Merge pull request #331 from marrink-lab/idp-new

fix issue 285
marrink-lab · Apr 22, 2024 · abd3e25 · abd3e25
2 parents 9690866 + bf0a8c7
commit abd3e25
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diff --git a/polyply/data/martini3/aminoacids.ff b/polyply/data/martini3/aminoacids.ff
diff --git a/polyply/data/martini3/citations.bib b/polyply/data/martini3/citations.bib
@@ -58,3 +58,11 @@ @article{M3_PDMS
   year={2022},
   publisher={Royal Society of Chemistry}
 }
+
+@article{M3_GO,
+title={GōMartini 3: From large conformational changes in proteins to environmental bias corrections},
+author={Souza, Paulo C. T. and Araujo, Luis P. Borges and Brasnett, Chris and Moreira, Rodrigo A. and Grunewald, Fabian and Park, Peter and Wang, Liguo and Razmazma, Hafez and Borges-Araujo, Ana C. and Cofas-Vargas, Luis F. and Monticelli, Luca and Mera-Adasme, Raul and Melo, Manuel N. and Wu, Sangwook and Marrink, Siewert J. and Poma, Adolfo B. and Thallmair, Sebastian},
+url={https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1},
+doi={10.1101/2024.04.15.589479},
+year={2024},
+}
diff --git a/polyply/src/generate_templates.py b/polyply/src/generate_templates.py
@@ -174,19 +174,23 @@ def compute_volume(block, coords, nonbond_params, treshold=1e-18):
     res_center_of_geometry = center_of_geometry(points)
     geom_vects = np.zeros((n_atoms, 3))
     idx = 0
-
+    radii = []
     for node, coord in coords.items():
         atom_key = block.nodes[node]["atype"]
         rad = float(nonbond_params[frozenset([atom_key, atom_key])]["nb1"])
         diff = coord - res_center_of_geometry
         if np.linalg.norm(diff) > treshold:
             geom_vects[idx, :] = diff + u_vect(diff) * rad
             idx += 1
-
-    if geom_vects.shape[0] > 1:
+        else:
+            radii.append(rad)
+    # make sure geom_vects is not just an array of zeros
+    # this can happen when multiple beads are stacked for
+    # example
+    if np.any(geom_vects):
         radgyr = radius_of_gyration(geom_vects)
     else:
-        radgyr = rad
+        radgyr = max(radii)
 
     return radgyr
 

diff --git a/polyply/src/minimizer.py b/polyply/src/minimizer.py
@@ -183,7 +183,8 @@ def target_function(positions):
                 energy += new
         return energy
 
-    opt_results = scipy.optimize.minimize(target_function, positions, method='L-BFGS-B',
+    opt_results = scipy.optimize.minimize(target_function, positions,
+                                          method='L-BFGS-B',
                                           options={'ftol': 0.001, 'maxiter': 100})
 
     # evaluate if optimization was successful

diff --git a/polyply/tests/test_data/library_tests/martini3/PROT/PNt.fasta b/polyply/tests/test_data/library_tests/martini3/PROT/PNt.fasta
@@ -0,0 +1,2 @@
+> PNt PROTEIN
+DWNNQSIVKTGERQHGIHIQGSDPGGVRTASGTTIKVSGRQAQGILLENPAAELQFRNGSVTSSGQLSDDGIRRFLGTVTVKAGKLVADHATLANVGDTWDDDGIALYVAGEQAQASIADSTLQGAGGVQIERGANVTVQRSAIVDGGLHIGALQSLQPEDLPPSRVVLRDTNVTAVPASGAPAAVSVLGASELTLDGGHITGGRAAGVAAMQGAVVHLQRATIRRGDALAGGAVPGGAVPGGAVPGGFGPGGFGPVLDGWYGVDVSGSSVELAQSIVEAPELGAAIRVGRGARVTVPGGSLSAPHGNVIETGGARRFAPQAAPLSITLQAGAH