_all() (ocelot.curator.Contribution.Contribution method) curate_cifstring() (in module ocelot.curator.Contribution) curate_one() (ocelot.curator.Contribution.Contribution method) CuratedData (class in ocelot.curator.DataSchema) CuratorError

D

data2cifdata() (ocelot.routines.disparser.DisParser static method) DataAccess (class in ocelot.curator.DataSchema) DataEntry (class in ocelot.curator.DataSchema) DataProvider (class in ocelot.curator.DataSchema) DataSchemaError DBChromophore (class in ocelot.task.dbwrite) DBChromophoreConformer (class in ocelot.task.dbwrite) DBConfiguration (class in ocelot.task.dbwrite) DBCrystal (class in ocelot.task.dbwrite) DBMolConformer (class in ocelot.task.dbwrite) DBschema (class in ocelot.task.dbwrite) DFTD3 (class in ocelot.task.dftd3) dimer_run() (ocelot.task.zindo.ZindoJob static method)

DimerCollection (class in ocelot.schema.conformer) dimerjob_from_two_molecules() (ocelot.task.zindo.ZindoJob class method) DisorderParserError DisorderUnit (class in ocelot.routines.disparser) DisParser (class in ocelot.routines.disparser) DispersionRelationLine (class in ocelot.task.bzcal) dissc_to_config() (ocelot.routines.disparser.ConfigConstructor static method) dist_pt2line() (in module ocelot.routines.geometry) distmat() (ocelot.schema.conformer.BasicConformer property) draw() (ocelot.schema.graph.BasicGraph method) draw_chemgraph() (in module ocelot.schema.graph) draw_mol() (ocelot.schema.rdfunc.RdFunc static method) draw_smiles() (ocelot.schema.rdfunc.RdFunc static method)

E

eigens (ocelot.task.emtensor.EmTensor attribute) ElectronicCoupling (class in ocelot.task.calec) EmTensor (class in ocelot.task.emtensor) ev_to_ha() (in module ocelot.routines.mathop)

expand() (ocelot.routines.loop.Loopsearcher method) extract_abs() (ocelot.task.wtuning.WtuningJob static method) extract_energy() (ocelot.task.reorg.Reorganization static method) (ocelot.task.wtuning.WtuningJob static method)

F

fd_effmass_st3() (in module ocelot.task.emtensor) fd_effmass_st5() (in module ocelot.task.emtensor) fd_reci_2ndder() (in module ocelot.routines.mathop) find_connected_psites() (in module ocelot.routines.disparser_functions) find_counterpart() (ocelot.routines.disparser.DisorderUnit static method) fingerprint() (ocelot.schema.rdfunc.RdFunc static method) fit() (ocelot.task.bzcal.LineSegment method) fit_linedata() (ocelot.task.bzcal.DispersionRelationLine method) Fitter (class in ocelot.routines.geometry) fp_similarity() (ocelot.schema.rdfunc.RdFunc static method) frac2cart() (in module ocelot.routines.geometry) frac_direction() (ocelot.task.bzcal.LineSegment property) FragConformer (class in ocelot.schema.conformer) FragmentGraph (class in ocelot.schema.graph) from_basicgraph() (ocelot.schema.graph.MolGraph class method) from_ciffile() (ocelot.routines.disparser.DisParser class method) (ocelot.task.readcif.ReadCif class method) from_cifstring() (ocelot.schema.configuration.Config class method) from_dict() (ocelot.curator.DataSchema.DataAccess class method) (ocelot.schema.configuration.Config class method) (ocelot.schema.conformer.BasicConformer class method) (ocelot.schema.conformer.BoneConformer class method) (ocelot.schema.conformer.ConformerDimer class method) (ocelot.schema.conformer.FragConformer class method) (ocelot.schema.conformer.MolConformer class method) (ocelot.schema.conformer.SidechainConformer class method) (ocelot.schema.graph.BasicGraph class method) (ocelot.schema.graph.FragmentGraph class method)

