From e976c905efc8c1ecab74b38653aa54c2e7861e46 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Oct 2018 17:17:45 +0200
Subject: [PATCH] gather all references of docu in one place
---
core/doc/graph_minimizer.rst | 5 --
doc/CMakeLists.txt | 1 +
doc/index.rst | 7 +--
doc/references.rst | 61 +++++++++++++++++++++++++
loop/doc/structure_db.rst | 8 ----
modelling/doc/loop_closing.rst | 4 --
scoring/doc/other_scoring_functions.rst | 1 -
sidechain/doc/index.rst | 1 -
sidechain/doc/loading.rst | 6 ---
9 files changed, 64 insertions(+), 30 deletions(-)
create mode 100644 doc/references.rst
diff --git a/core/doc/graph_minimizer.rst b/core/doc/graph_minimizer.rst
index a1ddb963..fb8b8986 100644
--- a/core/doc/graph_minimizer.rst
+++ b/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.
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index c79f0aa9..a715f27d 100644
--- a/doc/CMakeLists.txt
+++ b/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!)
diff --git a/doc/index.rst b/doc/index.rst
index de9b7d84..87ac769f 100644
--- a/doc/index.rst
+++ b/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>
diff --git a/doc/references.rst b/doc/references.rst
new file mode 100644
index 00000000..b5583344
--- /dev/null
+++ b/doc/references.rst
@@ -0,0 +1,61 @@
+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.
+
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index dd7288d0..6728fccf 100644
--- a/loop/doc/structure_db.rst
+++ b/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.
diff --git a/modelling/doc/loop_closing.rst b/modelling/doc/loop_closing.rst
index 7ec7230b..cc1b1edf 100644
--- a/modelling/doc/loop_closing.rst
+++ b/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.
diff --git a/scoring/doc/other_scoring_functions.rst b/scoring/doc/other_scoring_functions.rst
index f505232e..95e0eb49 100644
--- a/scoring/doc/other_scoring_functions.rst
+++ b/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).
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index c0a24dce..b6425e79 100644
--- a/sidechain/doc/index.rst
+++ b/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.
diff --git a/sidechain/doc/loading.rst b/sidechain/doc/loading.rst
index 58342cd6..0c716dc8 100644
--- a/sidechain/doc/loading.rst
+++ b/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.
-
--
GitLab