KeyError: '1amh'

[BinhongLiu]

Another error appeared. Thank you for helping me!

the log is here:

(COLLAPSE) [ac1daawz21@login04 COLLAPSE-main]$ python search_site.py data/examples/1a0h.pdb B H363 data/datasets/pdb_embeddings.pkl --cutoff 1e-3 --verbose --num_iter 3 search_site.py:43: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. pdb_meta = pdb_meta.append(pd.Series(data=['N/A'] * pdb_meta.shape[1], index=pdb_meta.columns, name=query_pdb)) ['103l_A' '103l_A' '103l_A' '103l_A' '103l_A'] 59445 Database size: 346005 Iteration 1: 230 new results Iteration 2: 199 new results Iteration 3: 871 new results Traceback (most recent call last): File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3802, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 203, in pandas._libs.index.IndexEngine._get_loc_duplicates File "pandas/_libs/index.pyx", line 211, in pandas._libs.index.IndexEngine._maybe_get_bool_indexer File "pandas/_libs/index.pyx", line 107, in pandas._libs.index._unpack_bool_indexer KeyError: '1amh'

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "search_site.py", line 126, in main(args) File "search_site.py", line 99, in main results[cols] = results['PDB'].apply(lambda x: pdb_meta.loc[x[:4], cols]) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/series.py", line 4771, in apply return SeriesApply(self, func, convert_dtype, args, kwargs).apply() File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/apply.py", line 1123, in apply return self.apply_standard() File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/apply.py", line 1174, in apply_standard mapped = lib.map_infer( File "pandas/_libs/lib.pyx", line 2924, in pandas._libs.lib.map_infer File "search_site.py", line 99, in results[cols] = results['PDB'].apply(lambda x: pdb_meta.loc[x[:4], cols]) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexing.py", line 1067, in getitem return self._getitem_tuple(key) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexing.py", line 1247, in _getitem_tuple return self._getitem_lowerdim(tup) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexing.py", line 967, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexing.py", line 1312, in _getitem_axis return self._get_label(key, axis=axis) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexing.py", line 1260, in _get_label return self.obj.xs(label, axis=axis) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/generic.py", line 4056, in xs loc = index.get_loc(key) File "/work/home/ac1daawz21/miniconda3/envs/COLLAPSE/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3804, in get_loc raise KeyError(key) from err KeyError: '1amh'

[awfderry]

Are you using the latest version of pdb_metadata.csv? Check that the index of the dataframe includes 1amh

[BinhongLiu]

My apology. The error was gone when I used the latest version of pdb_metadata.csv. Thank you so much!