from_file() (ocelot.schema.configuration.Config class method) (ocelot.schema.conformer.BasicConformer class method) from_json() (ocelot.curator.DataSchema.DataEntry class method) from_jsonfile() (ocelot.curator.DataSchema.DataEntry class method) from_klines_files() (ocelot.task.bzcal.DispersionRelationLine class method) from_labeled_clean_pstructure() (ocelot.schema.configuration.Config class method) from_mongo() (ocelot.curator.DataSchema.DataEntry class method) from_mopinput() (ocelot.routines.mopac.MopacInput class method) from_pmgmol() (ocelot.schema.conformer.BasicConformer class method) (ocelot.schema.conformer.FragConformer class method) from_psite() (ocelot.routines.disparser.AtomLabel class method) from_pstructure() (ocelot.schema.configuration.Config class method) from_publication_doi() (ocelot.curator.DataSchema.DataProvider class method) from_rdmol() (ocelot.schema.graph.BasicGraph class method) from_siteids() (ocelot.schema.conformer.BasicConformer class method) (ocelot.schema.conformer.FragConformer class method) from_sites() (ocelot.schema.conformer.BasicConformer class method) (ocelot.schema.conformer.BoneConformer class method) (ocelot.schema.conformer.FragConformer class method) (ocelot.schema.conformer.MolConformer class method) (ocelot.schema.conformer.SidechainConformer class method) from_smiles() (ocelot.schema.graph.BasicGraph class method) (ocelot.task.confgen.ConfGen class method) from_str() (ocelot.schema.conformer.BasicConformer class method) from_string() (ocelot.schema.rdfunc.RdFunc static method) from_vasprun() (ocelot.task.emtensor.EmTensor class method) from_vasprun_file() (ocelot.task.bzcal.DispersionRelationLine class method)

G

g09_build_cfrag() (ocelot.task.calec.ElectronicCoupling static method) g09_calculate_coupling() (ocelot.task.calec.ElectronicCoupling static method) g09_calculate_fock() (ocelot.task.calec.ElectronicCoupling static method) g09_get_alpha_orbital_energies() (ocelot.task.calec.ElectronicCoupling static method) g09_get_basis_functions() (ocelot.task.calec.ElectronicCoupling static method) g09_get_homo_lumo() (ocelot.task.calec.ElectronicCoupling static method) g09_get_mo_coefficients() (ocelot.task.calec.ElectronicCoupling static method) gauss_in_gen() (in module ocelot.task.wtuning) gauss_run() (ocelot.task.wtuning.WtuningJob static method) gen_input() (ocelot.task.nics.NICSjob method) gen_instructions() (ocelot.routines.disparser.ConfigConstructor static method) genconfs() (ocelot.task.confgen.ConfGen method) genconfs_ETKDG() (ocelot.task.confgen.ConfGen static method) genconfs_prune_by_energy() (ocelot.task.confgen.ConfGen method) generate_edges() (ocelot.routines.loop.Loopsearcher method) genlinepts() (in module ocelot.routines.geometry) geo_opt() (ocelot.task.wtuning.WtuningJob method) geo_partition() (ocelot.schema.conformer.MolConformer static method) geoc() (ocelot.routines.disparser.DisorderUnit property) (ocelot.schema.conformer.BasicConformer property) GeometryError get_3ddescriptors() (ocelot.schema.rdfunc.RdFunc static method) get_aids() (ocelot.schema.rdfunc.RdFunc static method) get_atomic_charge() (ocelot.routines.conformerparser.ACParser static method) get_avg_norms() (ocelot.schema.conformer.RingConformer static method) get_BO() (ocelot.routines.conformerparser.ACParser static method) get_bond_order() (ocelot.schema.rdfunc.RdFunc static method) get_bondmat() (ocelot.schema.conformer.BasicConformer static method) get_bondmat_based_on_siteid() (ocelot.schema.conformer.BasicConformer method) get_bonds() (ocelot.routines.conformerparser.ACParser static method) get_bone_and_frags_from_nxgraph() (ocelot.schema.graph.MolGraph static method) get_bone_config() (ocelot.schema.configuration.Config method) get_chrom_and_frags_from_nxgraph() (ocelot.schema.graph.MolGraph static method) get_closest_sites() (ocelot.schema.conformer.BasicConformer method) get_conjugate_group() (ocelot.schema.rdfunc.RdFunc static method) get_conjugate_group_with_halogen() (ocelot.schema.rdfunc.RdFunc static method) get_connected_pblock() (in module ocelot.routines.disparser_functions) get_dimers_array() (ocelot.schema.configuration.Config method) get_dist_and_trans() (ocelot.routines.pbc.PBCparser static method) get_distmat() (ocelot.schema.conformer.BasicConformer static method) get_em() (ocelot.task.bzcal.LineSegment static method) get_ems() (ocelot.task.bzcal.LineSegment method) get_hh_coupling() (ocelot.task.zindo.ZindoJob static method) get_hopping_network_s1() (ocelot.task.hop.Hop method) get_hopping_network_s2() (ocelot.task.hop.Hop method) get_intger_mesh() (ocelot.task.hop.Hop static method) get_joints_and_subgraph() (ocelot.schema.graph.MolGraph static method)

