icolos.utils.enums package

Submodules

icolos.utils.enums.composite_agents_enums module

class icolos.utils.enums.composite_agents_enums.BaseAgentEnum

Bases: object

DESCRIPTION = 'description'

ENVIRONMENT = 'environment'

ENVIRONMENT_EXPORT = 'export'

ENVIRONMENT_EXPORT_KEY = 'key'

ENVIRONMENT_EXPORT_VALUE = 'value'

GLOBAL_SETTINGS = 'global_settings'

GLOBAL_VARIABLES = 'global_variables'

HEADER = 'header'

ID = 'id'

LOGGING = 'logging'

LOGGING_LOGFILE = 'logfile'

STEPS = 'steps'

VERSION = 'version'

class icolos.utils.enums.composite_agents_enums.SchedulerEnum

Bases: BaseAgentEnum

SCHEDULER = 'scheduler'

class icolos.utils.enums.composite_agents_enums.WorkflowEnum

Bases: BaseAgentEnum

WORKFLOW = 'workflow'

icolos.utils.enums.compound_enums module

class icolos.utils.enums.compound_enums.CompoundContainerEnum

Bases: object

class icolos.utils.enums.compound_enums.CompoundTagsEnum

Bases: object

CONFORMER_ENERGY_TAG = 'conformer_energy'

FORMAL_CHARGE_TAG = 'formal_charge'

class icolos.utils.enums.compound_enums.ConformerContainerEnum

Bases: object

EXTRA_DATA_COORDFILE = 'coord_file'

EXTRA_DATA_COSMOFILE = 'cosmo_file'

class icolos.utils.enums.compound_enums.EnumerationContainerEnum

Bases: object

icolos.utils.enums.entry_points module

class icolos.utils.enums.entry_points.ExecutorEnum

Bases: object

RUNTIME_GLOBAL_VARIABLE_CONFIGDIR = 'config_dir'

RUNTIME_GLOBAL_VARIABLE_ENTRYPOINTDIR = 'entrypoint_dir'

RUNTIME_GLOBAL_VARIABLE_PACKAGEDIR = 'package_dir'

RUNTIME_GLOBAL_VARIABLE_WORKDIR = 'work_dir'

icolos.utils.enums.execution_enums module

class icolos.utils.enums.execution_enums.ExecutionPlatformEnum(value)

Bases: str, Enum

An enumeration.

CORE = 'core'

CORES = 'cores'

GPU = 'gpu'

GRES = 'gres'

LOCAL = 'local'

MEM = 'mem'

PARTITION = 'partition'

SERIAL = 'serial'

SLURM = 'slurm'

TIME = 'time'

icolos.utils.enums.flow_control_enums module

class icolos.utils.enums.flow_control_enums.FlowControlInitializationEnum

Bases: object

FLOW_CONTROL_INIT_DICT = {StepBaseEnum.STEP_ACTIVE_LEARNING: <class 'icolos.core.workflow_steps.active_learning.virtual_screening.StepActiveLearning'>, StepBaseEnum.STEP_ITERATOR: <class 'icolos.core.flow_control.iterator.StepIterator'>}

icolos.utils.enums.general_utils_enums module

class icolos.utils.enums.general_utils_enums.CheckFileGenerationEnum

Bases: object

GENERATED_EMPTY = 'generated_empty'

GENERATED_SUCCESS = 'generated_success'

NOT_GENERATED = 'not_generated'

class icolos.utils.enums.general_utils_enums.JSONSchemasEnum

Bases: object

HEADER_SCHEMA = 'header'

STEPS_SCHEMA = 'steps'

STEP_SCHEMA = 'step'

WORKFLOW_SCHEMA = 'workflow'

icolos.utils.enums.input_enums module

class icolos.utils.enums.input_enums.InputEnum

Bases: object

JSON_NAMES = 'names'

JSON_SMILES = 'smiles'

SOURCE_FIELD_COMPOUNDS = 'compounds'

TARGET_FIELD_COMPOUNDS = 'compounds'

TARGET_FIELD_CONFORMERS = 'conformers'

icolos.utils.enums.logging_enums module

class icolos.utils.enums.logging_enums.LoggingConfigEnum

Bases: object

DEBUG = 'debug'

ERROR = 'error'

EXCEPTION = 'exception'

INFO = 'info'

LOGGER_AGENT = 'agent'

LOGGER_BLANK = 'blank'

LOGGER_ENTRYPOINT = 'entrypoint'

LOGGER_IO = 'io'

LOGGER_STEP = 'step'

PATH_CONFIG_DEBUG = 'src/icolos/config/logging/debug.json'

PATH_CONFIG_DEFAULT = 'src/icolos/config/logging/default.json'

PATH_CONFIG_TUTORIAL = 'src/icolos/config/logging/tutorial.json'

PATH_CONFIG_VERBOSE = 'src/icolos/config/logging/verbose.json'

WARNING = 'warning'

icolos.utils.enums.parallelization module

class icolos.utils.enums.parallelization.ParallelizationEnum(value)

Bases: str, Enum

An enumeration.

STATUS_FAILED = 'failed'

STATUS_READY = 'ready'

STATUS_RUNNING = 'running'

STATUS_SUCCESS = 'success'

icolos.utils.enums.program_parameters module

class icolos.utils.enums.program_parameters.AutoDockVinaEnum

Bases: object

ADV_PDBQT = '.pdbqt'

REMARK_TAG = 'REMARK'

RESULT_LINE_IDENTIFIER = 'VINA RESULT'

RESULT_LINE_POS_RMSDTOBEST_LB = 3

RESULT_LINE_POS_RMSDTOBEST_UB = 4

RESULT_LINE_POS_SCORE = 2

VINA = 'vina'

VINA_CALL = 'vina'

VINA_CENTER_X = '--center_x'

VINA_CENTER_Y = '--center_y'

VINA_CENTER_Z = '--center_z'

VINA_CONFIGURATION = '--config'

VINA_CPU = '--cpu'

VINA_ENERGY_RANGE = '--energy_range'

VINA_EXHAUSTIVENESS = '--exhaustiveness'

VINA_FLEX = '--flex'

VINA_HELP = '--help'

VINA_HELP_ADVANCED = '--help_advanced'

VINA_LIGAND = '--ligand'

VINA_LOCAL_ONLY = '--local_only'

VINA_NUM_MODES = '--num_modes'

VINA_OUT = '--out'

VINA_RANDOMIZE_ONLY = '--randomize_only'

VINA_RECEPTOR = '--receptor'

VINA_SCORE_ONLY = '--score_only'

VINA_SEED = '--seed'

VINA_SIZE_X = '--size_x'

VINA_SIZE_Y = '--size_y'

VINA_SIZE_Z = '--size_z'

VINA_VERSION = '--version'

VINA_VERSION_IDENTIFICATION_STRING = 'AutoDock Vina 1.1.2'

VINA_WEIGHT_GAUSS1 = '--weight_gauss1'

VINA_WEIGHT_GAUSS2 = '--weight_gauss2'

VINA_WEIGHT_HYDROGEN = '--weight_hydrogen'

VINA_WEIGHT_HYDROPHOBIC = '--weight_hydrophobic'

VINA_WEIGHT_REPULSION = '--weight_repulsion'

VINA_WEIGHT_ROT = '--weight_rot'

class icolos.utils.enums.program_parameters.CosmoOutputEnum

Bases: object

ELEMENT = 'element'

GENERAL_BLOCK_ANNOTATIONS = {'E_cosmo': {'element': 0, 'pattern': 'E_COSMO+dE'}, 'HB_acc': {'element': 0, 'pattern': 'H-bond moment (accept)'}, 'HB_don': {'element': 0, 'pattern': 'H-bond moment (donor)'}, 'area': {'element': 0, 'pattern': 'Area'}, 'dipole': {'element': 0, 'pattern': 'Dipole moment'}, 'sigma1': {'element': 0, 'pattern': 'Sigma moments'}, 'sigma2': {'element': 1, 'pattern': 'Sigma moments'}, 'sigma3': {'element': 2, 'pattern': 'Sigma moments'}, 'sigma4': {'element': 3, 'pattern': 'Sigma moments'}, 'sigma5': {'element': 4, 'pattern': 'Sigma moments'}, 'sigma6': {'element': 5, 'pattern': 'Sigma moments'}, 'volume': {'element': 0, 'pattern': 'Volume'}}

GENERAL_BLOCK_PATTERN_STRING = '--- Compound 1 (mol) ---'

PATTERN = 'pattern'

SOLVENT_BLOCK_BODY_ANNOTATIONS = {'G_{solvent}': {'element': 0, 'pattern': 'Free energy of molecule in mix'}, 'Gsolv_{solvent}': {'element': 0, 'pattern': 'Gibbs Free Energy of Solvation'}}

SOLVENT_BLOCK_BODY_START_PATTERN = 'Compound: 1  (mol)'

SOLVENT_BLOCK_CURRENT_FRACTION_VALUE = '1.0000'

SOLVENT_BLOCK_HEADER_COMPOUNDS_PATTERN = 'Compound   '

SOLVENT_BLOCK_HEADER_MOLFRACTION_PATTERN = 'Mole Fraction'

SOLVENT_BLOCK_PATTERN_STRING = 'Gibbs Free Energy of Solvation'

SOLVENT_BLOCK_START_PATTERN = '----------------------'

SOLVENT_REPLACEHOLDER = '{solvent}'

SOLVENT_TRANSLATE_SOLVENT = {'1-octanol': 'octanol', 'acetonitr': 'acn', 'chcl3': 'chcl3', 'cyclohexa': 'cychex', 'dimethyls': 'dmso', 'h2o': 'h2o', 'methanol': 'meoh', 'thf': 'thf'}

class icolos.utils.enums.program_parameters.CrestEnum

Bases: object

CERST_NMR = '-nmr'

CREST = 'crest'

CREST_BTHR = '-bthr'

CREST_CHRG = '-chrg'

CREST_CROSS = '-cross'

CREST_DRY = '-dry'

CREST_EQV = '-eqv'

CREST_ETHR = '-ethr'

CREST_EWIN = '-ewin'

CREST_G = '-g'

CREST_GFF = '-gff'

CREST_GFN1 = '-gfn1'

CREST_GFN2 = '-gfn2'

CREST_H = '-h'

CREST_HELP_IDENTIFICATION_STRING = 'Conformer-Rotamer Ensemble Sampling Tool'

CREST_NICEPRINT = '-niceprint'

CREST_NOCROSS = '-nocross'

CREST_NOZS = '-nozs'

CREST_OPT = '-opt'

CREST_PRSC = '-prsc'

CREST_PTHR = '-pthr'

