cdr_graft.py Command Help

Command: $SCHRODINGER/run -FROM bioluminate cdr_graft.py

usage: 
    $SCHRODINGER/run -FROM bioluminate cdr_graft.py mouse_struct [<options>]
    

positional arguments:
  structure_file        The mouse structure to be humanized.

options:
  -h, --help            show this help message and exit
  -use_humanization_cdr USE_HUMANIZATION_CDR
                        Use the special CDR definition for humanization (Kabat
                        numbering with modified CDR definition). Default is
                        yes.
  -scheme {Chothia,Kabat,EnhancedChothia,IMGT,AHo}
                        Specify the antibody numbering scheme: Chothia, Kabat,
                        EnhancedChothia, IMGT, AHo. Default is Chothia.
  -species {HOMO SAPIENS,MUS MUSCULUS}
                        Destination species. Default is "$(default)".
  -cdr_params CDR_PARAMS
                        Pass the keyword/value pair to antibody CDR parameters
                        in the form <keyword>=<value>.
  -antibody_database DATABASE
                        Specify the antibody structure database to search
                        human framework structure.
  -fr_structure FR_STRUCTURE
                        Specify the antibody framework structure.
  -fr_heavy_sequences HEAVY_SEQS
                        Specify the human heavy chain sequence database (fasta
                        format).
  -fr_light_sequences LIGHT_SEQS
                        Specify the human light chain sequence database (fasta
                        format).
  -light_junction_sequences LIGHT_JUNC
                        Specify the human light chain junction sequence
                        (J-region) database (fasta format).
  -heavy_junction_sequences HEAVY_JUNC
                        Specify the human heavy chain junction sequence
                        (J-region) database (fasta format).
  -graft_residues [GRAFT_RESIDUES ...]
                        Other than CDR regions, specify additional residues to
                        be grafted. Choices are VZ (Vernier Zone), CSR
                        (Canonical Stuctural Residues), IR (VH/VL Interface
                        Residues), and/or a list of residue IDs such as H:73
                        L:89 etc.
  -stability_calc STAB_CALC
                        Specify the stability calculation type: scan and
                        combi. Default is off.
  -model_color MODEL_COLOR
                        Pass the keyword/value pair to specify the model
                        coloring in the form <keyword>=<value>. The defaults
                        are FR=wheat, CDR=purple, VZ='light blue', CSR=green,
                        VZ+CSR=red, IR=orange. Available color choices are:
                        black,gray,dark blue,blue,light
                        blue,aquamarine,turquoise,spring green,dark
                        green,green,lime green,yellow
                        green,yellow,orange,maroon,red,pink,plum,purple,blue
                        purple,white,brown,coral,dim gray,hot
                        pink,olive,peru,sienna,steel blue,thistle,wheat.
  -v                    show program's version number and exit
  -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:
  -NOLAUNCH             Set up subjob inputs, but don't run the jobs.