get_labels_with_same_ei() (ocelot.routines.disparser.AtomLabel method) get_labels_with_tag() (ocelot.routines.disparser.AtomLabel static method) get_line_ems() (ocelot.task.bzcal.DispersionRelationLine method) get_ll_coupling() (ocelot.task.zindo.ZindoJob static method) get_nbrmap() (ocelot.schema.conformer.BasicConformer static method) get_nbrmap_based_on_siteid() (ocelot.schema.conformer.BasicConformer method) get_nearest_label() (ocelot.routines.disparser.DisParser method) get_overlap() (ocelot.task.calec.ElectronicCoupling static method) get_plane_param() (in module ocelot.routines.geometry) get_pmg_dict() (in module ocelot.routines.disparser_functions) get_points_of_interest() (ocelot.task.bzcal.LineSegment static method) get_proj_point2plane() (in module ocelot.routines.geometry) get_property_basename() (in module ocelot.curator.Contribution) get_property_header() (in module ocelot.curator.Contribution) get_property_lattice() (in module ocelot.curator.Contribution) get_property_md5() (in module ocelot.curator.Contribution) get_psite_by_atomlable() (ocelot.routines.disparser.AtomLabel static method) get_psites_from_data() (ocelot.routines.disparser.DisParser method) get_reci_mat() (in module ocelot.task.emtensor) get_rings() (ocelot.schema.conformer.FragConformer method) (ocelot.schema.graph.MolGraph method) get_site_by_coords() (ocelot.schema.conformer.BasicConformer method) get_site_byid() (ocelot.schema.conformer.SiteidOperation method) get_site_location_by_key() (ocelot.routines.disparser.DisParser static method) get_sites_byids() (ocelot.schema.conformer.SiteidOperation method) get_sub_rdmol() (ocelot.schema.rdfunc.RdFunc static method) get_symmop() (in module ocelot.routines.disparser_functions) get_UA_pairs() (ocelot.routines.conformerparser.ACParser static method) get_unique_files() (in module ocelot.curator.Contribution) get_valence_electrons() (ocelot.task.zindo.ZindoJob static method) get_valence_info() (ocelot.routines.conformerparser.ACParser method) get_vanilla_configs() (ocelot.routines.disparser.DisParser static method) get_volume() (ocelot.schema.rdfunc.RdFunc static method) get_xyz_string() (ocelot.schema.conformer.DimerCollection method) get_zzmstensor() (ocelot.task.nics.NICSjob static method) GetBestRMSConf() (ocelot.task.confgen.ConfGen static method) GetBestRMSMatrix() (ocelot.task.confgen.ConfGen static method) getid() (ocelot.task.dbwrite.DBChromophore method) (ocelot.task.dbwrite.DBChromophoreConformer method) (ocelot.task.dbwrite.DBConfiguration method) (ocelot.task.dbwrite.DBCrystal method) (ocelot.task.dbwrite.DBMolConformer method) (ocelot.task.dbwrite.DBschema method) getmolweight() (ocelot.schema.rdfunc.RdFunc static method) getUADU() (ocelot.routines.conformerparser.ACParser static method) graph_similarity() (ocelot.schema.graph.BasicGraph method) GraphError group_dimers() (ocelot.task.hop.Hop static method)

H

hash_nxgraph() (ocelot.schema.graph.BasicGraph static method) hash_via_smiles() (ocelot.schema.graph.BasicGraph static method) hashconfig() (ocelot.schema.configuration.Config method)

hashstr2int() (in module ocelot.schema.graph) Hop (class in ocelot.task.hop) hopping() (ocelot.task.hop.Hop static method)

I

IdChg (class in ocelot.task.idchg) ideal_conf_num() (ocelot.task.confgen.ConfGen static method) identify_heuristic() (ocelot.task.pkid.PackingIdentifier method) identify_hirshfield() (ocelot.task.pkid.PackingIdentifier method) IJK (class in ocelot.task.hop) index2siteid() (ocelot.schema.conformer.BasicConformer property) infodict() (ocelot.routines.disparser.AsymmUnit method) init_rdmol() (ocelot.routines.conformerparser.ACParser method) inpstring() (ocelot.task.zindo.ZindoJob static method) input_gen_gauss() (ocelot.task.calec.ElectronicCoupling method) intersection() (ocelot.schema.conformer.BasicConformer method) intkey() (in module ocelot.routines.fileop)