CREST_RTHR = '-rthr'

CREST_SHAKE = '-shake'

CREST_T = '-T'

CREST_TSTEP = '-tstep'

CREST_UHF = '-uhf'

CREST_V3 = '-v3'

CREST_XNAM = '-xnam'

CREST_ZS = '-zs'

class icolos.utils.enums.program_parameters.CrestOutputEnum

Bases: object

COORD = 'coord'

COORD_ORIGINAL = 'coord.original'

CREST_BEST_XYZ = 'crest_best.xyz'

CREST_CONFORMERS_SDF = 'crest_conformers.sdf'

CREST_CONFORMERS_XYZ = 'crest_conformers.xyz'

CREST_ENERGIES = 'crest.energies'

CREST_ROTAMERS_XYZ = 'crest_rotamers.xyz'

CRE_MEMBERS = 'cre_members'

PREFIX_ENERGIES_XYZ = '        '

XTBTOPO_MOL2 = 'xtbtopo.mol'

class icolos.utils.enums.program_parameters.DSSPEnum

Bases: object

MKDSSP = 'mkdssp'

class icolos.utils.enums.program_parameters.FeatureCounterEnum

Bases: object

PROPERTY_NUM_AROMATIC_RINGS = 'num_aromatic_rings'

PROPERTY_NUM_RINGS = 'num_rings'

class icolos.utils.enums.program_parameters.FepPlusEnum

Bases: object

DICT = 'dict'

FEP_ABSOLUTE_EXECUTOR = '$SCHRODINGER/fep_absolute_binding'

FEP_EXECUTOR = '$SCHRODINGER/fep_plus'

FEP_HELP = '-h'

FEP_MAPPER = '$SCHRODINGER/run -FROM scisol fep_mapper.py'

FEP_MAPPER_HELP_SUCCESS_STRING = 'If given, the match will be allowed'

JSC_LIST = 'ssh $SCHRODINGER_JOBSERVER "export SCHRODINGER=/opt/schrodinger/suite/installations/default && /opt/schrodinger/suite/installations/default/jsc list"'

JSC_TAIL_FILE = 'ssh $SCHRODINGER_JOBSERVER "export SCHRODINGER=/opt/schrodinger/suite/installations/default && /opt/schrodinger/suite/installations/default/jsc tail-file'

PATH = 'path'

class icolos.utils.enums.program_parameters.GlideEnum

Bases: object

GLIDE = 'glide'

GLIDE_AMIDE_MODE = 'AMIDE_MODE'

GLIDE_ATTACHED = '-ATTACHED'

GLIDE_CALL = '$SCHRODINGER/glide'

GLIDE_EXPANDED_SAMPLING = 'EXPANDED_SAMPLING'

GLIDE_GRIDFILE = 'GRIDFILE'

GLIDE_HELP = '-h'

GLIDE_HELP_IDENTIFICATION_STRING = 'positional arguments:'

GLIDE_HOST = '-HOST'

GLIDE_LIGANDFILE = 'LIGANDFILE'

GLIDE_LOG_FAIL_STRINGS = {'*** Error in', '======= Backtrace: =========', 'Glide cannot recover from this signal and will now abort.'}

GLIDE_LOG_FINISHED_STRINGS = {'Exiting Glide'}

GLIDE_LOG_SUCCESS_STRING = 'glide_sort command succeeded'

GLIDE_NENHANCED_SAMPLING = 'NENHANCED_SAMPLING'

GLIDE_NJOBS = '-NJOBS'

GLIDE_NREQUIRED_CONS = 'NREQUIRED_CONS'

GLIDE_OVERWRITE = '-OVERWRITE'

GLIDE_POSES_PER_LIG = 'POSES_PER_LIG'

GLIDE_POSE_OUTTYPE = 'POSE_OUTTYPE'

GLIDE_POSE_OUTTYPE_LIGANDLIB = 'ligandlib_sd'

GLIDE_POSE_OUTTYPE_POSEVIEWER = 'poseviewer'

GLIDE_POSTDOCKSTRAIN = 'POSTDOCKSTRAIN'

GLIDE_POSTDOCK_NPOSE = 'POSTDOCK_NPOSE'

GLIDE_PRECISION = 'PRECISION'

GLIDE_REWARD_INTRA_HBONDS = 'REWARD_INTRA_HBONDS'

GLIDE_TMPLAUNCHDIR = '-TMPLAUNCHDIR'

GLIDE_USE_CONS = 'USE_CONS'

GLIDE_WAIT = '-WAIT'

class icolos.utils.enums.program_parameters.GoldEnum

Bases: object

GOLD_CALL = 'gold_auto'

GOLD_HELP = '-h'

GOLD_HELP_IDENTIFICATION_STRING = 'Usage: gold_auto'

GOLD_QUIET = '-q'

REMARK_TAG = 'REMARK'

class icolos.utils.enums.program_parameters.GoldOutputEnum

Bases: object

class icolos.utils.enums.program_parameters.GromacsEnum

Bases: object

ACPYPE_BINARY = 'acpype'

AMBER_PARAMETRISED_COMPONENTS = ['ABU', 'ACE', 'AIB', 'ALA', 'ARG', 'ARGN', 'ASN', 'ASN1', 'ASP', 'ASP1', 'ASPH', 'ASPP', 'ASH', 'CT3', 'CYS', 'CYS1', 'CYS2', 'CYSH', 'DALA', 'GLN', 'GLU', 'GLUH', 'GLUP', 'GLH', 'GLY', 'HIS', 'HIS1', 'HISA', 'HISB', 'HISH', 'HISD', 'HISE', 'HISP', 'HSD', 'HSE', 'HSP', 'HYP', 'ILE', 'LEU', 'LSN', 'LYS', 'LYSH', 'MELEU', 'MET', 'MEVAL', 'NAC', 'NME', 'NHE', 'NH2', 'PHE', 'PHEH', 'PHEU', 'PHL', 'PRO', 'SER', 'THR', 'TRP', 'TRPH', 'TRPU', 'TYR', 'TYRH', 'TYRU', 'VAL', 'PGLU', 'HID', 'HIE', 'HIP', 'LYP', 'LYN', 'CYN', 'CYM', 'CYX', 'DAB', 'ORN', 'HYP', 'NALA', 'NGLY', 'NSER', 'NTHR', 'NLEU', 'NILE', 'NVAL', 'NASN', 'NGLN', 'NARG', 'NHID', 'NHIE', 'NHIP', 'NHISD', 'NHISE', 'NHISH', 'NTRP', 'NPHE', 'NTYR', 'NGLU', 'NASP', 'NLYS', 'NORN', 'NDAB', 'NLYSN', 'NPRO', 'NHYP', 'NCYS', 'NCYS2', 'NMET', 'NASPH', 'NGLUH', 'CALA', 'CGLY', 'CSER', 'CTHR', 'CLEU', 'CILE', 'CVAL', 'CASN', 'CGLN', 'CARG', 'CHID', 'CHIE', 'CHIP', 'CHISD', 'CHISE', 'CHISH', 'CTRP', 'CPHE', 'CTYR', 'CGLU', 'CASP', 'CLYS', 'CORN', 'CDAB', 'CLYSN', 'CPRO', 'CHYP', 'CCYS', 'CCYS2', 'CMET', 'CASPH', 'CGLUH', 'DA', 'DG', 'DC', 'DT', 'DA5', 'DG5', 'DC5', 'DT5', 'DA3', 'DG3', 'DC3', 'DT3', 'DAN', 'DGN', 'DCN', 'DTN', 'A', 'U', 'C', 'G', 'RA', 'RU', 'RC', 'RG', 'RA5', 'RT5', 'RU5', 'RC5', 'RG5', 'RA3', 'RT3', 'RU3', 'RC3', 'RG3', 'RAN', 'RTN', 'RUN', 'RCN', 'RGN', 'SOL', 'WAT', 'HOH', 'OHH', 'TIP', 'T3P', 'T4P', 'T5P', 'T3H', 'K', 'NA', 'CA', 'MG', 'CL', 'ZN', 'CU1', 'CU', 'LI', 'NA+', 'RB', 'CS', 'F', 'CL-', 'BR', 'I', 'OH', 'Cal', 'IB+']

ANTECHAMBER = 'antechamber'

ATOMS = ['HETATM', 'ATOM']

ATOMS_DIRECTIVE = '[ atoms ]'

ATOMTYPES = '[ atomtypes ]'

BONDS = '[ bonds ]'

CLUSTER = 'gmx cluster'

CLUSTER_TS = 'Rscript $MDPLOT/MDplot/inst/bash/MDplot_bash.R clusters_ts'

DEFAULTS = '[ defaults ]'

DO_DSSP = 'gmx do_dssp'

EDITCONF = 'gmx editconf'

GENION = 'gmx genion'

GENRESTR = 'gmx genrestr'

GROMPP = 'gmx grompp'

IONS = ['ZN', 'MG', 'CU', 'CA', 'NA', 'CL', 'RB', 'CS', 'F', 'BR', 'I', 'OH', 'K']

LIG_EXT = 'lig'

LIG_ID = 'lig_id.lig'

MAKE_NDX = 'gmx make_ndx'

MDRUN = 'gmx mdrun'

MMPBSA = 'gmx_MMPBSA'

MOLECULES = '[ molecules ]'

MOLECULETYPES = '[ moleculetype ]'

MPI_MDRUN = 'gmx_mpi mdrun'

PDB2GMX = 'gmx pdb2gmx'

PDB2GMX_FAIL_ID_STRING = 'Required option was not provided'

PRIMARY_COMPONENTS = ['Protein', 'DNA', 'RNA']

RMS = 'gmx rms'

SELECT = 'gmx select'

SOLVATE = 'gmx solvate'

SOLVENTS = ['HOH ', 'SOL', 'WAT']

SYSTEM = '[ system ]'

TERMINATIONS = ['ENDMDL', 'END']

TRJCAT = 'gmx trjcat'

TRJCONV = 'gmx trjconv'

class icolos.utils.enums.program_parameters.JazzyEnum

Bases: object

HELP = '--help'

HELP_IDENTIFICATION_STRING = 'Show this message'

JAZZY = 'jazzy'

RESULT_DGA = 'dga'

RESULT_DGP = 'dgp'

RESULT_DGTOT = 'dgtot'

RESULT_SA = 'sa'

RESULT_SDC = 'sdc'

RESULT_SDX = 'sdx'

RESULT_SMILES = 'smiles'

RESULT_STATUS = '__status'

RESULT_STATUS_SUCCESS = 'success'

VEC = 'vec'

VEC_OPT = '--opt'

VEC_OPT_MMF94 = 'MMF94'

