Sync with production env

.gitignore

@@ -11,3 +11,9 @@ transfer_logs/*
 logs/*
 test_xchem/test_xchem/settings.py
 db/migrations/*
+# Warren added - to get instance on Diamond in sync with Git repo
+luigi.log
+*.cif
+mArh.json 
+bkup/*
+#.nfs00000000a33355f40000008a

make_investigation.py

@@ -0,0 +1,286 @@
+from rdkit.Chem.rdMolDescriptors import CalcMolFormula
+from rdkit import Chem
+from setup_django import setup_django 
+setup_django()
+# This line gets moved... move it back...
+from xchem_db.xchem_db.models import *
+import argparse
+import os
+
+if __name__ == "__main__":
+  parser = argparse.ArgumentParser()
+  parser.add_argument("-t", "--target", help = "Target name e.g. Mpro", required=True)
+  parser.add_argument("-x", "--exclude", default='', help = "Proposals to Exclude, seperated by commas")
+  parser.add_argument("-o", "--output", help = "Output File", required=True)
+
+  args = vars(parser.parse_args())  
+
+
+  skeleton = {
+    "_pdbx_investigation": {
+        "id": args["target"],
+        "type": "Fragment screening",
+        "db": "fragalysis",
+        "project": args["target"],
+        "url": f'https://fragalysis.diamond.ac.uk/viewer/react/preview/target/{args["target"]}',
+        "details": "Fragment screening project"
+    },
+    "_pdbx_investigation_frag_screening": {
+        "investigation_id": args["target"],
+        "campaign_id": '1',
+        "target": args["target"],
+        "common_unp": "FILLME",
+        "facility": "DLS",
+        "proc_pipeline": "XChem",
+        "internal_id": "FILLME"
+    },
+    "_pdbx_investigation_series": {
+        "frag_screening_campaign_id": [1, 1],
+        "id": [1, 2],
+        "fragment_lib": ["FILLME", 'FILLME'],
+        "fragment_batch": ["v1.0", "v1.0"],
+        "description": ["Placeholder Description", "Placeholder Description"]
+    },
+    "_pdbx_investigation_exp": {
+        "series_id": [],
+        "exp_id": [],
+        "exp_acc": [],
+        "exp_poly": [],
+        "exp_non_poly": [],
+        "exp_method": [],
+        "db": [],
+        "db_ac": [],
+        "exp_details": [],
+        "exp_url": []
+    },
+    "_pdbx_investigation_frag_screening_exp": {
+        "id": [],
+        "exp_id": [],
+        "instance_id": [],
+        "exp_fragment": [],
+        "bound_fragments": [],
+        "hit": [],
+        "hit_assessment": [],
+        "exp_details": []
+    },
+    "_pdbi_entity_poly_link": {
+        "id": [1],
+        "entity_id": [1]
+    },
+    "_pdbi_entity_nonpoly_link": {
+        "id": [],
+        "entity_id": []
+    },
+    "_pdbi_entity_poly": {
+        "entity_id": "1",
+        "type": "polypeptide(L)",
+        "src_method": "man",
+        "pdbx_seq_one_letter_code": "?",
+        "db_name": "?",
+        "db_code": "?",
+        "pdbx_db_accession": "?"
+    },
+    "_pdbi_entity_nonpoly": {
+        "entity_id": [],
+        "name": [],
+        "src_method": [],
+        "comp_id": [],
+        "formula": [],
+        "formula_weight": [],
+        "inchi_descriptor": []
+    },
+    "_pdbi_entity_frag_library": {
+        "entity_id": [],
+        "parent_id": [],
+        "series_id": [],
+        "name": [],
+        "details": [],
+        "src_method": [],
+        "comp_id": [],
+        "formula": [],
+        "formula_weight": [],
+        "inchi_descriptor": []
+    },
+    "_pdbx_contact_author": {
+        "id": [],
+        "address_1": [],
+        "address_2": [],
+        "address_3": [],
+        "legacy_address": [],
+        "city": [],
+        "state_province": [],
+        "postal_code": [],
+        "email": [],
+        "fax": [],
+        "name_first": [],
+        "name_last": [],
+        "name_mi": [],
+        "name_salutation": [],
+        "country": [],
+        "continent": [],
+        "phone": [],
+        "role": [],
+        "organization_type": [],
+        "identifier_ORCID": []
+    },
+    "_audit_author": {
+        "pdbx_ordinal": [],
+        "address": [],
+        "name": [],
+        "identifier_ORCID": []
+    },
+    "_pdbx_audit_support": {
+        "ordinal": [],
+        "funding_organization": [],
+        "country": [],
+        "grant_number": [],
+        "details": []
+    },
+    "_pdbx_database_status": {
+        "entry_id": "FILLME",
+        "status_code": "FILLME",
+        "dep_release_code": "FILLME",
+        "author_release_status_code": "FILLME",
+        "recvd_initial_deposition_date": "FILLME",
+        "date_accepted_terms_and_conditions": "FILLME"
+    }
+  }
+
+  exclude_list = args["exclude"].split(',')
+  print(args["target"])
+  crystal_set2 = Refinement.objects.filter(
+        crystal_name__crystal_name__contains=args["target"])
+  if exclude_list == '':
+    crystal_set = crystal_set2
+  else :
+    crystal_set = [x for x in crystal_set2 if x.crystal_name.visit.proposal.proposal not in exclude_list]
+
+  print(f"Processing {len(crystal_set)} Structures")  
+
+  outcomes = {1: 'Collecting', 2: 'Preprocessing', 3: 'Refinement',
+      4: 'Review', 5: 'Accepted', 6: 'Accepted', 7: 'Rejected'}
+
+  for crystal in crystal_set:
+    print(crystal.crystal_name.crystal_name)
+    if crystal.bound_conf:
+        strfil = crystal.bound_conf
+    elif crystal.pdb_latest:
+        strfil = crystal.pdb_latest
+    else:
+        strfil = None
+    if strfil:
+        if not os.path.exists(strfil):
