Restructure example gallery

biotite-dev · Apr 19, 2024 · 315b10d · 315b10d
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Showing 99 changed files with 80 additions and 38 deletions.
diff --git a/doc/conf.py b/doc/conf.py
@@ -85,7 +85,12 @@
 version = biotite.__version__
 release = biotite.__version__
 
-exclude_patterns = ["build"]
+exclude_patterns = [
+    # These are automatically incorporated by sphinx_gallery
+    "examples/scripts/**/README.rst",
+    # Execution times are not reported to the user
+    "sg_execution_times.rst",
+]
 
 pygments_style = "sphinx"
 
@@ -156,8 +161,14 @@
 }
 
 sphinx_gallery_conf = {
-    "examples_dirs"             : "examples/scripts",
-    "gallery_dirs"              : "examples/gallery",
+    "examples_dirs"             : [
+        "examples/scripts/sequence",
+        "examples/scripts/structure"
+    ],
+    "gallery_dirs"              : [
+        "examples/gallery/sequence",
+        "examples/gallery/structure"
+    ],
     "within_subsection_order"   : FileNameSortKey,
     # Do not run example scripts with a trailing '_noexec'
     "filename_pattern"          : "^((?!_noexec).)*$",

diff --git a/doc/examples/index.rst b/doc/examples/index.rst
@@ -0,0 +1,13 @@
+########
+Examples
+########
+
+This gallery shows how to perform different kind of analyses on real data using
+*Biotite*.
+Some of them are real world examples, others are fictional applications.
+
+.. toctree::
+    :maxdepth: 1
+
+    gallery/sequence/index
+    gallery/structure/index
diff --git a/doc/examples/scripts/README.txt b/doc/examples/scripts/README.txt
diff --git a/doc/examples/scripts/sequence/1_homology/README.rst b/doc/examples/scripts/sequence/1_homology/README.rst
@@ -0,0 +1,2 @@
+Homology and alignment
+----------------------
diff --git a/...ples/scripts/sequence/avidin_alignment.py → ...s/sequence/1_homology/avidin_alignment.py b/...ples/scripts/sequence/avidin_alignment.py → ...s/sequence/1_homology/avidin_alignment.py
diff --git a/...es/scripts/sequence/bionigma_alignment.py → ...sequence/1_homology/bionigma_alignment.py b/...es/scripts/sequence/bionigma_alignment.py → ...sequence/1_homology/bionigma_alignment.py
diff --git a/...les/scripts/sequence/genome_comparison.py → .../sequence/1_homology/genome_comparison.py b/...les/scripts/sequence/genome_comparison.py → .../sequence/1_homology/genome_comparison.py
diff --git a/...xamples/scripts/sequence/genome_search.py → ...ipts/sequence/1_homology/genome_search.py b/...xamples/scripts/sequence/genome_search.py → ...ipts/sequence/1_homology/genome_search.py
diff --git a/...amples/scripts/sequence/gpcr_evolution.py → ...pts/sequence/1_homology/gpcr_evolution.py b/...amples/scripts/sequence/gpcr_evolution.py → ...pts/sequence/1_homology/gpcr_evolution.py
diff --git a/...amples/scripts/sequence/hcn_hydropathy.py → ...pts/sequence/1_homology/hcn_hydropathy.py b/...amples/scripts/sequence/hcn_hydropathy.py → ...pts/sequence/1_homology/hcn_hydropathy.py
diff --git a/...amples/scripts/sequence/hcn_similarity.py → ...pts/sequence/1_homology/hcn_similarity.py b/...amples/scripts/sequence/hcn_similarity.py → ...pts/sequence/1_homology/hcn_similarity.py
diff --git a/doc/examples/scripts/sequence/homolog_msa.py → ...cripts/sequence/1_homology/homolog_msa.py b/doc/examples/scripts/sequence/homolog_msa.py → ...cripts/sequence/1_homology/homolog_msa.py
diff --git a/...les/scripts/sequence/lexa_conservation.py → .../sequence/1_homology/lexa_conservation.py b/...les/scripts/sequence/lexa_conservation.py → .../sequence/1_homology/lexa_conservation.py
diff --git a/...mples/scripts/sequence/luxa_comparison.py → ...ts/sequence/1_homology/luxa_comparison.py b/...mples/scripts/sequence/luxa_comparison.py → ...ts/sequence/1_homology/luxa_comparison.py
diff --git a/...amples/scripts/sequence/pi3k_alignment.py → ...pts/sequence/1_homology/pi3k_alignment.py b/...amples/scripts/sequence/pi3k_alignment.py → ...pts/sequence/1_homology/pi3k_alignment.py
diff --git a/doc/examples/scripts/sequence/plotepiscan.py → ...cripts/sequence/1_homology/plotepiscan.py b/doc/examples/scripts/sequence/plotepiscan.py → ...cripts/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]

