Generate Ionization States and Calculate LogD
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Role-based/Computational Chemist
Role-based/Medicinal Chemist
Solution-based/Hit to Lead/Properties/pKa
Task-based/Library Prep & Design
Description
This floe is a dataset preparation floe. It predicts micro- and macro-pKas of provided molecules. Based on predicted micro-pKas, it also calculates the most dominant state(s) of the molecule and LogD at a chosen pH from 0.0 to 14.0 (default 7.4). The predicted dominant state is saved as the primary molecule field by default. But it can also be saved to a new field. For multiple significant states, multiple records are created.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Small Molecule Dataset to Predict pKa On (new_mols): Small molecule dataset to predict pKa on.
Required
Type: data_source
Outputs
Significant Microstates (significant_micro_states): Dataset of significant microstates.
Required
Type: dataset_out
Default: Significant micro-states
Significant ionization state molecule field (Ionization_state_field): The field to store the significant state of the molecule. By default it replaces the PrimaryMolField.
Type: field_parameter::mol
Failed Descriptors Calculation (newmols_desc_failed): Dataset of molecules with failed descriptors calculation.
Required
Type: dataset_out
Default: Descriptors failed
Options
Get multiple significant states (get_multiple_states): Choose whether to generate multiple significant states at chosen environment pH and fraction cutoffs
Required
Type: boolean
Default: False
Choices: [True, False]
Calculate LogD (calc_logD): Choose whether to calculate LogD value
Required
Type: boolean
Default: True
Choices: [True, False]
Environment pH (env_pH): pH of environment in which micro states of the molecule are to be estimated. The value will be rounded to the nearest tenth.
Required
Type: decimal
Default: 7.4
Advanced options
Cutoff for ionizable groups count (ion_groups_count_cutoff): The maximum number of ionizable groups to be processed in detailed micro/macro-pKa prediction and protonation micro-equilibria. These groups are chosen by estimated intrinsic pKa to be around chosen environment pH (default 7.4).
Required
Type: integer
Default: 4
Choices: [2, 3, 4, 5]
Percentage cutoff for macro-state (macro_state_fraction_cutoff): Only macro states higher than this percentage cutoff at chosen environment pH will be saved to significant states output dataset.
Required
Type: integer
Default: 20
Percentage cutoff for micro-states within the macro state (tautomer_fraction_cutoff): Only micro states having fraction (tautomer fraction) higher than this percentage cutoff within a selected macro state, will be saved to significant states output dataset.
Required
Type: integer
Default: 35
Supporting experimental pKa data file (supporting_data_filename): Name of the supporting data descriptors file you have already created using the floe ‘Prepare supporting experimental pKa data file’
Type: file_in