make citing consistent

loop/doc/loop_closing.rst

@@ -8,11 +8,11 @@ Loops, represented as :class:`BackboneList` objects, often need to undergo
 conformational changes to fit into gaps defined by stem residues.
 |project| implements two algorithms performing this task.
 
-There is cyclic coordinate descent (CCD):
-Adrian A. Canutescu and Roland L. Dunbrack Jr. "Cyclic coordinate descent: A robotics algorithm for protein loop closure." Protein Sci. 12(5):963–972. (2003)
+  * There is cyclic coordinate descent (CCD) [canutescu2003]_
+
+
+  * and kinematic closure (KIC) [mandell2009]_
 
-and kinematic closure (KIC):
-Mandell DJ, Coutsias EA and Kortemme T. "Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling." Nat Methods. 6(8):551-2. (2009)
 
 In case of small gaps or small issues in the :class:`BackboneList` you might
 also consider the :class:`BackboneRelaxer`.
@@ -204,3 +204,10 @@ can be relaxed by the relaxer.
 
     :raises:            :class:`RuntimeError` if **bb_list** has not the same
                         size or sequence as the initial one.
+
+
+
+
+.. [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.
\ No newline at end of file

sidechain/doc/disulfid.rst

@@ -7,12 +7,8 @@ When calculating the pairwise interaction energy between two rotamers building
 a disulfid bond, one would get an unfavourable energy due to "clashes" between
 the sulfur atoms. It is possible to improve performance in sidechain
 reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description of
-disulfid bonds described in:
-
-Canutescu AA, Shelenkov AA, Dunbrack RL Jr.
-A graph-theory algorithm for rapid protein side-chain prediction.
-Protein Sci (2003).
+disulfid bonds. PROMOD3 implements a simple geometrical description 
+[canutescu2003]_ .
 
 Two methods are implemented to evaluate this disulfid score on either rigid of 
 flexible rotamers. The above paper proposes two rotamers to be in a disulfid
@@ -41,3 +37,5 @@ bonded state, if the resulting score is below 45.
                         of :class:`FRMRotamer` as input, the minimal score
                         between all possible subrotamer combinations gets
                         returned.
+
+.. [canutescu2003] 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

@@ -7,15 +7,10 @@
 .. currentmodule:: promod3.sidechain
 
 Tools and algorithms to model sidechains given backbone coordinates. 
-The full module is heavily based on SCWRL4:
-
-G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. 
-Improved prediction of protein side-chain conformations with SCWRL4. 
-Proteins (2009). 
-
-The paper describes the modelling of sidechains using two different rotamer 
-models. A rigid model, as well as a flexible model. Both models are implemented
-in PROMOD3 and can be applied in flexible ways.
+The full module is heavily based on SCWRL4 [krivov2009]_ .
+The according paper describes the modelling of sidechains using two different
+rotamer models. A rigid model, as well as a flexible model. Both models are
+implemented in PROMOD3 and can be applied in flexible ways.
 
 Reconstruct Function
 --------------------------------------------------------------------------------
@@ -190,3 +185,5 @@ Contents:
    Graph <graph>
    The Settings - Control Things... <sidechain_settings>
    Disulfid Bond Evaluation <disulfid>
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.