added scratch/

scripts/scratch/check_ligand.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+import os
+from biopandas.pdb import PandasPdb
+
+#%%
+homedir = os.path.expanduser('~')
+os.chdir(homedir + '/git/LSHTM_analysis/scripts/examples')
+
+#%%
+file_list = ['7bvf_b.pdb', 'pnca_complex.pdb', 'alr_complex.pdb']
+
+file_list = ['7bvf_b.pdb']
+#file_list = ['pnca_complex.pdb']
+file_list = ['alr_complex.pdb']
+BORING_LIGANDS = ["HOH","CA","SO4","IOD","NA","CL","GOL","PO4"]
+#%% df with list
+ligands_dict = {}
+for pdb_id in file_list:
+    ppdb = PandasPdb()
+    pdb_file = ppdb.read_pdb(pdb_id)        
+    het = pdb_file.df['HETATM']
+    het_list = list(set(het['residue_name']))
+    ligands = [ l for l in het_list if l not in BORING_LIGANDS]
+    lig_dict = {pdb_id:ligands}
+    #lig_dict = {pdb_id:het_list} # include BORING_LIGANDS
+    
+    ligands_dict.update(lig_dict)
+    print(ligands_dict)
+    print('pdb_code:', pdb_file.code) # works only in case of valid pdb
+    print('pdb_code:', pdb_file.pdb_path) #works for bespoke pdb but prints the full path
+    print('pdb_code:', os.path.basename(pdb_file.pdb_path)) # prints only the last part i.e filename
+#%%   test with one
+ppdb = PandasPdb()
+pdb_file = ppdb.read_pdb('7bvf_b.pdb')        
+het = pdb_file.df['HETATM']
+het_list = list(set(het['residue_name']))
+print(het_list)
+ligands = [ l for l in het_list if l not in BORING_LIGANDS]
+print(ligands) 
+
+#%% extract last part from file path
+print(os.path.basename(homedir + '/git/LSHTM_analysis/scripts/examples'))
+print(os.path.basename('alr_complex.pdb'))
+foo = os.path.basename(pdb_file.pdb_path)
+print(foo)