VEC_OPT_MMF94S = 'MMF94s'

VEC_OPT_UFF = 'UFF'

VEC_STRENGHT_ONLY = '--strength_only'

VIS = 'vis'

VIS_BASE64 = '--base64'

VIS_FIG_SIZE = '--fig_size'

VIS_FLATTEN_MOLECULE = '--flatten_molecule'

VIS_HELP = '--help'

VIS_HIGHLIGHT_ATOMS = '--highlight_atoms'

VIS_IGNORE_SA = '--ignore_sa'

VIS_IGNORE_SDC = '--ignore_sdc'

VIS_IGNORE_SDX = '--ignore_sdx'

VIS_OPT = '--opt'

VIS_OPT_MMF94 = 'MMF94'

VIS_OPT_MMF94S = 'MMF94s'

VIS_OPT_UFF = 'UFF'

VIS_SA_THRESHOLD = '--sa_threshold'

VIS_SDC_THRESHOLD = '--sdc_threshold'

class icolos.utils.enums.program_parameters.KallistoEnum

Bases: object

ALP = 'alp'

BONDS = 'bonds'

CNS = 'cns'

EEQ = 'eeq'

EXS = 'exs'

HELP = '--help'

HELP_IDENTIFICATION_STRING = 'Show this message'

KALLISTO = 'kallisto'

LIG = 'lig'

PROX = 'prox'

RMS = 'rms'

SHIFT = '--shift'

SILENT = '--silent'

SORT = 'sort'

STM = 'stm'

VDW = 'vdw'

class icolos.utils.enums.program_parameters.LigprepEnum

Bases: object

LIGPREP = 'ligprep'

LIGPREP_AC = '-ac'

LIGPREP_BFF = '-bff'

LIGPREP_EPIK = '-epik'

LIGPREP_F = '-f'

LIGPREP_FF_OPLS3e = '16'

LIGPREP_FF_OPLS_2005 = '14'

LIGPREP_G = '-g'

LIGPREP_HELP = '-h'

LIGPREP_HELP_IDENTIFICATION_STRING = 'usage: ligprep [options]'

LIGPREP_HOST = '-HOST'

LIGPREP_HOST_LOCALHOST = 'localhost'

LIGPREP_INPUT_ISMI = '-ismi'

LIGPREP_INP_CONFIG = '-inp'

LIGPREP_LOG_ENDING = '.log'

LIGPREP_NJOBS = '-NJOBS'

LIGPREP_NSTRUCTS = '-NSTRUCTS'

LIGPREP_OUTPUT_OSD = '-osd'

LIGPREP_PH = '-ph'

LIGPREP_PHT = '-pht'

LIGPREP_S = '-s'

LIGPREP_WAIT = '-WAIT'

class icolos.utils.enums.program_parameters.MacromodelEnum

Bases: object

MACROMODEL = 'macromodel'

MACROMODEL_HELP = '-h'

MACROMODEL_HELP_IDENTIFICATION_STRING = 'MacroModel Startup Script'

MACROMODEL_NJOBS = '-NJOBS'

MACROMODEL_WAIT = '-WAIT'

class icolos.utils.enums.program_parameters.ModelBuilderEnum

Bases: object

BEST_BUILDCONFIG_OUTPATH = '--best-buildconfig-outpath'

BEST_MODEL_OUTPATH = '--best-model-outpath'

CONFIG = '--config'

MERGED_MODEL_OUTPATH = '--merged-model-outpath'

OPTBUILD_ENTRY_POINT = 'optbuild.py'

PERSISTENCE_MODE = '--model-persistence-mode'

PERSISTENCE_MODE_PLAINSKLEARN = 'plain_sklearn'

PERSISTENCE_MODE_SKLEARNWITHOPTUNAAZ = 'sklearn_with_optunaz'

class icolos.utils.enums.program_parameters.OMEGAEnum

Bases: object

CLASSIC_CANON_ORDER = '-canonOrder'

CLASSIC_EWINDOW = '-ewindow'

CLASSIC_FROMCT = '-fromCT'

CLASSIC_INPUT = '-in'

CLASSIC_MAXCONFS = '-maxconfs'

CLASSIC_OUTPUT = '-out'

CLASSIC_PARAM = '-param'

CLASSIC_PREFIX = '-prefix'

CLASSIC_PROGRESS = '-progress'

CLASSIC_RMS = '-rms'

CLASSIC_SDENERGY = '-sdEnergy'

CLASSIC_STRICT = '-strict'

CLASSIC_STRICTSTEREO = '-strictstereo'

CLASSIC_VERBOSE = '-verbose'

DENSE_INPUT = '-in'

DENSE_OUTPUT = '-out'

DENSE_PARAM = '-param'

DENSE_PREFIX = '-prefix'

DENSE_PROGRESS = '-progress'

DENSE_VERBOSE = '-verbose'

MACROCYCLE_EWINDOW = '-ewindow'

MACROCYCLE_INPUT = '-in'

MACROCYCLE_ITERATION_CYCLE_SIZE = '-iteration_cycle_size'

MACROCYCLE_MAXCONFS = '-maxconfs'

MACROCYCLE_MAX_ITERATIONS = '-max_iterations'

MACROCYCLE_OUTPUT = '-out'

MACROCYCLE_PARAM = '-param'

MACROCYCLE_PREFIX = '-prefix'

MACROCYCLE_REF_TOLERANCE = '-ref_tolerance'

MACROCYCLE_RMS = '-rms'

MACROCYCLE_RMSD_DEDUPLICATE = '-rmsd_deduplicate'

OMEGA = 'oeomega'

OMEGA_HELP = '--help'

OMEGA_HELP_IDENTIFICATION_STRING = 'To cite OMEGA please'

OMEGA_MODE_CLASSIC = 'classic'

OMEGA_MODE_DENSE = 'dense'

OMEGA_MODE_MACROCYCLE = 'macrocycle'

OMEGA_MODE_POSE = 'pose'

OMEGA_MODE_ROCS = 'rocs'

POSE_INPUT = '-in'

POSE_OUTPUT = '-out'

POSE_PREFIX = '-prefix'

POSE_PROGRESS = '-progress'

POSE_VERBOSE = '-verbose'

ROCS_INPUT = '-in'

ROCS_OUTPUT = '-out'

ROCS_PARAM = '-param'

ROCS_PREFIX = '-prefix'

ROCS_PROGRESS = '-progress'

ROCS_VERBOSE = '-verbose'

class icolos.utils.enums.program_parameters.OMEGAOutputEnum

Bases: object

CLASSIC_ENERGY_OUTPUT_TAG = 'mmff94smod_NoEstat'

OUTPUT_SDF_NAME = 'omega_out.sdf'

class icolos.utils.enums.program_parameters.OpenBabelEnum

Bases: object

OBABEL = 'obabel'

OBABEL_IDENTIFICATION_STRING = '-O<outfilename>'

OBABEL_INPUTFORMAT_PDB = '-ipdb'

OBABEL_INPUTFORMAT_PDBQT = '-ipdbqt'

OBABEL_INPUTFORMAT_SDF = '-isdf'

OBABEL_INPUTFORMAT_XYZ = '-ixyz'

OBABEL_M = '-m'

OBABEL_O = '-O'

OBABEL_OUTPUT_FORMAT_PDB = '-opdb'

OBABEL_OUTPUT_FORMAT_PDBQT = '-opdbqt'

OBABEL_OUTPUT_FORMAT_SDF = '-osdf'

OBABEL_OUTPUT_FORMAT_XYZ = '-oxyz'

OBABEL_P = '-p'

OBABEL_PARTIALCHARGE = '--partialcharge'

OBABEL_PARTIALCHARGE_GASTEIGER = 'gasteiger'

OBABEL_X = '-x'

OBABEL_X_R = 'r'

class icolos.utils.enums.program_parameters.OpenBabelOutputEnum

Bases: object

class icolos.utils.enums.program_parameters.PMXAtomMappingEnum

Bases: object

D = '--d'

DMCS = '--dMCS'

H2HEAVY = '--H2Heavy'

H2HPOLAR = '--H2Hpolar'

HELP = '--help'

I1 = '-i1'

I2 = '-i2'

LIGAND_DIR = 'input/ligands'

LOG = '-log'

N1 = '-n1'

N2 = '-n2'

NO_ALIGNMENT = '--no-alignment'

NO_CHIRALITY = '--no-chirality'

NO_H2H = '--no-H2H'

NO_MCS = '--no-mcs'

O1 = '-o1'

O2 = '-o2'

OPDB1 = '-opdb1'

OPDB2 = '-opdb2'

OPDBM1 = '-opdbm1'

OPDBM2 = '-opdbm2'

RINGSONLY = '--RingsOnly'

SCORE = '-score'

SWAP = '--swap'

TIMEOUT = '--timeout'

class icolos.utils.enums.program_parameters.PMXEnum

Bases: object

ABFE = '$PMX abfe'

ANALYSE = '$PMX analyse'

ANALYSE_HELP = '-h'

ANALYSE_HELP_SUCCESS_STRING = 'Calculates free energies from fast'

ASSEMBLE_SYSTEMS = 'assemble_systems.py'

ATOMMAPPING = '$PMX atomMapping'

BOX_WATER_IONS = 'box_water_ions.py'

DOUBLEBOX = '$PMX doublebox'

GENLIB = '$PMX genlib'

GENTOP = '$PMX gentop'

HYBRID_STR_TOP = 'hybridStrTop'

LIGANDHYBRID = '$PMX ligandHybrid'

MUTATE = '$PMX mutate'

PDB = 'pdb'

PREPARE_SIMULATIONS = 'prepare_simulations.py'

PREPARE_TRANSITIONS = 'prepare_transitions.py'

RUN_ANALYSIS = 'run_analysis.py'

RUN_SIMULATIONS = 'run_simulations.py'

class icolos.utils.enums.program_parameters.PMXLigandHybridEnum

Bases: object

D = '--d'

DEANG = '--deAng'

FIT = '--fit'

HELP = '--help'

I1 = '-i1'

I2 = '-i2'

ITP1 = '-itp1'

ITP2 = '-itp2'

LOG = '-log'

N1 = '-n1'

N2 = '-n2'

OA = '-oA'

OB = '-oB'

OFFITP = '-offitp'

OITP = '-oitp'

PAIRS = '-pairs'

SCDUMA = '--scDUMa'

SCDUMD = '--scDUMd'

SCDUMM = '--scDUMm'

SPLIT = '--split'

class icolos.utils.enums.program_parameters.PantherEnum

Bases: object

PANTHER_CONFIG = 'panther_config.in'

PANTHER_ENTRYPOINT = 'panther.py'

PANTHER_OUTPUT_FILE = 'neg_image.mol2'

PANTHER_PTYHON2 = 'python2'

class icolos.utils.enums.program_parameters.PdbFixerEnum

Bases: object

FIXER = 'pdbfixer'

class icolos.utils.enums.program_parameters.PrimeEnum

Bases: object

PRIME_HELP = '-h'

PRIME_HELP_IDENTIFICATION_STRING = 'run $SCHRODINGER/prime_mmgbsa -h for a complete listing of all options.'

PRIME_MMGBSA = 'prime_mmgbsa'

PRIME_MMGBSA_TOTAL_ENERGY = 'r_psp_MMGBSA_dG_Bind'

PRIME_MMGBSA_TOTAL_ENERGY_NS = 'r_psp_MMGBSA_dG_Bind(NS)'

PRIME_NJOBS = '-NJOBS'

PRIME_OUTTYPE = '-out_type'

PRIME_OUTTYPE_LIGAND = 'LIGAND'

PRIME_WAIT = '-WAIT'

class icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum

Bases: object

AWS_BINARY_LOC = 'ssh <location> /opt/schrodinger/suite/installations/default/'

FMP_STATS = 'fmp_stats'

FMP_STATS_CALL = '$SCHRODINGER/run -FROM scisol fmp_stats.py'

LICADMIN = 'licadmin'

LICADMIN_STAT = 'STAT'

MULTISIM_EXEC = '$SCHRODINGER/utilities/multisim'

POSEVIEWER_FILE_KEY = 'pv.maegz'

PREPWIZARD = 'prepwizard'

PREPWIZARD_CALL = '$SCHRODINGER/utilities/prepwizard'

PROTEIN_INTERACTION = 'protein_interaction'

PROTEIN_INTERACTION_CALL = '$SCHRODINGER/run protein_interaction_analysis.py'

SCHRODINGER_MODULE = 'module load schrodinger/2021-2-js-aws'

SDCONVERT = 'sdconvert'

SDCONVERT_A = '-a'

SDCONVERT_CALL = '$SCHRODINGER/utilities/sdconvert'

SDCONVERT_FORMAT_MAE = 'mae'

SDCONVERT_FORMAT_MM = 'mm'

SDCONVERT_FORMAT_PDB = 'pdb'

SDCONVERT_FORMAT_SD = 'sd'

SDCONVERT_HELP = ''

SDCONVERT_HELP_IDENTIFICATION_STRING = 'mae : Maestro format'

SDCONVERT_I = '-i'

SDCONVERT_NOAROM = '-noarom'

SDCONVERT_NOSTEREO = '-nostereo'

SDCONVERT_O = '-o'

SDCONVERT_TITLE = '-title'

STRUCTCAT = 'structcat'

STRUCTCAT_CALL = '$SCHRODINGER/utilities/structcat'

STRUCTCAT_FORMAT_MAE = 'mae'

STRUCTCAT_FORMAT_MOL2 = 'mol2'

STRUCTCAT_FORMAT_PDB = 'pdb'

STRUCTCAT_FORMAT_SD = 'sd'

STRUCTCAT_FORMAT_SDF = 'sdf'

STRUCTCAT_HELP = '-h'

STRUCTCAT_HELP_IDENTIFICATION_STRING = '<format> must be one of'

STRUCTCAT_I = '-i'

STRUCTCAT_O = '-o'

STRUCTCONVERT = 'structconvert'

STRUCTCONVERT_CALL = '$SCHRODINGER/utilities/structconvert'

STRUCT_SPLIT = 'structsplit'

STRUCT_SPLIT_CALL = '$SCHRODINGER/run split_structure.py'

class icolos.utils.enums.program_parameters.ShaepEnum

Bases: object

CONFORMER_PATH = 'conformer.sdf'

NEGATIVE_IMAGE_OUTPUT_FILE = 'neg_image.mol2'

OUTPUT_SIMILARITY = 'similarity.txt'

SHAEP_EXECUTABLE = 'shaep'

TAG_ESP_SIMILARITY = 'esp_similarity'

TAG_SHAPE_SIMILARITY = 'shape_similarity'

class icolos.utils.enums.program_parameters.SlurmEnum

Bases: object

CANCELLED = 'CANCELLED'

COMPLETED = 'COMPLETED'

FAILED = 'FAILED'

NODE_FAIL = 'NODE_FAIL'

PENDING = 'PENDING'

RUNNING = 'RUNNING'

SBATCH = 'sbatch'

STATE = 'State'

class icolos.utils.enums.program_parameters.StepPMXEnum

Bases: object

ABFE = 'abfe'

BOXD = 'boxd'

BOXSHAPE = 'boxshape'

CONC = 'conc'

EXEC_MODE = 'exec_mode'

MDRUN_EXECUTABLE = 'mdrun_executable'

NNAME = 'nname'

PNAME = 'pname'

PREV_STEP = 'previous_step'

RBFE = 'rbfe'

RUN_TYPE = 'run_type'

SIM_TYPE = 'sim_type'

SIM_TYPES = 'sim_types'

STRICT = 'strict'

WATER = 'water'

class icolos.utils.enums.program_parameters.TurbomoleEnum

Bases: object

CONTROL = 'control'

CONTROL_COSMO_INSERTION = '$cosmo_isorad'

CONTROL_COSMO_OUT = '$cosmo_out file=n'

CONTROL_COSMO_REPLACE = '$cosmo_out file=mol.cosmo'

COORD = 'coord'

CT_CONFIG = 'cosmotherm_config'

CT_CONFIG_DEFAULTPATH = 'src/icolos/config/cosmo/default_cosmo.config'

CT_COSMOTHERM = 'cosmotherm'

CT_COSMOTHERM_CONFIG_FILE = 'cosmotherm.inp'

CT_COSMOTHERM_FAIL_STRING = 'COSMOtherm ERROR Termination'

CT_COSMOTHERM_OUTPUT_FILE = 'cosmotherm.out'

CT_COSMOTHERM_TAB_ENDING = 'cosmother.tab'

TM_CONFIG_BASENAME = 'tm_config_basename'

TM_CONFIG_COSMO = 'tm_config_cosmo'

TM_CONFIG_DIR = 'tm_config_dir'

TM_CONFIG_ENDING = '.tm'

TM_COSMOPREP = 'cosmoprep'

TM_COSMOPREP_SUCCESS_STRING = 'cosmoprep ended normally'

TM_DEFINE = 'define'

TM_DEFINE_SUCCESS_STRING = 'define ended normally'

TM_JOBEX = 'jobex'

TM_JOBEX_C = '-c'

TM_JOBEX_FAIL_IDENTIFICATION_STRING = 'jobex ended abnormally'

TM_JOBEX_GCART = '-gcart'

TM_JOBEX_SUCCESS_STRING = 'jobex ended normally'

TM_OUTPUT_COORDFILE = 'coord'

TM_OUTPUT_COSMOFILE = 'mol.cosmo'

TM_OUTPUT_FINAL_SDF = 'final.sdf'

TM_OUTPUT_FINAL_XYZ = 'final.xyz'

TM_RIDFT = 'ridft'

TM_RIDFT_FAIL_IDENTIFICATION_STRING = 'ridft ended abnormally'

TM_RIDFT_SUCCESS_STRING = 'ridft ended normally'

TM_T2X = 't2x'

TM_T2X_C = '-c'

TM_TURBOTMPDIR = 'TURBOTMPDIR'

TM_X2T = 'x2t'

TM_X2T_SUCCESS_STRING = '$coord'

class icolos.utils.enums.program_parameters.XTBEnum

Bases: object

XTB = 'xtb'

XTB_ACC = '--acc'

XTB_CHRG = '--chrg'

XTB_CYCLES = '--cycles'

XTB_ETEMP = '--etemp'

XTB_GBSA = '--gbsa'

XTB_GFN = '--gfn'

XTB_HELP = '--help'

XTB_HELP_IDENTIFICATION_STRING = 'normal termination of xtb'

XTB_ITERATION = '--iteration'

XTB_MOPAC = '--mopac'

XTB_OPT = '--opt'

XTB_ORCA = '--orca'

XTB_P = '-P'

XTB_PERIODIC = '--periodic'

XTB_QMDFF = '--qmdff'

XTB_TM = '--tm'

XTB_UHF = '--uhf'

class icolos.utils.enums.program_parameters.XTBOutputEnum

Bases: object

CHARGES = 'charges'

FAILURE = 'failure'

GRADIENT_TAG = 'gradient norm / Eh/a0'

SUCCESS = 'success'

TOTAL_ENERGY_TAG = 'total energy / Eh'

WBO = 'wbo'

XTBOPT_LOG = 'xtbopt.log'

XTBOPT_SDF = 'xtbopt.sdf'

XTBRESTART = 'xtbrestart'

XTBTOPO_SDF = 'xtbtopo.sdf'

icolos.utils.enums.step_enums module

class icolos.utils.enums.step_enums.IteratorEnum(value)

Bases: str, Enum

An enumeration.

ALL = 'all'

N_ITERS = 'n_iters'

SINGLE = 'single'

class icolos.utils.enums.step_enums.StepActiveLearningEnum

Bases: object

ACQUISITION_BATCH_SIZE = 'acquisition_batch_size'

ACQUISITION_FUNCTION = 'acquisition_function'

BATCH_SIZE = 'batch_size'

CRITERIA = 'criteria'

DYNAMIC_STOP = 'dynamic_stop'

EI = 'ei'

EPOCHS = 'number_of_reinvent_epochs'

EPSILON = 'epsilon'

EVALUATE = 'evaluate'

FRACTION_PER_EPOCH = 'fraction_per_epoch'

FRAGMENTS = 'fragments'

GRAPH = 'graph'

GREEDY = 'greedy'

GREEDY_EPSILON = 'greedy_epsilon'

ID = 'ID'

IDX = 'IDX'

INITIAL_POOLING_EPOCHS = 'initial_pooling_epochs'

INIT_SAMPLE_FACTOR = 'init_sample_factor'

LATENT_DISTANCE = 'latent_distance'

MAX_SAMPLED_FRACTION = 'max_sampled_fraction'

MODEL = 'model'

MOLECULE = 'Molecule'

MORGAN_FP = 'MorganFP'

N_ROUNDS = 'n_rounds'

ORACLE_CONFIG = 'oracle_config'

ORACLE_LABEL = 'oracle_label'

ORACLE_TYPE = 'oracle_type'

PI = 'pi'

RANDOM = 'random'

RANDOM_FOREST_REGRESSOR = 'rf'

REPLICAS = 'replicas'

RETRAIN = 'retrain'

SAVE_DIR = 'save_dir'

SMILES = 'SMILES'

SOAP_VECTOR = 'soap_vector'

SUPPORT_VECTOR_REGRESSOR = 'svr'

SURROGATE_MODEL_TYPE = 'surrogate_model_type'

TANIMOTO = 'tanimoto'

TANIMOTO_TRUE_BELIEVER = 'tanimoto_true_believer'

TS = 'ts'

UCB = 'ucb'

VALIDATION_LIB = 'validation_lib'

VIRTUAL_LIB = 'virtual_lib'

WARMUP = 'warmup'

class icolos.utils.enums.step_enums.StepAutoDockVinaEnum

Bases: object

ADV_RECEPTOR_PATH = 'receptor_path'

ADV_SEARCH_SPACE = 'search_space'

ADV_SEARCH_SPACE_CENTER_X = '--center_x'

ADV_SEARCH_SPACE_CENTER_Y = '--center_y'

ADV_SEARCH_SPACE_CENTER_Z = '--center_z'

ADV_SEARCH_SPACE_SIZE_X = '--size_x'

ADV_SEARCH_SPACE_SIZE_Y = '--size_y'

ADV_SEARCH_SPACE_SIZE_Z = '--size_z'

ADV_SEED = 'seed'

CONFIGURATION = 'configuration'

NUMBER_POSES = 'number_poses'

class icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum

Bases: object

ADV_PDBQT = '.pdbqt'

EXTRACT_BOX = 'extract_box'

EXTRACT_BOX_REFERENCE_LIGAND_FORMAT = 'reference_ligand_format'

EXTRACT_BOX_REFERENCE_LIGAND_FORMAT_PDB = 'PDB'

EXTRACT_BOX_REFERENCE_LIGAND_FORMAT_SDF = 'SDF'

EXTRACT_BOX_REFERENCE_LIGAND_PATH = 'reference_ligand_path'

INPUT_RECEPTOR_PDB = 'input_receptor_pdb'

OUTPUT_RECEPTOR_PDBQT = 'output_receptor_pdbqt'

PH = 'pH'

class icolos.utils.enums.step_enums.StepBaseEnum(value)

Bases: str, Enum

An enumeration.

ANNOTATION_GRID_FILENAME = 'grid_filename'

ANNOTATION_GRID_ID = 'grid_id'

ANNOTATION_GRID_PATH = 'grid_path'

ANNOTATION_TAG_DOCKING_SCORE = 'docking_score'

ANNOTATION_TAG_G_SCORE = 'g_score'

EXEC = 'execution'

EXEC_BINARYLOCATION = 'binary_location'

EXEC_FAILUREPOLICY = 'failure_policy'

EXEC_FAILUREPOLICY_NTRIES = 'n_tries'

EXEC_PARALLELIZATION = 'parallelization'

EXEC_PARALLELIZATION_CORES = 'jobs'

EXEC_PARALLELIZATION_MAXLENSUBLIST = 'max_length_sublists'

EXEC_PLATFORM = 'platform'

EXEC_PREFIXEXECUTION = 'prefix_execution'

EXEC_RESOURCES = 'resources'

EXEC_RESOURCES_ADDITIONAL_LINES = 'additional_lines'

EXEC_RESOURCES_CORES = 'cores'

EXEC_RESOURCES_GRES = 'gres'

EXEC_RESOURCES_MEM = 'mem'

EXEC_RESOURCES_MODULES = 'modules'

EXEC_RESOURCES_OTHER_ARGS = 'other_args'

EXEC_RESOURCES_PARTITION = 'partition'

EXEC_RESOURCES_TASKS = 'tasks'

FILETYPE_TXT = 'txt'

FILE_SIZE_THRESHOLD = '2000000000.0'

FILE_TYPE_PDB = 'pdb'

FORMAT_CMS = 'CMS'

FORMAT_CSV = 'CSV'

FORMAT_DTR = 'DTR'

FORMAT_JSON = 'JSON'

FORMAT_MOL2 = 'MOL2'

FORMAT_PDB = 'PDB'

FORMAT_PKL = 'PKL'

FORMAT_PLAIN = 'PLAIN'

FORMAT_SDF = 'SDF'

FORMAT_SMI = 'SMI'

FORMAT_SMILES = 'SMILES'

FORMAT_TXT = 'TXT'

FORMAT_XTB = 'XTB'

GRID_IDS = 'grid_ids'

INPUT = 'input'

INPUT_COMPOUNDS = 'compounds'

INPUT_CSV_COLUMNS = 'columns'

INPUT_CSV_DELIMITER = 'delimiter'

INPUT_CSV_NAMES_COLUMN = 'names'

INPUT_CSV_SMILES_COLUMN = 'smiles'

INPUT_ENFORCE_COMPOUND_IDS = 'compound_ids'

INPUT_ENFORCE_ENUMERATION_IDS = 'enumeration_ids'

INPUT_ENFORCE_IDS = 'enforce_ids'

INPUT_ENUMERATIONS = 'enumerations'

INPUT_EXTENSION = 'extension'

INPUT_FIELD = 'field'

INPUT_FORMAT = 'format'

INPUT_GENERIC = 'generic'

INPUT_GMX = 'gmx_state'

INPUT_MERGE = 'merge'

INPUT_MERGE_BY_ID = 'id'

INPUT_MERGE_BY_NAME = 'name'

INPUT_MERGE_BY_SMILE = 'smile'

INPUT_MERGE_COMPOUNDS = 'compounds'

INPUT_MERGE_COMPOUNDS_BY = 'merge_compounds_by'

INPUT_MERGE_ENUMERATIONS = 'enumerations'

INPUT_MERGE_ENUMERATIONS_BY = 'merge_enumerations_by'

INPUT_SOURCE = 'source'

INPUT_SOURCES = 'sources'

INPUT_SOURCE_TYPE = 'source_type'

INPUT_SOURCE_TYPE_DIR = 'dir'

INPUT_SOURCE_TYPE_FILE = 'file'

INPUT_SOURCE_TYPE_PATH = 'path'

INPUT_SOURCE_TYPE_STEP = 'step'

INPUT_SOURCE_TYPE_STRING = 'string'

INPUT_SOURCE_TYPE_URL = 'url'

PIPE_INPUT = 'pipe_input'

SETTINGS = 'settings'

SETTINGS_ADDITIONAL = 'additional'

SETTINGS_ARGUMENTS = 'arguments'

SETTINGS_ARGUMENTS_FLAGS = 'flags'

SETTINGS_ARGUMENTS_PARAMETERS = 'parameters'

STEPID = 'step_id'

STEP_ACTIVE_LEARNING = 'ACTIVE_LEARNING'

STEP_AUTODOCKVINA_DOCKING = 'VINA_DOCKING'

STEP_AUTODOCKVINA_TARGET_PREPARATION = 'VINA_TARGET_PREPARATION'

STEP_BOLTZMANN_WEIGHTING = 'BOLTZMANN_WEIGHTING'

STEP_CLUSTER = 'CLUSTER'

STEP_CLUSTERING = 'CLUSTERING'

STEP_COSMO = 'COSMO'

STEP_CREST = 'CREST'

STEP_DATA_MANIPULATION = 'DATA_MANIPULATION'

STEP_DESMOND = 'DESMOND'

STEP_DESMOND_SETUP = 'DESMOND_SETUP'

STEP_DISPATCHER = 'DISPATCHER'

STEP_DO_DSSP = 'DO_DSSP'

STEP_DSSP = 'DSSP'

STEP_EDITCONF = 'EDITCONF'

STEP_EMBEDDING = 'EMBEDDING'

STEP_ESP_SIM = 'ESP_SIM'

STEP_FEATURE_COUNTER = 'FEATURE_COUNTER'

STEP_FEP_ABSOLUTE = 'FEP_ABSOLUTE'

STEP_FEP_PLUS_ANALYSIS = 'FEP_PLUS_ANALYSIS'

STEP_FEP_PLUS_EXEC = 'FEP_PLUS_EXEC'

STEP_FEP_PLUS_SETUP = 'FEP_PLUS_SETUP'

STEP_FILTER = 'FILTER'

STEP_GENION = 'GENION'

STEP_GLIDE = 'GLIDE'

STEP_GMX_MMPBSA = 'GMX_MMPBSA'

STEP_GMX_RMSD = 'GMX_RMSD'

STEP_GOLD_DOCKING = 'GOLD_DOCKING'

STEP_GROMPP = 'GROMPP'

STEP_INITIALIZATION = 'INITIALIZATION'

STEP_ITERATOR = 'ITERATOR'

STEP_JAZZY = 'JAZZY'

STEP_KALLISTO = 'KALLISTO'

STEP_LIGPREP = 'LIGPREP'

STEP_LOMAP = 'LOMAP'

STEP_MACROMODEL = 'MACROMODEL'

STEP_MDPOCKET = 'MDPOCKET'

STEP_MDRUN = 'MDRUN'

STEP_MODEL_BUILDING = 'MODEL_BUILDING'

STEP_OMEGA = 'OMEGA'

STEP_PANTHER = 'PANTHER'

STEP_PDB2GMX = 'PDB2GMX'

STEP_PDB_FIXER = 'PDB_FIXER'

STEP_PEPTIDE_EMBEDDER = 'PEPTIDE_EMBEDDER'

STEP_PKA_PREDICTION = 'PKA_PREDICTION'

STEP_PMX_ABFE_SETUP = 'PMX_ABFE_SETUP'

STEP_PMX_ANALYSE = 'PMX_ANALYSE'

STEP_PMX_ASSEMBLE_SYSTEMS = 'PMX_ASSEMBLE_SYSTEMS'

STEP_PMX_ATOMMAPPING = 'PMX_ATOMMAPPING'

STEP_PMX_BOX_WATER_IONS = 'PMX_BOX_WATER_IONS'

STEP_PMX_DOUBLEBOX = 'PMX_DOUBLEBOX'

STEP_PMX_GENLIB = 'PMX_GENLIB'

STEP_PMX_GENTOP = 'PMX_GENTOP'

STEP_PMX_LIGANDHYBRID = 'PMX_LIGANDHYBRID'

STEP_PMX_MUTATE = 'PMX_MUTATE'

STEP_PMX_PREPARE_SIMULATIONS = 'PMX_PREPARE_SIMULATIONS'

STEP_PMX_PREPARE_TRANSITIONS = 'PMX_PREPARE_TRANSITIONS'

STEP_PMX_RUN_ANALYSIS = 'PMX_RUN_ANALYSIS'

STEP_PMX_RUN_SIMULATIONS = 'PMX_RUN_SIMULATIONS'

STEP_PMX_SETUP = 'PMX_SETUP'

STEP_PREDICTION = 'PREDICTION'

STEP_PREPWIZARD = 'PREPWIZARD'

STEP_PRIME = 'PRIME'

STEP_PROSPECTIVE_REINVENT = 'PROSPECTIVE_REINVENT'

STEP_PROTEIN_INTERACTIONS = 'PROTEIN_INTERACTION'

STEP_RESIDUE_SCANNING = 'RESIDUE_SCANNING'

STEP_RMSD = 'RMSD'

STEP_RMSFILTER = 'RMSFILTER'

STEP_SHAEP = 'SHAEP'

STEP_SOLVATE = 'SOLVATE'

STEP_TRJCAT = 'TRJCAT'

STEP_TRJCONV = 'TRJCONV'

STEP_TS_CLUSTER = 'TS_CLUSTER'

STEP_TURBOMOLE = 'TURBOMOLE'

STEP_TYPE = 'type'

STEP_XTB = 'XTB'

TOKEN_GUARD = 'token_guard'

WRITEOUT = 'writeout'

WRITEOUT_COMP = 'compounds'

WRITEOUT_COMP_AGGREGATION = 'aggregation'

WRITEOUT_COMP_AGGREGATION_HIGHESTISBEST = 'highest_is_best'

WRITEOUT_COMP_AGGREGATION_KEY = 'key'

WRITEOUT_COMP_AGGREGATION_MODE = 'mode'

WRITEOUT_COMP_AGGREGATION_MODE_ALL = 'all'

WRITEOUT_COMP_AGGREGATION_MODE_BESTPERCOMPOUND = 'best_per_compound'

WRITEOUT_COMP_AGGREGATION_MODE_BESTPERENUMERATION = 'best_per_enumeration'

WRITEOUT_COMP_CATEGORY = 'category'

WRITEOUT_COMP_CATEGORY_CONFORMERS = 'conformers'

WRITEOUT_COMP_CATEGORY_ENUMERATIONS = 'enumerations'

WRITEOUT_COMP_CATEGORY_EXTRADATA = 'extra_data'

WRITEOUT_COMP_KEY = 'key'

WRITEOUT_COMP_SELECTED_TAGS = 'selected_tags'

WRITEOUT_COMP_SELECTED_TAGS_HIGHESTISBEST = 'highest_is_best'

WRITEOUT_COMP_SELECTED_TAGS_KEY = 'key'

WRITEOUT_CONFIG = 'config'

WRITEOUT_DESTINATION = 'destination'

WRITEOUT_DESTINATION_AUTOMATIC = 'automatic'

WRITEOUT_DESTINATION_BASE_NAME = 'base_name'

WRITEOUT_DESTINATION_DIR = 'dir'

WRITEOUT_DESTINATION_FORMAT = 'format'

WRITEOUT_DESTINATION_MERGE = 'merge'

WRITEOUT_DESTINATION_MODE = 'mode'

WRITEOUT_DESTINATION_RESOURCE = 'resource'

WRITEOUT_DESTINATION_TYPE = 'type'

WRITEOUT_DESTINATION_TYPE_FILE = 'file'

WRITEOUT_DESTINATION_TYPE_REINVENT = 'reinvent'

WRITEOUT_DESTINATION_TYPE_REST = 'rest'

WRITEOUT_DESTINATION_TYPE_STDERR = 'stderr'

WRITEOUT_DESTINATION_TYPE_STDOUT = 'stdout'

WRITEOUT_GENERIC = 'generic'

WRITEOUT_GENERIC_KEY = 'key'

WRITEOUT_GMX = 'gmx_state'

class icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum

Bases: object

PROPERTIES = 'properties'

PROPERTIES_INPUT = 'input'

PROPERTIES_OUTPUT = 'output'

WEIGHT = 'weight'

WEIGHT_INPUT = 'input'

WEIGHT_OUTPUT_PREFIX = 'output_prefix'

WEIGHT_PROPERTIES = 'properties'

class icolos.utils.enums.step_enums.StepCavExploreEnum

Bases: object

CAVITY_CONFIG_DIR = 'cavity_config_dir'

CAVITY_CONFIG_FILE = 'cavity_config_file'

CAVITY_LOCATION = 'cavity_location'

EPS = 'eps'

FIELDS = 'fields'

FIELD_KEY_CMS = 'cms'

FIELD_KEY_DTR = 'dtr'

FIELD_KEY_DX = 'dx'

FRAME_LIST_FILE = 'list_of_frames.txt'

ISO_VALUE = 'iso_value'

MDPOCKET_COMMAND = 'mdpocket'

MIN_SAMPLES = 'min_samples'

MPI_THREADS = 'mpi_threads'

NAME_CA = 'name CA'

OUTPUT_FILE = 'output_file'

PROTEIN = 'protein'

SELECTION_TEXT = 'selection_text'

THRESHOLD = 'threshold'

TRAJ_TYPE = 'format'

class icolos.utils.enums.step_enums.StepClusteringEnum

Bases: object

FEATURES = 'features'

FREE_ENERGY_SOLVENT_TAGS = 'free_energy_solvent_tags'

MAX_ITER = 'max_iter'

N_CLUSTERS = 'n_clusters'

TOP_N_PER_SOLVENT = 'top_n_per_solvent'

class icolos.utils.enums.step_enums.StepCressetEnum

Bases: object

SUCCESS = 'success'

class icolos.utils.enums.step_enums.StepDSSPEnum

Bases: object

class icolos.utils.enums.step_enums.StepDataManipulationEnum

Bases: object

ACTION = 'action'

ACTION_ATTACH_CONFORMERS_AS_EXTRA = 'attach_conformers_as_extra'

ACTION_NO_ACTION = 'no_action'

ASSEMBLE_COMPLEXES = 'assemble_complexes'

COLLECT_ITERATOR_RESULTS = 'collect_iterator_results'

COMPUTE_MCS = 'compute_mcs'

CONVERT_MAE_TO_PDB = 'mae2pdb'

FILTER = 'filter'

KEY_MATCHED = 'matched'

MATCH_SOURCE = 'source'

RECEPTOR = 'receptor'

class icolos.utils.enums.step_enums.StepDesmondEnum

Bases: object

CFG_FIELDS = 'cfg_fields'

CONFIG = 'config'

MSJ_FIELDS = 'msj_fields'

PREPROCESS_MSJ = 'config.msj'

PRODUCTION_CFG = 'prod.cfg'

PRODUCTION_MSJ = 'production.msj'

SETUP_MSJ_FIELDS = 'setup_msj_fields'

TOKEN_STR = 'DESMOND_GPGPU:16'

class icolos.utils.enums.step_enums.StepEmbeddingEnum

Bases: object

EMBED_AS = 'embed_as'

EMBED_AS_CONFORMERS = 'conformers'

EMBED_AS_ENUMERATIONS = 'enumerations'

METHOD = 'method'

METHOD_RDKIT = 'RDKIT'

RDKIT_PROTONATE = 'protonate'

class icolos.utils.enums.step_enums.StepFeatureCounterEnum

Bases: object

FEATURE = 'feature'

LEVEL = 'level'

LEVEL_CONFORMER = 'conformer'

LEVEL_ENUMERATION = 'enumeration'

class icolos.utils.enums.step_enums.StepFepPlusEnum

Bases: object

DATA_TERMINUS = 'fep_mapper_cleanup: Loading output graph'

EDGE_HEADER_LINE = '* Edge calculated properties (units in kcal/mol)'

FEP_EXEC_COMPLETE = 'Multisim completed.'

FEP_EXEC_PARTIAL_COMPLETE = 'Multisim partially completed.'

FEP_MAPPER_OUTPUT = 'out'

FIELD_KEY_POSEVIEWER = 'poseviewer'

FILE_NAME = '--name'

FMP_OUTPUT_FILE = 'out.fmp'

HOST_FLAG = '-HOST'

JOBID_STRING = 'JobId:'

JOBNAME_FLAG = '-JOBNAME'

LOGFILE = 'multisim.log'

NODE_HEADER_LINE = '* Node calculated properties (units in kcal/mol)'

RECEPTOR_MAEGZ = 'receptor.maegz'

REFERENCE_DG = 'ref_dg'

RETRIES = '-RETRIES'

SIMILARITY = '* Similarity'

SIMULATION_PROTOCOL = '* Simulation Protocol'

STRUCTCAT_MAEGZ_OUTFILE = 'concatenated.mae'

STRUCTCAT_SDF_OUTFILE = 'concatenated.sdf'

STRUCT_SPLIT_BASE = 'split'

WAIT_FLAG = '-WAIT'

XRAY_SPLIT = 'xray_split'

XRAY_STRUCTURES = 'xray_structures'

class icolos.utils.enums.step_enums.StepFilterEnum

Bases: object

AGGREGATION = 'aggregation'

COMPOUNDS = 'compounds'

CONFORMERS = 'conformers'

CRITERIA = 'criteria'

ENUMERATIONS = 'enumerations'

FILTER_LEVEL = 'filter_level'

HIGHEST_IS_BEST = 'highest_is_best'

RETURN_N = 'return_n'

class icolos.utils.enums.step_enums.StepGlideEnum

Bases: object

CONFIGURATION = 'configuration'

FILL_DUMMY_CONFS = 'fill_dummy_confs'

GLIDE_DOCKING_SCORE = 'r_i_docking_score'

GLIDE_GSCORE = 'r_i_glide_gscore'

GLIDE_LOG = '.log'

GLIDE_MAEGZ_DEFAULT_EXTENSION = '_pv.maegz'

GLIDE_POSEVIEWER_FILE_KEY = 'structures_pv.maegz'

GLIDE_SDF = '.sdf'

GLIDE_SDF_DEFAULT_EXTENSION = '_lib.sdfgz'

GLIDE_SOURCE_FILE_INDEX = 'i_m_source_file_index'

MAESTRO_IN_FILE = 'maestro_in_file'

MAESTRO_IN_FILE_PATH = 'path'

TIME_LIMIT_PER_TASK = 'time_limit_per_task'

class icolos.utils.enums.step_enums.StepGoldEnum

Bases: object

AUTOMATIC_SETTINGS = 'AUTOMATIC SETTINGS'

AUTOSCALE = 'autoscale'

BLOCK_INDENT = '  '

CAVITY_FILE = 'cavity_file'

CONFIGURATION = 'configuration'

CONFIGURATION_START = 'GOLD CONFIGURATION FILE'

CONSTRAINTS = 'CONSTRAINTS'

COVALENT_BONDING = 'COVALENT BONDING'

DATA_FILES = 'DATA FILES'

FITNESS_FUNCTION_SETTINGS = 'FITNESS FUNCTION SETTINGS'

