OCDocker package¶
Subpackages¶
- OCDocker.DB package
- OCDocker.Docking package
- Subpackages
- Submodules
- OCDocker.Docking.PLANTS module
PLANTSbox_to_plants()generate_digest()generate_plants_files_database()get_binding_site()get_docked_poses()get_pose_index_from_file_path()read_log()run_plants()run_prepare_ligand()run_prepare_receptor()run_rescore()write_config_file()write_pose_list()write_rescoring_config_file()run_docking()read_rescore_logs()
- OCDocker.Docking.Smina module
- OCDocker.Docking.Vina module
- OCDocker.Docking.Gnina module
- OCDocker.Docking.BaseVinaLike module
- OCDocker.Docking.PLANTS module
- Module contents
- OCDocker.CLI package
- OCDocker.OCScore package
- OCDocker.Processing package
- OCDocker.Rescoring package
- OCDocker.Toolbox package
- Submodules
- OCDocker.Toolbox.Basetools module
- OCDocker.Toolbox.Constants module
- OCDocker.Toolbox.Conversion module
- OCDocker.Toolbox.Downloading module
- OCDocker.Toolbox.FilesFolders module
- OCDocker.Toolbox.IO module
- OCDocker.Toolbox.Logging module
- OCDocker.Toolbox.MoleculeProcessing module
- OCDocker.Toolbox.Preparation module
- OCDocker.Toolbox.Printing module
- OCDocker.Toolbox.Reproducibility module
- OCDocker.Toolbox.Running module
- OCDocker.Toolbox.Security module
- OCDocker.Toolbox.Validation module
- Module contents
- Submodules
Submodules¶
- OCDocker.Config module
VinaConfigSminaConfigSminaConfig.executableSminaConfig.energy_rangeSminaConfig.exhaustivenessSminaConfig.num_modesSminaConfig.scoringSminaConfig.scoring_functionsSminaConfig.custom_scoringSminaConfig.custom_atomsSminaConfig.local_onlySminaConfig.minimizeSminaConfig.randomize_onlySminaConfig.minimize_itersSminaConfig.accurate_lineSminaConfig.minimize_early_termSminaConfig.approximationSminaConfig.factorSminaConfig.force_capSminaConfig.user_gridSminaConfig.user_grid_lambda
GninaConfigGninaConfig.executableGninaConfig.flexGninaConfig.flexresGninaConfig.flexdist_ligandGninaConfig.flexdistGninaConfig.flex_limitGninaConfig.flex_maxGninaConfig.autobox_ligandGninaConfig.autobox_addGninaConfig.autobox_extendGninaConfig.no_ligGninaConfig.covalent_rec_atomGninaConfig.covalent_lig_atom_patternGninaConfig.covalent_lig_atom_positionGninaConfig.covalent_fix_lig_atom_positionGninaConfig.covalent_bond_orderGninaConfig.covalent_optimize_ligGninaConfig.exhaustivenessGninaConfig.num_modesGninaConfig.scoringGninaConfig.scoring_functionsGninaConfig.custom_scoringGninaConfig.custom_atomsGninaConfig.score_onlyGninaConfig.local_onlyGninaConfig.minimizeGninaConfig.randomize_onlyGninaConfig.num_mc_stepsGninaConfig.max_mc_stepsGninaConfig.num_mc_savedGninaConfig.temperatureGninaConfig.minimize_itersGninaConfig.accurate_lineGninaConfig.simple_ascentGninaConfig.minimize_early_termGninaConfig.minimize_single_fullGninaConfig.approximationGninaConfig.factorGninaConfig.force_capGninaConfig.user_gridGninaConfig.user_grid_lambdaGninaConfig.print_termsGninaConfig.print_atom_typesGninaConfig.cnn_scoringGninaConfig.cnnGninaConfig.cnn_modelsGninaConfig.cnn_modelGninaConfig.cnn_rotationGninaConfig.cnn_mix_emp_forceGninaConfig.cnn_mix_emp_energyGninaConfig.cnn_empirical_weightGninaConfig.cnn_center_xGninaConfig.cnn_center_yGninaConfig.cnn_center_zGninaConfig.cnn_verboseGninaConfig.out_flexGninaConfig.atom_termsGninaConfig.atom_term_dataGninaConfig.pose_sort_orderGninaConfig.full_flex_outputGninaConfig.cpuGninaConfig.seedGninaConfig.min_rmsd_filterGninaConfig.quietGninaConfig.addHGninaConfig.stripHGninaConfig.deviceGninaConfig.no_gpu
PLANTSConfigDock6ConfigLeDockConfigODDTConfigDatabaseConfigToolsConfigPathsConfigOCDockerConfigOCDockerConfig.vinaOCDockerConfig.sminaOCDockerConfig.gninaOCDockerConfig.plantsOCDockerConfig.dock6OCDockerConfig.ledockOCDockerConfig.oddtOCDockerConfig.databaseOCDockerConfig.toolsOCDockerConfig.pathsOCDockerConfig.output_levelOCDockerConfig.multiprocessOCDockerConfig.overwriteOCDockerConfig.tmp_dirOCDockerConfig.ocdocker_pathOCDockerConfig.dudez_archiveOCDockerConfig.pdbbind_archiveOCDockerConfig.parsed_archiveOCDockerConfig.logdirOCDockerConfig.oddt_models_dirOCDockerConfig.available_coresOCDockerConfig.from_config_file()OCDockerConfig.from_dict()
get_config()reset_config()set_config()
- OCDocker.Error module
- OCDocker.Initialise module
- OCDocker.Ligand module
LigandLigand.RadiusOfGyrationLigand.FpDensityMorgan1Ligand.FpDensityMorgan2Ligand.FpDensityMorgan3Ligand.__init__()Ligand.pathLigand.moleculeLigand.box_pathLigand.from_json_descriptorsLigand.sanitizeLigand.normalize_smiles_with_openbabelLigand.nameLigand.__repr__()Ligand.create_box()Ligand.get_centroid()Ligand.get_descriptors()Ligand.is_same_molecule()Ligand.is_same_molecule_SMILES()Ligand.is_valid()Ligand.print_attributes()Ligand.to_dict()Ligand.to_json()Ligand.to_smiles()Ligand.descriptors_namesLigand.single_descriptorsLigand.allDescriptorsLigand.findAUTOCORR2D_1()Ligand.findAUTOCORR2D_10()Ligand.findAUTOCORR2D_100()Ligand.findAUTOCORR2D_101()Ligand.findAUTOCORR2D_102()Ligand.findAUTOCORR2D_103()Ligand.findAUTOCORR2D_104()Ligand.findAUTOCORR2D_105()Ligand.findAUTOCORR2D_106()Ligand.findAUTOCORR2D_107()Ligand.findAUTOCORR2D_108()Ligand.findAUTOCORR2D_109()Ligand.findAUTOCORR2D_11()Ligand.findAUTOCORR2D_110()Ligand.findAUTOCORR2D_111()Ligand.findAUTOCORR2D_112()Ligand.findAUTOCORR2D_113()Ligand.findAUTOCORR2D_114()Ligand.findAUTOCORR2D_115()Ligand.findAUTOCORR2D_116()Ligand.findAUTOCORR2D_117()Ligand.findAUTOCORR2D_118()Ligand.findAUTOCORR2D_119()Ligand.findAUTOCORR2D_12()Ligand.findAUTOCORR2D_120()Ligand.findAUTOCORR2D_121()Ligand.findAUTOCORR2D_122()Ligand.findAUTOCORR2D_123()Ligand.findAUTOCORR2D_124()Ligand.findAUTOCORR2D_125()Ligand.findAUTOCORR2D_126()Ligand.findAUTOCORR2D_127()Ligand.findAUTOCORR2D_128()Ligand.findAUTOCORR2D_129()Ligand.findAUTOCORR2D_13()Ligand.findAUTOCORR2D_130()Ligand.findAUTOCORR2D_131()Ligand.findAUTOCORR2D_132()Ligand.findAUTOCORR2D_133()Ligand.findAUTOCORR2D_134()Ligand.findAUTOCORR2D_135()Ligand.findAUTOCORR2D_136()Ligand.findAUTOCORR2D_137()Ligand.findAUTOCORR2D_138()Ligand.findAUTOCORR2D_139()Ligand.findAUTOCORR2D_14()Ligand.findAUTOCORR2D_140()Ligand.findAUTOCORR2D_141()Ligand.findAUTOCORR2D_142()Ligand.findAUTOCORR2D_143()Ligand.findAUTOCORR2D_144()Ligand.findAUTOCORR2D_145()Ligand.findAUTOCORR2D_146()Ligand.findAUTOCORR2D_147()Ligand.findAUTOCORR2D_148()Ligand.findAUTOCORR2D_149()Ligand.findAUTOCORR2D_15()Ligand.findAUTOCORR2D_150()Ligand.findAUTOCORR2D_151()Ligand.findAUTOCORR2D_152()Ligand.findAUTOCORR2D_153()Ligand.findAUTOCORR2D_154()Ligand.findAUTOCORR2D_155()Ligand.findAUTOCORR2D_156()Ligand.findAUTOCORR2D_157()Ligand.findAUTOCORR2D_158()Ligand.findAUTOCORR2D_159()Ligand.findAUTOCORR2D_16()Ligand.findAUTOCORR2D_160()Ligand.findAUTOCORR2D_161()Ligand.findAUTOCORR2D_162()Ligand.findAUTOCORR2D_163()Ligand.findAUTOCORR2D_164()Ligand.findAUTOCORR2D_165()Ligand.findAUTOCORR2D_166()Ligand.findAUTOCORR2D_167()Ligand.findAUTOCORR2D_168()Ligand.findAUTOCORR2D_169()Ligand.findAUTOCORR2D_17()Ligand.findAUTOCORR2D_170()Ligand.findAUTOCORR2D_171()Ligand.findAUTOCORR2D_172()Ligand.findAUTOCORR2D_173()Ligand.findAUTOCORR2D_174()Ligand.findAUTOCORR2D_175()Ligand.findAUTOCORR2D_176()Ligand.findAUTOCORR2D_177()Ligand.findAUTOCORR2D_178()Ligand.findAUTOCORR2D_179()Ligand.findAUTOCORR2D_18()Ligand.findAUTOCORR2D_180()Ligand.findAUTOCORR2D_181()Ligand.findAUTOCORR2D_182()Ligand.findAUTOCORR2D_183()Ligand.findAUTOCORR2D_184()Ligand.findAUTOCORR2D_185()Ligand.findAUTOCORR2D_186()Ligand.findAUTOCORR2D_187()Ligand.findAUTOCORR2D_188()Ligand.findAUTOCORR2D_189()Ligand.findAUTOCORR2D_19()Ligand.findAUTOCORR2D_190()Ligand.findAUTOCORR2D_191()Ligand.findAUTOCORR2D_192()Ligand.findAUTOCORR2D_2()Ligand.findAUTOCORR2D_20()Ligand.findAUTOCORR2D_21()Ligand.findAUTOCORR2D_22()Ligand.findAUTOCORR2D_23()Ligand.findAUTOCORR2D_24()Ligand.findAUTOCORR2D_25()Ligand.findAUTOCORR2D_26()Ligand.findAUTOCORR2D_27()Ligand.findAUTOCORR2D_28()Ligand.findAUTOCORR2D_29()Ligand.findAUTOCORR2D_3()Ligand.findAUTOCORR2D_30()Ligand.findAUTOCORR2D_31()Ligand.findAUTOCORR2D_32()Ligand.findAUTOCORR2D_33()Ligand.findAUTOCORR2D_34()Ligand.findAUTOCORR2D_35()Ligand.findAUTOCORR2D_36()Ligand.findAUTOCORR2D_37()Ligand.findAUTOCORR2D_38()Ligand.findAUTOCORR2D_39()Ligand.findAUTOCORR2D_4()Ligand.findAUTOCORR2D_40()Ligand.findAUTOCORR2D_41()Ligand.findAUTOCORR2D_42()Ligand.findAUTOCORR2D_43()Ligand.findAUTOCORR2D_44()Ligand.findAUTOCORR2D_45()Ligand.findAUTOCORR2D_46()Ligand.findAUTOCORR2D_47()Ligand.findAUTOCORR2D_48()Ligand.findAUTOCORR2D_49()Ligand.findAUTOCORR2D_5()Ligand.findAUTOCORR2D_50()Ligand.findAUTOCORR2D_51()Ligand.findAUTOCORR2D_52()Ligand.findAUTOCORR2D_53()Ligand.findAUTOCORR2D_54()Ligand.findAUTOCORR2D_55()Ligand.findAUTOCORR2D_56()Ligand.findAUTOCORR2D_57()Ligand.findAUTOCORR2D_58()Ligand.findAUTOCORR2D_59()Ligand.findAUTOCORR2D_6()Ligand.findAUTOCORR2D_60()Ligand.findAUTOCORR2D_61()Ligand.findAUTOCORR2D_62()Ligand.findAUTOCORR2D_63()Ligand.findAUTOCORR2D_64()Ligand.findAUTOCORR2D_65()Ligand.findAUTOCORR2D_66()Ligand.findAUTOCORR2D_67()Ligand.findAUTOCORR2D_68()Ligand.findAUTOCORR2D_69()Ligand.findAUTOCORR2D_7()Ligand.findAUTOCORR2D_70()Ligand.findAUTOCORR2D_71()Ligand.findAUTOCORR2D_72()Ligand.findAUTOCORR2D_73()Ligand.findAUTOCORR2D_74()Ligand.findAUTOCORR2D_75()Ligand.findAUTOCORR2D_76()Ligand.findAUTOCORR2D_77()Ligand.findAUTOCORR2D_78()Ligand.findAUTOCORR2D_79()Ligand.findAUTOCORR2D_8()Ligand.findAUTOCORR2D_80()Ligand.findAUTOCORR2D_81()Ligand.findAUTOCORR2D_82()Ligand.findAUTOCORR2D_83()Ligand.findAUTOCORR2D_84()Ligand.findAUTOCORR2D_85()Ligand.findAUTOCORR2D_86()Ligand.findAUTOCORR2D_87()Ligand.findAUTOCORR2D_88()Ligand.findAUTOCORR2D_89()Ligand.findAUTOCORR2D_9()Ligand.findAUTOCORR2D_90()Ligand.findAUTOCORR2D_91()Ligand.findAUTOCORR2D_92()Ligand.findAUTOCORR2D_93()Ligand.findAUTOCORR2D_94()Ligand.findAUTOCORR2D_95()Ligand.findAUTOCORR2D_96()Ligand.findAUTOCORR2D_97()Ligand.findAUTOCORR2D_98()Ligand.findAUTOCORR2D_99()Ligand.findAsphericity()Ligand.findBCUT2D_CHGHI()Ligand.findBCUT2D_CHGLO()Ligand.findBCUT2D_LOGPHI()Ligand.findBCUT2D_LOGPLOW()Ligand.findBCUT2D_MRHI()Ligand.findBCUT2D_MRLOW()Ligand.findBCUT2D_MWHI()Ligand.findBCUT2D_MWLOW()Ligand.findBalabanJ()Ligand.findBertzCT()Ligand.findChi0()Ligand.findChi0n()Ligand.findChi0v()Ligand.findChi1()Ligand.findChi1n()Ligand.findChi1v()Ligand.findChi2n()Ligand.findChi2v()Ligand.findChi3n()Ligand.findChi3v()Ligand.findChi4n()Ligand.findChi4v()Ligand.findEState_VSA1()Ligand.findEState_VSA10()Ligand.findEState_VSA11()Ligand.findEState_VSA2()Ligand.findEState_VSA3()Ligand.findEState_VSA4()Ligand.findEState_VSA5()Ligand.findEState_VSA6()Ligand.findEState_VSA7()Ligand.findEState_VSA8()Ligand.findEState_VSA9()Ligand.findEccentricity()Ligand.findExactMolWt()Ligand.findFpDensityMorgan1()Ligand.findFpDensityMorgan2()Ligand.findFpDensityMorgan3()Ligand.findFractionCSP3()Ligand.findHallKierAlpha()Ligand.findHeavyAtomCount()Ligand.findHeavyAtomMolWt()Ligand.findInertialShapeFactor()Ligand.findKappa1()Ligand.findKappa2()Ligand.findKappa3()Ligand.findLabuteASA()Ligand.findMaxAbsEStateIndex()Ligand.findMaxAbsPartialCharge()Ligand.findMaxEStateIndex()Ligand.findMaxPartialCharge()Ligand.findMinAbsEStateIndex()Ligand.findMinAbsPartialCharge()Ligand.findMinEStateIndex()Ligand.findMinPartialCharge()Ligand.findMolLogP()Ligand.findMolMR()Ligand.findMolWt()Ligand.findNHOHCount()Ligand.findNOCount()Ligand.findNPR1()Ligand.findNPR2()Ligand.findNumAliphaticCarbocycles()Ligand.findNumAliphaticHeterocycles()Ligand.findNumAliphaticRings()Ligand.findNumAromaticCarbocycles()Ligand.findNumAromaticHeterocycles()Ligand.findNumAromaticRings()Ligand.findNumHAcceptors()Ligand.findNumHDonors()Ligand.findNumHeteroatoms()Ligand.findNumRadicalElectrons()Ligand.findNumRotatableBonds()Ligand.findNumSaturatedCarbocycles()Ligand.findNumSaturatedHeterocycles()Ligand.findNumSaturatedRings()Ligand.findNumValenceElectrons()Ligand.findPEOE_VSA1()Ligand.findPEOE_VSA10()Ligand.findPEOE_VSA11()Ligand.findPEOE_VSA12()Ligand.findPEOE_VSA13()Ligand.findPEOE_VSA14()Ligand.findPEOE_VSA2()Ligand.findPEOE_VSA3()Ligand.findPEOE_VSA4()Ligand.findPEOE_VSA5()Ligand.findPEOE_VSA6()Ligand.findPEOE_VSA7()Ligand.findPEOE_VSA8()Ligand.findPEOE_VSA9()Ligand.findPMI1()Ligand.findPMI2()Ligand.findPMI3()Ligand.findRadiusOfGyration()Ligand.findRingCount()Ligand.findSMR_VSA1()Ligand.findSMR_VSA10()Ligand.findSMR_VSA2()Ligand.findSMR_VSA3()Ligand.findSMR_VSA4()Ligand.findSMR_VSA5()Ligand.findSMR_VSA6()Ligand.findSMR_VSA7()Ligand.findSMR_VSA8()Ligand.findSMR_VSA9()Ligand.findSlogP_VSA1()Ligand.findSlogP_VSA10()Ligand.findSlogP_VSA11()Ligand.findSlogP_VSA12()Ligand.findSlogP_VSA2()Ligand.findSlogP_VSA3()Ligand.findSlogP_VSA4()Ligand.findSlogP_VSA5()Ligand.findSlogP_VSA6()Ligand.findSlogP_VSA7()Ligand.findSlogP_VSA8()Ligand.findSlogP_VSA9()Ligand.findSpherocityIndex()Ligand.findTPSA()Ligand.findVSA_EState1()Ligand.findVSA_EState10()Ligand.findVSA_EState2()Ligand.findVSA_EState3()Ligand.findVSA_EState4()Ligand.findVSA_EState5()Ligand.findVSA_EState6()Ligand.findVSA_EState7()Ligand.findVSA_EState8()Ligand.findVSA_EState9()Ligand.findfr_Al_COO()Ligand.findfr_Al_OH()Ligand.findfr_Al_OH_noTert()Ligand.findfr_ArN()Ligand.findfr_Ar_COO()Ligand.findfr_Ar_N()Ligand.findfr_Ar_NH()Ligand.findfr_Ar_OH()Ligand.findfr_COO()Ligand.findfr_COO2()Ligand.findfr_C_O()Ligand.findfr_C_O_noCOO()Ligand.findfr_C_S()Ligand.findfr_HOCCN()Ligand.findfr_Imine()Ligand.findfr_NH0()Ligand.findfr_NH1()Ligand.findfr_NH2()Ligand.findfr_N_O()Ligand.findfr_Ndealkylation1()Ligand.findfr_Ndealkylation2()Ligand.findfr_Nhpyrrole()Ligand.findfr_SH()Ligand.findfr_aldehyde()Ligand.findfr_alkyl_carbamate()Ligand.findfr_alkyl_halide()Ligand.findfr_allylic_oxid()Ligand.findfr_amide()Ligand.findfr_amidine()Ligand.findfr_aniline()Ligand.findfr_aryl_methyl()Ligand.findfr_azide()Ligand.findfr_azo()Ligand.findfr_barbitur()Ligand.findfr_benzene()Ligand.findfr_benzodiazepine()Ligand.findfr_bicyclic()Ligand.findfr_diazo()Ligand.findfr_dihydropyridine()Ligand.findfr_epoxide()Ligand.findfr_ester()Ligand.findfr_ether()Ligand.findfr_furan()Ligand.findfr_guanido()Ligand.findfr_halogen()Ligand.findfr_hdrzine()Ligand.findfr_hdrzone()Ligand.findfr_imidazole()Ligand.findfr_imide()Ligand.findfr_isocyan()Ligand.findfr_isothiocyan()Ligand.findfr_ketone()Ligand.findfr_ketone_Topliss()Ligand.findfr_lactam()Ligand.findfr_lactone()Ligand.findfr_methoxy()Ligand.findfr_morpholine()Ligand.findfr_nitrile()Ligand.findfr_nitro()Ligand.findfr_nitro_arom()Ligand.findfr_nitro_arom_nonortho()Ligand.findfr_nitroso()Ligand.findfr_oxazole()Ligand.findfr_oxime()Ligand.findfr_para_hydroxylation()Ligand.findfr_phenol()Ligand.findfr_phenol_noOrthoHbond()Ligand.findfr_phos_acid()Ligand.findfr_phos_ester()Ligand.findfr_piperdine()Ligand.findfr_piperzine()Ligand.findfr_priamide()Ligand.findfr_prisulfonamd()Ligand.findfr_pyridine()Ligand.findfr_quatN()Ligand.findfr_sulfide()Ligand.findfr_sulfonamd()Ligand.findfr_sulfone()Ligand.findfr_term_acetylene()Ligand.findfr_tetrazole()Ligand.findfr_thiazole()Ligand.findfr_thiocyan()Ligand.findfr_thiophene()Ligand.findfr_unbrch_alkane()Ligand.findfr_urea()Ligand.findqed()
