Rowan RDKit

batch_charges

batch_charges(
    mols,
    method="aimnet2_wb97md3",
    engine="aimnet2",
    mode="auto",
    timeout=600,
    name="Charges API Workflow",
    folder_uuid=None,
)

Computes atom-centered charges for the given Molecules.

Parameters:

Name	Type	Description	Default
`mols`	`Iterable[RdkitMol]`	RDKit Molecule	required
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`engine`	`str`	Engine to run the charges. See list of available engines	`'aimnet2'`
`mode`	`str`	The mode to run the calculation in. See list of available modes for options.	`'auto'`
`timeout`	`int`	timeout in seconds	`600`
`name`	`str`	name of the job	`'Charges API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`list[ChargesResults]`	list of dictionaries with the charges and the conformer index

batch_conformers

batch_conformers(
    mols,
    num_conformers=10,
    method="aimnet2_wb97md3",
    mode="rapid",
    return_energies=False,
    timeout=600,
    name="Conformer API Workflow",
    folder_uuid=None,
)

Generate conformers for a Molecule.

Parameters:

Name	Type	Description	Default
`mols`	`Iterable[RdkitMol]`	RDKit molecule object	required
`num_conformers`		number of conformers to generate	`10`
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`mode`	`str`	conformer generation mode. See list of available modes for options.	`'rapid'`
`return_energies`	`bool`	whether to return energies in Hartree too	`False`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Conformer API Workflow'`

Returns:

Type	Description
`list[ConformerResult]`	list of dictonaries with RDKit Molecule and energies

batch_energy

batch_energy(
    mols,
    method="aimnet2_wb97md3",
    engine="aimnet2",
    mode="auto",
    timeout=600,
    name="Energy API Workflow",
    folder_uuid=None,
)

Computes the energy for the given molecule.

Parameters:

Name	Type	Description	Default
`mols`	`Iterable[RdkitMol]`	RDKit Molecule	required
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`engine`	`str`	Engine to run the energy. See list of available engines	`'aimnet2'`
`mode`	`str`	Mode to run the energy. See list of available modes for options.	`'auto'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Energy API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`list[list[ConformerEnergyResult]]`	list of dictionaries with the energy in Hartree and the conformer index

batch_optimize

batch_optimize(
    mols,
    method="aimnet2_wb97md3",
    engine="aimnet2",
    mode="auto",
    return_energies=False,
    timeout=600,
    name="Optimize API Workflow",
    folder_uuid=None,
)

Optimize each of a Molecule's conformers and then return the Molecule.

Parameters:

Name	Type	Description	Default
`mols`	`Iterable[RdkitMol]`	input Molecule	required
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`engine`	`str`	Engine to run the optimization. See list of available engines	`'aimnet2'`
`mode`	`str`	Mode to run the optimization. See list of available modes for options.	`'auto'`
`return_energies`	`bool`	whether to return energies in Hartree too	`False`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Optimize API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`list[OptimizeResult]`	dictionaries with optimized conformer(s) and optional list of energies per conformer

batch_pka

batch_pka(
    mols,
    mode="rapid",
    timeout=600,
    name="pKa API Workflow",
    pka_range=(2, 12),
    deprotonate_elements=None,
    protonate_elements=None,
    folder_uuid=None,
)

Calculate the pKa of a batch of Molecules.

Parameters:

Name	Type	Description	Default
`mols`	`Iterable[RdkitMol]`	list of RDKit Molecules	required
`mode`	`pKaMode`	pKa calculation mode. See list of available modes for options.	`'rapid'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'pKa API Workflow'`
`pka_range`	`tuple[int, int]`	range of pKa values to calculate	`(2, 12)`
`deprotonate_elements`	`list[int] \| None`	elements to deprotonate	`None`
`protonate_elements`	`list[int] \| None`	elements to protonate	`None`

Returns:

Type	Description
`list[PKaResults]`	list of dictionary of pKa values indexed by atom

batch_tautomers

batch_tautomers(
    mols, mode="reckless", timeout=600, name="Tautomers API Workflow", folder_uuid=None
)

Generate possible tautomers of a Molecule.

Parameters:

Name	Type	Description	Default
`mols`	`Iterable[RdkitMol]`	RDKit Molecule	required
`mode`	`TautomerMode`	Tautomer mode. See list of available modes for options.	`'reckless'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Tautomers API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`list[TautomerResults]`	list of lists of dictionaries containing RDKit Molecule, relative energies, and weights

run_charges

run_charges(
    mol,
    method="aimnet2_wb97md3",
    engine="aimnet2",
    mode="auto",
    timeout=600,
    name="Charges API Workflow",
    folder_uuid=None,
)

Computes atom-centered charges for the given Molecule.

Parameters:

Name	Type	Description	Default
`mol`	`RdkitMol`	RDKit Molecule	required
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`engine`	`str`	Engine to run the charges. See list of available engines	`'aimnet2'`
`mode`	`str`	The mode to run the calculation in. See list of available modes for options.	`'auto'`
`timeout`	`int`	timeout in seconds	`600`
`name`	`str`	name of the job	`'Charges API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`ChargesResults`	dictionary with the charges and the conformer index

run_conformers

run_conformers(
    mol,
    num_conformers=10,
    method="aimnet2_wb97md3",
    mode="rapid",
    return_energies=False,
    timeout=600,
    name="Conformer API Workflow",
    folder_uuid=None,
)

Generate conformers for a Molecule.

Parameters:

Name	Type	Description	Default
`mol`	`RdkitMol`	RDKit Molecule	required
`num_conformers`		number of conformers to generate	`10`
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`mode`	`str`	Mode for conformer generation. See list of available modes for options.	`'rapid'`
`return_energies`	`bool`	whether to return energies in Hartree too	`False`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Conformer API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`ConformerResult`	dictionary with the RDKit Molecule and energies

run_energy

run_energy(
    mol,
    method="aimnet2_wb97md3",
    engine="aimnet2",
    mode="auto",
    timeout=600,
    name="Energy API Workflow",
    folder_uuid=None,
)

Computes the energy for the given molecule.

Parameters:

Name	Type	Description	Default
`mol`	`RdkitMol`	RDKit Molecule	required
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`engine`	`str`	Engine to run the energy. See list of available engines	`'aimnet2'`
`mode`	`str`	Mode to run the energy. See list of available modes for options.	`'auto'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Energy API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`list[ConformerEnergyResult]`	dictionary with the energy in Hartree and the conformer index

run_optimize

run_optimize(
    mol,
    method="aimnet2_wb97md3",
    engine="aimnet2",
    mode="auto",
    return_energies=False,
    timeout=600,
    name="Optimize API Workflow",
    folder_uuid=None,
)

Optimize each of a molecule's conformers and then return the molecule.

Parameters:

Name	Type	Description	Default
`mol`	`RdkitMol`	RDKit Molecule	required
`method`	`str`	Method to use for the calculation. See list of available methods	`'aimnet2_wb97md3'`
`engine`	`str`	Engine to run the optimization. See list of available engines	`'aimnet2'`
`return_energies`	`bool`	whether to return energies in Hartree too	`False`
`mode`	`str`	Mode to run the optimization. See list of available modes for options.	`'auto'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Optimize API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`OptimizeResult`	dictionary with the optimized conformer(s) and optional list of energies per conformer

run_pka

run_pka(
    mol,
    mode="rapid",
    timeout=600,
    name="pKa API Workflow",
    pka_range=(2, 12),
    deprotonate_elements=None,
    protonate_elements=None,
    folder_uuid=None,
)

Calculate the pKa of a Molecule.

Parameters:

Name	Type	Description	Default
`mol`	`RdkitMol`	RDKit Molecule	required
`mode`	`pKaMode`	pKa calculation Mode. See list of available modes for options.	`'rapid'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'pKa API Workflow'`
`pka_range`	`tuple[int, int]`	range of pKa values to calculate	`(2, 12)`
`deprotonate_elements`	`list[int] \| None`	elements to deprotonate	`None`
`protonate_elements`	`list[int] \| None`	elements to protonate	`None`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`PKaResults`	dictionary of pKa values indexed by atom

run_tautomers

run_tautomers(
    mol, mode="reckless", timeout=600, name="Tautomers API Workflow", folder_uuid=None
)

Generate possible tautomers of a Molecule.

Parameters:

Name	Type	Description	Default
`mol`	`RdkitMol`	RDKit Molecule	required
`mode`	`TautomerMode`	Tautomer mode. See list of available modes for options.	`'reckless'`
`timeout`	`int`	time in seconds before the Workflow times out	`600`
`name`	`str`	name for the job	`'Tautomers API Workflow'`
`folder_uuid`	`str \| None`	folder UUID	`None`

Returns:

Type	Description
`TautomerResults`	list of dictionaries containing RDKit Molecule, relative energies, and weights