gather all references of docu in one place

core/doc/graph_minimizer.rst

@@ -228,8 +228,3 @@ a set :math:`X=[x_1, x_2, ..., x_n]` that minimizes:
                         representing the single solutions minimizing
                         the overall energy function.
                         The second element is the according energy value.          
-
-
-.. [goldstein1994] Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.
-
-.. [leach1998] Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.

doc/CMakeLists.txt

@@ -14,6 +14,7 @@ buildsystem.rst
 contributing.rst
 gettingstarted.rst
 portableIO.rst
+references.rst
 )
 
 # add documentation tests (must be done before rest below!)

doc/index.rst

@@ -16,12 +16,9 @@ Documentation
 
    Users <users>
    Developers <developers>
+   References <references>
 
 .. toctree::
    :maxdepth: 1
 
-   changelog
-
-
-.. [biasini2013] Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, Johner N, Schenk AD, Philippsen A and Schwede T (2013). OpenStructure: an integrated software framework for computational structural biology. Acta Cryst.
-
+   Changelog <changelog>

doc/references.rst

+References
+==========
+
+.. [biasini2013] Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, 
+                 Johner N, Schenk AD, Philippsen A and Schwede T (2013). 
+                 OpenStructure: an integrated software framework for 
+                 computational structural biology. Acta Cryst.
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). 
+                   Cyclic coordinate descent: A robotics algorithm for protein 
+                   loop closure. Protein Sci.
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). 
+                    A graph-theory algorithm for rapid protein side-chain 
+                    prediction. Protein Sci.
+
+.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). 
+                     Residue depth: a novel parameter for the analysis of 
+                     protein structure and stability. Structure.
+
+.. [goldstein1994] Goldstein RF (1994). 
+                   Efficient rotamer elimination applied to protein side-chains 
+                   and related spin glasses. Biophys J.
+
+.. [Jones1999] Jones DT (1999). 
+               Protein secondary structure prediction based on position-specific 
+               scoring matrices. J. Mol. Biol. 
+
+.. [kabsch1983] Kabsch W, Sander C (1983). 
+                Dictionary of protein secondary structure: pattern recognition of 
+                hydrogen-bonded and geometrical features. Biopolymers.
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). 
+                Improved prediction of protein side-chain conformations with 
+                SCWRL4. Proteins.
+
+.. [leach1998] Leach AR, Lemon AP (1998). 
+               Exploring the conformational space of protein side chains using 
+               dead-end elimination and the A* algorithm. Proteins.
+
+.. [lovell2000] Lovell SC, Word JM, Richardson JS, Richardson DC (2000). 
+                The penultimate rotamer library. Proteins.
+
+.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). 
+                 Sub-angstrom accuracy in protein loop reconstruction by 
+                 robotics-inspired conformational sampling. Nat Methods.
+
+.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). 
+                    A smoothed backbone-dependent rotamer library for proteins 
+                    derived from adaptive kernel density estimates and 
+                    regressions. Structure.
+
+.. [soding2005] Söding J (2005). 
+                Protein homology detection by HMM-HMM comparison. 
+                Bioinformatics.
+
+.. [zhou2005] Zhou H, Zhou Y (2005). 
+              Fold Recognition by Combining Sequence Profiles Derived From 
+              Evolution and From Depth-Dependent Structural Alignment of 
+              Fragments. Proteins.
+

loop/doc/structure_db.rst

@@ -981,11 +981,3 @@ The PsipredPrediction class
   .. method:: __len__()
 
     :returns:           Number of elements in container
-
-
-
-.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
-.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
-.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
-.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202. 
-.. [kabsch1983] Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.

modelling/doc/loop_closing.rst

@@ -374,8 +374,4 @@ Example usage:
     :rtype:  :class:`~promod3.loop.MmSystemCreator`
 
 
-.. rubric:: Citations
 
-.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.
-
-.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.

scoring/doc/other_scoring_functions.rst

@@ -53,4 +53,3 @@ Scoring Functions from SCWRL3
 
 
 
-.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).

sidechain/doc/index.rst

@@ -37,4 +37,3 @@ Contents:
    subrotamer_optimizer
 
 
-.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.

sidechain/doc/loading.rst

@@ -54,9 +54,3 @@ is directly provided in binary format and can be loaded with
 
   :returns: The read library
   :rtype:   :class:`BBDepRotamerLib`
-
-
-.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.
-
-.. [lovell2000] Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.
-