Merge pull request #3 from lightdock/0.1.1

Merge 0.1.1 -> master

Author: brianjimenez

Cargo.toml

@@ -1,13 +1,13 @@
 [package]
 name = "lightdock"
-version = "0.1.0"
+version = "0.1.1"
 authors = ["Brian Jimenez Garcia <br.jimenezgarcia@gmail.com>"]
 edition = "2018"
 
 [dependencies]
 rand = "0.7.3"
 serde = { version = "1.0.106", features = ["derive"] }
 serde_json = "1.0.51"
-lib3dmol = "0.3.2"
+lib3dmol = "0.4.0"
 lazy_static = "1.4.0"
 npy = "0.4.0"

example/ab_icode/init/initial_positions_0.dat

@@ -0,0 +1,20 @@
+ATOM      0 H    XXX    1       -4.818  20.973  28.462
+ATOM      1 H    XXX    1       -8.636  19.145  28.816
+ATOM      2 H    XXX    1      -12.291  26.572  21.145
+ATOM      3 H    XXX    1       -9.856  24.030  25.359
+ATOM      4 H    XXX    1      -28.041  31.392  -6.931
+ATOM      5 H    XXX    1      -38.609  10.605  -0.494
+ATOM      6 H    XXX    1       -7.074  15.310  29.478
+ATOM      7 H    XXX    1      -37.561  18.092  -9.162
+ATOM      8 H    XXX    1      -38.438  16.290  -5.221
+ATOM      9 H    XXX    1      -36.801  19.717 -12.638
+ATOM     10 H    XXX    1       -2.200  25.440  23.557
+ATOM     11 H    XXX    1       -4.406  24.425  25.443
+ATOM     12 H    XXX    1      -35.989  28.746  -2.675
+ATOM     13 H    XXX    1      -13.685  22.824  25.558
+ATOM     14 H    XXX    1       -5.061  11.453  29.826
+ATOM     15 H    XXX    1      -14.541  17.574  27.910
+ATOM     16 H    XXX    1      -36.625  14.132 -12.218
+ATOM     17 H    XXX    1      -40.818  19.662  -0.851
+ATOM     18 H    XXX    1      -33.517  27.201  -7.769
+ATOM     19 H    XXX    1      -38.070  23.004  -5.622

example/ab_icode/init/initial_positions_1.dat

@@ -0,0 +1,2 @@
+R H.ASP.52A
+R H.LEU.82C

example/ab_icode/init/initial_positions_10.dat

@@ -0,0 +1,35 @@
+{
+    "anm_lig": 10,
+    "anm_rec": 10,
+    "anm_seed": 324324,
+    "flip": false,
+    "glowworms": 200,
+    "ligand_pdb": "ligand.pdb",
+    "ligand_restraints": {
+        "active": [],
+        "blocked": [],
+        "passive": []
+    },
+    "membrane": false,
+    "noh": true,
+    "now": true,
+    "noxt": true,
+    "receptor_pdb": "receptor.pdb",
+    "receptor_restraints": {
+        "active": [
+            "H.ASP.52A",
+            "H.LEU.82C"
+        ],
+        "blocked": [],
+        "passive": []
+    },
+    "restraints": "restraints.list",
+    "starting_points_seed": 324324,
+    "surface_density": 50.0,
+    "swarm_radius": 10.0,
+    "swarms": 20,
+    "transmembrane": false,
+    "use_anm": true,
+    "verbose_parser": false,
+    "write_starting_positions": false
+}

example/ab_icode/init/initial_positions_11.dat

@@ -33,6 +33,7 @@ struct SetupFile {
     starting_points_seed: u32, 
     verbose_parser: bool, 
     noxt: bool, 
+    now: bool,
     restraints: Option<String>, 
     use_anm: bool, 
     glowworms: u32, 

example/ab_icode/init/initial_positions_12.dat

@@ -150,7 +150,10 @@ impl DockingModel {
         let mut atom_index: u64 = 0;
         for chain in structure.chains.iter() {
             for residue in chain.lst_res.iter() {
-                let res_id = format!("{}.{}.{}", chain.name, residue.name.trim(), residue.res_num);
+                let mut res_id = format!("{}.{}.{}", chain.name, residue.name.trim(), residue.res_num);
+                if let Some(c) = residue.res_icode {
+                    res_id.push(c);
+                }
 
                 for atom in residue.lst_atom.iter() {
                     // Membrane beads MMB.BJ