`ValueError` in `CSpred.calc_sing_pdb`

[rvhonorato]

Hi there, when tying to run CSpred.py I am getting a ValueError.

It was very tricky for me to install the package - this is what I ended up doing:

For system packages i had to install cmake, openblas and gcc-fortran - these are needed for scipy.

I also had to install reduce, as in the first execution it would give me an error: which: no reduce in $PATH

Installation:

# clone repository
git clone https://github.com/THGLab/CSpred
cd CSpred
git checkout SideChain

# setup python env
python3.8 -m venv .venv # does not work on 3.9+
source .venv/bin/activate
pip install -r requirements.txt

# download models
mkdir models/
cd models/
## datadryad needs the `user-agent` to resolve the link
wget --user-agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36" \
  -O models.tgz \
  "https://datadryad.org/stash/downloads/file_stream/242856"
tar -zxvf models.tgz
rm models.tgz
cd ..

# put the binaries in the `PATH`
export PATH=$PATH:`pwd`/bins:`pwd`/bins/mTM-align:`pwd`/bins/ncbi-blast-2.9.0+/bin

# get a model from pdb
wget -O 1ccn.pdb "https://files.rcsb.org/download/1CCN.pdb"

# execute
python CSpred.py 1ccn.pdb

Error log

python CSpred.py 1ccn.pdb                   
Calculating UCBShift-Y predictions ...
Calculating using 4 references with maximal identity 1.00
Generating features ...
Warning! No hydrogen atoms found in the structure. Using a structure without hydrogen atoms will significantly detoriate the performance!!!
Hbond KeyError at ('A', (' ', 1, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 2, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 3, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 4, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 5, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 6, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 7, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 8, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 9, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 10, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 11, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 12, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 13, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 14, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 15, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 16, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 17, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 18, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 19, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 20, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 21, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 22, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 23, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 24, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 25, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 26, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 27, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 28, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 29, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 30, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 31, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 32, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 33, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 34, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 35, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 36, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 37, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 38, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 39, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 40, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 41, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 42, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 43, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 44, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 45, ' ')).  Skipping this residue
Hbond KeyError at ('A', (' ', 46, ' ')).  Skipping this residue
Calculating UCBShift-X predictions for C ...
Traceback (most recent call last):
  File "CSpred.py", line 222, in <module>
    preds = calc_sing_pdb(args.input, args.pH, TP=not args.shiftx_only, ML=not args.shifty_only, test=args.test)
  File "CSpred.py", line 162, in calc_sing_pdb
    r0_pred = r0.predict(atom_feats.values)
  File "/home/rodrigo/repos/CSpred/.venv/lib/python3.8/site-packages/sklearn/ensemble/_forest.py", line 766, in predict
    X = self._validate_X_predict(X)
  File "/home/rodrigo/repos/CSpred/.venv/lib/python3.8/site-packages/sklearn/ensemble/_forest.py", line 412, in _validate_X_predict
    return self.estimators_[0]._validate_X_predict(X, check_input=True)
  File "/home/rodrigo/repos/CSpred/.venv/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 380, in _validate_X_predict
    X = check_array(X, dtype=DTYPE, accept_sparse="csr")
  File "/home/rodrigo/repos/CSpred/.venv/lib/python3.8/site-packages/sklearn/utils/validation.py", line 567, in check_array
    raise ValueError("Found array with %d sample(s) (shape=%s) while a"
ValueError: Found array with 0 sample(s) (shape=(0, 275)) while a minimum of 1 is required.

The error message is not very clear (and I'm not a NMR expert) - could it be that I am providing the wrong input molecule?

[kvr2007]

Hello! The main warning that you get is written in the beginning of the message:

Warning! No hydrogen atoms found in the structure. Using a structure without hydrogen atoms will significantly detoriate the performance!!!

Basically, you need to first add hydrogens on the PDB file. There is a number of ways to do it, e.g. phenix.reduce or in UCSF ChimeraX