Package: settmhc
SETTMHCSETTMHC is a peptide-MHC class I binding predictor software based on multimodal sequence-structure information.SETTMHC also includes other two modules: pMHC complex structure mdeling and a persistent homology method to analysis pMHC complex surface topology features as structure representations.InstallationSystemLinuxOne-step installationBefor using theenvironment.yaml, make sure thePyrosettadownload channel is modified in the file.Using conda, just runconda env create -n SETTMHC -f environment.yaml, but it may cause some dependencies issues.Build step by stepDue to the two structure modeling methods, the environment build may be cumbersome.python > 3.71. Requirements forAPE-Gen1.1 Conda packagesconda install -c bioconda sminaconda install -c omnia pdbfixerconda install -c conda-forge mdtrajconda install -c schrodinger pymolorconda install -c conda-forge pymol-open-sourceconda install -c bioconda autodock-vinaconda install -c conda-forge openmm=7.5.11.2 Install RCDDownload RCD v1.4 fromhttps://chaconlab.org/modeling/rcd/rcd-downloadAddxxxx/RCD_v1.40_Linux_20190228/binto PATH to make 'rcd' command availableMake sure the lib path containing 'libmkl_intel_lp64.so' is added to LD_LIBRARY_PATH, you may get the lib path byfind /home -name libmkl_intel_lp64.so. If there is no such object, runconda install -c intel mkland add the lib path to LD_LIBRARY_PATH.2. Requirements forRosettaMHCDownloadPyrosettaconda install biopythonDownloadClustal omegaand add it to PATH3. Install SETTMHC from pipBefore install settmhc, you may installpytorch 1.9.0(cpu only or with cuda) manually depending on your device.pip install settmhcUsageSETTMHC binding prediction for pMHCDownload the model files first, defaluts to~/.local/share/settmhc/, or you can addexport SETTMHC_MODEL_DIR="path you like"to your~/.bashrcbeforehand.settmhc --downloadYou can run prediction with peptides and hlas input:settmhc --peptides KELEGILLL ALLGLTLGV --hlas HLA-A*02:01 HLA-A*11:01 -o output.csvOr just input a csv file contains HLA and peptides, for more details in input.csv, see demo/demo.csv, whichAnnotationcolumn is optional.settmhc -i input.csv -o output.csvOr specify a pMHC complex PDB filesettmhc -pdb 1DUZ.pdb --protein A --peptide CSeesettmhc -hfor more argument information.pMHC complex structre modelingusage: pmhc-model [-h] [--software {APE-Gen,RosettaMHC}] [--output_dir OUTPUT_DIR] [--filename FILENAME]
                  [--list_supported_hlas] [--template_pdb TEMPLATE_PDB] [--mhc_chain MHC_CHAIN]
                  [--peptide_chain PEPTIDE_CHAIN]
                  peptide_input receptor_class

Peptide-MHC complex structure Generator

positional arguments:
  peptide_input         Sequence of peptide
  receptor_class        MHC class I allele

optional arguments:
  -h, --help            show this help message and exit
  --software {APE-Gen,RosettaMHC}
                        Software used for pMHC structure generation, defaults to 'APE-Gen' (default: APE-Gen)
  --output_dir OUTPUT_DIR
                        Output PDB file saved path (default: structures)
  --filename FILENAME   Saved PDB file name,e.g.,default='pmhc001', and the output file will be like 'pmhc001.pdb'
                        (default: pmhc001)
  --list_supported_hlas
                        List all the supported 110 HLA alleles (default: False)

RosettaMHC simple arguments:
  --template_pdb TEMPLATE_PDB
                        Provide template structure in PDB to perform threading (default: None)
  --mhc_chain MHC_CHAIN
                        HLA chain in the template PDB file (default: A)
  --peptide_chain PEPTIDE_CHAIN
                        Peptide chain in the template PDB file (default: C)To model pMHC structure, only input one pair of peptide and HLA allele at a time.pmhc-model KELEGILLL HLA-A*02:01Persistent homology method for structure analysisusage: pshm [-h] -i INPUT [-o OUTPUT] [-l LENGTH] [-f FILTRATION] [-u UNIT] [-c CUTOFF] [--protein PROTEIN]
            [--ligand LIGAND]

A persistent homology method for pMHC interface structure feature generation

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input file for structure feature generation (default: None)
  -o OUTPUT, --output OUTPUT
                        Output file for pshm results containing the 16×360 feature matrix (default: None)
  -l LENGTH, --length LENGTH
                        Max length for RipsComplex (default: 15)
  -f FILTRATION, --filtration FILTRATION
                        Max length for filtration process, usually the same as RipsComplex max length (default: 15)
  -u UNIT, --unit UNIT  Filtration unit (length for each filtration shell) (default: 0.5)
  -c CUTOFF, --cutoff CUTOFF
                        HLA and peptide atom distance cutoff for HLA atoms filter (default: 10)
  --protein PROTEIN     HLA chain in the PDB file (default: A)
  --ligand LIGAND       Peptide chain in the PDB file (default: C)The default arguments for RipsComplex building are used for SETTMHC training.pshm -i 1DUZ.pdb -o 1duz_features.csv --protein A --ligand -CPotential issuesAn error may occur during the applicationAttributeError: module 'distutils' has no attribute 'version'due to the high version of setuptools.You can fix this bypip install setuptools==59.5.0