findFpDensityMorgan1()findFpDensityMorgan2()findFpDensityMorgan3()findAUTOCORR2D_1()findAUTOCORR2D_10()findAUTOCORR2D_100()findAUTOCORR2D_101()findAUTOCORR2D_102()findAUTOCORR2D_103()findAUTOCORR2D_104()findAUTOCORR2D_105()findAUTOCORR2D_106()findAUTOCORR2D_107()findAUTOCORR2D_108()findAUTOCORR2D_109()findAUTOCORR2D_11()findAUTOCORR2D_110()findAUTOCORR2D_111()findAUTOCORR2D_112()findAUTOCORR2D_113()findAUTOCORR2D_114()findAUTOCORR2D_115()findAUTOCORR2D_116()findAUTOCORR2D_117()findAUTOCORR2D_118()findAUTOCORR2D_119()findAUTOCORR2D_12()findAUTOCORR2D_120()findAUTOCORR2D_121()findAUTOCORR2D_122()findAUTOCORR2D_123()findAUTOCORR2D_124()findAUTOCORR2D_125()findAUTOCORR2D_126()findAUTOCORR2D_127()findAUTOCORR2D_128()findAUTOCORR2D_129()findAUTOCORR2D_13()findAUTOCORR2D_130()findAUTOCORR2D_131()findAUTOCORR2D_132()findAUTOCORR2D_133()findAUTOCORR2D_134()findAUTOCORR2D_135()findAUTOCORR2D_136()findAUTOCORR2D_137()findAUTOCORR2D_138()findAUTOCORR2D_139()findAUTOCORR2D_14()findAUTOCORR2D_140()findAUTOCORR2D_141()findAUTOCORR2D_142()findAUTOCORR2D_143()findAUTOCORR2D_144()findAUTOCORR2D_145()findAUTOCORR2D_146()findAUTOCORR2D_147()findAUTOCORR2D_148()findAUTOCORR2D_149()findAUTOCORR2D_15()findAUTOCORR2D_150()findAUTOCORR2D_151()findAUTOCORR2D_152()findAUTOCORR2D_153()findAUTOCORR2D_154()findAUTOCORR2D_155()findAUTOCORR2D_156()findAUTOCORR2D_157()findAUTOCORR2D_158()findAUTOCORR2D_159()findAUTOCORR2D_16()findAUTOCORR2D_160()findAUTOCORR2D_161()findAUTOCORR2D_162()findAUTOCORR2D_163()findAUTOCORR2D_164()findAUTOCORR2D_165()findAUTOCORR2D_166()findAUTOCORR2D_167()findAUTOCORR2D_168()findAUTOCORR2D_169()findAUTOCORR2D_17()findAUTOCORR2D_170()findAUTOCORR2D_171()findAUTOCORR2D_172()findAUTOCORR2D_173()findAUTOCORR2D_174()findAUTOCORR2D_175()findAUTOCORR2D_176()findAUTOCORR2D_177()findAUTOCORR2D_178()findAUTOCORR2D_179()findAUTOCORR2D_18()findAUTOCORR2D_180()findAUTOCORR2D_181()findAUTOCORR2D_182()findAUTOCORR2D_183()findAUTOCORR2D_184()findAUTOCORR2D_185()findAUTOCORR2D_186()findAUTOCORR2D_187()findAUTOCORR2D_188()findAUTOCORR2D_189()findAUTOCORR2D_19()findAUTOCORR2D_190()findAUTOCORR2D_191()findAUTOCORR2D_192()findAUTOCORR2D_2()findAUTOCORR2D_20()findAUTOCORR2D_21()findAUTOCORR2D_22()findAUTOCORR2D_23()findAUTOCORR2D_24()findAUTOCORR2D_25()findAUTOCORR2D_26()findAUTOCORR2D_27()findAUTOCORR2D_28()findAUTOCORR2D_29()findAUTOCORR2D_3()findAUTOCORR2D_30()findAUTOCORR2D_31()findAUTOCORR2D_32()findAUTOCORR2D_33()findAUTOCORR2D_34()findAUTOCORR2D_35()findAUTOCORR2D_36()findAUTOCORR2D_37()findAUTOCORR2D_38()findAUTOCORR2D_39()findAUTOCORR2D_4()findAUTOCORR2D_40()findAUTOCORR2D_41()findAUTOCORR2D_42()findAUTOCORR2D_43()findAUTOCORR2D_44()findAUTOCORR2D_45()findAUTOCORR2D_46()findAUTOCORR2D_47()findAUTOCORR2D_48()findAUTOCORR2D_49()findAUTOCORR2D_5()findAUTOCORR2D_50()findAUTOCORR2D_51()findAUTOCORR2D_52()findAUTOCORR2D_53()findAUTOCORR2D_54()findAUTOCORR2D_55()findAUTOCORR2D_56()findAUTOCORR2D_57()findAUTOCORR2D_58()findAUTOCORR2D_59()findAUTOCORR2D_6()findAUTOCORR2D_60()findAUTOCORR2D_61()findAUTOCORR2D_62()findAUTOCORR2D_63()findAUTOCORR2D_64()findAUTOCORR2D_65()findAUTOCORR2D_66()findAUTOCORR2D_67()findAUTOCORR2D_68()findAUTOCORR2D_69()findAUTOCORR2D_7()findAUTOCORR2D_70()findAUTOCORR2D_71()findAUTOCORR2D_72()findAUTOCORR2D_73()findAUTOCORR2D_74()findAUTOCORR2D_75()findAUTOCORR2D_76()findAUTOCORR2D_77()findAUTOCORR2D_78()findAUTOCORR2D_79()findAUTOCORR2D_8()findAUTOCORR2D_80()findAUTOCORR2D_81()findAUTOCORR2D_82()findAUTOCORR2D_83()findAUTOCORR2D_84()findAUTOCORR2D_85()findAUTOCORR2D_86()findAUTOCORR2D_87()findAUTOCORR2D_88()findAUTOCORR2D_89()findAUTOCORR2D_9()findAUTOCORR2D_90()findAUTOCORR2D_91()findAUTOCORR2D_92()findAUTOCORR2D_93()findAUTOCORR2D_94()findAUTOCORR2D_95()findAUTOCORR2D_96()findAUTOCORR2D_97()findAUTOCORR2D_98()findAUTOCORR2D_99()findAsphericity()findBCUT2D_CHGHI()findBCUT2D_CHGLO()findBCUT2D_LOGPHI()findBCUT2D_LOGPLOW()findBCUT2D_MRHI()findBCUT2D_MRLOW()findBCUT2D_MWHI()findBCUT2D_MWLOW()findBalabanJ()findBertzCT()findChi0()findChi0n()findChi0v()findChi1()findChi1n()findChi1v()findChi2n()findChi2v()findChi3n()findChi3v()findChi4n()findChi4v()findEState_VSA1()findEState_VSA10()findEState_VSA11()findEState_VSA2()findEState_VSA3()findEState_VSA4()findEState_VSA5()findEState_VSA6()findEState_VSA7()findEState_VSA8()findEState_VSA9()findEccentricity()findExactMolWt()findFractionCSP3()findHallKierAlpha()findHeavyAtomCount()findHeavyAtomMolWt()findInertialShapeFactor()findKappa1()findKappa2()findKappa3()findLabuteASA()findMaxAbsEStateIndex()findMaxAbsPartialCharge()findMaxEStateIndex()findMaxPartialCharge()findMinAbsEStateIndex()findMinAbsPartialCharge()findMinEStateIndex()findMinPartialCharge()findMolLogP()findMolMR()findMolWt()findNHOHCount()findNOCount()findNPR1()findNPR2()findNumAliphaticCarbocycles()findNumAliphaticHeterocycles()findNumAliphaticRings()findNumAromaticCarbocycles()findNumAromaticHeterocycles()findNumAromaticRings()findNumHAcceptors()findNumHDonors()findNumHeteroatoms()findNumRadicalElectrons()findNumRotatableBonds()findNumSaturatedCarbocycles()findNumSaturatedHeterocycles()findNumSaturatedRings()findNumValenceElectrons()findPEOE_VSA1()findPEOE_VSA10()findPEOE_VSA11()findPEOE_VSA12()findPEOE_VSA13()findPEOE_VSA14()findPEOE_VSA2()findPEOE_VSA3()findPEOE_VSA4()findPEOE_VSA5()findPEOE_VSA6()findPEOE_VSA7()findPEOE_VSA8()findPEOE_VSA9()findPMI1()findPMI2()findPMI3()findRadiusOfGyration()findRingCount()findSMR_VSA1()findSMR_VSA10()findSMR_VSA2()findSMR_VSA3()findSMR_VSA4()findSMR_VSA5()findSMR_VSA6()findSMR_VSA7()findSMR_VSA8()findSMR_VSA9()findSlogP_VSA1()findSlogP_VSA10()findSlogP_VSA11()findSlogP_VSA12()findSlogP_VSA2()findSlogP_VSA3()findSlogP_VSA4()findSlogP_VSA5()findSlogP_VSA6()findSlogP_VSA7()findSlogP_VSA8()findSlogP_VSA9()findSpherocityIndex()findTPSA()findVSA_EState1()findVSA_EState