diff --git a/...s/scripts/sequence/residue_coevolution.py → ...equence/1_homology/residue_coevolution.py b/...s/scripts/sequence/residue_coevolution.py → ...equence/1_homology/residue_coevolution.py
diff --git a/...ts/sequence/thca_synthase_polymorphism.py → .../1_homology/thca_synthase_polymorphism.py b/...ts/sequence/thca_synthase_polymorphism.py → .../1_homology/thca_synthase_polymorphism.py
diff --git a/doc/examples/scripts/sequence/2_sequencing/README.rst b/doc/examples/scripts/sequence/2_sequencing/README.rst
@@ -0,0 +1,2 @@
+Sequence read quality control and mapping
+-----------------------------------------
diff --git a/doc/examples/scripts/sequence/gene_counts.py → ...ipts/sequence/2_sequencing/gene_counts.py b/doc/examples/scripts/sequence/gene_counts.py → ...ipts/sequence/2_sequencing/gene_counts.py
diff --git a/...mples/scripts/sequence/genome_assembly.py → .../sequence/2_sequencing/genome_assembly.py b/...mples/scripts/sequence/genome_assembly.py → .../sequence/2_sequencing/genome_assembly.py
diff --git a/...mples/scripts/sequence/quality_control.py → .../sequence/2_sequencing/quality_control.py b/...mples/scripts/sequence/quality_control.py → .../sequence/2_sequencing/quality_control.py
diff --git a/...examples/scripts/sequence/read_quality.py → ...pts/sequence/2_sequencing/read_quality.py b/...examples/scripts/sequence/read_quality.py → ...pts/sequence/2_sequencing/read_quality.py
diff --git a/doc/examples/scripts/sequence/3_profile/README.rst b/doc/examples/scripts/sequence/3_profile/README.rst
@@ -0,0 +1,2 @@
+Sequence profiles
+-----------------
diff --git a/...xamples/scripts/sequence/anderson_logo.py → ...ripts/sequence/3_profile/anderson_logo.py b/...xamples/scripts/sequence/anderson_logo.py → ...ripts/sequence/3_profile/anderson_logo.py
diff --git a/...es/scripts/sequence/rbs_identification.py → .../sequence/3_profile/rbs_identification.py b/...es/scripts/sequence/rbs_identification.py → .../sequence/3_profile/rbs_identification.py
diff --git a/doc/examples/scripts/sequence/4_annotation/README.rst b/doc/examples/scripts/sequence/4_annotation/README.rst
@@ -0,0 +1,2 @@
+Features and annotations
+------------------------
diff --git a/doc/examples/scripts/sequence/operon_map.py → ...ripts/sequence/4_annotation/operon_map.py b/doc/examples/scripts/sequence/operon_map.py → ...ripts/sequence/4_annotation/operon_map.py
diff --git a/doc/examples/scripts/sequence/plasmid_map.py → ...ipts/sequence/4_annotation/plasmid_map.py b/doc/examples/scripts/sequence/plasmid_map.py → ...ipts/sequence/4_annotation/plasmid_map.py
diff --git a/...es/scripts/sequence/plasmid_map_custom.py → ...quence/4_annotation/plasmid_map_custom.py b/...es/scripts/sequence/plasmid_map_custom.py → ...quence/4_annotation/plasmid_map_custom.py
diff --git a/.../scripts/sequence/region_visualization.py → ...ence/4_annotation/region_visualization.py b/.../scripts/sequence/region_visualization.py → ...ence/4_annotation/region_visualization.py
diff --git a/...xamples/scripts/sequence/sigma_domains.py → ...ts/sequence/4_annotation/sigma_domains.py b/...xamples/scripts/sequence/sigma_domains.py → ...ts/sequence/4_annotation/sigma_domains.py
diff --git a/doc/examples/scripts/sequence/5_misc/README.rst b/doc/examples/scripts/sequence/5_misc/README.rst
@@ -0,0 +1,2 @@
+Miscellaneous
+-------------
diff --git a/...les/scripts/sequence/blosum_dendrogram.py → ...ipts/sequence/5_misc/blosum_dendrogram.py b/...les/scripts/sequence/blosum_dendrogram.py → ...ipts/sequence/5_misc/blosum_dendrogram.py
diff --git a/doc/examples/scripts/sequence/codon_usage.py → ...es/scripts/sequence/5_misc/codon_usage.py b/doc/examples/scripts/sequence/codon_usage.py → ...es/scripts/sequence/5_misc/codon_usage.py
diff --git a/...xamples/scripts/sequence/color_schemes.py → .../scripts/sequence/5_misc/color_schemes.py b/...xamples/scripts/sequence/color_schemes.py → .../scripts/sequence/5_misc/color_schemes.py
diff --git a/...scripts/sequence/color_schemes_protein.py → .../sequence/5_misc/color_schemes_protein.py b/...scripts/sequence/color_schemes_protein.py → .../sequence/5_misc/color_schemes_protein.py
diff --git a/...ts/sequence/local_alignment_statistics.py → ...ence/5_misc/local_alignment_statistics.py b/...ts/sequence/local_alignment_statistics.py → ...ence/5_misc/local_alignment_statistics.py
diff --git a/...es/scripts/sequence/orf_identification.py → ...pts/sequence/5_misc/orf_identification.py b/...es/scripts/sequence/orf_identification.py → ...pts/sequence/5_misc/orf_identification.py
diff --git a/doc/examples/scripts/sequence/README.rst b/doc/examples/scripts/sequence/README.rst
@@ -0,0 +1,2 @@
+Sequence examples
+=================
diff --git a/doc/examples/scripts/sequence/README.txt b/doc/examples/scripts/sequence/README.txt
diff --git a/doc/examples/scripts/structure/1_protein/README.rst b/doc/examples/scripts/structure/1_protein/README.rst
@@ -0,0 +1,2 @@
+Protein backbone and secondary structure
+----------------------------------------
diff --git a/...es/scripts/structure/pb_alignment.license → .../structure/1_protein/pb_alignment.license b/...es/scripts/structure/pb_alignment.license → .../structure/1_protein/pb_alignment.license
