fix disulphide bond node filtering #205 (#209)

* fix disulphide bond node filtering #205

* Local dataset (#208) (#211)

* add load local pdb_files to ProteinGraphDataset

* load local pdb_files from a list

* test and black and isort and add CHANGELOG.md

* docstring formatting

* comment jupyter; just run  and ssh or vscode to interact with container

* install dependency of jupyter nbextension

* Fixed Dockerfile and unit tests

* Update chage log

Co-authored-by: xutingfeng <xutingfeng@big.ac.cn>
Co-authored-by: Arian Jamasb <arjamasb@gmail.com>
Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk>

Co-authored-by: Nicktf <49584439+1511878618@users.noreply.github.com>
Co-authored-by: xutingfeng <xutingfeng@big.ac.cn>
Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk>

* fix typo

Co-authored-by: Nicktf <49584439+1511878618@users.noreply.github.com>
Co-authored-by: xutingfeng <xutingfeng@big.ac.cn>
Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk>

CHANGELOG.md

@@ -1,9 +1,9 @@
-### 1.5.2
+### 1.5.2 - UNRELEASED
 
-### Protein
+#### Protein
 * [Bugfix] - [#206](https://github.com/a-r-j/graphein/pull/206) Fixes `KeyError` when using `graphein.protein.edges.distance.node_coords`
 
-### GRN
+#### GRN
 * [Bugfix] - [#208](https://github.com/a-r-j/graphein/pull/208) - Resolves SSL issues with RegNetwork.
 
 #### ML
@@ -16,6 +16,7 @@
 #### CI
 * [Bugfix] - [#208](https://github.com/a-r-j/graphein/pull/208) explicitly installs `jupyter_contrib_nbextensions` in Docker.
 
+
 ### 1.5.1
 
 #### Protein

graphein/protein/edges/distance.py

@@ -237,6 +237,10 @@ def add_disulfide_interactions(
     disulfide_df = filter_dataframe(
         disulfide_df, "atom_name", DISULFIDE_ATOMS, True
     )
+    # Ensure only residues in the graph are kept
+    disulfide_df = filter_dataframe(
+        disulfide_df, "node_id", list(G.nodes), True
+    )
     distmat = compute_distmat(disulfide_df)
     interacting_atoms = get_interacting_atoms(2.2, distmat)
     add_interacting_resis(G, interacting_atoms, disulfide_df, ["disulfide"])