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Fix chain break representation in input.md

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Updated the documentation for the 'contig' field to correct the representation of chain breaks from '\0' to '/0'.
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Rachel Clune
2026-02-12 09:45:38 -08:00
committed by GitHub
parent a814636801
commit b100462717
1 changed files with 4 additions and 4 deletions
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8
models/rfd3/docs/input.md
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@@ -120,7 +120,7 @@ Below is a table of all of the inputs that the `InputSpecification` accepts. Use
| -------------------------------------------------------------- | ----------------- | --------------------------------------------------------------------- |
| `input` | `str` | Path to and file name of **PDB/CIF**. Required if you provide contig+length. |
| `atom_array_input` | internal | Pre-loaded [`AtomArray`](https://www.biotite-python.org/latest/apidoc/biotite.structure.AtomArray.html) (not recommended). |
| `contig` | `InputSelection` | (Can only pass a contig string.) Indexed motif specification, e.g., `"A1-80,10,\0,B5-12"`. |
| `contig` | `InputSelection` | (Can only pass a contig string.) Indexed motif specification, e.g., `"A1-80,10,/0,B5-12"`. |
| `unindex` | `InputSelection` | (Can only pass a contig string or dictionary.) Unindexed motif components, the specified residues can be anywhere in the final sequence. See [Unindexing Specifics](#unindexing-specifics) for more information. |
| `length` | `str` | Total design length constraint; `"min-max"` or int for specified length. |
| `ligand` | `str` | Ligand(s) by chemical component name (from [RSCB PDB](https://www.rcsb.org/)) or index. |
@@ -186,7 +186,7 @@ Graphical representation of the different ways to specify portions of a structur
A 'contig string' is a string that contains residue information and is used in many of the settings in the table above. Here are some formatting specifics:
- Different pieces of information included in the string are separated by commas
- Ranges of residues are specified by a dash (`-`) between the starting and ending residue
- Chain breaks are represented by `\0`
- Chain breaks are represented by `/0`
- Residue numbers or ranges with a chain label before the number come from the input structure
- Residue numbers or ranges without a chain label before the number will be designed. If given a range, the designed region will have a length that is uniformly random within the specified range.
@@ -194,13 +194,13 @@ For example:
```yaml
my_calculation:
input: path/to/my/input.pdb
contig: A40-60,70,A120-170,A203,\0,B3-45,60-80
contig: A40-60,70,A120-170,A203,/0,B3-45,60-80
```
- `A40-60`: the design will start with residues 40-60 from the A chain of the input structure.
- `70`: RFD3 will design a chain with exactly 70 residues that will connect to A60
- `A120-170`: RFD3 will include a bond between the last designed residue and residue A120, and then include residues A120-A170 from the input structure.
- `A203`: A bond will be created between A170 and A203 and A203 will be in the final structure. However, residues A171-A202 will not be in the final structure.
- `\0`: Chain break. There is no peptide bond between A203 and B3 in the output structure
- `/0`: Chain break. There is no peptide bond between A203 and B3 in the output structure
- `B3-B45`: Residues B3 thru B45 are taken from the input structure.
- `60-80`: A design region is added B45 that will be between 60 and 80 residues long.