diff --git a/...xamples/scripts/structure/pb_alignment.py → ...ripts/structure/1_protein/pb_alignment.py b/...xamples/scripts/structure/pb_alignment.py → ...ripts/structure/1_protein/pb_alignment.py
diff --git a/...es/scripts/structure/peptide_assembly.png → .../structure/1_protein/peptide_assembly.png b/...es/scripts/structure/peptide_assembly.png → .../structure/1_protein/peptide_assembly.png
diff --git a/...les/scripts/structure/peptide_assembly.py → ...s/structure/1_protein/peptide_assembly.py b/...les/scripts/structure/peptide_assembly.py → ...s/structure/1_protein/peptide_assembly.py
diff --git a/...ripts/structure/peptide_assembly_pymol.py → ...cture/1_protein/peptide_assembly_pymol.py b/...ripts/structure/peptide_assembly_pymol.py → ...cture/1_protein/peptide_assembly_pymol.py
diff --git a/...xamples/scripts/structure/ramachandran.py → ...ripts/structure/1_protein/ramachandran.py b/...xamples/scripts/structure/ramachandran.py → ...ripts/structure/1_protein/ramachandran.py
diff --git a/...es/scripts/structure/residue_chirality.py → .../structure/1_protein/residue_chirality.py b/...es/scripts/structure/residue_chirality.py → .../structure/1_protein/residue_chirality.py
diff --git a/...es/scripts/structure/sheet_arrangement.py → .../structure/1_protein/sheet_arrangement.py b/...es/scripts/structure/sheet_arrangement.py → .../structure/1_protein/sheet_arrangement.py
diff --git a/...es/scripts/structure/transketolase_sse.py → .../structure/1_protein/transketolase_sse.py b/...es/scripts/structure/transketolase_sse.py → .../structure/1_protein/transketolase_sse.py
diff --git a/doc/examples/scripts/structure/2_nucleotide/README.rst b/doc/examples/scripts/structure/2_nucleotide/README.rst
@@ -0,0 +1,2 @@
+Nucleic acid base pairs and secondary structure
+-----------------------------------------------
diff --git a/doc/examples/scripts/structure/base_pairs.py → ...ipts/structure/2_nucleotide/base_pairs.py b/doc/examples/scripts/structure/base_pairs.py → ...ipts/structure/2_nucleotide/base_pairs.py
diff --git a/...ples/scripts/structure/leontis_westhof.py → ...structure/2_nucleotide/leontis_westhof.py b/...ples/scripts/structure/leontis_westhof.py → ...structure/2_nucleotide/leontis_westhof.py
diff --git a/...amples/scripts/structure/transfer_rnas.py → ...s/structure/2_nucleotide/transfer_rnas.py b/...amples/scripts/structure/transfer_rnas.py → ...s/structure/2_nucleotide/transfer_rnas.py
diff --git a/...xamples/scripts/structure/watson_crick.py → ...ts/structure/2_nucleotide/watson_crick.py b/...xamples/scripts/structure/watson_crick.py → ...ts/structure/2_nucleotide/watson_crick.py
diff --git a/doc/examples/scripts/structure/3_molecule/README.rst b/doc/examples/scripts/structure/3_molecule/README.rst
@@ -0,0 +1,2 @@
+Small molecules
+---------------
diff --git a/...mples/scripts/structure/alkane_isomers.py → ...ts/structure/3_molecule/alkane_isomers.py b/...mples/scripts/structure/alkane_isomers.py → ...ts/structure/3_molecule/alkane_isomers.py
diff --git a/...ipts/structure/molecular_visualization.py → ...ure/3_molecule/molecular_visualization.py b/...ipts/structure/molecular_visualization.py → ...ure/3_molecule/molecular_visualization.py
diff --git a/...s/scripts/structure/peoe_visualization.py → ...tructure/3_molecule/peoe_visualization.py b/...s/scripts/structure/peoe_visualization.py → ...tructure/3_molecule/peoe_visualization.py
diff --git a/doc/examples/scripts/structure/4_contacts/README.rst b/doc/examples/scripts/structure/4_contacts/README.rst
@@ -0,0 +1,2 @@
+Proximity and contacts
+----------------------
diff --git a/...les/scripts/structure/adjacency_matrix.py → .../structure/4_contacts/adjacency_matrix.py b/...les/scripts/structure/adjacency_matrix.py → .../structure/4_contacts/adjacency_matrix.py
diff --git a/...mples/scripts/structure/contact_sites.png → ...ts/structure/4_contacts/contact_sites.png b/...mples/scripts/structure/contact_sites.png → ...ts/structure/4_contacts/contact_sites.png
diff --git a/...amples/scripts/structure/contact_sites.py → ...pts/structure/4_contacts/contact_sites.py b/...amples/scripts/structure/contact_sites.py → ...pts/structure/4_contacts/contact_sites.py
diff --git a/.../scripts/structure/contact_sites_pymol.py → ...ructure/4_contacts/contact_sites_pymol.py b/.../scripts/structure/contact_sites_pymol.py → ...ructure/4_contacts/contact_sites_pymol.py
diff --git a/...ples/scripts/structure/disulfide_bonds.py → ...s/structure/4_contacts/disulfide_bonds.py b/...ples/scripts/structure/disulfide_bonds.py → ...s/structure/4_contacts/disulfide_bonds.py
diff --git a/...amples/scripts/structure/domain_hbonds.py → ...pts/structure/4_contacts/domain_hbonds.py b/...amples/scripts/structure/domain_hbonds.py → ...pts/structure/4_contacts/domain_hbonds.py
diff --git a/doc/examples/scripts/structure/leaflet.png → .../scripts/structure/4_contacts/leaflet.png b/doc/examples/scripts/structure/leaflet.png → .../scripts/structure/4_contacts/leaflet.png
diff --git a/doc/examples/scripts/structure/leaflet.py → ...s/scripts/structure/4_contacts/leaflet.py b/doc/examples/scripts/structure/leaflet.py → ...s/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,

diff --git a/...amples/scripts/structure/leaflet_pymol.py → ...pts/structure/4_contacts/leaflet_pymol.py b/...amples/scripts/structure/leaflet_pymol.py → ...pts/structure/4_contacts/leaflet_pymol.py
diff --git a/doc/examples/scripts/structure/6_modeling/README.rst b/doc/examples/scripts/structure/6_modeling/README.rst
@@ -0,0 +1,2 @@
+Molecular dynamics and docking
+------------------------------
diff --git a/doc/examples/scripts/structure/docking.png → .../scripts/structure/6_modeling/docking.png b/doc/examples/scripts/structure/docking.png → .../scripts/structure/6_modeling/docking.png
diff --git a/doc/examples/scripts/structure/docking.py → ...s/scripts/structure/6_modeling/docking.py b/doc/examples/scripts/structure/docking.py → ...s/scripts/structure/6_modeling/docking.py
diff --git a/...amples/scripts/structure/docking_pymol.py → ...pts/structure/6_modeling/docking_pymol.py b/...amples/scripts/structure/docking_pymol.py → ...pts/structure/6_modeling/docking_pymol.py
diff --git a/...examples/scripts/structure/md_analysis.py → ...ripts/structure/6_modeling/md_analysis.py b/...examples/scripts/structure/md_analysis.py → ...ripts/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,

