README update

Author: OliverBScott

README.md

@@ -13,6 +13,13 @@
     <img width="80%", src="https://github.com/UCLCheminformatics/ScaffoldGraph/blob/master/img/scaffoldgraph.jpg?raw=true" />
 </p>
 
+[Features](https://github.com/UCLCheminformatics/ScaffoldGraph#features) | 
+[Installation](https://github.com/UCLCheminformatics/ScaffoldGraph#installation) |
+[Quick-start](https://github.com/UCLCheminformatics/ScaffoldGraph#quick-start) |
+[Contributing](https://github.com/UCLCheminformatics/ScaffoldGraph#contributing) |
+[References](https://github.com/UCLCheminformatics/ScaffoldGraph#references) |
+[Citation](https://github.com/UCLCheminformatics/ScaffoldGraph#citation)
+
 ## Features
 
 * **Scaffold Network generation** (Varin, 2011)
@@ -180,7 +187,7 @@ Where "command" is one of: tree, network, hiers, aggregate or select.
        
     Note: selecting subsets of a graph will not be possible if a name is not supplied 
         
-- ### Output Formats
+- #### Output Formats
 
     - ##### TSV Format (default)
     
@@ -211,20 +218,20 @@ Where "command" is one of: tree, network, hiers, aggregate or select.
   
 --------------------------------------------------------------------------------
 
-#### Library usage
+### Library usage
 
 ScaffoldGraph makes it simple to construct a graph using the library API.
 The resultant graphs follow the same API as a NetworkX DiGraph.
 
-```python
-import scaffoldgraph as sg
-
-# construct a scaffold network from an SDF file
-network = sg.ScaffoldNetwork.from_sdf('my_sdf_file.sdf')
-
-# construct a scaffold tree from a SMILES file
-tree = sg.ScaffoldTree.from_smiles('my_smiles_file.smi')
-```
+    ```python
+    import scaffoldgraph as sg
+    
+    # construct a scaffold network from an SDF file
+    network = sg.ScaffoldNetwork.from_sdf('my_sdf_file.sdf')
+    
+    # construct a scaffold tree from a SMILES file
+    tree = sg.ScaffoldTree.from_smiles('my_smiles_file.smi')
+    ```
 
 
 --------------------------------------------------------------------------------
@@ -237,25 +244,25 @@ tree = sg.ScaffoldTree.from_smiles('my_smiles_file.smi')
     It is simple to construct a graph from multiple input source in parallel,
     using the concurrent.futures module and the sg.utils.aggregate function.
     
-    ```python
-    from concurrent.futures import ProcessPoolExecutor
-    from functools import partial
-    import scaffoldgraph as sg
-    import os
-  
-    directory = './data'
-    sdf_files = [f for f in os.listdir(directory) if f.endswith('.sdf')]
-  
-    func = partial(sg.ScaffoldNetwork.from_sdf, ring_cutoff=10)
-    
-    graphs = []
-    with ProcessPoolExecutor(max_workers=4) as executor:
-        futures = executor.map(func, sdf_files)
-        for future in futures:
-            graphs.append(future)
-    
-    network = sg.utils.aggregate(graphs)
-    ```
+        ```python
+        from concurrent.futures import ProcessPoolExecutor
+        from functools import partial
+        import scaffoldgraph as sg
+        import os
+      
+        directory = './data'
+        sdf_files = [f for f in os.listdir(directory) if f.endswith('.sdf')]
+      
+        func = partial(sg.ScaffoldNetwork.from_sdf, ring_cutoff=10)
+        
+        graphs = []
+        with ProcessPoolExecutor(max_workers=4) as executor:
+            futures = executor.map(func, sdf_files)
+            for future in futures:
+                graphs.append(future)
+        
+        network = sg.utils.aggregate(graphs)
+        ```
     
 - **Creating custom scaffold prioritisation rules**
 
@@ -267,71 +274,71 @@ tree = sg.ScaffoldTree.from_smiles('my_smiles_file.smi')
     When subclassing a name property must be defined and either a condition, get_property or filter function.
     Examples are shown below:
     
-    ```python
-    import scaffoldgraph as sg
-    from scaffoldgraph.prioritization import *
-    
-    """
-    Scaffold filter rule (must implement name and condition)
-    The filter will retain all scaffolds which return a True condition
-    """
-  
-    class CustomRule01(ScaffoldFilterRule):
-        """Do not remove rings with >= 12 atoms if there are smaller rings to remove"""
-  
-        def condition(self, child, parent):
-              removed_ring = child.rings[parent.removed_ring_idx]
-              return removed_ring.size < 12
+        ```python
+        import scaffoldgraph as sg
+        from scaffoldgraph.prioritization import *
+        
+        """
+        Scaffold filter rule (must implement name and condition)
+        The filter will retain all scaffolds which return a True condition
+        """
+      
+        class CustomRule01(ScaffoldFilterRule):
+            """Do not remove rings with >= 12 atoms if there are smaller rings to remove"""
+      
+            def condition(self, child, parent):
+                  removed_ring = child.rings[parent.removed_ring_idx]
+                  return removed_ring.size < 12
+                
+            @property
+            def name(self):
+                return 'custom rule 01'
+              
+        """
+        Scaffold min/max filter rule (must implement name and get_property)
+        The filter will retain all scaffolds with the min/max property value
+        """
+      
+        class CustomRule02(ScaffoldMinFilterRule):
+            """Smaller rings are removed first"""
+      
+            def get_property(self, child, parent):
+                  return child.rings[parent.removed_ring_idx].size
+                
+            @property
+            def name(self):
+                return 'custom rule 02'
             
-        @property
-        def name(self):
-            return 'custom rule 01'
           
-    """
-    Scaffold min/max filter rule (must implement name and get_property)
-    The filter will retain all scaffolds with the min/max property value
-    """
-  
-    class CustomRule02(ScaffoldMinFilterRule):
-        """Smaller rings are removed first"""
-  
-        def get_property(self, child, parent):
-              return child.rings[parent.removed_ring_idx].size
-            
-        @property
-        def name(self):
-            return 'custom rule 02'
-        
+        """
+        Scaffold base filter rule (must implement name and filter)
+        The filter method must return a list of filtered parent scaffolds
+        This rule is used when a more complex rule is required, this example
+        defines a tiebreaker rule. Only one scaffold must be left at the end
+        of all filter rules in a rule set
+        """
       
-    """
-    Scaffold base filter rule (must implement name and filter)
-    The filter method must return a list of filtered parent scaffolds
-    This rule is used when a more complex rule is required, this example
-    defines a tiebreaker rule. Only one scaffold must be left at the end
-    of all filter rules in a rule set
-    """
-  
-    class CustomRule03(BaseScaffoldFilterRule):
-        """Tie-breaker rule (alphabetical)"""
-
-        def filter(self, child, parents):
-            return [sorted(parents, key=lambda p: p.smiles)[0]]
-
-        @property
-        def name(self):
-            return 'cutstom rule 03'  
-    ```
+        class CustomRule03(BaseScaffoldFilterRule):
+            """Tie-breaker rule (alphabetical)"""
+    
+            def filter(self, child, parents):
+                return [sorted(parents, key=lambda p: p.smiles)[0]]
+    
+            @property
+            def name(self):
+                return 'cutstom rule 03'  
+        ```
     
     Custom rules can subsequently be added to a rule set and supplied to the scaffold tree constructor:
     
-    ```python
-    ruleset = ScaffoldRuleSet(name='custom rules')
-    ruleset.add_rule(CustomRule01())
-    ruleset.add_rule(CustomRule02())
-    ruleset.add_rule(CustomRule03())
-  
-    graph = sg.ScaffoldTree.from_sdf('my_sdf_file.sdf', prioritization_rules=ruleset)
-    ```
+        ```python
+        ruleset = ScaffoldRuleSet(name='custom rules')
+        ruleset.add_rule(CustomRule01())
+        ruleset.add_rule(CustomRule02())
+        ruleset.add_rule(CustomRule03())
+      
+        graph = sg.ScaffoldTree.from_sdf('my_sdf_file.sdf', prioritization_rules=ruleset)
+        ```
 
 --------------------------------------------------------------------------------
 
@@ -347,7 +354,7 @@ Contributions to ScaffoldGraph will most likely fall into the following categori
       Request please provide a clear description of the encountered bug. If unsure feel free to post an issue
 
 Please send Pull Requests to: 
-http://github.com/UCLCheminformatics/scaffoldgraph
+http://github.com/UCLCheminformatics/ScaffoldGraph
 
 ### Testing
 
@@ -374,4 +381,10 @@ ScaffoldGraph uses Travis CI for continuous integration
 * Varin, T., Schuffenhauer, A., Ertl, P., and Renner, S. (2011). Mining for bioactive scaffolds with scaffold networks: Improved compound set enrichment from primary screening data. Journal of Chemical Information and Modeling, 51(7), 1528–1538.
 * Varin, T., Gubler, H., Parker, C., Zhang, J., Raman, P., Ertl, P. and Schuffenhauer, A. (2010) Compound Set Enrichment: A Novel Approach to Analysis of Primary HTS Data. Journal of Chemical Information and Modeling, 50(12), 2067-2078.
 * Wetzel, S., Klein, K., Renner, S., Rennerauh, D., Oprea, T. I., Mutzel, P., and Waldmann, H. (2009). Interactive exploration of chemical space with scaffold hunter. Nat Chem Biol, 1875(8), 581–583.
-* Wilkens, J., Janes, J. and Su, A. (2005). HierS:  Hierarchical Scaffold Clustering Using Topological Chemical Graphs. Journal of Medicinal Chemistry, 48(9), 3182-3193.
+* Wilkens, J., Janes, J. and Su, A. (2005). HierS:  Hierarchical Scaffold Clustering Using Topological Chemical Graphs. Journal of Medicinal Chemistry, 48(9), 3182-3193.
+
+---------------------------------------------------------------------------------
+
+## Citation
+
+Pending...