basic stats for collator and aligner

src/xchemalign/aligner.py

@@ -14,6 +14,7 @@
 import os
 import traceback
 import shutil
+import time
 from pathlib import Path
 
 import yaml
@@ -207,6 +208,7 @@ def __init__(self, version_dir, metadata, assemblies, logger=None):
             self.logger = logger
         else:
             self.logger = utils.Logger()
+        self.num_alignments = 0
         self.errors = []
         self.warnings = []
 
@@ -802,6 +804,7 @@ def _extract_components(self, crystals, aligner_meta):
         self.logger.info('extracting components')
 
         num_errors = 0
+        num_pdbs = 0
         for k1, v1 in aligner_meta.get(Constants.META_XTALS, {}).items():  # k = xtal
             if Constants.META_ALIGNED_FILES in v1:
                 self.logger.info('handling', k1)
@@ -811,7 +814,6 @@ def _extract_components(self, crystals, aligner_meta):
                     .get(Constants.META_XTAL_CIF, {})
                     .get(Constants.META_FILE)
                 )
-
                 for k2, v2 in v1[Constants.META_ALIGNED_FILES].items():  # chain
                     for k3, v3 in v2.items():  # ligand
                         for k4, v4 in v3.items():  # version
@@ -830,6 +832,7 @@ def _extract_components(self, crystals, aligner_meta):
                                         self.logger.error("validation errors - can't extract components")
                                         num_errors += 1
                                     else:
+                                        num_pdbs += 1
                                         pdbxtal.create_apo_file()
                                         pdbxtal.create_apo_solv_desolv()
 
@@ -866,6 +869,7 @@ def _extract_components(self, crystals, aligner_meta):
                                                 )
                                                 traceback.print_exc()
 
+        self.num_alignments = num_pdbs
         return num_errors
 
 
@@ -901,7 +905,10 @@ def main():
             logger.error("There are errors, cannot continue")
             exit(1)
         else:
+            t0 = time.time()
             a.run()
+            t1 = time.time()
+            logger.info("Handled {} alignments in {} secs".format(a.num_alignments, round(t1 - t0)))
             # write a summary of errors and warnings
             logger.report()
             logger.close()

src/xchemalign/collator.py

@@ -16,6 +16,7 @@
 import shutil
 import datetime
 import re
+import time
 import traceback
 from distutils import dir_util
 import yaml
@@ -161,6 +162,7 @@ def __init__(self, config_file, log_file=None, log_level=0, include_git_info=Fal
         self.new_or_updated_xtals = None
         self.compound_codes = {}
         self.compound_smiles = {}
+        self.num_crystals = 0
         if not log_file:
             log_file = self.output_path / 'collator.log'
         self.logger = utils.Logger(logfile=log_file, level=log_level)
@@ -742,6 +744,7 @@ def _copy_files(self, meta):
 
             event_tables = self._find_event_tables()
             forbidden_unattested_ligand_events = {}
+            pdb_count = 0
             for xtal_name, xtal in meta[Constants.META_XTALS].items():
                 dir = cryst_path / xtal_name
 
@@ -900,6 +903,7 @@ def _copy_files(self, meta):
                             "Failed to copy PDB file {} to {}".format(fdata[0], self.output_path / fdata[1])
                         )
                     else:
+                        pdb_count += 1
                         data_to_add[Constants.META_XTAL_PDB] = {
                             Constants.META_FILE: str(fdata[1]),
                             Constants.META_SHA256: fdata[2],
@@ -1054,6 +1058,8 @@ def _copy_files(self, meta):
                         if ligand_binding_events:
                             data_to_add[Constants.META_BINDING_EVENT] = ligand_binding_events
 
+                self.num_crystals = pdb_count
+
                 new_xtal_data = {}
                 for k, v in historical_xtal_data.items():
                     new_xtal_data[k] = v
@@ -1305,8 +1311,11 @@ def main():
             logger.close()
             exit(1)
         else:
+            t0 = time.time()
             c.run(meta)
+            t1 = time.time()
             # write a summary of errors and warnings
+            logger.info("Handled {} crystals in {} secs".format(c.num_crystals, round(t1 - t0)))
             logger.report()
             logger.close()
             if logger.logfilename: