Initial commit of example scripts for API paper

Author: Alex-AMC

Diff for: api_paper_2024/example_1/ReadMe.md

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+# Extending Substructure Searching using the CSD Python API 
+
+By searching the CSD using a SMARTS query through the CSD Python API and further inspect molecules as required.
+Using SMARTS, it is possible to express a complex Isoflavone query which is recursive in nature.
+
+
+## To Run: 
+```bash
+python isovflavone_search.py
+```

Diff for: api_paper_2024/example_1/data_files/demo_subset_of_pubchem.sdf

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+#!/usr/bin/env python
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2024-05-02: created by the Cambridge Crystallographic Data Centre
+#
+
+"""
+Credit - this code was written by Jason C. Cole, Natalie Johnson and Alex Moldovan
+"""
+
+from ccdc.io import EntryReader
+from ccdc.search import SubstructureSearch, SMARTSSubstructure
+
+
+class TrihydroxyIsoflavoneHitfinder(SubstructureSearch.HitProcessor):
+    """Post process hits - pick out hits that are only tri-substituted
+       and then retrieve information from them to tabulate.
+    """
+
+    def __init__(self, query_string, database='CSD'):
+
+        self._query = SMARTSSubstructure(query_string)
+        self._query_string = query_string
+        self._hits = []
+        self._extracted_data = []
+        self._entry_reader = EntryReader(database)
+        self._hits_without_filtering = []
+        self._database = database
+
+    @staticmethod
+    def _hydroxyl_or_hydroxylate(atom):
+        return (atom.atomic_number == 8) and \
+            (len(atom.neighbours) == 1 and atom.formal_charge == -1.0) or \
+            (len(atom.neighbours) == 2 and (
+                    atom.neighbours[0].atomic_number == 1 or atom.neighbours[1].atomic_number == 1))
+
+    def _find_hydroxyls(self, hit):
+        return [atom for atom in hit.match_atoms() if self._hydroxyl_or_hydroxylate(atom)]
+
+    def _count_bound_hydroxyls(self, hit):
+        return len(self._find_hydroxyls(hit))
+
+    def _get_entry_data_other(self, identifier):
+        entry = self._entry_reader.entry(identifier)
+        return entry.attributes
+
+    def _get_entry_data_csd(self, identifier):
+        entry = self._entry_reader.entry(identifier)
+
+        synonyms = entry.synonyms
+        chemical_name = entry.chemical_name
+        return {"Chemical Name": chemical_name, "Synonyms": synonyms}
+
+    def _substitution_pattern(self, hit):
+        # Get the labelled atoms in the query
+
+        pattern = []
+        label_index_lookup = {i: self._query.label_to_atom_index(i) for i in self._query._matches.keys()}
+        print(label_index_lookup)
+        match_atoms = hit.match_atoms()
+        for k in label_index_lookup.keys():
+
+            atom = match_atoms[label_index_lookup[k]]
+
+            if self._hydroxyl_or_hydroxylate(atom):
+                pattern.append(str(k))
+
+        return ",".join(sorted(pattern))
+
+    def _get_entry_data(self, hit):
+        if self.database == 'CSD':
+            d = self._get_entry_data_csd(hit.identifier)
+        else:
+            d = self._get_entry_data_other(hit.identifier)
+        return d | {"Substitution Pattern": self._substitution_pattern(hit)}
+
+    def add_hit(self, hit):
+        """
+        This is the key method that gets called in the search
+        """
+        self._hits_without_filtering.append(hit)
+        if self._count_bound_hydroxyls(hit) == 3:
+            self._hits.append(hit)
+
+    def tabulate(self):
+        """
+        Generate a dictionary of dictionaries of relevant data from the hits
+        """
+        data = {}
+        for hit in self._hits:
+            data[hit.identifier] = self._get_entry_data(hit)
+
+        return data
+
+    def run(self):
+        searcher = SubstructureSearch()
+        searcher.add_substructure(self._query)
+        super().search(searcher, self._entry_reader)
+
+
+if __name__ == "__main__":
+
+    sub = "$([#1]),$([OH1]),$([OX1H0]),$(O[CH3]),$(Oc1ccccc1)"
+    query_string = f"c(!@[{sub}:1])1c(!@[{sub}:2])c(!@[{sub}:3])c(!@[{sub}:4])c(OC(!@[{sub}:5])=C(c2c(!@[{sub}:6])c(!@[{sub}:7])c(!@[{sub}:8])c(!@[{sub}:9])c(!@[{sub}:10])2)C(=O)c1)" # noqa
+
+
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-d','--database', default='CSD',help='Path to the file to search or "CSD" to use the CSD')
+    args = parser.parse_args()
+
+    database = 'tiny.sdf'
+    filtered_search = TrihydroxyIsoflavoneHitfinder(query_string, args.database)
+    filtered_search.run()
+
+    data = filtered_search.tabulate()
+    sorted_ids = sorted(data.keys())
+    info_keys = sorted(data[sorted_ids[0]].keys())
+
+    print(f"Without filtering, we have: {len(filtered_search._hits_without_filtering)} hits")
+    print(f"After filtering we have: {len(filtered_search._hits)} hits")
+
+    print(",".join(["Identifier"] + info_keys))
+    for key in sorted_ids:
+        datum = data[key]
+
+        print(",".join([key] + [str(datum[x]) for x in info_keys]))

Diff for: api_paper_2024/example_1/isovflavone_search.py

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+#!/usr/bin/env python
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2024-05-02: created by the Cambridge Crystallographic Data Centre
+#
+
+import sys
+
+from ccdc.entry import Entry
+from ccdc.io import EntryReader, EntryWriter
+
+
+def process_structures(input_file, output_file):
+    with EntryReader(input_file) as er, EntryWriter(output_file) as ew:
+        for e in er:
+            attribs = e.attributes
+            molecule = e.molecule
+            molecule.assign_bond_types('all')
+            ne = Entry.from_molecule(molecule, attributes=attribs)
+            ew.write(ne)
+
+
+if __name__ == "__main__":
+    input_file = sys.argv[1]
+    output_file = sys.argv[2]
+    process_structures(input_file, output_file)

Diff for: api_paper_2024/example_1/process_pubchem_structures.py

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+# Mining third-party resources for structural context
+
+The CSD Python API, combined with other Python and REST APIs, can be very powerful for mining for such relationships.
+Each CCDC refcode has associated publication information, and many have an associated publication document object
+identifier (DOI). ##TODO Add very quick summary of tool. 
+
+## Dependencies
+
+- habanero
+
+Optional:
+
+- wordcloud
+- nltk (after install please consult https://www.nltk.org/data.html)
+
+```conda install -c conda-forge habanero wordcloud nltk```
+
+## To Run
+
+Add script folder through CSD Python API drop down menu.
+With a structure opened, click  `about_entry.py` in menu dropdown.