diff --git a/...ples/scripts/structure/mmtf_trajectory.py → ...s/structure/6_modeling/mmtf_trajectory.py b/...ples/scripts/structure/mmtf_trajectory.py → ...s/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()

diff --git a/...amples/scripts/structure/normal_modes.gif → ...pts/structure/6_modeling/normal_modes.gif b/...amples/scripts/structure/normal_modes.gif → ...pts/structure/6_modeling/normal_modes.gif
diff --git a/...xamples/scripts/structure/normal_modes.py → ...ipts/structure/6_modeling/normal_modes.py b/...xamples/scripts/structure/normal_modes.py → ...ipts/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

diff --git a/...s/scripts/structure/normal_modes_pymol.py → ...tructure/6_modeling/normal_modes_pymol.py b/...s/scripts/structure/normal_modes_pymol.py → ...tructure/6_modeling/normal_modes_pymol.py
diff --git a/...ples/scripts/structure/rotamer_library.py → ...s/structure/6_modeling/rotamer_library.py b/...ples/scripts/structure/rotamer_library.py → ...s/structure/6_modeling/rotamer_library.py
diff --git a/...les/scripts/structure/solvation_shells.py → .../structure/6_modeling/solvation_shells.py b/...les/scripts/structure/solvation_shells.py → .../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)

