--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/structure_pipeline.py	Wed Oct 07 09:31:40 2020 +0000
@@ -0,0 +1,59 @@
+import argparse
+
+from chembl_structure_pipeline import checker, standardizer
+
+
+def load_mols(input_file):
+    """
+    Returns a list of strings, each a molblock
+    """
+    with open(input_file) as f:
+        mols = [''.join(('\n', mol.strip())) for mol in f.read().strip().split('$$$$\n')]
+    return mols
+
+
+def write_mols(mols, output_file):
+    """
+    Writes a list of molblocks to an SDF
+    """
+    with open(output_file, 'w') as f:
+        f.write('\n$$$$'.join(mols))
+
+
+def standardize_molblock(mol):
+    return standardizer.standardize_molblock(mol)
+
+
+def get_parent_molblock(mol):
+    return standardizer.get_parent_molblock(mol)[0]
+
+
+def check_molblock(mol):
+    issues = checker.check_molblock(mol)
+    max_penalty_score = str(max([issue[0] for issue in issues])) if issues else '0'
+    message = '; '.join([issue[1] for issue in issues])
+    mol_with_issues = '\n'.join((mol, '> <MaxPenaltyScore>', max_penalty_score, '> <IssueMessages>', message))
+    return mol_with_issues
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
+    parser.add_argument('-i', '--input', help='SDF/MOL input')
+    parser.add_argument('-o', '--output', help="Standardized output")
+    parser.add_argument('--standardize', action='store_true', help="Standardize molblock")
+    parser.add_argument('--get_parent', action='store_true', help="Get parent molblock.")
+    parser.add_argument('--check', action='store_true', help="Check molblock")
+    args = parser.parse_args()
+
+    mols = load_mols(args.input)
+    if args.standardize:
+        mols = [standardize_molblock(mol) for mol in mols]
+    if args.get_parent:
+        mols = [get_parent_molblock(mol) for mol in mols]
+    if args.check:
+        mols = [check_molblock(mol) for mol in mols]
+    write_mols(mols, args.output)
+
+
+if __name__ == "__main__":
+    main()