Merge branch 'main' into documentation

Author: rclune

README.md

@@ -19,7 +19,7 @@ Open source code for RFdiffusion2 as described in the following pre-print.
 More detailed information about how to run, install, and use RFdiffusion2 can be found [here](https://rosettacommons.github.io/RFdiffusion2/). 
 
 <!-- ## Table of Contents
-- [Set-up](readme_link.html#set-up)
+- [Setup](readme_link.html#setup)
 - [Inference Example](readme_link.html#inference)
 - [Viewing Designs](readme_link.html#viewing-designs)
   - [PyMOL and designs on the same machine](readme_link.html#same_machine_pymol)
@@ -58,7 +58,7 @@ provided image and alternative instructions for how to install RFdiffusion2 from
 
    *Note: You can also run RFdiffusion2 with [Singularity](https://sylabs.io/singularity/).*
 
-   RFdiffusion2 (RFD2) uses [Apptainer](https://apptainer.org) to simplify the environment set-up.
+   RFdiffusion2 (RFD2) uses [Apptainer](https://apptainer.org) to simplify the environment setup.
    If you do not already have Apptainer on your system, please follow the [Apptainer installation instructions](https://apptainer.org/docs/admin/main/installation.html) for your operating system.
 
    If you manage your packages on linux with `apt` you can simply run:
@@ -83,7 +83,7 @@ provided image and alternative instructions for how to install RFdiffusion2 from
 
 For other usage examples, see the [Usage page](rosettacommons.github.io/RFdiffusion2/usage/usage.html) in the external documentation. 
 
-The blow commands run several demos that show off some of the inference capabilities of RFdiffusion2 including: 
+The below commands run several demos that show off some of the inference capabilities of RFdiffusion2 including: 
 - enzyme design from an atomic motif and small molecule
 - enzyme design from an atomic motif of unknown sequence positions and a small molecule
 - small-molecule binder design with RASA conditioning 
@@ -154,7 +154,7 @@ It is still possible to view designs on a remote computer from your local PyMOL,
 
 You will need to know an IP address that will point back to your computer, typically you can use 127.0.0.1.
 
-You will also need to add the -R option when you are signing into your cluster and provide the path back to yourPyMOL server:
+You will also need to add the -R option when you are signing into your cluster and provide the path back to your PyMOL server:
 ```
 ssh username@hostname -R 9123:localhost:9123
 ```

doc/source/installation.md

@@ -23,7 +23,7 @@ FATAL: kernel reported a bad superblock for squashfs image partition,possible ca
 To fix this issue you can rebuild the sif on your HPC cluster: 
 ```
 apptainer build --sandbox rfd2_sandbox /path/to/bakerlab_rf_diffusion_aa.sif
-apptainer build rfd2_zlib.sif rfd2 sandbox
+apptainer build rfd2_zlib.sif rfd2_sandbox
 ```
 Thank you to those who posted in [Issue 10](https://github.com/RosettaCommons/RFdiffusion2/issues/10) for reporting this problem and documenting a
 solution.  
@@ -54,7 +54,7 @@ If you have trouble with these files but they *should* work based on your system
         ```
         conda env create -f cuda121_env.yml
         conda activate rfd2_env
-        pip install -r requirements_121.txt
+        pip install -r requirements_cuda121.txt
         ```
     This will force the dependencies you want installed by CUDA to be installed before pip is used. 
 2. Check to make sure the python that is being referenced is the one from your conda environment once it is activated. On clusters different modules you have imported might overrule the python in your conda environment. You can either manually give the path to your Python or change your system settings or environment variables to prefer the environment's python installation.

doc/source/usage/ori_tokens.md

@@ -0,0 +1,3 @@
+## ORI Tokens
+
+ORI Tokens