kinase_conservation_analysis.py Command Help

Command: $SCHRODINGER/run -FROM psp kinase_conservation_analysis.py

usage: kinase_conservation_analysis.py [-h] [-distance_cutoff DISTANCE_CUTOFF]
                                       -ligand_asl LIGAND_ASL -protein_db
                                       {kinase,nhr,gpcr}
                                       [-angle_cutoff ANGLE_CUTOFF]
                                       -receptor_chain RECEPTOR_CHAIN [-pval]
                                       [-groups {TKL,RGC,AGC,CMGC,STE,OTHER,TK,CAMK,CK1} [{TKL,RGC,AGC,CMGC,STE,OTHER,TK,CAMK,CK1} ...]]
                                       [-jobname JOBNAME] [-HOST <hostname>]
                                       [-WAIT] [-D] [-NOJOBID] [-NJOBS NJOBS]
                                       [-RETRIES RETRIES] [-NOLAUNCH]
                                       query_structure

Given a holo structure, annotates its protein sequence with ligand binding
residues within a given distance cuttoff (7.0 Angstrom by default). Then uses
BLOSUM matrix to calculate a position specific conservation score of the
ligand binding residues.

positional arguments:
  query_structure       A target ligand/receptor (holo) complex structure.

options:
  -h, --help            show this help message and exit
  -distance_cutoff DISTANCE_CUTOFF
                        A distance cutoff from ligand to collect residues on
                        receptor protein (default: 7.0)
  -ligand_asl LIGAND_ASL
                        ASL defining the ligand atoms (default: None)
  -protein_db {kinase,nhr,gpcr}
                        Specify the protein database for conservation
                        analysis.
  -angle_cutoff ANGLE_CUTOFF
                        A side chain angle cutoff to determine if a residue is
                        pointing to the ligand (default: 105.0)
  -receptor_chain RECEPTOR_CHAIN
                        A chain ID of the receptor
  -pval                 A flag to print p-values and associated z-scores in
                        .csv file
  -groups {TKL,RGC,AGC,CMGC,STE,OTHER,TK,CAMK,CK1} [{TKL,RGC,AGC,CMGC,STE,OTHER,TK,CAMK,CK1} ...]
                        Run conservation analysis within selected groups.
  -jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
                        Set the base name of outputs

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -D, -DEBUG            Show details of Job Control operation.
  -NOJOBID              Run the job directly, without Job Control layer.

Standard Options:
  -NJOBS NJOBS          Divide the overall job into NJOBS subjobs.
  -RETRIES RETRIES      If a subjob fails for any reason, it will be retried
                        RETRIES times. (Default: 2)
  -NOLAUNCH             Set up subjob inputs, but don't run the jobs.