Tests for 5t35

Author: brianjimenez

README.md

@@ -59,3 +59,41 @@
 
 ![2uuy/2uuy_1.png](2uuy/2uuy_1.png)
 
+
+
+## 5t35
+
+### Default 1 restraint
+
+```bash
+./run.sh 1
+```
+
+![protacs/5t35/5t35_1.png](protacs/5t35/5t35_1.png)
+
+
+### Dense sampling enabled, 1 restraint
+
+```bash
+./run.sh 1 20 -ds
+```
+
+![protacs/5t35/5t35_1_20_ds.png](protacs/5t35/5t35_1_20_ds.png)
+
+
+### 50 swarms per restraint, 2 restraints
+
+```bash
+./run.sh 2 50
+```
+
+![protacs/5t35/5t35_2_50.png](protacs/5t35/5t35_2_50.png)
+
+
+### Dense sampling enabled, 2 restraint
+
+```bash
+./run.sh 2 20 -ds
+```
+
+![protacs/5t35/5t35_2_20_ds.png](protacs/5t35/5t35_2_20_ds.png)

protacs/5t35/1_restraints.list

@@ -0,0 +1 @@
+R D.759.301

protacs/5t35/2_restraints.list

@@ -0,0 +1,2 @@
+R D.ARG.69
+R D.759.301

protacs/5t35/5t35_1.png

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+rm -rf init setup.json lightdock* swarm_* resi.list;
+
+if [ "$#" == "3" ]; then
+    SPR="-spr $2";
+    DS="-ds";
+elif [ "$#" == "2" ]; then
+    SPR="-spr $2";
+    DS="";
+elif [ "$#" == "1" ]; then
+    SPR="";
+    DS="";
+else
+    echo "Wrong arguments";
+    exit 1;
+fi
+
+lightdock3_setup.py receptor.pdb ligand.pdb --noxt --now --noh -rst ${1}_restraints.list ${SPR} ${DS};
+
+for i in `cut -c 9- ${1}_restraints.list`;do echo "resi $i"; done > resi.list;
+
+residues=$(paste -d' ' -s resi.list);
+
+pymol lightdock_receptor.pdb init/swarm_centers.pdb -d "select lightdock_receptor; color white, sele; show surface, sele; select swarm_centers; color red, sele; show spheres, sele; select all and ${residues}; color blue, sele; z vis;";

protacs/5t35/5t35_1_20_ds.png

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+
+from prody import parsePDB
+import sys
+
+
+pdb_file = sys.argv[1]
+molecule = parsePDB(pdb_file)
+
+selection = molecule.select("within 10 of (chain D and resnum 301 or chain D and resnum 69) and surface or (chain D and resnum 301 or chain D and resnum 69)")
+for a in selection:
+    print(f"{a.getChid()}.{a.getResname()}.{a.getResnum()} {a.getName()}")