ConvertFile

task: Enter
subtask: Convert
host: chemml
function: ConvertFile
input tokens (receivers): file_path : the path to the file that needs to be converted

types: (“<type ‘str’>”, “<type ‘dict’>”)
output tokens (senders): converted_file_paths : list of paths to the converted files

types: <type ‘list’>
required packages: ChemML, 0.4.1

Babel, 2.3.4
config file view: ##

<< host = chemml << function = ConvertFile

<< to_format = required_required

<< file_path = required_required

<< from_format = required_required

>> id file_path

>> id converted_file_paths

Note

The documentation page for function parameters: https://openbabel.org/wiki/Babel

PyScript

task: Enter
subtask: python script
host: chemml
function: PyScript
input tokens (receivers): iv4 : input variable, of any format

types: ()

iv5 : input variable, of any format

types: ()

iv6 : input variable, of any format

types: ()

iv1 : input variable, of any format

types: ()

iv2 : input variable, of any format

types: ()

iv3 : input variable, of any format

types: ()
output tokens (senders): ov2 : output variable, of any format

types: ()

ov3 : output variable, of any format

types: ()

ov1 : output variable, of any format

types: ()

ov6 : output variable, of any format

types: ()

ov4 : output variable, of any format

types: ()

ov5 : output variable, of any format

types: ()
required packages: ChemML, 0.4.1

pandas, 0.20.3
config file view: ##

<< host = chemml << function = PyScript

<< line08 = type python code

<< line09 = type python code

<< line01 = type python code

<< line02 = input tokens are available as ...

<< line03 = ... python variables

<< line04 = type python code

<< line05 = type python code

<< line20 = type python code

<< line07 = type python code

<< line06 = type python code

<< line17 = type python code

<< line16 = type python code

<< line15 = type python code

<< line14 = type python code

<< line13 = type python code

<< line12 = type python code

<< line11 = type python code

<< line10 = type python code

<< line19 = type python code

<< line18 = type python code

>> id iv4

>> id iv5

>> id iv6

>> id iv1

>> id iv2

>> id iv3

>> id ov2

>> id ov3

>> id ov1

>> id ov6

>> id ov4

>> id ov5

Note

The documentation page for function parameters:

XYZreader

task: Enter
subtask: xyz
host: chemml
function: XYZreader
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): molecules : dictionary of molecules with [‘mol’, ‘file’] keys

types: (“<type ‘dict’>”,)
required packages: ChemML, 0.4.1
config file view: ##

<< host = chemml << function = XYZreader

<< path_root = None

<< skip_lines = [2, 0]

<< reader = auto

<< path_pattern = required_required

<< Z = {'Ru': 44.0, 'Re': 75.0, 'Rf': 104.0, 'Rg': 111.0, 'Ra': 88.0, 'Rb': 37.0, 'Rn': 86.0, 'Rh': 45.0, 'Be': 4.0, 'Ba': 56.0, 'Bh': 107.0, 'Bi': 83.0, 'Bk': 97.0, 'Br': 35.0, 'H': 1.0, 'P': 15.0, 'Os': 76.0, 'Ge': 32.0, 'Gd': 64.0, 'Ga': 31.0, 'Pr': 59.0, 'Pt': 78.0, 'Pu': 94.0, 'C': 6.0, 'Pb': 82.0, 'Pa': 91.0, 'Pd': 46.0, 'Cd': 48.0, 'Po': 84.0, 'Pm': 61.0, 'Hs': 108.0, 'Uup': 115.0, 'Uus': 117.0, 'Uuo': 118.0, 'Ho': 67.0, 'Hf': 72.0, 'Hg': 80.0, 'He': 2.0, 'Md': 101.0, 'Mg': 12.0, 'K': 19.0, 'Mn': 25.0, 'O': 8.0, 'Mt': 109.0, 'S': 16.0, 'W': 74.0, 'Zn': 30.0, 'Eu': 63.0, 'Zr': 40.0, 'Er': 68.0, 'Ni': 28.0, 'No': 102.0, 'Na': 11.0, 'Nb': 41.0, 'Nd': 60.0, 'Ne': 10.0, 'Np': 93.0, 'Fr': 87.0, 'Fe': 26.0, 'Fl': 114.0, 'Fm': 100.0, 'B': 5.0, 'F': 9.0, 'Sr': 38.0, 'N': 7.0, 'Kr': 36.0, 'Si': 14.0, 'Sn': 50.0, 'Sm': 62.0, 'V': 23.0, 'Sc': 21.0, 'Sb': 51.0, 'Sg': 106.0, 'Se': 34.0, 'Co': 27.0, 'Cn': 112.0, 'Cm': 96.0, 'Cl': 17.0, 'Ca': 20.0, 'Cf': 98.0, 'Ce': 58.0, 'Xe': 54.0, 'Tm': 69.0, 'Cs': 55.0, 'Cr': 24.0, 'Cu': 29.0, 'La': 57.0, 'Li': 3.0, 'Lv': 116.0, 'Tl': 81.0, 'Lu': 71.0, 'Lr': 103.0, 'Th': 90.0, 'Ti': 22.0, 'Te': 52.0, 'Tb': 65.0, 'Tc': 43.0, 'Ta': 73.0, 'Yb': 70.0, 'Db': 105.0, 'Dy': 66.0, 'Ds': 110.0, 'At': 85.0, 'I': 53.0, 'In': 49.0, 'U': 92.0, 'Y': 39.0, 'Ac': 89.0, 'Ag': 47.0, 'Ir': 77.0, 'Am': 95.0, 'Al': 13.0, 'As': 33.0, 'Ar': 18.0, 'Au': 79.0, 'Es': 99.0, 'Uut': 113.0, 'Mo': 42.0}

