bug fixes from 0.5.20 release

BradyAJohnston · May 26, 2022 · 56bf6f2 · 56bf6f2
1 parent 04bb366
commit 56bf6f2
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Showing 5 changed files with 136 additions and 123 deletions.
diff --git a/release/molecular_nodes_0.5.21.zip b/release/molecular_nodes_0.5.21.zip
diff --git a/serpens_plugin_file.blend b/serpens_plugin_file.blend
diff --git a/src/CustomNodes.py b/src/CustomNodes.py
@@ -181,11 +181,11 @@ def create_node_group(node_name, input_list, label_prefix = "Chain "):
 
     # create an empty node group group inside of the node tree
     # link the just-created custom node group data to the node group in the tree
-    new_node_group = node_mod.node_group.nodes.new("GeometryNodeGroup")
-    new_node_group.node_tree = bpy.data.node_groups[chain_group.name]
+    # new_node_group = node_mod.node_group.nodes.new("GeometryNodeGroup")
+    # new_node_group.node_tree = bpy.data.node_groups[chain_group.name]
 
     # resize the newly created node to be a bit wider
-    node_mod.node_group.nodes[-1].width = 200
+    # node_mod.node_group.nodes[-1].width = 200
 
 
 # the chain_id_list and output_name are passed in from the operator when it is called
@@ -196,5 +196,5 @@ def create_node_group(node_name, input_list, label_prefix = "Chain "):
 # finally make the selection node!
 create_node_group(node_name, chain_list)
 
-node = bpy.context.selected_nodes[0]
-bpy.ops.transform.translate('INVOKE_DEFAULT')
+# node = bpy.context.selected_nodes[0]
+# bpy.ops.transform.translate('INVOKE_DEFAULT')
diff --git a/src/import_structure.py b/src/import_structure.py
@@ -448,9 +448,9 @@ def get_value(vec, x):
             return 0
 
     create_model(
-        name=name,
-        collection=collection,
-        locations=list(map(lambda x: [get_value(prop_x, x), get_value(prop_y, x), get_value(prop_z, x)], range(len(first_model.atoms())))))
+        name = name,
+        collection = collection,
+        locations = list(map(lambda x: [get_value(prop_x, x), get_value(prop_y, x), get_value(prop_z, x)], range(len(first_model.atoms())))))
 
 
 def get_bond_list(model, connect_cutoff=0.35, search_distance=2):

diff --git a/src/mda_test.py b/src/mda_test.py
@@ -25,109 +25,109 @@ def verify_user_sitepackages(mda_path):
     warning("Unable to Import MDAnalysis")
 
 dict_elements = {
-    "H":  1,
-    "He":  2,
-    "Li":  3,
-    "Be":  4,
-    "B":  5,
-    "C":  6,
-    "N":  7,
-    "O":  8,
-    "F":  9,
-    "Ne": 10,
-    "Na": 11,
-    "Mg": 12,
-    "Al": 13,
-    "Si": 14,
-    "P": 15,
-    "S": 16,
-    "Cl": 17,
-    "Ar": 18,
-    "K": 19,
-    "Ca": 20,
-    "Sc": 21,
-    "Ti": 22,
-    "V": 23,
-    "Cr": 24,
-    "Mn": 25,
-    "Fe": 26,
-    "Co": 27,
-    "Ni": 28,
-    "Cu": 29,
-    "Zn": 30,
-    "Ga": 31,
-    "Ge": 32,
-    "As": 33,
-    "Se": 34,
-    "Br": 35,
-    "Kr": 36,
-    "Rb": 37,
-    "Sr": 38,
-    "Y": 39,
-    "Zr": 40,
-    "Nb": 41,
-    "Mo": 42,
-    "Tc": 43,
-    "Ru": 44,
-    "Rh": 45,
-    "Pd": 46,
-    "Ag": 47,
-    "Cd": 48,
-    "In": 49,
-    "Sn": 50,
-    "Sb": 51,
-    "Te": 52,
-    "I": 53,
-    "Xe": 54,
-    "Cs": 55,
-    "Ba": 56,
-    "La": 57,
-    "Ce": 58,
-    "Pr": 59,
-    "Nd": 60,
-    "Pm": 61,
-    "Sm": 62,
-    "Eu": 63,
-    "Gd": 64,
-    "Tb": 65,
-    "Dy": 66,
-    "Ho": 67,
-    "Er": 68,
-    "Tm": 69,
-    "Yb": 70,
-    "Lu": 71,
-    "Hf": 72,
-    "Ta": 73,
-    "W": 74,
-    "Re": 75,
-    "Os": 76,
-    "Ir": 77,
-    "Pt": 78,
-    "Au": 79,
-    "Hg": 80,
-    "Tl": 81,
-    "Pb": 82,
-    "Bi": 83,
-    "Po": 84,
-    "At": 85,
-    "Rn": 86,
-    "Fr": 87,
-    "Ra": 88,
-    "Ac": 89,
-    "Th": 90,
-    "Pa": 91,
-    "U": 92,
-    "Np": 93,
-    "Pu": 94,
-    "Am": 95,
-    "Cm": 96,
-    "Bk": 97,
-    "Cf": 98,
-    "Es": 99,
-    "Fm": 100,
-    "Md": 101,
-    "No": 102,
-    "Lr": 103,
+    "H"  :  1,
+    "He" :  2,
+    "Li" :  3,
+    "Be" :  4,
+    "B"  :  5,
+    "C"  :  6,
+    "N"  :  7,
+    "O"  :  8,
+    "F"  :  9,
+    "Ne" : 10,
+    "Na" : 11,
+    "Mg" : 12,
+    "Al" : 13,
+    "Si" : 14,
+    "P"  : 15,
+    "S"  : 16,
+    "Cl" : 17,
+    "Ar" : 18,
+    "K"  : 19,
+    "Ca" : 20,
+    "Sc" : 21,
+    "Ti" : 22,
+    "V"  : 23,
+    "Cr" : 24,
+    "Mn" : 25,
+    "Fe" : 26,
+    "Co" : 27,
+    "Ni" : 28,
+    "Cu" : 29,
+    "Zn" : 30,
+    "Ga" : 31,
+    "Ge" : 32,
+    "As" : 33,
+    "Se" : 34,
+    "Br" : 35,
+    "Kr" : 36,
+    "Rb" : 37,
+    "Sr" : 38,
+    "Y"  : 39,
+    "Zr" : 40,
+    "Nb" : 41,
+    "Mo" : 42,
+    "Tc" : 43,
+    "Ru" : 44,
+    "Rh" : 45,
+    "Pd" : 46,
+    "Ag" : 47,
+    "Cd" : 48,
+    "In" : 49,
+    "Sn" : 50,
+    "Sb" : 51,
+    "Te" : 52,
+    "I"  : 53,
+    "Xe" : 54,
+    "Cs" : 55,
+    "Ba" : 56,
+    "La" : 57,
+    "Ce" : 58,
+    "Pr" : 59,
+    "Nd" : 60,
+    "Pm" : 61,
+    "Sm" : 62,
+    "Eu" : 63,
+    "Gd" : 64,
+    "Tb" : 65,
+    "Dy" : 66,
+    "Ho" : 67,
+    "Er" : 68,
+    "Tm" : 69,
+    "Yb" : 70,
+    "Lu" : 71,
+    "Hf" : 72,
+    "Ta" : 73,
+    "W"  : 74,
+    "Re" : 75,
+    "Os" : 76,
+    "Ir" : 77,
+    "Pt" : 78,
+    "Au" : 79,
+    "Hg" : 80,
+    "Tl" : 81,
+    "Pb" : 82,
+    "Bi" : 83,
+    "Po" : 84,
+    "At" : 85,
+    "Rn" : 86,
+    "Fr" : 87,
+    "Ra" : 88,
+    "Ac" : 89,
+    "Th" : 90,
+    "Pa" : 91,
+    "U"  : 92,
+    "Np" : 93,
+    "Pu" : 94,
+    "Am" : 95,
+    "Cm" : 96,
+    "Bk" : 97,
+    "Cf" : 98,
+    "Es" : 99,
+    "Fm" : 100,
+    "Md" : 101,
+    "No" : 102,
+    "Lr" : 103,
     "Vac": 104
 }
 
@@ -141,29 +141,42 @@ def verify_user_sitepackages(mda_path):
 # file_top = "C:\\Users\\BradyJohnston\\Downloads\\6vsb_2_2_2_traj_xtc\\last_frame_nos.pdb"
 # file_traj = "C:\\Users\\BradyJohnston\\Downloads\\6vsb_2_2_2_traj_xtc\\trj_nos.xtc"
 
+# setup the universe using MDAnalysis, for use later in the script
 u = mda.Universe(file_top, file_traj)
 
 # output_name = "spike"
 output_name = molecule_name
 
-try:
-    parent_coll = bpy.data.collections['MolecularNodes']
-    parent_coll.name == "MolecularNodes"
-    # make the collection active, for creating and disabling new
-    bpy.context.view_layer.active_layer_collection = bpy.context.view_layer.layer_collection.children[
-        'MolecularNodes']
-except:
+# try to get the collection, returns None if collection doesn't exist
+parent_coll = bpy.data.collections.get('MolecularNodes')
+
+# if the collection doesn't exist, create it
+if not parent_coll:
     parent_coll = bpy.data.collections.new('MolecularNodes')
     bpy.context.scene.collection.children.link(parent_coll)
-    # make the collection active, for creating and disabling new
-    bpy.context.view_layer.active_layer_collection = bpy.context.view_layer.layer_collection.children[
-        'MolecularNodes']
+
+# make the MolecularNodes collection active
+bpy.context.view_layer.active_layer_collection = bpy.context.view_layer.layer_collection.children['MolecularNodes']
+
+# try:
+#     parent_coll = bpy.data.collections['MolecularNodes']
+#     parent_coll.name == "MolecularNodes"
+#     # make the collection active, for creating and disabling new
+#     bpy.context.view_layer.active_layer_collection = bpy.context.view_layer.layer_collection.children[
+#         'MolecularNodes']
+# except:
+#     parent_coll = bpy.data.collections.new('MolecularNodes')
+#     bpy.context.scene.collection.children.link(parent_coll)
+#     # make the collection active, for creating and disabling new
+#     bpy.context.view_layer.active_layer_collection = bpy.context.view_layer.layer_collection.children[
+#         'MolecularNodes']
 
 
 # create new collection that will house the data, link it to the parent collection
 col = bpy.data.collections.new(output_name)
 parent_coll.children.link(col)
 
+# create the properties collection
 col_properties = bpy.data.collections.new(output_name + "_properties")
 col.children.link(col_properties)
 
@@ -261,7 +274,7 @@ def create_prop_AtomicNum_ChainNum_NameNum(univ, name, collection):
         n_atoms=n
     )
 
-    return unique_chains
+    return list(unique_chains)
 
 
 def create_prop_aaSeqNum_atomNum_atomAAIDNum(univ, name, collection):
@@ -355,7 +368,7 @@ def create_prop_bvalue_isBackbone_isCA(univ, name, collection):
 
 
 # create the models that will hold the properties associated with each atom
-unique_chains = create_prop_AtomicNum_ChainNum_NameNum(
+unique_names = create_prop_AtomicNum_ChainNum_NameNum(
     univ=u,
     name=output_name + "_properties_1",
     collection=col_properties