diff --git a/...mples/scripts/structure/trajectory_sse.py → ...ts/structure/6_modeling/trajectory_sse.py b/...mples/scripts/structure/trajectory_sse.py → ...ts/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)

diff --git a/...ples/scripts/structure/water_exchange.png → ...s/structure/6_modeling/water_exchange.png b/...ples/scripts/structure/water_exchange.png → ...s/structure/6_modeling/water_exchange.png
diff --git a/...cripts/structure/water_exchange_noexec.py → ...cture/6_modeling/water_exchange_noexec.py b/...cripts/structure/water_exchange_noexec.py → ...cture/6_modeling/water_exchange_noexec.py
@@ -19,7 +19,7 @@
 However, the trajectories are based of publicly accessible structures
 of the open (PDB: 7NP3) and closed (PDB: 7NP4) state.
 
-.. image:: ../../scripts/structure/water_exchange.png
+.. image:: ../../../scripts/structure/6_modeling/water_exchange.png
 """
 
 # Code source: Daniel Bauer, Patrick Kunzmann

diff --git a/doc/examples/scripts/structure/7_misc/README.rst b/doc/examples/scripts/structure/7_misc/README.rst
@@ -0,0 +1,2 @@
+Miscellaneous
+-------------
diff --git a/...scripts/structure/biological_assembly.png → .../structure/7_misc/biological_assembly.png b/...scripts/structure/biological_assembly.png → .../structure/7_misc/biological_assembly.png
diff --git a/.../scripts/structure/biological_assembly.py → ...s/structure/7_misc/biological_assembly.py b/.../scripts/structure/biological_assembly.py → ...s/structure/7_misc/biological_assembly.py
diff --git a/...ts/structure/biological_assembly_pymol.py → ...cture/7_misc/biological_assembly_pymol.py b/...ts/structure/biological_assembly_pymol.py → ...cture/7_misc/biological_assembly_pymol.py
diff --git a/doc/examples/scripts/structure/diameter.py → ...ples/scripts/structure/7_misc/diameter.py b/doc/examples/scripts/structure/diameter.py → ...ples/scripts/structure/7_misc/diameter.py
diff --git a/doc/examples/scripts/structure/gap_bars.py → ...ples/scripts/structure/7_misc/gap_bars.py b/doc/examples/scripts/structure/gap_bars.py → ...ples/scripts/structure/7_misc/gap_bars.py
diff --git a/...ts/structure/glycan_visualization.license → ...cture/7_misc/glycan_visualization.license b/...ts/structure/glycan_visualization.license → ...cture/7_misc/glycan_visualization.license
diff --git a/...scripts/structure/glycan_visualization.py → .../structure/7_misc/glycan_visualization.py b/...scripts/structure/glycan_visualization.py → .../structure/7_misc/glycan_visualization.py
diff --git a/.../scripts/structure/ku_superimposition.png → ...s/structure/7_misc/ku_superimposition.png b/.../scripts/structure/ku_superimposition.png → ...s/structure/7_misc/ku_superimposition.png
diff --git a/...s/scripts/structure/ku_superimposition.py → ...ts/structure/7_misc/ku_superimposition.py b/...s/scripts/structure/ku_superimposition.py → ...ts/structure/7_misc/ku_superimposition.py
diff --git a/...pts/structure/ku_superimposition_pymol.py → ...ucture/7_misc/ku_superimposition_pymol.py b/...pts/structure/ku_superimposition_pymol.py → ...ucture/7_misc/ku_superimposition_pymol.py
diff --git a/...mples/scripts/structure/pdb_statistics.py → ...cripts/structure/7_misc/pdb_statistics.py b/...mples/scripts/structure/pdb_statistics.py → ...cripts/structure/7_misc/pdb_statistics.py
diff --git a/doc/examples/scripts/structure/README.rst b/doc/examples/scripts/structure/README.rst
@@ -0,0 +1,2 @@
+Structure examples
+==================
diff --git a/doc/examples/scripts/structure/README.txt b/doc/examples/scripts/structure/README.txt
diff --git a/doc/index.rst b/doc/index.rst
@@ -69,7 +69,7 @@ Biotite documentation
 
