to use easily :
export PYTHONPATH=/work/pylesh/python_local.bak:$PYTHONPATH source /work/pylesh/virtualenvs/dev/bin/activate
Use to find repeat motifs involving particular residues, i.e. aromatics, charges, etc. Bias toward favored residues in a amino acid matirx like in matrix.tsv.
script needs to be in directory with repeatdb.txt (included in repo) which contains data from repeatsdb.bio.unipd
optional arguments: -h, --help show this help message and exit -pdbs PDBS pdb ID list to check -output OUTPUT output directory -aa_matrix weight matrix for amino acid types to rank repeat rows based on desired amino acid composition -repeat_class type of repeat a la repeatsdb.bio.unipd, e.g. "III.1" -dist_targ neighboring repeat target spacing -dist_flex neighboring repeat spacing flexibility -angle_flex maximum cosine (in degrees) difference between displacement vectors considered repeatative -min_repeats mimium number of repeats to record -min_aa_score minimum AA composition sum based on scores in matrix -min_sasa minimum average residue sasa value for reported repeats -max_sasa maximum average residue sasa value for reported repeats -sasa_probe_radius probe radius for sasa calculations
#generate_cst.py -pdbs RepeatPose.pdb Makes cst file for each input pdb. For options see -h. Uses Pyrosetta directly and via SASA wrapper from Alex Ford's interface_fragment_matching for solvation calculation By default, make contraints for all Nitrogen to Oxygen ( and O to O contacts with at least one hydrogen in the system ) and disulfides.
#generate_backbones.py -pdbs RepeatPose1.pdb RepeatPose2.pdb ... given repeat pdbs Uses Pyrosetta directly and via Daniel Silva's RMSD aligner function in solenoid_tools
#expand_constraints.py
optional arguments: -h, --help show this help message and exit -ref_pdb REF_PDB reference pdb -ref_cst REF_CST corresponding to reference pdb -repeat_pdb_tag input pdb tag -out OUT Output directory
optional arguments: -h, --help show this help message and exit -pdb_stem PDB_STEM pdb stem, start of globs for pdbs and csts -thread THREAD number of parallel threads to run
usage: score_and_select.py [-h] -pdb_glob PDB_GLOB -native_pdb NATIVE_PDB -out OUT [-score SCORE] [-plot PLOT] [-norm NORM] [-name NAME]
for plotting pdb scores and selecting subsets based on absolute or per residue scores
For -plot function (on by default, 0 for off) you need a plotly account from https://plot.ly/python/. Github accounts work. You must provide
optional arguments: -h, --help show this help message and exit -pdb_glob pdb stem, start of globs for pdbs and csts -native_pdb pdb to compare designs against -out OUT folder to move files to -score SCORE select all structures with less than this REU / residue -plot PLOT 0|(1) plot scores with plotly -norm NORM 0|(1) normalize scores by residue -name NAME plot tag