PDB parser

Parse a PDB file

amo pdb_parser \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-pdb <INPUT_PDB_FILE> \
-chian A \
-type 0 \
-output [OUTPUT_DIRECTORY]

Residue distance map

Compute distances between pairwise of residues from a given PDB file.

amo residue_distmap \
# -threads 1 \
-hlog \
-jobname [JOB_NAME] \
-pdb <INPUT_PDB_FILE> \
-threshold 7.50 \
-atom_type CA \
-output [OUTPUT_DIRECTORY]

Voxelization of protein structure

amo pdb2voxel \
-index <STRING> \
-dirt <STRING> \
-output <STRING|optional>

-- Notes:
-- each line in the index file is similar to
-- 6qspA02.pdb,2.9325,32.8724,6.1531
-- where the 1st is the PDB file name, the 2nd to end are the coordinate (x, y, z) of the mass centroid
-- Options:
-- -type <BOOL>: represent an atom by using the Rubik's cube (3x3x3) or not
-- -index <STRING>: index for proteins those are converted to voxel representations
-- -dirt <STRING>: path to the directory where the proteins are stored
-- -backbone <BOOL>: backbone of a protein, now supports N, CA, C, O, CB
-- -atom_type <STRING>: what type of an atom is used for the voxel representation
-- -alpha <DOUBLE>: the edge length of the cube, default is 2048.0
-- -beta <INT>: number of voxels, default is 512
-- -threads <INT>: number of threads, default is 2

FASTA to structure (randomly)

amo fasta2pdb \
-threads 1 \
-hlog \
-jobname [JOB_NAME] \
-fastx <INPUT_FASTA_FILE> \ # e.g., DesG.fasta
-output [OUTPUT_DIRECTORY]