iop_route_params() (ocelot.task.wtuning.WtuningJob property) is_bone_close() (ocelot.schema.conformer.ConformerDimer property) is_close() (ocelot.schema.conformer.ConformerDimer property) is_hydrogen_explicit() (ocelot.task.confgen.ConfGen static method) is_identical() (ocelot.schema.conformer.ConformerDimer property) is_likely_counterpart() (ocelot.routines.disparser.DisorderUnit method) is_missing_hydrogen() (ocelot.schema.conformer.BasicConformer method) is_not_identical() (ocelot.schema.conformer.ConformerDimer property) is_subgraph() (ocelot.schema.graph.BasicGraph method) iscollinear() (ocelot.routines.geometry.Fitter static method) iscoplane_with() (ocelot.schema.conformer.RingConformer method) iscoplane_with_norm() (ocelot.schema.conformer.RingConformer method) issubset() (ocelot.schema.conformer.BasicConformer method)

K

kcart() (ocelot.task.emtensor.EmTensor property)

kmesh() (ocelot.task.emtensor.EmTensor property)

L

legit() (ocelot.task.zindo.ZindoJob property) length() (ocelot.schema.conformer.BondConformer property) (ocelot.task.bzcal.LineSegment property) lgfr (ocelot.task.nics.NICSjob attribute) linear_fit() (ocelot.routines.geometry.Fitter static method) LineSegment (class in ocelot.task.bzcal)

log_add() (ocelot.task.wtuning.WtuningJob method) loop2edges() (ocelot.routines.loop.Loopsearcher static method) Loopsearcher (class in ocelot.routines.loop) lp() (ocelot.schema.conformer.BoneConformer property) lq() (ocelot.schema.conformer.BoneConformer property) lsexternsion() (in module ocelot.routines.fileop)

M

make_symmetric() (ocelot.task.calec.ElectronicCoupling static method) max_wi() (ocelot.task.bzcal.LineSegment property) min_wi() (ocelot.task.bzcal.LineSegment property) minbonedist() (ocelot.schema.conformer.ConformerDimer property) mindist() (ocelot.schema.conformer.ConformerDimer property) module ocelot ocelot.curator ocelot.curator.Contribution ocelot.curator.DataSchema ocelot.routines ocelot.routines.conformerparser ocelot.routines.disparser ocelot.routines.disparser_functions ocelot.routines.fileop ocelot.routines.geometry ocelot.routines.loop ocelot.routines.mathop ocelot.routines.mopac ocelot.routines.pbc ocelot.schema ocelot.schema.configuration ocelot.schema.conformer ocelot.schema.graph ocelot.schema.rdfunc ocelot.task ocelot.task.bzcal ocelot.task.calec ocelot.task.confgen ocelot.task.dbwrite ocelot.task.dftd3 ocelot.task.emtensor ocelot.task.hop ocelot.task.idchg ocelot.task.nics ocelot.task.pkid ocelot.task.readcif ocelot.task.reorg ocelot.task.wtuning ocelot.task.zindo tests

mol2xyz_by_confid() (ocelot.schema.rdfunc.RdFunc static method) mol_as_json() (ocelot.schema.rdfunc.RdFunc static method) mol_from_json() (ocelot.schema.rdfunc.RdFunc static method) mol_overlap() (ocelot.schema.conformer.ConformerDimer method) MolConformer (class in ocelot.schema.conformer) molconformers (ocelot.schema.configuration.Config attribute) molconformers_all_legit() (ocelot.schema.configuration.Config method) MolGraph (class in ocelot.schema.graph) molgraph_set() (ocelot.schema.configuration.Config method) mongo_insert() (ocelot.curator.DataSchema.CuratedData method) (ocelot.curator.DataSchema.DataEntry method) mop2siteobjs() (in module ocelot.routines.mopac) MopacInput (class in ocelot.routines.mopac) MopacOutput (class in ocelot.routines.mopac) movefile() (in module ocelot.routines.fileop)

N

n_nonsignlebond_electrons() (ocelot.schema.rdfunc.RdFunc static method) nbrmap() (ocelot.schema.conformer.BasicConformer property) nics_line_scan_path() (ocelot.task.nics.NICSjob method) nics_sigma_structure() (ocelot.task.nics.NICSjob method)

NicsError NICSjob (class in ocelot.task.nics) nonblank_lines() (in module ocelot.routines.fileop) norm() (in module ocelot.routines.geometry) normal_along() (ocelot.schema.conformer.RingConformer method)

