Implement MSn Annotation (computational-metabolomics#12)

* Compatibility with conda version of geng; remove geng tool from package

* Incorporate pkl files into connectivity database

* Add nauty as dependency

* Add pickle as test dependency

* Switch from strings to pickles for connectivity graphs

* Use blob instead of text to store pickled dictionary

* No longer write substructures to .smi

* Add option to build to select only frequent substructures

* Add connectivity filter to k_configs

* Incorporate connectivity filter into MSn build method

* Build substructures for each set of masses independently

* Call itertools.product on substructures within multiprocessing portion of build

* Configure run script for current create_isomorphism_database inputs

* Built subsets should be empty list, not None

* Update variable names, remove debug options, update docstrings

* Add annotate_msn and generate_structures user functions

* Move stage at which multiprocessing step is performed

* Allow for multiple output options in build

* Remove ppm option for retrieving elemental composition from substructure db

* Allow list of mc/exact_mass to be passed to generate_structures

* Use TemporaryDirectory to store unittest results

* Let generate_structures return/yield smiles

* Implement build_msn to incorporate considerations for building structures from MS/MS

* Implement annotate_msn to provide an interface to build_msn

* Add/update build docstrings

* Remove unnecessary build parameters

* Pass data dictionary to user-facing build functions rather than separate mc, exact_mass, MSn masses

* Update variable naming conventions

* Add newline between smiles in out file

* Update SubstructureDb for removal of .pkl files

* Add function create_substructure_database

* Bring tests up to date with variable renaming

* Bring scripts up to date with variable renaming

* Simplify loading of test data and remove teardown

* Remove unused class ConnectivityDb and update SubstructureDb parameters

* Implement additional non-msn build tests

* Improve temporary table cleaning logic

* Fix issues with new build functions

* Allow tests to load auxiliary test data

* Implement msn tests and update k_config test for new parameter

* Correctly specify ppm in generate_structures

* Minor docstring and code reformatting

* Add small substructures to database prior to msn annotation

* Add type hinting to user-facing functions

* Improve and re-order docstring params

* Fix gen_subs_table SQLite syntax

* Update user-facing docs

* Update test and package data

* Update variable names and docs

* Allow specification of heavy atoms using min and max instead of a sequence

* Update gen_subs_table SQL statement to use max/min not sequence

* Add automated small substructure generation

Author: jackgisby

.gitignore

@@ -102,14 +102,6 @@ ENV/
 
 *~
 
-# DB Files
-*.pkl
-*.sqlite
-
-# ignore changes to scripts for testing
-scripts/*
-scripts/results/*
-
 # ignore lib files for testing
 */libgcc_s_dw2-1.dll
 */libstdc++-6.dll

environment.yml

@@ -11,3 +11,4 @@ dependencies:
  - rdkit
  - biopython
  - matplotlib
+ - nauty

metaboblend/auxiliary.py

@@ -27,13 +27,13 @@
 def calculate_complete_multipartite_graphs(max_atoms_available, max_n_substructures):
     """
     Calculates all possible configurations of multipartite graphs up to (inclusive) a given number of atoms available
-    ("sizes") and number of substructures ("boxes"). The possible bonding configurations for these graphs are
+    and number of substructures. The possible bonding configurations for these graphs are
     calculated by geng and RI, before they are used to combine substructures and generate novel metabolites.
 
     :param max_n_substructures: The maximal number of substructures (vertices). At least two substructures must be
         available for bonding for a graph to be created.
 
-    :param max_atoms_available: The maximal number of atoms available (maximal number of edges per vertice) in each
+    :param max_atoms_available: The maximal number of atoms available (maximal number of edges per vertex) in each
         substructure for bonding. At least one atom must be available for bonding for a graph to be created.
 
     :return: A string detailing each possible combination of atoms_available and n_substructures (p) and the
@@ -94,31 +94,31 @@ def draw_subgraph(edges, vn):
 
     plt.title(str(vn))
 
-    sG = nx.Graph()
-    sG.add_edges_from([(e[0], e[1]) for e in edges])
+    s_g = nx.Graph()
+    s_g.add_edges_from([(e[0], e[1]) for e in edges])
 
-    pos = nx.circular_layout(sG)
-    nx.draw(sG, pos)
+    pos = nx.circular_layout(s_g)
+    nx.draw(s_g, pos)
 
     cols = ["b", "r", "g", "y"]
-    cD = {}
+    c_d = {}
 
     i = 0
     for j, substructure in enumerate(vn):
         if len(substructure) == 1:
-            cD[(i,)] = cols[j]
+            c_d[(i,)] = cols[j]
             i += 1
 
         elif len(substructure) == 2:
-            cD[(i, i + 1)] = cols[j]
+            c_d[(i, i + 1)] = cols[j]
             i += 2
 
-    for k in cD.keys():
-        nx.draw_networkx_nodes(sG, pos=pos, nodelist=k, node_color=cD[k], node_size=800, alpha=1.0)
+    for k in c_d.keys():
+        nx.draw_networkx_nodes(s_g, pos=pos, nodelist=k, node_color=c_d[k], node_size=800, alpha=1.0)
 
-    nx.draw_networkx_labels(sG, pos=pos)
+    nx.draw_networkx_labels(s_g, pos=pos)
 
-    return plt, sG
+    return plt, s_g
 
 
 def graph_to_ri(graph: nx.Graph, name):
@@ -149,14 +149,14 @@ def graph_to_ri(graph: nx.Graph, name):
     return out
 
 
-def graph_info(p, sG, mappings):
+def graph_info(p, s_g, mappings):
     """
     Generates and sorts valence and edge information.
 
     :param p: String containing a connectivity subgraph configuration generated by
         :py:meth:`metaboblend.auxiliary.calculate_complete_multipartite_graphs`.
 
-    :param sG: A :py:meth:`networkx.Graph` connectivity subgraph generated by geng based on the output of
+    :param s_g: A :py:meth:`networkx.Graph` connectivity subgraph generated by geng based on the output of
         :py:meth:`metaboblend.auxiliary.calculate_complete_multipartite_graphs`.
 
     :param mappings: Mappings calculated by RI for the relabelling of a subgraph generated by geng. Used by get_valences
@@ -169,7 +169,7 @@ def graph_info(p, sG, mappings):
     frags = {}
 
     for m in mappings:
-        ug = nx.relabel_nodes(sG, m, copy=True)
+        ug = nx.relabel_nodes(s_g, m, copy=True)
         vn = get_degrees(p, ug)
 
         e = list(ug.edges())