FLAGS = 'FLAGS'

FLOOD_FILL = 'FLOOD FILL'

GENETIC_OPERATORS = 'GENETIC OPERATORS'

GOLD_CONFIG_FILE = 'gold_config_file'

GOLD_FITFUNC_PATH = 'gold_fitfunc_path'

LIGAND_DATA_FILE = 'ligand_data_file'

POPULATION = 'POPULATION'

PROTEIN_DATA = 'PROTEIN DATA'

PROTEIN_DATAFILE = 'protein_datafile'

SAVE_OPTIONS = 'SAVE OPTIONS'

TERMINATION = 'TERMINATION'

class icolos.utils.enums.step_enums.StepGoldTargetPreparationEnum

Bases: object

class icolos.utils.enums.step_enums.StepGromacsEnum

Bases: object

AMBERTOOLS_PREFIX = 'ambertools_prefix'

AUTO = 'auto'

CHARGE_METHOD = 'charge_method'

CLUSTERS_NUMBER = 'clustersNumber'

COFACTORS = 'cofactors'

COMPLEX_PDB = 'Complex.pdb'

COMPLEX_TOP = 'Complex.top'

COUPLING_GROUP = 'Other'

COUPLING_GROUPS = 'coupling_groups'

DEFAULT_MMPBSA_IN = 'src/icolos/config/amber/default_mmpbsa.in'

FIELDS = 'fields'

FIELD_KEY_CPT = 'cpt'

FIELD_KEY_EDR = 'edr'

FIELD_KEY_ITP = 'itp'

FIELD_KEY_LOG = 'log'

FIELD_KEY_MDP = 'mdp'

FIELD_KEY_NDX = 'ndx'

FIELD_KEY_PDB = 'pdb'

FIELD_KEY_STRUCTURE = 'gro'

FIELD_KEY_TOPOL = 'top'

FIELD_KEY_TPR = 'tpr'

FIELD_KEY_XTC = 'xtc'

FILE_SIZE_THRESHOLD = 2000000000

FORCEFIELD = 'forcefield'

FORCEFIELD_ITP = 'forcefield.itp'

FORCE_CONSTANTS = '1000 1000 1000'

GAFF = 'gaff'

GROMACS_LOAD = 'module load GROMACS/2021-fosscuda-2019a-PLUMED-2.7.1-Python-3.7.2'

INCLUDE_LIG_ITP = '#include "Ligand.itp"'

INDEX_FLAG = '-n'

INPUT_FILE = 'input_file'

LENGTHS = 'lengths'

LIGAND_ITP = 'Ligand.itp'

LIGAND_MOL2 = 'Ligand.mol2'

LIGAND_PDB = 'Ligand.pdb'

LIG_ID = 'lig_id'

LIG_MOLECULE_GRP = 'Ligand   1\n'

MAKE_NDX_COMMAND = 'make_ndx_command'

MMGBSA_DG = 'MMGBSA_DG'

MMPBSA_IN = 'mmpbsa.in'

MULTIDIR = 'multidir'

OPENFF = 'openff'

PARAM_METHOD = 'param_method'

POSRE_LIG = 'posre_lig.itp'

PROPS = 'props'

PROTEIN_OTHER = 'Protein_Other'

PROTEIN_PDB = 'Protein.pdb'

PROTEIN_TOP = 'Protein.top'

REPLICAS = 'replicas'

RESTRAINTS = 'restraints'

SIM_COMPLETE = 'Finished mdrun'

STD_CPT = 'state.cpt'

STD_EDR = 'ener.edr'

STD_INDEX = 'index.ndx'

STD_LOG = 'md.log'

STD_STRUCTURE = 'confout.gro'

STD_TOPOL = 'topol.top'

STD_TPR = 'topol.tpr'

STD_TRR = 'traj.trr'

STD_XTC = 'traj.xtc'

TC_GRPS = 'tc-grps'

THREADS = 'threads'

WATER_AND_IONS = 'Water_and_ions'

WATER_POSRE = '\n#ifdef POSRES_WATER\n[ position_restraints ]\n;  i funct       fcx        fcy        fcz\n   1    1       1000       1000       1000\n#endif\n'

class icolos.utils.enums.step_enums.StepJazzyEnum

Bases: object

FAILURE = 'failure'

SUCCESS = 'success'

class icolos.utils.enums.step_enums.StepKallistoEnum

Bases: object

FAILURE = 'failure'

FEATURES = 'features'

SUCCESS = 'success'

class icolos.utils.enums.step_enums.StepLigprepEnum

Bases: object

FILTER_FILE = 'filter_file'

LIGPREP_TAUTOMER_PROBABILITY = 'r_lp_tautomer_probability'

LIGPREP_VARIANTS = 's_lp_Variant'

class icolos.utils.enums.step_enums.StepMacromodelEnum

Bases: object

COM_FILE = 'com_file'

COM_FILE_DEFAULT = ' MMOD       0      1      0      0     0.0000     0.0000     0.0000     0.0000\n DEBG      55      0      0      0     0.0000     0.0000     0.0000     0.0000\n FFLD      16      1      0      0     1.0000     0.0000     0.0000     0.0000\n SOLV       3      1      0      0     0.0000     0.0000     0.0000     0.0000\n EXNB       0      0      0      0     0.0000     0.0000     0.0000     0.0000\n BDCO       0      0      0      0    89.4427 99999.0000     0.0000     0.0000\n READ       0      0      0      0     0.0000     0.0000     0.0000     0.0000\n CRMS       0      0      0      0     0.0000     0.8000     0.0000     0.0000\n LMCS    1000      0      0      0     0.0000     0.0000     3.0000     6.0000\n NANT       0      0      0      0     0.0000     0.0000     0.0000     0.0000\n MCNV       1      5      0      0     0.0000     0.0000     0.0000     0.0000\n MCSS       2      0      0      0    27.0000     0.0000     0.0000     0.0000\n MCOP       1      0      0      0     0.5000     0.0000     0.0000     0.0000\n DEMX       0    833      0      0    27.0000    54.0000     0.0000     0.0000\n MSYM       0      0      0      0     0.0000     0.0000     0.0000     0.0000\n AUOP       0      0      0      0   100.0000     0.0000     0.0000     0.0000\n AUTO       0      2      1      1     0.0000     1.0000     0.0000     2.0000\n CONV       2      0      0      0     0.0500     0.0000     0.0000     0.0000\n MINI       1      0   2500      0     0.0000     0.0000     0.0000     0.0000'

COM_FILE_PATH = 'com_file.com'

MAE_INPUT = 'input_mol.mae'

MAE_OUTPUT = 'output_mol.mae'

SDF_OUTPUT = 'output_mol.sdf'

class icolos.utils.enums.step_enums.StepModelBuilderEnum

Bases: object

DATA = 'data'

DATA_INPUT_COLUMN = 'input_column'

DATA_RESPONSE_COLUMN = 'response_column'

DATA_TESTSET_FILE = 'test_dataset_file'

DATA_TRAININGSET_FILE = 'training_dataset_file'

FIELD_KEY_BEST_CONFIGURATION = 'best_configuration'

FIELD_KEY_INPUT_DATA = 'input_data'

FIELD_KEY_PRODUCTION_MODEL = 'production_model'

TMP_INPUT_CONFIG = 'input_config.json'

TMP_INPUT_DATA = 'input_data.csv'

TMP_OUTPUT_BEST_MODEL = 'best_model.pkl'

TMP_OUTPUT_BEST_PARAMETERS = 'best_parameters.json'

TMP_OUTPUT_PRODUCTION_MODEL = 'production_model.pkl'

class icolos.utils.enums.step_enums.StepOpenFFEnum

Bases: object

FORCEFIELD = 'off_forcefield'

INTERCHANGE = 'interchange'

METHOD = 'method'

PARMED = 'parmed'

UNIQUE_MOLS = 'unique_molecules'

class icolos.utils.enums.step_enums.StepPMXSetupEnum

Bases: object

CHARGE_METHOD = 'charge_method'

REPLICAS = 'replicas'

class icolos.utils.enums.step_enums.StepPantherEnum

Bases: object

FIELDS = 'fields'

FIELDS_PARAMETERS_LIB = {'2-Radius': 'rad.lib', '3-Angle': 'angles.lib', '4-Charge': 'charges.lib'}

FIELD_KEY_COORDINATES = '5-Center'

FIELD_KEY_NEGATIVE_IMAGE = 'negative_image'

FIELD_KEY_PDB_FILE = '1-Pdb file'

OUTPUT_FILE = 'output_file'

PANTHER_CONFIG_DIR = 'panther_config_file'

PANTHER_CONFIG_FILE = 'panther_config_file'

PANTHER_LOCATION = 'panther_location'

class icolos.utils.enums.step_enums.StepPdbFixerEnum

Bases: object

ADD_MISSING_ATOMS = 'add_missing_atoms'

ADD_MISSING_HYDROGENS = 'add_missing_hydrogens'

FIND_MISSING_ATOMS = 'find_missing_atoms'

FIND_MISSING_RESIDUES = 'find_missing_residues'

REMOVE_CHAINS = 'remove_chains'

REPLACE_NONSTANDARD_RESIDUES = 'replace_nonstandard_residues'

class icolos.utils.enums.step_enums.StepPredictorEnum

Bases: object

FEATURES = 'features'

MODEL_PATH = 'model_path'

NAME_PREDICTED = 'name_predicted'

NAME_PREDICTED_DEFAULT = 'pred_value'

class icolos.utils.enums.step_enums.StepPrepwizEnum

Bases: object

COFACTOR_IDS = ['TDP', 'FAD', 'FMN', 'NAD', 'PNS', 'COA', 'PLP', 'GSH', 'BTN', 'FFO', 'B12', 'ASC', 'MQ7', 'UQ1', 'MGD', 'H4B', 'MDO', 'SAM', 'F43', 'COM', 'TP7', 'HEA', 'DPM', 'PQQ', 'TPQ', 'TRQ', 'LPA', 'HEM']

LIGANDS = 'ligands'

REMOVE_RES = 'remove_res'

class icolos.utils.enums.step_enums.StepPrimeEnum

Bases: object

MAE_COMPLEX = 'complex.mae'

MAE_INPUT = 'input_mol.mae'

MAE_OUTPUT = 'complex-out.maegz'

MMGBSA_SCORE = 'r_psp_MMGBSA_dG_Bind'

POSEVIEWER = 'poseviewer'

RECEPTOR = 'receptor'

SDF_INPUT = 'input_mol.sdf'

SDF_OUTPUT = 'output_mol.sdf'

class icolos.utils.enums.step_enums.StepRMSDEnum

Bases: object

METHOD = 'method'