+            continue
+    if strfil:
+        hets = {}
+        resids = []
+        with open(strfil, 'r') as pdb:
+            for line in pdb:
+                if line.startswith('HETATM'):
+                    resids.append(line[17:20].replace(' ', ''))
+        for non_poly in [x for x in set(resids) if 'LIG' not in x]:
+            block = []
+            oldresnum, resnum = None, None
+            with open(strfil, 'r') as pdb:
+                for line in pdb:
+                    if line.startswith('HETATM'):
+                        if non_poly in line:
+                            resnum = line[22:26].replace(' ', '')
+                            if oldresnum:
+                                if not oldresnum == resnum:
+                                    continue
+                            block.append(line)
+                            oldresnum = resnum
+            hets[non_poly] = Chem.MolFromPDBBlock(''.join(block))
+    smile_mol = [
+        Chem.MolFromSmiles(x.compound.smiles) for x in crystal.crystal_name.crystalcompoundpairs_set.all()]
+    code = [
+        x.compound.compound_string for x in crystal.crystal_name.crystalcompoundpairs_set.all()]
+    smile_mol += list(hets.values())
+    code_only_ligs = code
+    code += list(hets.keys())
+    if len(skeleton["_pdbx_investigation_exp"]["exp_id"]) < 1:
+        exp_id = 1
+    else:
+        exp_id = max(skeleton["_pdbx_investigation_exp"]["exp_id"])+1
+    entity_ids_used = []
+    for mol, cod in zip(smile_mol, code):
+        if mol is None:
+            continue
+        formula = CalcMolFormula(mol)
+        inchi = Chem.inchi.MolToInchi(mol)
+        wt = Chem.rdMolDescriptors.CalcExactMolWt(mol)
+        if cod not in skeleton["_pdbi_entity_nonpoly"]["name"]:
+            entity_id = len(skeleton["_pdbi_entity_nonpoly"]["entity_id"])+1
+            comp_id = len(skeleton["_pdbi_entity_nonpoly"]["comp_id"])+1
+            skeleton["_pdbi_entity_nonpoly"]["entity_id"].append(entity_id)
+            skeleton["_pdbi_entity_nonpoly"]["name"].append(cod)
+            skeleton["_pdbi_entity_nonpoly"]["src_method"].append('syn')
+            skeleton["_pdbi_entity_nonpoly"]["comp_id"].append(comp_id)
+            skeleton["_pdbi_entity_nonpoly"]["formula"].append(formula)
+            skeleton["_pdbi_entity_nonpoly"]["formula_weight"].append(wt)
+            skeleton["_pdbi_entity_nonpoly"]["inchi_descriptor"].append(inchi)
+            entity_ids_used.append(entity_id)
+        else:
+            entity_ids_used.append(
+                skeleton["_pdbi_entity_nonpoly"]["entity_id"][skeleton["_pdbi_entity_nonpoly"]["name"].index(cod)])
+    for eid in set(entity_ids_used):
+        skeleton["_pdbi_entity_nonpoly_link"]["id"].append(exp_id)
+        skeleton["_pdbi_entity_nonpoly_link"]["entity_id"].append(eid)
+    details = outcomes.get(crystal.outcome)
+    if details == 'Review':
+        r = ReviewResponses.objects.filter(crystal=crystal.crystal_name)
+        if len(r) > 0:
+            details = r[0].reason
+        else:
+            details = 'Refined but Not Reviewed'
+    for ex in code_only_ligs:
+        try:
+          lig_entity = skeleton["_pdbi_entity_nonpoly"]["entity_id"][skeleton["_pdbi_entity_nonpoly"]["name"].index(ex)]
+        except ValueError:
+          print(f"Skipping {ex}")
+          continue
+        skeleton["_pdbx_investigation_exp"]["series_id"].append("1")
+        skeleton["_pdbx_investigation_exp"]["exp_id"].append(exp_id)
+        skeleton["_pdbx_investigation_exp"]["exp_acc"].append(
+            crystal.crystal_name.crystal_name)  # Use names for the moment lol
+        skeleton["_pdbx_investigation_exp"]["exp_poly"].append(1)
+        skeleton["_pdbx_investigation_exp"]["exp_non_poly"].append(lig_entity)
+        skeleton["_pdbx_investigation_exp"]["exp_method"].append("X-ray")
+        skeleton["_pdbx_investigation_exp"]["db"].append("PDB")
+        skeleton["_pdbx_investigation_exp"]["db_ac"].append('XXXX')
+        skeleton["_pdbx_investigation_exp"]["exp_details"].append(details)
+        skeleton["_pdbx_investigation_exp"]["exp_url"].append(f'https://fragalysis.diamond.ac.uk/viewer/react/preview/direct/target/{args["target"]}/mols/{ex}/L/P/C')
+        # skeleton["_pdbx_investigation_exp"]["state"].append("?")
+
+  cif_file = [f'{args["target"]}\n', "#\n"]
+  for k, v in skeleton.items():
+    loop = False
+    lens = []
+    for keys, values in v.items():
+        if isinstance(values, int) or isinstance(values, str):
+            pass
+        else:
+            lens.append(len(values))
+    if len(lens) > 0:
+        loop = True
+    if not loop:
+        for keys, values in v.items():
+            if isinstance(values, str):
+                cif_file.append(f'{k}.{keys} "{values}"\n')
+            else:
+                cif_file.append(f'{k}.{keys} {values}\n')
+    else:
+        cif_file.append('loop_\n')
+        loop_data = []
+        for keys, values in v.items():
+            loop_data.append(values)
+            cif_file.append(f'{k}.{keys}\n')
+        for tup in zip(*loop_data):
+            conv = [f'{x}' if not isinstance(
+                x, str) else f'"{x}"' for x in tup]
+            cif_file.append(' '.join(conv)+'\n')
+    cif_file.append("#\n")
+
+  with open(args["output"], 'w') as f:
+    f.write(''.join(cif_file))

single_soakdb.py

@@ -7,7 +7,7 @@
 from functions import db_functions
 from functions import misc_functions
 from functions.pandda_functions import *
-from xchem_db.models import *
+from xchem_db.xchem_db.models import *
 from utils.refinement import RefinementObjectFiles
 
 from dateutil.parser import parse
@@ -211,30 +211,30 @@ def create_links(filename, link_dir):
         required=True,
     )
 
-    parser.add_argument(
-        "-o",
-        "--output_directory",
-        default='',
-        help="Output directory where bound-state pdb files will be",
-        required=True,
-    )
+    #parser.add_argument(
+    #    "-o",
+    #    "--output_directory",
+    #    default='',
+    #    help="Output directory where bound-state pdb files will be",
+    #    required=True,
+    #)
 
     args = vars(parser.parse_args())
 
     filename = args["soakdb_file"]
-    link_dir = args["output_directory"]
+    link_dir = ''
 
     print('Will process: ' + filename)
     print('symlinks to the bound-state pdbs will be found in: ' + link_dir)
 
     print('Checking wether ' + filename + ' is a new or existing entry in XCDB...')
-    status = check_file(filename)
+    status = 0 #check_file(filename)
     print(status)
     if status==0 or status==1:
         print('Transferring the data from the soakDB file into XCDB (this may take a while!)...')
         run_transfer(filename)
     print('Creating the symbolic links to the bound-state pdb files...')
-    create_links(filename, link_dir)
+    #create_links(filename, link_dir)
     print('Telling the database this file is now up-to-date...')
     sdb = SoakdbFiles.objects.get(filename=filename)
     sdb.status = 2