10()findVSA_EState2()findVSA_EState3()findVSA_EState4()findVSA_EState5()findVSA_EState6()findVSA_EState7()findVSA_EState8()findVSA_EState9()findfr_Al_COO()findfr_Al_OH()findfr_Al_OH_noTert()findfr_ArN()findfr_Ar_COO()findfr_Ar_N()findfr_Ar_NH()findfr_Ar_OH()findfr_COO()findfr_COO2()findfr_C_O()findfr_C_O_noCOO()findfr_C_S()findfr_HOCCN()findfr_Imine()findfr_NH0()findfr_NH1()findfr_NH2()findfr_N_O()findfr_Ndealkylation1()findfr_Ndealkylation2()findfr_Nhpyrrole()findfr_SH()findfr_aldehyde()findfr_alkyl_carbamate()findfr_alkyl_halide()findfr_allylic_oxid()findfr_amide()findfr_amidine()findfr_aniline()findfr_aryl_methyl()findfr_azide()findfr_azo()findfr_barbitur()findfr_benzene()findfr_benzodiazepine()findfr_bicyclic()findfr_diazo()findfr_dihydropyridine()findfr_epoxide()findfr_ester()findfr_ether()findfr_furan()findfr_guanido()findfr_halogen()findfr_hdrzine()findfr_hdrzone()findfr_imidazole()findfr_imide()findfr_isocyan()findfr_isothiocyan()findfr_ketone()findfr_ketone_Topliss()findfr_lactam()findfr_lactone()findfr_methoxy()findfr_morpholine()findfr_nitrile()findfr_nitro()findfr_nitro_arom()findfr_nitro_arom_nonortho()findfr_nitroso()findfr_oxazole()findfr_oxime()findfr_para_hydroxylation()findfr_phenol()findfr_phenol_noOrthoHbond()findfr_phos_acid()findfr_phos_ester()findfr_piperdine()findfr_piperzine()findfr_priamide()findfr_prisulfonamd()findfr_pyridine()findfr_quatN()findfr_sulfide()findfr_sulfonamd()findfr_sulfone()findfr_term_acetylene()findfr_tetrazole()findfr_thiazole()findfr_thiocyan()findfr_thiophene()findfr_unbrch_alkane()findfr_urea()findqed()get_centroid()get_smiles()load_mol()multiple_molecules_sdf()read_descriptors_from_json()split_molecules()func()class_func()
- OCDocker.Receptor module
ReceptorReceptor.nameReceptor.structureReceptor.pathReceptor.original_pathReceptor.clean_source_pathReceptor.SASAReceptor.DipoleMomentReceptor.IsoelectricPointReceptor.GRAVYReceptor.AromaticityReceptor.InstabilityIndexReceptor.TotalAALengthReceptor.AvgAALengthReceptor.countChainReceptor.descriptors_namesReceptor.single_descriptorsReceptor.allDescriptorsReceptor.__init__()Receptor.get_descriptors()Receptor.is_valid()Receptor.print_attributes()Receptor.to_dict()Receptor.to_json()
compute_aromaticity()compute_dipole_moment()compute_gravy()compute_instability_index()compute_isoelectric_point()compute_sasa()count_AAs_and_chains()count_surface_AA()get_res()load_mol()read_descriptors_from_json()renumber_pdb_residues()
Module contents¶
The main OCDocker package.
Usage:
import OCDocker as ocdocker
Packages¶
CLI: Command-line interface helpers.
DB: Database management utilities.
Docking: Docking routines.
OCScore: Scoring and ML utilities.
Processing: Pre/post-processing workflows.
Rescoring: Rescoring routines.
Toolbox: Shared toolbox utilities.
Modules¶
Config: Configuration helpers.
Error: Error reporting utilities.
Initialise: Runtime initialization helpers.
Ligand: Ligand model and descriptors.
Receptor: Receptor model and descriptors.