Add pose IDs to mmCIF keywords via $PoseID token substitution

src/pdbdepo/pdb_deposition.py

@@ -13,6 +13,7 @@
 
 import argparse
 import bz2
+import csv
 import datetime
 import glob
 import re
@@ -101,6 +102,7 @@ def process_input(
     mmcifgen_block,
     output_dir: Path,
     cmpd_codes_dict: dict = {},
+    pose_ids_dict: dict = {},
     debug=False,
 ):
     software_templates = read_software_templates()
@@ -276,6 +278,10 @@ def process_input(
                         mmcifgen_refine_values,
                     )
 
+            # build the comma-separated pose ID string for this crystal
+            pose_ids = pose_ids_dict.get(xtal_name, [])
+            pose_id_str = ', '.join(pose_ids)
+
             # add in the common metadata (generated by mmcif-gen)
             for item in mmcifgen_block:
                 to_add = True
@@ -287,6 +293,7 @@ def process_input(
                             template = item.loop.values[1]
                             template = template.replace('$CompoundCode', cmpd_code)
                             template = template.replace('$CrystalName', xtal_name)
+                            template = template.replace('$PoseID', pose_id_str)
                             cmpd_codes = cmpd_codes_dict.get(xtal_name)
                             if cmpd_codes:
                                 for i, cmpd_code in enumerate(cmpd_codes):
@@ -296,6 +303,19 @@ def process_input(
                                 template = template.replace('$ExternalCode' + str(i), '')
                             new_loop = structure_cif_block0.init_loop('', item.loop.tags)
                             new_loop.add_row([item.loop.values[0], template])
+                    elif any('$PoseID' in v for v in item.loop.values):
+                        to_add = False
+                        ncols = len(item.loop.tags)
+                        nrows = len(item.loop.values) // ncols
+                        new_loop = structure_cif_block0.init_loop('', item.loop.tags)
+                        for r in range(nrows):
+                            loop_row = [
+                                item.loop.values[r * ncols + c].replace('$PoseID', pose_id_str) for c in range(ncols)
+                            ]
+                            new_loop.add_row(loop_row)
+                elif item.pair is not None and '$PoseID' in item.pair[1]:
+                    structure_cif_block0.set_pair(item.pair[0], item.pair[1].replace('$PoseID', pose_id_str))
+                    to_add = False
                 if to_add:
                     # otherwise add the item as it is
                     added_item = structure_cif_block0.add_item(item)
@@ -1060,12 +1080,34 @@ def read_cmpd_codes(filename):
     return d
 
 
+def read_fragalysis_csv(filename):
+    """Read Fragalysis metadata CSV and return a dict mapping crystal name -> list of pose codes.
+
+    The CSV has pose code in column 1 (index 0) and crystal/experiment code in column 3 (index 2).
+    """
+    d = {}
+    if filename:
+        with open(filename, 'rt', newline='') as f:
+            reader = csv.reader(f)
+            next(reader)  # skip header
+            for tokens in reader:
+                if len(tokens) >= 3:
+                    pose_code = tokens[0].strip()
+                    crystal_name = tokens[2].strip()
+                    if crystal_name not in d:
+                        d[crystal_name] = []
+                    d[crystal_name].append(pose_code)
+    info('read pose IDs for', len(d), 'crystals')
+    return d
+
+
 def run(collator_path, metadata_csv, compound_codes_csv=None, fragalysis_csv=None, debug=False):
     info('run on ' + str(datetime.datetime.now()))
     info('using RDKit version ' + rdBase.rdkitVersion)
     # info('using InCHI version ' + Chem.GetInchiVersion())
 
     cmpd_codes_dict = read_cmpd_codes(compound_codes_csv)
+    pose_ids_dict = read_fragalysis_csv(fragalysis_csv)
 
     output_dir_p = collator_path / 'pdb_depo_files'
 
@@ -1101,6 +1143,7 @@ def run(collator_path, metadata_csv, compound_codes_csv=None, fragalysis_csv=Non
                 meta_mmcifgen,
                 output_dir_p,
                 cmpd_codes_dict=cmpd_codes_dict,
+                pose_ids_dict=pose_ids_dict,
                 debug=debug,
             )