Objective
Calculate molecular properties of aspirin (acetylsalicylic acid) using RDKit chemistry tools to assess its drug-likeness and pharmaceutical properties.
Scientific Question: How to calculate molecular properties of aspirin (acetylsalicylic acid) using rdkit chemistry tools to assess its drug-likeness and pharmaceutical properties.?
Inputs (Recipe Parameters)
molecule_smiles
smiles
SMILES representation of molecule
Example:
CC(=O)Oc1ccccc1C(=O)OOutputs (Expected Results)
result
data
Workflow result
Procedure (Unit Operations: 2 Stages)
Stage 1
Analysis Stage
Execute 3 operations
IN: input_data
→
OUT: stage_1_result
1
PROMPT:
analyze the molecular properties of aspirin (acetylsalicylic acid)
resolveIntention
resolveIntention
2
PROMPT:
calculate the MW of aspirin using its smiles notation
calculate_molecular_weight
calculate_molecular_weight
Params: smiles: {input.smiles}
3
PROMPT:
get the formula
get_molecular_formula
get_molecular_formula
Params: smiles: {input.smiles}
▼
Stage 2
Validation Stage
Execute 3 operations
IN: stage_1_result
→
OUT: stage_2_result
1
PROMPT:
check if aspirin follows lipinski's rule of five, which predicts drug-likeness
check_lipinski_ro5
check_lipinski_ro5
Params: smiles: {input.smiles}
2
PROMPT:
calculate the TPSA (tpsa), which is important for predicting membrane permeability
calculate_tpsa
calculate_tpsa
Params: smiles: {input.smiles}
3
PROMPT:
convert the smiles to inchi for database searching
smiles_to_inchi
smiles_to_inchi
Params: smiles: {input.smiles}
Equipment Mapping (PARAMUS Tools)
Required Capabilities: Chemistry
Tool Chain
| Tool | Purpose | Stages |
|---|---|---|
resolveIntention |
Used in workflow step 1 | |
execute |
Used in workflow step 2 | |
calculate_molecular_weight |
Used in workflow step 3 | |
get_molecular_formula |
Used in workflow step 4 | |
check_lipinski_ro5 |
Used in workflow step 5 | |
calculate_tpsa |
Used in workflow step 6 | |
smiles_to_inchi |
Used in workflow step 7 |
External Tools & Gap Analysis
| External Tool | Purpose | PARAMUS Alternative | Status |
|---|
Validation Criteria
Benchmarks
Test Cases
Execution Guidance
Duration
~3 minutes
Computational Cost
medium
Parallelizable Stages
None