>> id molecules

Note

The documentation page for function parameters:

load_cep_homo

task: Enter
subtask: datasets
host: chemml
function: load_cep_homo
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): smiles : pandas dataframe

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

homo : pandas dataframe

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

pandas, 0.20.3
config file view: ##

<< host = chemml << function = load_cep_homo

>> id smiles

>> id homo

Note

The documentation page for function parameters:

load_comp_energy

task: Enter
subtask: datasets
host: chemml
function: load_comp_energy
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): formation_energy : pandas dataframe

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

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 = load_comp_energy

>> id formation_energy

>> id entries

Note

The documentation page for function parameters:

load_crystal_structures

task: Enter
subtask: datasets
host: chemml
function: load_crystal_structures
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 = load_crystal_structures

>> id entries

Note

The documentation page for function parameters:

load_organic_density

task: Enter
subtask: datasets
host: chemml
function: load_organic_density
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): smiles : pandas dataframe

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

features : pandas dataframe

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

density : pandas dataframe

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

pandas, 0.20.3
config file view: ##

<< host = chemml << function = load_organic_density

>> id smiles

>> id features

>> id density

Note

The documentation page for function parameters:

load_xyz_polarizability

task: Enter
subtask: datasets
host: chemml
function: load_xyz_polarizability
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): coordinates : dictionary of molecules represented by their xyz coordinates and atomic numbers

types: (“<type ‘dict’>”,)

polarizability : pandas dataframe

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

pandas, 0.20.3
config file view: ##

<< host = chemml << function = load_xyz_polarizability

>> id coordinates

>> id polarizability

Note

The documentation page for function parameters:

read_excel

task: Enter
subtask: table
host: pandas
function: read_excel
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: pandas, 0.20.3
config file view: ##

<< host = pandas << function = read_excel

<< engine = None

<< squeeze = False

<< index_col = None

<< date_parser = None

<< na_values = None

<< parse_dates = False

<< dtype = None

<< skiprows = None

<< sheet_name = 0

<< header = 0

<< skip_footer = 0

<< convert_float = True

<< names = None

<< io = required_required

<< usecols = None

<< true_values = None

<< false_values = None

<< thousands = None

<< converters = None

>> id df

Note

The documentation page for function parameters: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_excel.html

read_table

task: Enter
subtask: table
host: pandas
function: read_table
input tokens (receivers): this block doesn’t receive anything
output tokens (senders): df : pandas dataframe

types: (“<class ‘pandas.core.frame.DataFrame’>”,)
required packages: pandas, 0.20.3
config file view: ##

<< host = pandas << function = read_table

<< comment = None

<< escapechar = None

<< float_precision = None

<< na_filter = True

<< iterator = False

<< sep = required_required

<< mangle_dupe_cols = True

<< skip_blank_lines = True

<< keep_default_na = True

<< false_values = None

<< header = infer

<< prefix = None

<< memory_map = False

<< names = None

<< skipfooter = 0

<< verbose = False

<< compact_ints = None

<< lineterminator = None

<< compression = infer

<< dayfirst = False

<< low_memory = True

<< encoding = None

<< parse_dates = False

<< skip_footer = 0

<< dtype = None

<< quotechar = "

<< thousands = None

<< converters = None

<< warn_bad_lines = True

<< as_recarray = None

<< engine = None

<< dialect = None

<< chunksize = None

<< tupleize_cols = None

<< na_values = None

<< infer_datetime_format = False

<< keep_date_col = False

<< use_unsigned = None

<< nrows = None

<< true_values = None

<< delim_whitespace = False

<< usecols = None

<< squeeze = False

<< buffer_lines = None

<< index_col = None

<< skipinitialspace = False

<< decimal = .

<< skiprows = None

<< filepath_or_buffer = required_required

<< date_parser = None

<< delimiter = None

<< error_bad_lines = True

<< doublequote = True

<< quoting = 0

>> id df

Note

The documentation page for function parameters: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_table.html