APEAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: APEAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = APEAttributeGenerator

<< packing_threshold = None

<< n_nearest_to_eval = None

<< radius_property = None

>> id entries

>> id df

Note

The documentation page for function parameters:

APRDFAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: APRDFAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = APRDFAttributeGenerator

<< cut_off_distance = 10.0

<< num_points = 6

<< elemental_properties = required_required

<< smooth_parameter = 4.0

>> id entries

>> id df

Note

The documentation page for function parameters:

BagofBonds

task: Represent
subtask: molecular descriptors
host: chemml
function: BagofBonds
input tokens (receivers): molecules : the molecule numpy array or data frame

types: (“<class ‘pandas.core.frame.DataFrame’>”, “<type ‘numpy.ndarray’>”, “<type ‘dict’>”)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = BagofBonds

<< const = 1

>> id molecules

>> id df

Note

The documentation page for function parameters:

ChargeDependentAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: ChargeDependentAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = ChargeDependentAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

ChemicalOrderingAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: ChemicalOrderingAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = ChemicalOrderingAttributeGenerator

<< weighted = True

<< shells = [1, 2, 3]

>> id entries

>> id df

Note

The documentation page for function parameters:

CompositionEntry

task: Represent
subtask: inorganic input
host: chemml
function: CompositionEntry
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = CompositionEntry

<< filepath = required_required

>> id entries

Note

The documentation page for function parameters:

CoordinationNumberAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: CoordinationNumberAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = CoordinationNumberAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

CoulombMatrix

task: Represent
subtask: molecular descriptors
host: chemml
function: CoulombMatrix
input tokens (receivers): molecules : the molecule numpy array or data frame

types: (“<class ‘pandas.core.frame.DataFrame’>”, “<type ‘numpy.ndarray’>”, “<type ‘dict’>”)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = CoulombMatrix

<< const = 1

<< CMtype = SC

<< nPerm = 3

<< max_n_atoms = auto

>> id molecules

>> id df

Note

The documentation page for function parameters:

CoulombMatrixAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: CoulombMatrixAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = CoulombMatrixAttributeGenerator

<< n_eigenvalues = 30

>> id entries

>> id df

Note

The documentation page for function parameters:

CrystalStructureEntry

task: Represent
subtask: inorganic input
host: chemml
function: CrystalStructureEntry
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = CrystalStructureEntry

<< directory_path = required_required

>> id entries

Note

The documentation page for function parameters:

DistanceMatrix

task: Represent
subtask: distance matrix
host: chemml
function: DistanceMatrix
input tokens (receivers): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = DistanceMatrix

<< norm_type = fro

<< nCores = 1

>> id df

>> id df

Note

The documentation page for function parameters:

Dragon

task: Represent
subtask: molecular descriptors
host: chemml
function: Dragon
input tokens (receivers): molfile : the molecule file path

types: (“<type ‘str’>”, “<type ‘dict’>”, “<type ‘list’>”)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
wrapper parameters: script : , (default:new)

choose one of: []
required packages: ChemML, 0.4.1

pandas, 0.20.3

Dragon, 7 or 6

lxml, 3.4.0
config file view: ##

<< host = chemml << function = Dragon

<< script = new

<< SaveExcludeConst = False

<< MaxSR = '35'

<< SaveFilePath = Dragon_descriptors.txt

<< output_directory = ./

<< DisconnectedCalculationOption = '0'

<< SaveExcludeNearConst = False

<< Add2DHydrogens = False

<< SaveProject = False

<< Decimal_Separator = .

<< SaveOnlyData = False

<< script = new

<< RejectDisconnectedStrucuture = False

<< SaveExclusionOptionsToVariables = False

<< LogEdge = True

<< LogPathWalk = True

<< SaveLabelsOnSeparateFile = False

<< version = 6

<< DefaultMolFormat = '1'

<< MaxSRDetour = '30'

<< HelpBrowser = /usr/bin/xdg-open

<< SaveExcludeRejectedMolecules = False

<< knimemode = False

<< RejectUnusualValence = False

<< SaveProjectFile = Dragon_project.drp

<< SaveStdOut = False

<< SaveFormatSubBlock = %b-%s-%n-%m.txt

<< blocks = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]

<< SaveExcludeCorrelated = False

<< molFile = required_required

<< consecutiveDelimiter = False

<< molInputFormat = SMILES

<< MaxAtomWalkPath = '2000'

<< SaveExcludeAllMisVal = False

<< SaveExcludeStdDev = False

<< Weights = ['Mass', 'VdWVolume', 'Electronegativity', 'Polarizability', 'Ionization', 'I-State']

<< external = False

<< RoundWeights = True

<< MaxSRforAllCircuit = '19'

<< fileName = None

<< RoundCoordinates = True

<< Missing_String = NaN

<< SaveExcludeMisVal = False

<< logFile = Dragon_log.txt

<< PreserveTemporaryProjects = True

<< SaveLayout = True

<< molInput = file

<< SaveFormatBlock = %b-%n.txt

<< MissingValue = NaN

<< SaveCorrThreshold = '0.95'

<< SaveType = singlefile

<< ShowWorksheet = False

<< delimiter = ,

<< RetainBiggestFragment = False

<< CheckUpdates = True

<< RoundDescriptorValues = True

<< SaveExcludeMisMolecules = False

<< SaveStdDevThreshold = '0.0001'

<< SaveFile = True

<< logMode = file

>> id molfile

>> id df

Note

The documentation page for function parameters:

EffectiveCoordinationNumberAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: EffectiveCoordinationNumberAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = EffectiveCoordinationNumberAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

ElementFractionAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: ElementFractionAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = ElementFractionAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

ElementPairPropertyAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: ElementPairPropertyAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = ElementPairPropertyAttributeGenerator

<< elemental_pair_properties = None

>> id entries

>> id df

Note

The documentation page for function parameters:

ElementalPropertyAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: ElementalPropertyAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
wrapper parameters: elemental_properties : , (default:None)

choose one of: []
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = ElementalPropertyAttributeGenerator

<< elemental_properties = None

<< use_default_properties = True

>> id entries

>> id df

Note

The documentation page for function parameters:

GCLPAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: GCLPAttributeGenerator
input tokens (receivers): energies : to be passed to the parameter energies

types: (“<class ‘pandas.core.frame.DataFrame’>”,)

phases : to be passed to the parameter phases

types: (“<class ‘pandas.core.frame.DataFrame’>”,)

entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = GCLPAttributeGenerator

<< count_phases = None

<< energies = []

<< phases = []

>> id energies

>> id phases

>> id entries

>> id df

Note

The documentation page for function parameters:

IonicCompoundProximityAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: IonicCompoundProximityAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = IonicCompoundProximityAttributeGenerator

<< max_formula_unit = 14

>> id entries

>> id df

Note

The documentation page for function parameters:

IonicityAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: IonicityAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = IonicityAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

LatticeSimilarityAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: LatticeSimilarityAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = LatticeSimilarityAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

LocalPropertyDifferenceAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: LocalPropertyDifferenceAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = LocalPropertyDifferenceAttributeGenerator

<< elemental_properties = required_required

<< shells = [1]

>> id entries

>> id df

Note

The documentation page for function parameters:

LocalPropertyVarianceAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: LocalPropertyVarianceAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = LocalPropertyVarianceAttributeGenerator

<< elemental_properties = required_required

<< shells = [1]

>> id entries

>> id df

Note

The documentation page for function parameters:

MeredigAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: MeredigAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = MeredigAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

PRDFAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: PRDFAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = PRDFAttributeGenerator

<< cut_off_distance = 10.0

<< n_points = 20

>> id entries

>> id df

Note

The documentation page for function parameters:

PackingEfficiencyAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: PackingEfficiencyAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = PackingEfficiencyAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

RDKitFingerprint

task: Represent
subtask: molecular descriptors
host: chemml
function: RDKitFingerprint
input tokens (receivers): molfile : the molecule file path

types: (“<type ‘str’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)

removed_rows : output variable, of any format

types: ()
required packages: ChemML, 0.4.1

pandas, 0.20.3

RDKit, 2016.03.1
config file view: ##

<< host = chemml << function = RDKitFingerprint

<< nBits = 1024

<< molfile = required_required

<< removeHs = True

<< vector = bit

<< radius = 2

<< arguments = []

<< path = None

<< FPtype = Morgan

>> id molfile

>> id df

>> id removed_rows

Note

The documentation page for function parameters:

StoichiometricAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: StoichiometricAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
wrapper parameters: use_default_norms : , (default:None)

choose one of: []
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = StoichiometricAttributeGenerator

<< use_default_norms = None

<< p_norms = None

>> id entries

>> id df

Note

The documentation page for function parameters:

StructuralHeterogeneityAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: StructuralHeterogeneityAttributeGenerator
input tokens (receivers): entries : list of entries from CrystalStructureEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = StructuralHeterogeneityAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

ValenceShellAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: ValenceShellAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = ValenceShellAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters:

YangOmegaAttributeGenerator

task: Represent
subtask: inorganic descriptors
host: chemml
function: YangOmegaAttributeGenerator
input tokens (receivers): entries : list of entries from CompositionEntry class.

types: (“<type ‘list’>”,)
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = YangOmegaAttributeGenerator

>> id entries

>> id df

Note

The documentation page for function parameters: