small changes for fixing docs

ConservedWaterSearch/hydrogen_orientation.py

@@ -50,7 +50,7 @@ def hydrogen_orientation_analysis(
       exist with satisfying water angles
 
     See :cite:`conservedwatersearch2022` for more information on water
-    classification :ref:`conservedwaters:theory, background and methods`.
+    classification :ref:`conservedwaters_theory_background_methods`.
     If orientations don't satisfy the criteria for any of the waters, an
     empty list is returned.
 

ConservedWaterSearch/water_clustering.py

@@ -40,7 +40,7 @@ class WaterClustering:
     First, oxygens are clustered using OPTICS or HDBSCAN, followed by
     analysis of orientations for classification of waters into one of 3
     proposed conserved water types (for more information see
-    :ref:`conservedwaters:theory, background and methods`):
+    :ref:`conservedwaters_theory_background_methods`):
 
         - FCW (Fully Conserved Water): hydrogens are strongly oriented in
           two directions with angle of 104.5
@@ -702,7 +702,7 @@ def water_type(self) -> list[str]:
           exsist with satisfying water angles
 
         For more information see :cite:`conservedwatersearch2022` and
-        :ref:`conservedwaters:theory, background and methods`).
+        :ref:`conservedwaters_theory_background_methods`).
 
         Returns:
             list[str]: Returns a list of strings containing water type

docs/source/HydrogenOrientationAnalysis.rst

@@ -2,7 +2,7 @@
 Hydrogen Orientation Analysis
 -----------------------------
 
-Analysis of hydrogen orientations is used to classify conserved waters into 3 different types: Fully Conserved Water (FCW), Half Conserved Water (HCW) and Weakly Conserved Waters (WCW). See :ref:`conservedwaters:theory, background and methods` for more information.
+Analysis of hydrogen orientations is used to classify conserved waters into 3 different types: Fully Conserved Water (FCW), Half Conserved Water (HCW) and Weakly Conserved Waters (WCW). See :ref:`conservedwaters_theory_background_methods` for more information.
 
 .. rubric:: Overview
 

docs/source/citing.rst

@@ -24,6 +24,3 @@ For citations, the following BibTeX entry can be used:
     URL = {https://doi.org/10.1021/acs.jcim.2c00801},
     }
 
-
-.. rubric:: References:
-.. bibliography:: references/references.bib

docs/source/conservedwaters.rst

@@ -1,15 +1,17 @@
+.. _conservedwaters_theory_background_methods:
+
 Theory, Background, and Methods
 ===============================
 
 Understanding Conserved Water Molecules
-------------------------------
+---------------------------------------
 
 Conserved water refers to water molecules that maintain specific, stable positions and orientations within biological systems, such as the active sites of proteins. These waters play pivotal roles in biochemical processes like protein-ligand binding and enzymatic reactions. Their presence and orientations significantly influence both the thermodynamics and kinetics of these processes. The importance of these water networks in influencing the thermodynamic signature of ligand-protein binding has been the subject of several studies. For example, researchers studied how water networks affect the thermodynamics of binding between phosphonopeptide inhibitors and the enzyme thermolysin. They found a direct correlation between the structure of the water networks and the thermodynamic profiles of the binding interactions :cite:`Betz2016,ENGLERT2010,Biela2012,Biela2013,Krimmer2014,Krimmer2016,Cramer2017`. In another study, mutations that disrupted nearby water networks were found to lower the affinity of ligand-protein binding in the *Haemophilus influenzae virulence* protein SiaP :cite:`Darby2019`. These findings highlight that the stabilization of water molecules through water network formation leads to more favorable binding signatures, emphasizing the critical role that conserved water plays in biochemical interactions.
 
 
 
 Overview of the Methodology
------------------------------
+---------------------------
 
 The developed method focuses on the identification and classification of conserved water molecules and their networks derived from molecular dynamics (MD) simulations :cite:`conservedwatersearch2022`. A distinguishing aspect of this approach is its two-fold analytical capability: it not only pinpoints the positions of oxygen atoms but also performs a novel analysis of hydrogen orientations. Additionally, the method incorporates a residence time criterion. It ensures that the water molecules in selected clusters are present in their respective positions for the majority of the simulation time, thus qualifying them as conserved water molecules. Working in conjunction with the hydrogen orientation analysis, this residence time criterion provides a robust classification of water molecules into three distinct types: Fully Conserved Water (FCW), Half Conserved Water (HCW), and Weakly Conserved Water (WCW), based on their preferred hydrogen orientations toward the receptor. This classification is a significant advancement over existing methods and provides critical insights into the roles and contributions of individual waters in the network. As a result, it offers a more comprehensive understanding of the water network's stability. The method is particularly useful in protein-ligand systems to understand water networks and their effects on binding thermodynamics, but it is general enough to be applicable to water networks at any type of surface. The method relies exclusively on data from MD simulations, eliminating the need for any crystal water data.