             .. grid-item::
 
-                .. button-ref:: examples/gallery/index
+                .. button-ref:: examples/index
                     :color: primary
                     :outline:
                     :expand:
@@ -83,12 +83,12 @@ Biotite documentation
            :gutter: 2
 
            .. grid-item-card::
-               :link: examples/gallery/sequence/lexa_conservation.html
-               :img-background: /examples/gallery/sequence/images/sphx_glr_lexa_conservation_002.png
+               :link: examples/gallery/sequence/1_homology/lexa_conservation.html
+               :img-background: /examples/gallery/sequence/1_homology/images/sphx_glr_lexa_conservation_002.png
 
            .. grid-item-card::
-               :link: examples/gallery/structure/transketolase_sse.html
-               :img-background: /examples/gallery/structure/images/sphx_glr_transketolase_sse_004.png
+               :link: examples/gallery/structure/1_protein/transketolase_sse.html
+               :img-background: /examples/gallery/structure/1_protein/images/sphx_glr_transketolase_sse_004.png
 
 
 .. raw:: html
@@ -112,8 +112,8 @@ Biotite documentation
         representations, ranging from sequence alignments to feature maps.
 
         .. card::
-            :img-background: /examples/gallery/sequence/images/sphx_glr_avidin_alignment_001.png
-            :link: examples/gallery/sequence/avidin_alignment.html
+            :img-background: /examples/gallery/sequence/1_homology/images/sphx_glr_avidin_alignment_001.png
+            :link: examples/gallery/sequence/1_homology/avidin_alignment.html
 
     .. grid-item::
 
@@ -131,8 +131,8 @@ Biotite documentation
 
 
         .. card::
-            :img-background: /examples/gallery/structure/images/sphx_glr_contact_sites_001.png
-            :link: examples/gallery/structure/contact_sites.html
+            :img-background: /examples/gallery/structure/4_contacts/images/sphx_glr_contact_sites_001.png
+            :link: examples/gallery/structure/4_contacts/contact_sites.html
 
     .. grid-item::
 
@@ -146,8 +146,8 @@ Biotite documentation
         instead of learning the respective REST API.
 
         .. card::
-            :img-background: /examples/gallery/structure/images/sphx_glr_pdb_statistics_001.png
-            :link: examples/gallery/structure/pdb_statistics.html
+            :img-background: /examples/gallery/structure/7_misc/images/sphx_glr_pdb_statistics_001.png
+            :link: examples/gallery/structure/7_misc/pdb_statistics.html
 
     .. grid-item::
 
@@ -164,8 +164,8 @@ Biotite documentation
         File creation and command line execution are handled under the hood.
 
         .. card::
-            :img-background: /examples/gallery/structure/images/sphx_glr_docking_002.png
-            :link: examples/gallery/structure/docking.html
+            :img-background: /examples/gallery/structure/6_modeling/images/sphx_glr_docking_002.png
+            :link: examples/gallery/structure/6_modeling/docking.html
 
 
 .. raw:: html
@@ -218,7 +218,7 @@ Biotite documentation
     tutorial/index
     install
     apidoc/index
-    examples/gallery/index
+    examples/index
     extensions
     contribute
     logo
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Sequence read quality control and mapping
		-----------------------------------------
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		@@ -0,0 +1,2 @@
		Features and annotations
		------------------------
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		@@ -0,0 +1,2 @@
		Protein backbone and secondary structure
		----------------------------------------
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		@@ -0,0 +1,2 @@
		Nucleic acid base pairs and secondary structure
		-----------------------------------------------
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		@@ -0,0 +1,2 @@
		Molecular dynamics and docking
		------------------------------