fixup! Restructure example gallery

doc/examples/scripts/sequence/1_homology/plotepiscan.py

@@ -40,7 +40,7 @@
 import biotite.sequence.io.fasta as fasta
 
 # Path to the data files
-array_seq_path = "../../download/Array_Seq.txt"
+array_seq_path = "../../../download/Array_Seq.txt"
 
 fasta_file = fasta.FastaFile.read(array_seq_path)
 
@@ -99,8 +99,8 @@ def read_scan(filename, pep_len=20, score_res=20):
     return df
 
 # Load epitope scan data
-fcr3_file_path  = "../../download/FCR3_10ug.csv"
-nf54_file_path  = "../../download/NF54_10ug.csv"
+fcr3_file_path  = "../../../download/FCR3_10ug.csv"
+nf54_file_path  = "../../../download/NF54_10ug.csv"
 
 # Define the score residues on the arrays
 files = [fcr3_file_path, nf54_file_path]

doc/examples/scripts/structure/4_contacts/leaflet.py

@@ -30,7 +30,7 @@
 
 # The bilayer structure file can be downloaded from
 # http://www.charmm-gui.org/archive/pure_bilayer/dppc.tar.gz
-PDB_FILE_PATH = "../../download/dppc_n128.pdb"
+PDB_FILE_PATH = "../../../download/dppc_n128.pdb"
 
 
 def find_leaflets(structure, head_atom_mask,

doc/examples/scripts/structure/6_modeling/md_analysis.py

@@ -30,8 +30,8 @@
 import matplotlib.pyplot as plt
 
 # Put here the path of the downloaded files
-templ_file_path = "../../download/lysozyme_md.pdb"
-traj_file_path  = "../../download/lysozyme_md.xtc"
+templ_file_path = "../../../download/lysozyme_md.pdb"
+traj_file_path  = "../../../download/lysozyme_md.xtc"
 
 # Gromacs does not set the element symbol in its PDB files,
 # but Biotite guesses the element names from the atom names,

doc/examples/scripts/structure/6_modeling/mmtf_trajectory.py

@@ -34,7 +34,7 @@
 import os.path
 
 # Put here the path of the downloaded trajectory file
-xtc_file_path = "../../download/lysozyme_md.xtc"
+xtc_file_path = "../../../download/lysozyme_md.xtc"
 
 xtc_file = xtc.XTCFile.read(xtc_file_path)
 coord = xtc_file.get_coord()

doc/examples/scripts/structure/6_modeling/normal_modes.py

@@ -43,7 +43,7 @@
 
 
 # A CSV file containing the eigenvectors for the CA atoms
-VECTOR_FILE = "../../download/glycosylase_anm_vectors.csv"
+VECTOR_FILE = "../../../download/glycosylase_anm_vectors.csv"
 # The corresponding structure
 PDB_ID = "1MUG"
 # The normal mode to be visualized

doc/examples/scripts/structure/6_modeling/solvation_shells.py

@@ -33,8 +33,8 @@
 import biotite.structure.io as strucio
 
 # Put here the path of the downloaded files
-templ_file_path = "../../download/waterbox_md.pdb"
-traj_file_path  = "../../download/waterbox_md.xtc"
+templ_file_path = "../../../download/waterbox_md.pdb"
+traj_file_path  = "../../../download/waterbox_md.xtc"
 
 # Load the trajectory
 traj = strucio.load_structure(traj_file_path, template=templ_file_path)

doc/examples/scripts/structure/6_modeling/trajectory_sse.py

@@ -26,8 +26,8 @@
 
 
 # Put here the path of the downloaded files
-templ_file_path = "../../download/lysozyme_md.pdb"
-traj_file_path  = "../../download/lysozyme_md.xtc"
+templ_file_path = "../../../download/lysozyme_md.pdb"
+traj_file_path  = "../../../download/lysozyme_md.xtc"
 
 
 xtc_file = xtc.XTCFile.read(traj_file_path)

doc/examples/scripts/structure/6_modeling/water_exchange_noexec.py

@@ -18,6 +18,8 @@
 example.
 However, the trajectories are based of publicly accessible structures
 of the open (PDB: 7NP3) and closed (PDB: 7NP4) state.
+
+.. image:: ../../../scripts/structure/6_modeling/water_exchange.png
 """
 
 # Code source: Daniel Bauer, Patrick Kunzmann
@@ -112,5 +114,4 @@ def cum_water_in_pore(traj, cutoff=6, key_residues=(507, 511)):
             va="center")
 fig.savefig("water_exchange.png", bbox_inches="tight")
 
-# sphinx_gallery_static_image = "water_exchange.png"
 plt.show()

doc/index.rst

@@ -69,7 +69,7 @@ Biotite documentation
 
             .. grid-item::
 
-                .. button-ref:: examples/gallery/index
+                .. button-ref:: examples/index
                     :color: primary
                     :outline:
                     :expand: