build_peptide.py Command Help

Command: $SCHRODINGER/run build_peptide.py

usage: 
$SCHRODINGER/run build_peptide.py input_file output_file [options]

Builds one or more peptides from single-letter amino acid codes.

Input is a file of one or more lines with amino acids
represented by standard one-letter codes. Each line in the input file will
create a structure in the output file. However, if FASTA files are specified,
peptides will be built for each FASTA entry. If PDB is the specified output,
an output file will be written for each peptide. Blank lines are ignored.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            File of one or more lines with single-letter codes of
                        amino acids
  output_file           Structure file in maestro or pdb format

options:
  -h, --help            show this help message and exit
  -c, -cap              Add capping groups to peptides.
  -z, -zwitterion       Create zwitterionic form of peptides. This option is
                        supported only when not adding caps
  -f, -fasta            Input file is in FASTA format.
  -s , -secondary_structure 
                        secondary structure of the peptide. Allowed:
                        AlphaHelix, PiHelix, ThreeTenHelix, CollagenHelix,
                        ParallelPleatedSheet, AntiparallelPleatedSheet,
                        Extended, LeftHandedAlphaHelix, default: AlphaHelix