METHOD_ALIGNMOL = 'alignmol'

METHOD_BEST = 'best'

RMSD_TAG = 'rmsd'

class icolos.utils.enums.step_enums.StepRMSFilterEnum

Bases: object

METHOD = 'method'

METHOD_ALIGNMOL = 'alignmol'

METHOD_BEST = 'best'

ORDER_ASCENDING = 'ascending'

ORDER_BY = 'order_by'

THRESHOLD = 'threshold'

class icolos.utils.enums.step_enums.StepShaepEnum

Bases: object

FIELD_KEY_NEGATIVE_IMAGE = 'negative_image'

NEG_IMAGE_EXT = 'mol2'

class icolos.utils.enums.step_enums.StepTurbomoleEnum

Bases: object

EXECUTION_MODE = 'execution_mode'

FAILED = 'failed'

SUCCESS = 'success'

class icolos.utils.enums.step_enums.TokenGuardEnum

Bases: object

TG = 'token_guard'

TG_BINARY_LOCATION = 'binary_location'

TG_PREFIX_EXECUTION = 'prefix_execution'

TG_TOKEN_POOLS = 'token_pools'

TG_WAIT_INTERVAL_SECONDS = 'wait_interval_seconds'

TG_WAIT_LIMIT_SECONDS = 'wait_limit_seconds'

icolos.utils.enums.step_initialization_enum module

class icolos.utils.enums.step_initialization_enum.StepInitializationEnum

Bases: object

STEP_INIT_DICT = {StepBaseEnum.STEP_BOLTZMANN_WEIGHTING: <class 'icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting'>, StepBaseEnum.STEP_CLUSTER: <class 'icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster'>, StepBaseEnum.STEP_CLUSTERING: <class 'icolos.core.workflow_steps.calculation.clustering.StepClustering'>, StepBaseEnum.STEP_COSMO: <class 'icolos.core.workflow_steps.calculation.cosmo.StepCosmo'>, StepBaseEnum.STEP_CREST: <class 'icolos.core.workflow_steps.confgen.crest.StepCREST'>, StepBaseEnum.STEP_DATA_MANIPULATION: <class 'icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation'>, StepBaseEnum.STEP_DESMOND: <class 'icolos.core.workflow_steps.schrodinger.desmond_exec.StepDesmondExec'>, StepBaseEnum.STEP_DESMOND_SETUP: <class 'icolos.core.workflow_steps.schrodinger.desmond_preprocessor.StepDesmondSetup'>, StepBaseEnum.STEP_DISPATCHER: <class 'icolos.core.step_dispatch.dispatcher.StepDispatcher'>, StepBaseEnum.STEP_DO_DSSP: <class 'icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP'>, StepBaseEnum.STEP_DSSP: <class 'icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP'>, StepBaseEnum.STEP_EDITCONF: <class 'icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf'>, StepBaseEnum.STEP_EMBEDDING: <class 'icolos.core.workflow_steps.io.embedder.StepEmbedding'>, StepBaseEnum.STEP_ESP_SIM: <class 'icolos.core.workflow_steps.calculation.esp_sim.StepEspSim'>, StepBaseEnum.STEP_FEATURE_COUNTER: <class 'icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter'>, StepBaseEnum.STEP_FEP_ABSOLUTE: <class 'icolos.core.workflow_steps.schrodinger.fep_absolute.StepSchrodingerAbsoluteFEP'>, StepBaseEnum.STEP_FEP_PLUS_ANALYSIS: <class 'icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis'>, StepBaseEnum.STEP_FEP_PLUS_EXEC: <class 'icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec'>, StepBaseEnum.STEP_FEP_PLUS_SETUP: <class 'icolos.core.workflow_steps.schrodinger.fep_plus_setup.StepFepPlusSetup'>, StepBaseEnum.STEP_GENION: <class 'icolos.core.workflow_steps.gromacs.genion.StepGMXGenion'>, StepBaseEnum.STEP_GLIDE: <class 'icolos.core.workflow_steps.schrodinger.glide.StepGlide'>, StepBaseEnum.STEP_GMX_MMPBSA: <class 'icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa'>, StepBaseEnum.STEP_GMX_RMSD: <class 'icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd'>, StepBaseEnum.STEP_GOLD_DOCKING: <class 'icolos.core.workflow_steps.ccdc.docking.StepGold'>, StepBaseEnum.STEP_GROMPP: <class 'icolos.core.workflow_steps.gromacs.grompp.StepGMXGrompp'>, StepBaseEnum.STEP_INITIALIZATION: <class 'icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound'>, StepBaseEnum.STEP_JAZZY: <class 'icolos.core.workflow_steps.calculation.jazzy.StepJazzy'>, StepBaseEnum.STEP_KALLISTO: <class 'icolos.core.workflow_steps.calculation.kallisto.StepKallisto'>, StepBaseEnum.STEP_LIGPREP: <class 'icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep'>, StepBaseEnum.STEP_LOMAP: <class 'icolos.core.workflow_steps.calculation.lomap.StepLomap'>, StepBaseEnum.STEP_MACROMODEL: <class 'icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel'>, StepBaseEnum.STEP_MDPOCKET: <class 'icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket'>, StepBaseEnum.STEP_MDRUN: <class 'icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun'>, StepBaseEnum.STEP_MODEL_BUILDING: <class 'icolos.core.workflow_steps.prediction.model_building.StepModelBuilder'>, StepBaseEnum.STEP_OMEGA: <class 'icolos.core.workflow_steps.confgen.omega.StepOmega'>, StepBaseEnum.STEP_PANTHER: <class 'icolos.core.workflow_steps.calculation.panther.StepPanther'>, StepBaseEnum.STEP_PDB2GMX: <class 'icolos.core.workflow_steps.gromacs.pdb2gmx.StepGMXPdb2gmx'>, StepBaseEnum.STEP_PDB_FIXER: <class 'icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer'>, StepBaseEnum.STEP_PEPTIDE_EMBEDDER: <class 'icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder'>, StepBaseEnum.STEP_PMX_ABFE_SETUP: <class 'icolos.core.workflow_steps.pmx.abfe.StepPMXabfe'>, StepBaseEnum.STEP_PMX_ASSEMBLE_SYSTEMS: <class 'icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems'>, StepBaseEnum.STEP_PMX_ATOMMAPPING: <class 'icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping'>, StepBaseEnum.STEP_PMX_BOX_WATER_IONS: <class 'icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons'>, StepBaseEnum.STEP_PMX_DOUBLEBOX: <class 'icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox'>, StepBaseEnum.STEP_PMX_GENLIB: <class 'icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib'>, StepBaseEnum.STEP_PMX_GENTOP: <class 'icolos.core.workflow_steps.pmx.gentop.StepPMXgentop'>, StepBaseEnum.STEP_PMX_LIGANDHYBRID: <class 'icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid'>, StepBaseEnum.STEP_PMX_MUTATE: <class 'icolos.core.workflow_steps.pmx.mutate.StepPMXmutate'>, StepBaseEnum.STEP_PMX_PREPARE_SIMULATIONS: <class 'icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations'>, StepBaseEnum.STEP_PMX_PREPARE_TRANSITIONS: <class 'icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions'>, StepBaseEnum.STEP_PMX_RUN_ANALYSIS: <class 'icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis'>, StepBaseEnum.STEP_PMX_RUN_SIMULATIONS: <class 'icolos.core.workflow_steps.pmx.run_simulations.StepPMXRunSimulations'>, StepBaseEnum.STEP_PMX_SETUP: <class 'icolos.core.workflow_steps.pmx.setup_workpath.StepPMXSetup'>, StepBaseEnum.STEP_PREDICTION: <class 'icolos.core.workflow_steps.prediction.predictor.StepPredictor'>, StepBaseEnum.STEP_PREPWIZARD: <class 'icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard'>, StepBaseEnum.STEP_PRIME: <class 'icolos.core.workflow_steps.schrodinger.prime.StepPrime'>, StepBaseEnum.STEP_PROSPECTIVE_REINVENT: <class 'icolos.core.workflow_steps.active_learning.prospective_reinvent.StepProspectiveREINVENT'>, StepBaseEnum.STEP_PROTEIN_INTERACTIONS: <class 'icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction'>, StepBaseEnum.STEP_RESIDUE_SCANNING: <class 'icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning'>, StepBaseEnum.STEP_RMSD: <class 'icolos.core.workflow_steps.calculation.rmsd.StepRMSD'>, StepBaseEnum.STEP_RMSFILTER: <class 'icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter'>, StepBaseEnum.STEP_SHAEP: <class 'icolos.core.workflow_steps.calculation.shaep.StepShaep'>, StepBaseEnum.STEP_SOLVATE: <class 'icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate'>, StepBaseEnum.STEP_TRJCAT: <class 'icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat'>, StepBaseEnum.STEP_TRJCONV: <class 'icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv'>, StepBaseEnum.STEP_TS_CLUSTER: <class 'icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS'>, StepBaseEnum.STEP_TURBOMOLE: <class 'icolos.core.workflow_steps.calculation.turbomole.StepTurbomole'>, StepBaseEnum.STEP_AUTODOCKVINA_DOCKING: <class 'icolos.core.workflow_steps.autodockvina.docking.StepAutoDockVina'>, StepBaseEnum.STEP_AUTODOCKVINA_TARGET_PREPARATION: <class 'icolos.core.workflow_steps.autodockvina.target_preparation.StepAutoDockVinaTargetPreparation'>, StepBaseEnum.STEP_XTB: <class 'icolos.core.workflow_steps.confgen.xtb.StepXTB'>}

icolos.utils.enums.write_out_enums module

class icolos.utils.enums.write_out_enums.RunVariablesEnum

Bases: object

COMPOUND_ID = 'compound_id'

COMPOUND_NAME = 'compound_name'

CONFORMER_ID = 'conformer_id'

CONFORMER_STRING = 'conformer_string'

ENUMERATION_ID = 'enumeration_id'

ENUMERATION_STRING = 'enumeration_string'

POSTFIX = ']'

PREFIX = '['

class icolos.utils.enums.write_out_enums.WriteOutEnum

Bases: object

COMPOUND_NAME = 'compound_name'

INDEX_STRING = 'index_string'

JSON_NA = ''

JSON_NAMES = 'names'

JSON_RESULTS = 'results'

JSON_VALUES = 'values'

JSON_VALUES_KEY = 'values_key'

PDB = 'pdb'

RDKIT_NAME = '_Name'

SDF = 'sdf'

Module contents