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@ -145,27 +145,28 @@ python -m rf2aa.run_inference --config-name nucleic_acid
<a id="p-sm-complex"></a>
### Predicting Protein Small Molecule Complexes
To predict protein small molecule complexes, the syntax to input the protein remains the same. Adding in the small molecule works similarly to other inputs.
Here is an example (from `rf2aa/config/inference/protein_sm.yaml`):
Here is an example (from `rf2aa/config/inference/protein_complex_sm.yaml`):
```
defaults:
- base
job_name: 7qxr
job_name: "3fap"
protein_inputs:
A:
fasta_file: examples/protein/7qxr.fasta
fasta_file: examples/protein/3fap_A.fasta
B:
fasta_file: examples/protein/3fap_B.fasta
sm_inputs:
B:
input: examples/small_molecule/NSW_ideal.sdf
C:
input: examples/small_molecule/ARD_ideal.sdf
input_type: "sdf"
```
Small molecule inputs are provided as sdf files or smiles strings and users are **required** to provide both an input and an input_type field for every small molecule that they want to provide. Metal ions can also be provided as sdf files or smiles strings.
To predict the example:
```
python -m rf2aa.run_inference --config-name protein_sm
python -m rf2aa.run_inference --config-name protein_complex_sm
```
<a id="higher-order"></a>
### Predicting Higher Order Complexes