docs and json progress

models/rfd3/README.md

@@ -74,10 +74,6 @@ you will need to change the path in the `.json` file(s) before running.
 
 <table>
   <tr>
-    <td align="center">
-      <h3><a href="./docs/na_binder_design.md">Nucleic acid binder design</a></h3>
-      <img src="docs/.assets/dna.png" height="150" />
-    </td>
     <td align="center">
       <h3><a href="./docs/sm_binder_design.md">Small molecule binder design</a></h3>
       <img src="docs/.assets/sm.png" height="150" />
@@ -86,6 +82,11 @@ you will need to change the path in the `.json` file(s) before running.
       <h3><a href="./docs/protein_binder_design.md">Protein binder design</a></h3>
       <img src="docs/.assets/ppi.png" height="150" />
     </td>
+     <td align="center">
+      <h3><a href="./docs/na_binder_design.md">Nucleic acid binder design</a></h3>
+      <img src="docs/.assets/dna.png" height="150" />
+    </td>
+
   </tr>
   <tr>
     <td align="center">
@@ -96,6 +97,11 @@ you will need to change the path in the `.json` file(s) before running.
       <h3><a href="./docs/symmetry.md">Symmetric design</a></h3>
       <img src="docs/.assets/symm.png" height="150" />
     </td>
+    <td align="center">
+      <h3><a href="./docs/multipolymer.md">Multipolymer design</a></h3>
+      <img src="docs/.assets/multipolymer.png" height="150" />
+    </td>
+
   </tr>
 </table>
 

models/rfd3/docs/examples/atom23_design.json

@@ -0,0 +1,73 @@
+{
+    "W05": {
+        "ss_dbn": ".(((((((((((((((((((..[[[[[[.)))))(((....)))(((....)))))))))))))))))((((((..]]]]]].)))))).",
+        "select_fixed_atoms": false,
+        "contig": "90-90R",
+        "length": "90-90",
+        "input": "../input_pdbs/AMP.pdb"
+    },
+    "AMP_aptamer": {
+        "input": "../input_pdbs/AMP.pdb",
+	"ligand": "AMP",
+	"contig": "40-50R",
+        "length": "40-50",
+        "ori_jitter": 1,
+        "select_buried": {"AMP": "ALL"},
+        "select_hbond_acceptor": {
+            "AMP": "N7,O4',O1P,O2P,O3P,N3,N1"
+        },
+        "select_hbond_donor": {
+            "AMP": "N6,O3',O2'"
+        }
+    },
+    "FMN_aptamer": {
+        "input": "../input_pdbs/FMN_3x21.pdb",
+	"ligand": "FMN",
+	"contig": "40-50R",
+        "length": "40-50",
+        "ori_jitter": 1,
+        "select_buried": {"FMN": "ALL"},
+        "select_hbond_acceptor": {
+            "FMN": "O2,O4,N1,N5,O5',O2P,O3P"
+        },
+        "select_hbond_donor": {
+            "FMN": "N3,O2',O3',O4'"
+        }
+    },
+    "AMP_aptamer_noh": {
+        "input": "../input_pdbs/AMP.pdb",
+	"ligand": "AMP",
+	"contig": "40-50R",
+        "length": "40-50",
+        "ori_jitter": 1,
+        "select_buried": {"AMP": "ALL"}
+    },
+    "FMN_aptamer_noh": {
+        "input": "../input_pdbs/FMN_3x21.pdb",
+	"ligand": "FMN",
+	"contig": "40-50R",
+        "length": "40-50",
+        "ori_jitter": 1,
+        "select_buried": {"FMN": "ALL"}
+    },
+    "unindexed_rnasep": {
+        "input": "../input_pdbs/rnase_p_3q1q_active_site_small.pdb",
+        "contig": "50-80R,/0,100-120,/0,C1-4,C79-86",
+        "length": "162-212",
+        "ligand": "MG,PO4",
+        "unindex": "B49,B50,B51,B52,B321,/0,A56-58,/0",
+        "select_fixed_atoms": {
+            "B49": "ALL",
+            "B50": "ALL",
+            "B51": "ALL",
+            "B52": "ALL",
+            "B321": "ALL",
+            "A56-58": "ALL",
+            "C1-4": "ALL",
+            "C79-86": "ALL"
+        }
+    }
+
+    
+
+}

models/rfd3/docs/input.md

@@ -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"`. When running inference with an atom223 checkpoint, contigs can include `R` or `D` suffixes to denote designed polymer type is RNA or DNA e.g. "A1-80,10-10R,20-20D,30-30,/0,B5-12" (designs a 10 length RNA chain, 20 length DNA chain and a 30 length protein chain).            |
 | `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. |
@@ -136,6 +136,7 @@ Below is a table of all of the inputs that the `InputSpecification` accepts. Use
 | `symmetry`                                                     | `SymmetryConfig`  | See {doc}`examples/symmetry`.                                               |
 | `ori_token`                                                    | `list[float]`     | `[x,y,z]` origin override to control COM (center of mass) placement of designed structure. |
 | `infer_ori_strategy`                                           | `str`             | `"com"` or `"hotspots"`.  The center of mass of the diffused region will typically be within 5Å of the ORI token. Using `hotspots` will place the ORI token 10Å outward from the center of mass of the specified hotspots. Using `com` will place the token at the center of mass of the input structure.|
+| `ori_jitter`                                           | `float`             | default `None`. Per batch, move the ori token in a random direction by a distance sampled from a geomtric distribution with the mean as the specified float value in Angstrom.|
 | `plddt_enhanced`                                               | `bool`            | Default `True`. Enables pLDDT (predicted Local Distance Difference Test) enhancement. |
 | `is_non_loopy`                                                 | `bool \| None`            | Default `None`. If `True`/`False`, produces output structures with fewer/more loops.|
 | `partial_t`                                                    | `float`           | Noise (Å) for partial diffusion, enables partial diffusion (sets the noise level.) Recommended values are 5.0-15.0 Å. See [Partial Diffusion](#partial-diffusion) for more information. |