licoricelin/palmfold

RdRp structural classifier

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 v221108

Structural classifier of RNA viral RNA-dependent RNA polymerase (RdRp). Given a protein structure file (.pdb), palmfold performs structural alignments against a constellation of RdRp and non-RdRp polymerase (XdXp) structures and scores the matches. It will evaluate if the input structure is predicted to be RdRp, independent of sequence information.

Usage

python3 palmfold.py -i ./pdb -p ./pol -o ./test

arguments:

  -h, --help`
  						show this help message and exit
  						
  --inputpath INPUTPATH, -i INPUTPATH
                        Directory containing "*.pdb[.gz]" files to be classified. [./pdb]

  --palmprints PALMPRINTS, -p PALMPRINTS
                        path to "./palmfold/pol/" containing palmprint pdb models. [./pol]

  --outpath OUTPATH, -o OUTPATH
                        Directory for writing output files. [./out]

  --threshold THRESHOLD, -t THRESHOLD
                        Polymerase+ classification threshold for TMAlign. [0.5]

  --verbose, -v
    					Print INFO messages, else prints WARN and ERROR only

Install

Dependencies

• Python3 & Bio library : pip3 install "Bio"
• TMalign (binary link), available in $PATH

# Clone respository
git clone https://github.com/ababaian/palmfold.git

cd palmfold

# Unit test for palmfold
python3 palmfold.py -i ./pdb -p ./pol -o ./test