The file accepted by the Monomer Import page of Biotoolkit Monomers.
File
| Property |
Value |
| Formats |
.xlsx (first sheet), .csv, .txt (CSV content), .sdf |
| Template |
monomer_import_template.xlsx, from the Template File button of the Import Monomer Help dialog |
| Header row |
Required, first row. Column names in upper case, in any order. Unknown columns are ignored. |
| CSV delimiter |
Comma |
| Encoding |
UTF-8 |
| One file per upload |
Yes. Files are listed in File History for twelve months. |
An SDF is converted to the tabular form before processing: the molfile of each record becomes the structure, the record's data fields map to the columns below, and R-groups are read from fields named R1 to R10 whose value is the cap group name. A record whose Symbol field is empty or - is skipped.
Columns
| Column |
Required |
Type and limit |
Normalisation |
Description |
SYMBOL |
yes |
text, 500 characters |
trimmed |
Symbol used in HELM sequences. Unique within your organisation and the polymer type, and not held by a public monomer. Together with POLYMER_TYPE, it is the key that decides between creating and updating. |
NAME |
yes |
text, 1000 characters |
trimmed |
Full name. Unique within your organisation and the polymer type. |
SMILES |
yes |
text |
trimmed |
Structure with [*:n] attachment points. CXSMILES accepted. See Attachment Points and CAP Groups. |
POLYMER_TYPE |
yes |
text, 100 characters |
upper-cased |
PEPTIDE, RNA or CHEM. |
MONOMER_TYPE |
yes |
text, 100 characters |
trimmed, case as listed |
Backbone, Branch or Undefined. Must be valid for the polymer type. A CHEM monomer is stored as Undefined whatever is submitted. |
NATURAL_ANALOG |
for PEPTIDE and RNA |
text, 10 characters |
upper-cased |
Natural analog code for the polymer type. A CHEM monomer is stored as - whatever is submitted. See Monomer Types, Polymer Types and Natural Analogs. |
AUTHOR |
no |
text, 500 characters |
trimmed |
Free text. |
RGROUPS |
no |
text |
upper-cased |
Semicolon-separated label:cap pairs, for example R1:H;R2:OH. Labels R1 to R25, caps from the vocabulary. When absent, every attachment point found in the SMILES is capped with H. |
A missing NAME or MONOMER_TYPE is reported before the structure is processed, with a plain message naming the column.
Cap group vocabulary
| Code |
Name |
SMILES template |
H |
Hydrogen |
[*:{n}][H] |
OH |
Hydroxyl |
O[*:{n}] |
NH2 |
Amino |
N[*:{n}] |
Azide |
Azide |
[*:{n}]N=[N+]=[N-] |
Ethynyl |
Ethynyl |
[*:{n}]C#C |
Codes are matched case-insensitively and stored in the spelling above. Your organisation may have additional codes; the error message on an invalid cap lists the current vocabulary.
Row outcomes
| Outcome |
Condition |
| Created |
No private monomer with this SYMBOL and POLYMER_TYPE in your organisation |
| Updated |
A private monomer with this SYMBOL and POLYMER_TYPE exists; its fields are replaced. A material change increments its version. |
| Failed |
Any error below. Other rows are unaffected. |
Error file
Produced when at least one row failed. It is the input file with the failed rows only and an extra ERROR_MESSAGE column. Downloaded from the Error File column of File History.
| Message |
Meaning |
Symbol is required |
SYMBOL empty |
SMILES is required |
SMILES empty |
Polymer type is required |
POLYMER_TYPE empty |
Unknown polymer type: <value>. Expected values: <list> |
POLYMER_TYPE not in the list |
Unknown monomer type: <value>. Expected values: <list> |
MONOMER_TYPE not in the list, or not valid for the polymer type |
Invalid cap group "<value>" for <label>. Valid values: <list> |
A cap outside the vocabulary |
Invalid R-group format "<pair>". Expected format: R1:H or R2:OH |
A pair in RGROUPS is not label:cap |
Monomer with this structure is already registered: <symbol>. If you expected a distinct structure, verify your input carries full stereochemistry … |
Same canonical structure as a live monomer of the polymer type, private or public. Delivered inside a JSON envelope with outcome and message. |
Cannot modify protected public monomer '<symbol>' (public seed data) |
Symbol held by a public monomer. Same envelope. |
Biotoolkit service is unavailable. Please try again later. |
The chemistry service did not answer. Re-import the rows later. |
| Any other text |
The structure was rejected by the chemistry service. The message is the service's, with the technical prefix removed. |
Upload-time errors
Shown on the page instead of in the error file.
| Message |
Meaning |
Please add your import file. |
No file selected |
An error has occurred, check your file format and if the problem persists contact an administrator. |
The file could not be read or registered. Check the extension and the header row. |
File History columns
| Column |
Content |
| File Name |
Uploaded name. Click to download the file. |
| Status |
Processing while rows are handled, then a terminal status; Error as soon as one row failed |
| Total Rows, Parsed Rows, Success Rows, Error Rows |
Row counts |
| Parsing Progress, Progress Percentage, Success Percentage, Error Percentage |
Derived from the counts |
| Started At, Completed At, Duration Seconds |
Timing, dates as YYYY-MM-DD |
| Summary |
One-line outcome |
| Created By, Created At |
Who uploaded, when. This is the only place the uploader is recorded: the monomers themselves show Unknown as creator. |
| Error File |
Download button when an error file exists |
Example
SYMBOL,NAME,SMILES,POLYMER_TYPE,MONOMER_TYPE,NATURAL_ANALOG,AUTHOR,RGROUPS
Ahp,2-Aminoheptanoic acid,CCCCC[C@H](N[*:1])C([*:2])=O,PEPTIDE,Backbone,L,M. Curie,R1:H;R2:OH
MeNva,N-methyl-norvaline,CCC[C@H](N(C)[*:1])C([*:2])=O,PEPTIDE,Backbone,V,M. Curie,R1:H;R2:OH
PEG3,Triethylene glycol linker,[*:1]OCCOCCOCCO[*:2],CHEM,Undefined,-,M. Curie,R1:H;R2:H