MolDraw › Chemistry tools › Batch Chemical Converter
Batch Chemical Converter (CSV in, CSV out)
In short: Convert a whole list of SMILES, names, CAS numbers, PubChem CIDs, InChI or InChIKeys at once. Get canonical SMILES, formula, molecular weight, exact mass, InChI, InChIKey, IUPAC name, LogP, TPSA, H-bond donors and acceptors and a Lipinski check, then download CSV, TSV or SDF. It is free, works in your web browser and needs no download.
Paste one identifier per line or open a CSV, TSV or TXT file. SMILES are processed on your device, up to 5,000 rows per run. Names, CAS numbers and other identifiers are looked up in PubChem first; those rows are marked online.
CC(=O)Oc1ccccc1C(=O)O, gives C9H8O4, MW 180.159 g/mol, exact mass 180.0423, TPSA 63.6 Ų, 1 donor, 4 acceptors and a Lipinski Pass. Then press Download CSV.Outputs
Ready.
How to convert a list of chemicals
- Paste your list, or press Open CSV / TSV / TXT. One value per line works, and so does a spreadsheet saved as CSV.
- Check the line under the box. It says how many rows and columns were read and which separator was found.
- For a table, choose the Identifier column and tick First row is a header if row 1 holds column names.
- Leave Input type on Detect for each row, or force SMILES, Name, CAS number, PubChem CID, InChI or InChIKey.
- Tick the Outputs you need. Outputs marked online need an internet lookup.
- Press Convert. The progress bar shows rows done, errors and online lookups. Press Stop to end early and keep what is done.
- Check the preview, then press Download CSV, Download TSV or Download SDF.
Inputs and outputs
| Input | Example | How it is read |
|---|---|---|
| SMILES | CN1C=NC2=C1C(=O)N(C(=O)N2C)C | On your device |
| Name (common or IUPAC) | caffeine | Online, PubChem |
| CAS Registry Number | 58-08-2 | Check digit tested, then PubChem |
| PubChem CID | 2519 | Online, PubChem |
| InChI | InChI=1S/C8H10N4O2/… | Online, PubChem |
| InChIKey | RYYVLZVUVIJVGH-UHFFFAOYSA-N | Online, PubChem |
What each output means
| Output | Meaning | Source |
|---|---|---|
| Canonical SMILES | One standard SMILES per structure, so duplicates match | Local |
| Molecular formula | Hill order (C, H, then A–Z), net charge added | Local |
| MW (g/mol) | Average molar mass from standard atomic weights | Local |
| Exact mass | Monoisotopic mass (most abundant isotope of each element), for mass spectrometry | Local |
| InChI, InChIKey | Standard IUPAC identifiers for database searches | Online |
| IUPAC name | Systematic name from PubChem, when the compound is listed | Online |
| cLogP | Calculated octanol–water partition coefficient | Local |
| TPSA (Ų) | Topological polar surface area from N and O contributions | Local |
| HBD, HBA | H-bond donors (N–H, O–H) and acceptors (N and O atoms) | Local |
| Lipinski | Pass if at most one rule-of-five limit is broken | Local |
Worked examples
Aspirin from SMILES
CC(=O)Oc1ccccc1C(=O)O
C9H8O4, exact mass 180.0423, TPSA 63.6 Ų, HBD 1, HBA 4.
MW 180.159 g/mol, Lipinski Pass
Caffeine from its CAS number
58-08-2 passes the check digit test and is looked up online.
C8H10N4O2, TPSA 58.4 Ų, HBD 0.
MW 194.19 g/mol, InChIKey RYYVLZVUVIJVGH-UHFFFAOYSA-N
A spreadsheet with IDs
Columns id;smiles;IC50 separated by semicolons.
The separator and the SMILES column are found automatically.
Your id and IC50 columns are kept next to the results
Atorvastatin
MW 558.6 g/mol and cLogP above 5.
Two rule-of-five limits are broken.
Lipinski Fail (MW > 500; LogP > 5)
Common mistakes
- Names in a SMILES column. With Input type set to SMILES, "aspirin" fails. Use Detect for each row for mixed lists.
- Excel changed your CAS numbers. Spreadsheets can turn 7732-18-5 into a date. Format the column as text before saving.
- Salts and mixtures. A SMILES with a dot, such as
[Na+].[Cl-], is treated as one entry. MW and formula include every part. - Header read as data. If row 1 holds column names, tick First row is a header, or it will appear as a failed row.
- Comparing LogP values from different methods. cLogP and XLogP3 are both estimates. Use one method for a whole series.
- Very long name lists. Online lookups run at about four per second. Convert names to SMILES once, then work from the SMILES file.
Want to see a structure? Paste any SMILES into MolDraw, a free online chemical structure editor, to draw, edit and export it as PNG, SVG or MOL.
Open MolDraw editorFrequently asked questions
How do I convert a list of SMILES to molecular weights at once?
Paste the SMILES one per line, or open a CSV file and pick the SMILES column. Keep MW (g/mol) ticked and press Convert. When it finishes, press Download CSV. SMILES are processed on your device, so up to 5,000 rows take only seconds.
Which inputs need an internet lookup?
SMILES are read on your device. Names, CAS numbers, PubChem CIDs, InChI and InChIKeys are first looked up in the free PubChem database to get the structure. InChI, InChIKey and IUPAC name outputs are also looked up online. Online rows are marked online in the preview and are limited to about four per second.
Can I upload a CSV with several columns?
Yes. The converter detects comma, tab, semicolon and pipe separators, quoted cells and a byte order mark. It guesses the header row and the identifier column, and you can change both. Tick Keep my other columns to copy your IDs or activity values into the output.
What does the Lipinski column mean?
Lipinski's rule of five flags poor oral absorption when a compound breaks more than one of: MW ≤ 500, LogP ≤ 5, at most 5 H-bond donors and at most 10 H-bond acceptors. Pass means zero or one violation. The violations column lists which limits were broken.
Why does my LogP differ from PubChem's XLogP3?
There are several ways to estimate LogP. This converter uses a calculated cLogP from atom contributions, while PubChem reports XLogP3. The two usually agree within about one unit. Compare compounds with the same method.
What is in the SDF download?
One record per converted row: a 2D structure with coordinates, the input as the title line, and each chosen output (formula, MW, LogP and so on) as an SDF data field. Most chemistry programs and databases can open it.
Why did a row fail?
The Status column gives the reason: for example a SMILES with an unclosed ring or bracket, a CAS number with a wrong check digit, or a name PubChem does not know. Fix the input and run the converter again. The other rows are not affected.
Related chemistry tools
Last updated: