source/__init__.py

@@ -8,12 +8,12 @@
 #  Start of project                  : 2011-08-31 by CB
 #  First publication in Blender      : 2011-11-11 by CB
 #  Fusion of the PDB, XYZ and Panel  : 2019-03-22 by CB
-#  Last modified                     : 2024-05-28 by CB
+#  Last modified                     : 2024-07-27 by JF
 #
 #  Contributing authors
 #  ====================
+#  John Ferrier (ferrier.j@northeastern.edu)
 #  
-#  So far ... none ... .
 #
 #
 #  Acknowledgements

source/xyz_gui.py

@@ -27,7 +27,6 @@ from .xyz_export import export_xyz
 class IMPORT_OT_xyz(Operator, ImportHelper):
     bl_idname = "import_mesh.xyz"
     bl_label  = "Import XYZ (*.xyz)"
-    bl_description = "Import a XYZ atomic structure"
     bl_options = {'PRESET', 'UNDO'}
 
     filename_ext = ".xyz"
@@ -162,7 +161,7 @@ class IMPORT_OT_xyz(Operator, ImportHelper):
                    self.use_center_all,
                    self.use_camera,
                    self.use_lamp,
-                   filepath_xyz)
+                   filepath_xyz, self.use_frames)   # Added self.use_frames for animation purposes in xyz_import.py [ read_xyz_file() ]
 
         # Load frames
         if len(ALL_FRAMES) > 1 and self.use_frames:

source/xyz_import.py

@@ -4,6 +4,7 @@
 
 import os
 import bpy
+import re
 from math import pi, sqrt
 from mathutils import Vector, Matrix
 
@@ -192,17 +193,49 @@ def read_elements():
         ELEMENTS.append(li)
 
 
+def extract_number(file_name):
+    match = re.findall(r'\d+', file_name)
+    return int(''.join(match)) if match else 0
+
+
 # filepath_pdb: path to pdb file
 # radiustype  : '0' default
 #               '1' atomic radii
 #               '2' van der Waals
-def read_xyz_file(filepath_xyz,radiustype):
+def read_xyz_file(filepath_xyz,radiustype, use_frames):
 
     number_frames = 0
     total_number_atoms = 0
 
+    #### Added .xyz sequence for animations! Original author has animation functions built in but 
+    # never allowed for ALL_FRAMES to be built out. Just added a functionality for ALL_FRAMES.
+    # Files need to be in the format of my_cool_file_1.xyz, my_cool_file_2.xyz, ..., my_cool_file_x.xyz
+    # No other numbers, as extract_number() puts all numbers together for sorting. Guess it could work if
+    # the pre-emptive numbers are all the same... This was mostly just a quick fix for my use-case though.
+    # - JF
+
+    # Get the file directory
+    file_dir    = os.path.dirname( filepath_xyz )
+    files       = []
+
+    # If the use_frames option is selected on import, create a full list of the .xyz files in the dir
+    if use_frames:
+        for file in os.listdir( file_dir ):
+            if file.endswith('.xyz'):
+                files.append( file )
+
+        # Sort the list of .xyz files
+        files = sorted( files, key = extract_number )
+
+    else:
+        # If not, just append the single file
+        files.append( filepath_xyz )
+
+    # Cycle through each sorted file
+    for xyzf in files:
+
         # Open the file ...
-    filepath_xyz_p = open(filepath_xyz, "r")
+        filepath_xyz_p = open( os.path.join( file_dir, xyzf ), "r")
 
         #Go through the whole file.
         FLAG = False
@@ -441,7 +474,7 @@ def import_xyz(Ball_type,
                put_to_center_all,
                use_camera,
                use_light,
-               filepath_xyz):
+               filepath_xyz, use_frames):
 
     # List of materials
     atom_material_list = []
@@ -454,7 +487,7 @@ def import_xyz(Ball_type,
     # ------------------------------------------------------------------------
     # READING DATA OF ATOMS
 
-    Number_of_total_atoms = read_xyz_file(filepath_xyz, radiustype)
+    Number_of_total_atoms = read_xyz_file(filepath_xyz, radiustype, use_frames)
 
     # We show the atoms of the first frame.
     first_frame = ALL_FRAMES[0]
@@ -540,7 +573,7 @@ def import_xyz(Ball_type,
             sum_vec = Vector((0.0,0.0,0.0))
 
             # Sum of all atom coordinates
-            for (i, atoms_of_one_type) in enumerate(frame):
+            for i, atoms_of_one_type in enumerate(frame):
 
                 # This is a guarantee that only the total number of atoms of the
                 # first frame is used. Condition is, so far, that the number of