O

ocelot module ocelot.curator module ocelot.curator.Contribution module ocelot.curator.DataSchema module ocelot.routines module ocelot.routines.conformerparser module ocelot.routines.disparser module ocelot.routines.disparser_functions module ocelot.routines.fileop module ocelot.routines.geometry module ocelot.routines.loop module ocelot.routines.mathop module ocelot.routines.mopac module ocelot.routines.pbc module ocelot.schema module ocelot.schema.configuration module ocelot.schema.conformer module ocelot.schema.graph module ocelot.schema.rdfunc module

ocelot.task module ocelot.task.bzcal module ocelot.task.calec module ocelot.task.confgen module ocelot.task.dbwrite module ocelot.task.dftd3 module ocelot.task.emtensor module ocelot.task.hop module ocelot.task.idchg module ocelot.task.nics module ocelot.task.pkid module ocelot.task.readcif module ocelot.task.reorg module ocelot.task.wtuning module ocelot.task.zindo module omega_extract() (ocelot.task.wtuning.WtuningJob static method) omega_FindC() (ocelot.task.wtuning.WtuningJob method) omega_format() (ocelot.task.wtuning.WtuningJob method) omega_gauss_do() (ocelot.task.wtuning.WtuningJob method) omega_iopstr() (ocelot.task.wtuning.WtuningJob property) omega_tune() (ocelot.task.wtuning.WtuningJob method) omega_wtune() (ocelot.task.wtuning.WtuningJob method) orient() (ocelot.schema.conformer.BasicConformer method)

P

PackingIdentifier (class in ocelot.task.pkid) parse() (ocelot.routines.conformerparser.ACParser method) parse2linsegs() (ocelot.task.bzcal.DispersionRelationLine static method) parse_bonds() (ocelot.routines.conformerparser.ACParser method) parse_charges() (ocelot.routines.mopac.MopacOutput method) parse_out() (ocelot.task.idchg.IdChg static method) parse_results() (ocelot.task.dftd3.DFTD3 static method) parse_rlx_or_sp() (ocelot.routines.mopac.MopacOutput method) parse_thermo() (ocelot.routines.mopac.MopacOutput method) parse_tmo() (ocelot.task.zindo.ZindoJob method) partition() (ocelot.schema.graph.MolGraph method) partition_to_bone_frags() (ocelot.schema.graph.MolGraph method)

PBCparser (class in ocelot.routines.pbc) plane_fit() (ocelot.routines.geometry.Fitter static method) plot_path() (ocelot.task.nics.NICSjob method) plotlinebs() (ocelot.task.bzcal.DispersionRelationLine method) plt_bone_overlap() (ocelot.schema.conformer.ConformerDimer method) plt_pizz_xypath() (ocelot.task.nics.NICSjob static method) pltend() (ocelot.task.bzcal.LineSegment property) pmgmol() (ocelot.schema.conformer.BasicConformer property) pmgmol_to_rdmol() (in module ocelot.routines.conformerparser) prepare_data() (ocelot.routines.disparser.DisParser method) props_for_hash() (ocelot.schema.graph.BasicGraph property) prune_by_rmsd() (ocelot.task.confgen.ConfGen static method)

R

ra2pi2rb() (in module ocelot.task.emtensor) ra2rb() (in module ocelot.task.emtensor) ra_to_rb() (in module ocelot.routines.mathop) RawData (class in ocelot.curator.DataSchema) rb2ra() (in module ocelot.task.emtensor) rb2ra2pi() (in module ocelot.task.emtensor) RdFunc (class in ocelot.schema.rdfunc) read() (ocelot.task.readcif.ReadCif method) read_and_trim() (in module ocelot.curator.Contribution) read_kpoints_line() (ocelot.task.bzcal.DispersionRelationLine static method) read_obj() (in module ocelot.routines.fileop) read_vasprun() (ocelot.task.bzcal.DispersionRelationLine static method) ReadCif (class in ocelot.task.readcif) readfile() (in module ocelot.curator.Contribution)

removefile() (in module ocelot.routines.fileop) reorg_energy() (ocelot.task.reorg.Reorganization method) Reorganization (class in ocelot.task.reorg) retrieve_name() (in module ocelot.routines.fileop) RingConformer (class in ocelot.schema.conformer) rings (ocelot.schema.conformer.MolConformer attribute) rotate_along() (ocelot.schema.conformer.BasicConformer method) rotate_along_axis() (in module ocelot.routines.geometry) rotate_along_de_matrix() (ocelot.schema.conformer.BasicConformer static method) rotate_along_with_matrix() (ocelot.schema.conformer.BasicConformer method) rotation_matrix() (in module ocelot.routines.geometry) run() (ocelot.task.dftd3.DFTD3 method) (ocelot.task.hop.Hop method) (ocelot.task.idchg.IdChg method)

