Add functionalities related to aromatic rings

doc/apidoc.json

@@ -347,6 +347,11 @@
             "dot_bracket",
             "dot_bracket_from_structure",
             "base_pairs_from_dot_bracket"
+        ],
+        "Aromatic rings": [
+            "find_aromatic_rings",
+            "find_stacking_interactions",
+            "PiStacking"
         ]
     },
     "biotite.structure.info" : {

doc/references.bib

@@ -103,6 +103,20 @@ @article{Bondi1964
   doi = {10.1021/j100785a001}
 }
 
+@article{Bouysset2021,
+  title = {{{ProLIF}}: A Library to Encode Molecular Interactions as Fingerprints},
+  shorttitle = {{{ProLIF}}},
+  author = {Bouysset, Cédric and Fiorucci, Sébastien},
+  year = {2021},
+  month = sep,
+  journal = {Journal of Cheminformatics},
+  volume = {13},
+  number = {1},
+  pages = {72},
+  issn = {1758-2946},
+  doi = {10.1186/s13321-021-00548-6}
+}
+
 @article{Brevern2000,
   title = {Bayesian Probabilistic Approach for Predicting Backbone Structures in Terms of Protein Blocks},
   author = {de Brevern, A. G. and Etchebest, C. and Hazout, S.},
@@ -543,16 +557,17 @@ @article{Ma2002
 }
 
 @article{Mantina2009,
+  title = {Consistent van Der {{Waals Radii}} for the {{Whole Main Group}}},
   author = {Mantina, Manjeera and Chamberlin, Adam C. and Valero, Rosendo and Cramer, Christopher J. and Truhlar, Donald G.},
-  title = {Consistent van der Waals Radii for the Whole Main Group},
+  year = {2009},
+  month = may,
   journal = {The Journal of Physical Chemistry A},
   volume = {113},
   number = {19},
-  pages = {5806-5812},
-  year = {2009},
-  doi = {10.1021/jp8111556},
-  note = {PMID: 19382751},
-  url = {https://doi.org/10.1021/jp8111556}
+  pages = {5806--5812},
+  publisher = {American Chemical Society},
+  issn = {1089-5639},
+  doi = {10.1021/jp8111556}
 }
 
 @article{Mariani2013,
@@ -665,49 +680,12 @@ @article{Pearson1988
 }
 
 @article{RDKit,
-  author       = {Greg Landrum and
-                  Paolo Tosco and
-                  Brian Kelley and
-                  Ricardo Rodriguez and
-                  David Cosgrove and
-                  Riccardo Vianello and
-                  sriniker and
-                  Peter Gedeck and
-                  Gareth Jones and
-                  NadineSchneider and
-                  Eisuke Kawashima and
-                  Dan Nealschneider and
-                  Andrew Dalke and
-                  Matt Swain and
-                  Brian Cole and
-                  Samo Turk and
-                  Aleksandr Savelev and
-                  tadhurst-cdd and
-                  Alain Vaucher and
-                  Maciej Wójcikowski and
-                  Ichiru Take and
-                  Vincent F. Scalfani and
-                  Rachel Walker and
-                  Kazuya Ujihara and
-                  Daniel Probst and
-                  Juuso Lehtivarjo and
-                  Hussein Faara and
-                  guillaume godin and
-                  Axel Pahl and
-                  Jeremy Monat},
-  title        = {rdkit/rdkit: 2024\_09\_5 (Q3 2024) Release},
-  month        = jan,
-  year         = 2025,
-  publisher    = {Zenodo},
-  version      = {Release\_2024\_09\_5},
-  doi          = {10.5281/zenodo.14779836},
-  url          = {https://doi.org/10.5281/zenodo.14779836},
-  swhid        = {swh:1:dir:7f64ae1b0334f6273f3daedab96bf3e0229e530a
-                   ;origin=https://doi.org/10.5281/zenodo.591637;visi
-                   t=swh:1:snp:17d9293d284e1a05de2a78abb47df1ef544a3c
-                   cd;anchor=swh:1:rel:eaf5c3e1f69b9714806a37d25966b6
-                   4cc04f19b8;path=rdkit-rdkit-7ea9d81
-                  },
+  title = {Rdkit/Rdkit: 2024\_09\_5 ({{Q3}} 2024) {{Release}}},
+  shorttitle = {Rdkit/Rdkit},
+  author = {Landrum, Greg and Tosco, Paolo and Kelley, Brian and Rodriguez, Ricardo and Cosgrove, David and Vianello, Riccardo and {sriniker} and Gedeck, Peter and Jones, Gareth and NadineSchneider and Kawashima, Eisuke and Nealschneider, Dan and Dalke, Andrew and Swain, Matt and Cole, Brian and Turk, Samo and Savelev, Aleksandr and {tadhurst-cdd} and Vaucher, Alain and Wójcikowski, Maciej and Take, Ichiru and Scalfani, Vincent F. and Walker, Rachel and Ujihara, Kazuya and Probst, Daniel and Lehtivarjo, Juuso and Faara, Hussein and {godin}, guillaume and Pahl, Axel and Monat, Jeremy},
+  year = {2025},
+  month = jan,
+  doi = {10.5281/zenodo.14779836}
 }
 
 @article{Roberts2004,
@@ -955,6 +933,20 @@ @article{Westbrook2015
   pmid = {25540181}
 }
 
+@article{Wojcikowski2015,
+  title = {Open {{Drug Discovery Toolkit}} ({{ODDT}}): A New Open-Source Player in the Drug Discovery Field},
+  shorttitle = {Open {{Drug Discovery Toolkit}} ({{ODDT}})},
+  author = {Wójcikowski, Maciej and Zielenkiewicz, Piotr and Siedlecki, Pawel},
+  year = {2015},
+  month = jun,
+  journal = {Journal of Cheminformatics},
+  volume = {7},
+  number = {1},
+  pages = {26},
+  issn = {1758-2946},
+  doi = {10.1186/s13321-015-0078-2}
+}
+
 @article{Xia2021,
   title = {Domains and Functions of Spike Protein in {{SARS-Cov-2}} in the Context of Vaccine Design},
   author = {Xia, Xuhua},

src/biotite/structure/__init__.py

@@ -125,6 +125,7 @@
 from .rdf import *
 from .repair import *
 from .residues import *
+from .rings import *
 from .sasa import *
 from .sequence import *
 from .sse import *