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: