Initial commit

Code should function as-is but needs more comments and docstrings

README.md

@@ -1,2 +1,30 @@
-# per-residue-distance
-Calculates the per-residue atomic distance between two chains
+
+# Plotting code for per-residue atomic distances
+
+
+
+Obtain rotation-translation matrices from the PDBe FTP server:
+
+```https://ftp.ebi.ac.uk/pub/databases/pdbe-kb/superposition/<uniprot>[0]/<uniprot>/<uniprot>.json```
+
+E.g. 
+
+```wget https://ftp.ebi.ac.uk/pub/databases/pdbe-kb/superposition/A/A0QTT2/A0QTT2.json```
+
+
+Obtain updated mmCIF files (the normal, non-SIFTS mmCIF file type will not work) using:
+
+
+```https://www.ebi.ac.uk/pdbe/entry-files/download/<pdbid>_updated.cif```
+
+E.g.
+
+```wget https://www.ebi.ac.uk/pdbe/entry-files/download/7cyr_updated.cif```
+
+## Example 
+
+``` python
+python3 per_residue_distance.py --mmcif1 example_data/7cyr_updated.cif.gz --mmcif2 example_data/7cy2_updated.cif.gz --rt_matrices example_data/A0QTT2.json --pdb_id1 7cyr --pdb_id2 7cy2 --chain1 A --chain2 A
+```
+
+Chain IDs should be parsed as `label_asym_id` from the updated mmcif `atom_site` loop. 

example_data/A0QTT2.json

@@ -0,0 +1,95 @@
+{
+    "7cy2_A": {
+        "pdb_id": "7cy2",
+        "auth_asym_id": "A",
+        "struct_asym_id": "A",
+        "matrix": [
+            [
+                1.0,
+                0.0,
+                0.0,
+                0.0
+            ],
+            [
+                0.0,
+                1.0,
+                -0.0,
+                0.0
+            ],
+            [
+                -0.0,
+                -0.0,
+                1.0,
+                0.0
+            ],
+            [
+                0,
+                0,
+                0,
+                1
+            ]
+        ]
+    },
+    "7cyr_A": {
+        "pdb_id": "7cyr",
+        "auth_asym_id": "A",
+        "struct_asym_id": "A",
+        "matrix": [
+            [
+                0.938,
+                -0.289,
+                0.19,
+                -12.116
+            ],
+            [
+                -0.038,
+                0.46,
+                0.887,
+                4.053
+            ],
+            [
+                -0.344,
+                -0.84,
+                0.42,
+                4.58
+            ],
+            [
+                0,
+                0,
+                0,
+                1
+            ]
+        ]
+    },
+    "7cz2_A": {
+        "pdb_id": "7cz2",
+        "auth_asym_id": "A",
+        "struct_asym_id": "A",
+        "matrix": [
+            [
+                -0.085,
+                0.465,
+                0.881,
+                -24.287
+            ],
+            [
+                0.348,
+                0.843,
+                -0.412,
+                17.893
+            ],
+            [
+                -0.934,
+                0.271,
+                -0.233,
+                28.361
+            ],
+            [
+                0,
+                0,
+                0,
+                1
+            ]
+        ]
+    }
+}