S

screen_dimers() (ocelot.task.hop.Hop static method) sdict() (ocelot.schema.conformer.SiteidOperation property) set_atomic_charges() (ocelot.routines.conformerparser.ACParser method) set_atomic_radicals() (ocelot.routines.conformerparser.ACParser method) sha1hash() (in module ocelot.task.dbwrite) show_confs_diversity() (ocelot.task.confgen.ConfGen static method) SidechainConformer (class in ocelot.schema.conformer) SidechainGraph (class in ocelot.schema.graph) siteid2index() (ocelot.schema.conformer.BasicConformer property) SiteidError SiteidOperation (class in ocelot.schema.conformer) siteids() (ocelot.schema.conformer.SiteidOperation property)

sites() (ocelot.schema.conformer.ConformerDimer property) sites2mopinput() (ocelot.routines.mopac.MopacInput static method) sort_by_siteid() (ocelot.schema.conformer.BasicConformer method) sssr_alex() (ocelot.routines.loop.Loopsearcher method) status() (ocelot.schema.conformer.SiteidOperation property) string_acronym() (in module ocelot.curator.DataSchema) stringkey() (in module ocelot.routines.fileop) strip_occu_in_eigens() (ocelot.task.bzcal.DispersionRelationLine static method) substructurematch() (ocelot.schema.rdfunc.RdFunc static method) supercell_proj() (ocelot.task.hop.Hop static method) symbols() (ocelot.schema.conformer.BasicConformer property) (ocelot.schema.graph.BasicGraph property)

T

tests module time_limit() (in module ocelot.curator.Contribution) TimeoutException to() (ocelot.schema.conformer.BasicConformer method) to_addhmol() (ocelot.schema.conformer.MolConformer method) to_configs() (ocelot.routines.disparser.DisParser method) to_dict() (ocelot.task.wtuning.WtuningJob method) to_file() (ocelot.task.wtuning.WtuningJob method) to_fracrgb() (in module ocelot.schema.graph)

to_graph() (ocelot.schema.conformer.BasicConformer method) to_jsonfile() (ocelot.curator.DataSchema.DataEntry method) to_rdmol() (ocelot.schema.conformer.BasicConformer method) (ocelot.schema.graph.BasicGraph method) to_smarts() (ocelot.schema.rdfunc.RdFunc static method) to_xyz() (ocelot.schema.conformer.ConformerDimer method) (ocelot.schema.conformer.DimerCollection method) to_xyzstring() (ocelot.schema.conformer.ConformerDimer method) triangle_fill() (ocelot.task.calec.ElectronicCoupling static method) trim_diffraction() (in module ocelot.curator.Contribution)

U

unfilled() (ocelot.task.dbwrite.DBschema property) unify() (in module ocelot.routines.geometry) unique_ijk() (ocelot.task.hop.Hop static method)

unsaturation() (ocelot.schema.rdfunc.RdFunc static method) unwrap() (ocelot.routines.pbc.PBCparser static method) unwrap_and_squeeze() (ocelot.routines.pbc.PBCparser static method)

V

valence_electron() (in module ocelot.routines.conformerparser) (in module ocelot.task.zindo)

valences_not_too_large() (ocelot.routines.conformerparser.ACParser static method) vis_partition() (ocelot.schema.rdfunc.RdFunc static method) volume_slow() (ocelot.schema.conformer.BasicConformer property)

W

where_is_disorder() (ocelot.task.readcif.ReadCif static method) write_dimer() (ocelot.task.zindo.ZindoJob method) write_inp() (ocelot.task.idchg.IdChg method) write_kmesh() (ocelot.task.emtensor.EmTensor method)

write_mopinput() (ocelot.routines.mopac.MopacInput method) write_obj() (in module ocelot.routines.fileop) write_single() (ocelot.task.zindo.ZindoJob method) wtuning_cycle() (ocelot.task.wtuning.WtuningJob method) WtuningJob (class in ocelot.task.wtuning)

Z

zindo_cal() (ocelot.task.hop.Hop method)

ZindoJob (class in ocelot.task.zindo)