Error: The PDB file "complex_cavity_decoy.pdb" did not contain any valid atoms

[areyesromero]

Dear developers,

I have installed RNACavityMiner on a Linux-64 Ubuntu workstation. These are the prerequisites vs what I have: GCC 8.2.0: 9.3.0 openbabel: not installed as it is not supported in Python v3.8 RxDock: 0.1.0 PyMOL: 2.4.0, educational licensed. environment.yml: installed without problems with anaconda.

From what I have understood I have encountered two errors while running the commands "./../src/miner_grid.sh 1ANR_1.pdb" in the test folder:

1) Error: The PDB file "complex_cavity_decoy.pdb" did not contain any valid atoms 2) FileNotFoundError: [Errno 2] No such file or directory: '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/predicted_cavities.txt'

Any idea how to work around the issue?

Find below the full terminal output:

removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/features.csv' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/complex_cavity_decoy.pdb' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/receptor.pdb' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/cavity_decoy.xyz' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/receptor_grid.xyz' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/receptor_grid.pdb' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/1ANR_1.pdb' removed '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/receptor.log' removed directory '/home/atilio/RNA/RNACavityMiner/test/1ANR_1' '1ANR_1.pdb' -> '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/./1ANR_1.pdb' started making grids.. PyMOL not running, entering library mode (experimental) finished making grids.. started converting coordinate file to MOL2.. finished converting coordinate file to MOL2.. started determining center.. finished determining center.. preparting to featurize.. sed: can't read cavity_decoy.pdb: No such file or directory sed: can't read cavity_decoy.pdb: No such file or directory grep: cavity_decoy.pdb: No such file or directory started featurizing..

Error: The PDB file "complex_cavity_decoy.pdb" did not contain any valid atoms

processing features.. cat: raw_feature.txt: No such file or directory now estimating ligandability.. cat: /home/atilio/RNA/RNACavityMiner/test/1ANR_1/predicted_cavities.txt: No such file or directory starting to prune grids PyMOL not running, entering library mode (experimental) Traceback (most recent call last): File "/home/atilio/RNA/RNACavityMiner/py/grid_pruner.py", line 74, in prune_grid(rna = "receptor", score_file = a.score_in, outname = a.coord_out, quantile = 0.95, sasa_cutoff = 10.0) File "/home/atilio/RNA/RNACavityMiner/py/grid_pruner.py", line 36, in prune_grid df = pd.read_csv(score_file, header = 0, sep = ",") File "/home/atilio/anaconda3/envs/cavityminer/lib/python3.8/site-packages/pandas/io/parsers.py", line 686, in read_csv return _read(filepath_or_buffer, kwds) File "/home/atilio/anaconda3/envs/cavityminer/lib/python3.8/site-packages/pandas/io/parsers.py", line 452, in _read parser = TextFileReader(fp_or_buf, kwds) File "/home/atilio/anaconda3/envs/cavityminer/lib/python3.8/site-packages/pandas/io/parsers.py", line 936, in init self._make_engine(self.engine) File "/home/atilio/anaconda3/envs/cavityminer/lib/python3.8/site-packages/pandas/io/parsers.py", line 1168, in _make_engine self._engine = CParserWrapper(self.f, self.options) File "/home/atilio/anaconda3/envs/cavityminer/lib/python3.8/site-packages/pandas/io/parsers.py", line 1998, in init self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 361, in pandas._libs.parsers.TextReader.cinit File "pandas/_libs/parsers.pyx", line 653, in pandas._libs.parsers.TextReader._setup_parser_source FileNotFoundError: [Errno 2] No such file or directory: '/home/atilio/RNA/RNACavityMiner/test/1ANR_1/predicted_cavities.txt'

[atfrank]

This is most likely an issue with the installation of dependencies. I've updated the install instructions. Please re-try. I've pasted them below for your convenience.

create environment

conda create -n rnacavityminertest -y
conda activate rnacavityminertest

# Install dependencies
conda install -c schrodinger pymol -y
conda install -c conda-forge openbabel
conda install -c bioconda rxdock -y
conda install pandas

pip install --user --force scikit-learn==0.22.2.post1
pip install --user --force xgboost==0.90 

Clone RNACavityMiner

git clone https://github.com/atfrank/RNACavityMiner.git
cd RNACavityMiner/

Clone RNAPosers

git clone https://github.com/atfrank/RNAPosers.git
cd RNAPosers/
make clean
make
cd ..
cp RNAPosers/bin/featurize bin/
rm -rf RNAPosers

Then test with:

export CAVITYMINER="/Users/aaronfranklab/RNACavityMiner" # you'll need to change
cd test/
./../src/miner_grid.sh 1ANR_1.pdb

[atfrank]

@areyesromero based on our offline correspondence, it seems as if the problem has been solved with my latest update to the rego. After addressing installation issues, the remaining issue was that the decimal separator in awk in your locale was "," vs ".". This was resulting in an error when you reading in and operating on the data with Pandas in Python. I'm closing this issue.