You could use the DSSP program to calculate the secondary structures. Or you could use iCn3D (https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html) to load your PDB with the menu “File > Open File > PDB File (appendable)”, then output the secondary structure using the menu “File > Save Files > Secondary Structure”. The whole process can be converted to a Node.js script to run in command line.

It can be done using dssp, but its output format is not easy to parse. Assuming that BioPython is installed and dssp is somewhere in $PATH, this script will automate the process. It can be customized to adopt various conversions from the dssp format into 3-letter designation, which is explained in comments.

import os
import sys
import subprocess
import string
import argparse
from Bio.PDB import PDBParser
from Bio.PDB.DSSP import DSSP

parser = argparse.ArgumentParser(
                                 description='\n The program will extract DSSP secondary structure assignments.\n',
                                 epilog='\n \n',
                                 formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
                    'input_file', help='path to the input PDB file [required]')
args = parser.parse_args()

try:
    dssp_loc = subprocess.check_output("which dssp", shell=True)
#    sys.stdout.write('\n dssp found at %s\n' % dssp_loc)
except Exception:
    sys.stdout.write('\n dssp not found. It is available for download from https://github.com/cmbi/dssp \n\n')
    sys.exit(1)

if os.access(args.input_file, os.R_OK):
    p = PDBParser()
    pdb_file = args.input_file
    pdb_code = args.input_file.rsplit('.', 1)[0]
    structure = p.get_structure(pdb_code, pdb_file)
    model = structure[0]
    dssp = DSSP(model, pdb_file)

# Note that the recent DSSP executable from the DSSP-2 package was renamed from dssp to mkdssp. If using a recent DSSP release, you may need to provide the name of your DSSP executable:
#dssp = DSSP(model, pdb_file, dssp='mkdssp')
# DSSP data is accessed by a tuple - (chain id, residue id):
# The dssp data returned for a single residue is a tuple in the form:
#
# Tuple Index   Value
# 0     DSSP index
# 1     Amino acid
# 2     Secondary structure
# 3     Relative ASA
# 4     Phi
# 5     Psi
# 6     NH-->O_1_relidx
# 7     NH-->O_1_energy
# 8     O-->NH_1_relidx
# 9     O-->NH_1_energy
# 10    NH-->O_2_relidx
# 11    NH-->O_2_energy
# 12    O-->NH_2_relidx
# 13    O-->NH_2_energy

    aa_key = ''
    ss_key = ''

    for i in range(len(dssp)):
        aa_key = aa_key + str(dssp[list(dssp.keys())[i]][1])
        ss_key = ss_key + str(dssp[list(dssp.keys())[i]][2])

# Code                    Description
#   H                     Alpha Helix
#   B                     Beta Bridge
#   E                     Strand
#   G                     Helix-3
#   I                     Helix-5
#   T                     Turn
#   S                     Bend
#  ' '                    Coil (unstructured)
#SS-Scheme 1: H,G,I->H ; E,B->E ; T,S->C
#SS-Scheme 2: H,G->H ; E,B->E ; I,T,S->C THIS IS DEFAULT
#SS-Scheme 3: H,G->H ; E->E ; I,B,T,S->C
#SS-Scheme 4: H->H ; E,B->E ; G,I,T,S->C
#SS-Scheme 5: H->H ; E->E ; G,I,B,T,S->C

    ss_key = string.replace(ss_key, '-', 'C')
#Scheme 1
#    ss_key = string.replace(ss_key, 'G', 'H')
#    ss_key = string.replace(ss_key, 'I', 'H')
#    ss_key = string.replace(ss_key, 'B', 'E')
#    ss_key = string.replace(ss_key, 'T', 'C')
#    ss_key = string.replace(ss_key, 'S', 'C')
#Scheme 2
    ss_key = string.replace(ss_key, 'G', 'H')
    ss_key = string.replace(ss_key, 'B', 'E')
    ss_key = string.replace(ss_key, 'I', 'C')
    ss_key = string.replace(ss_key, 'T', 'C')
    ss_key = string.replace(ss_key, 'S', 'C')
#Scheme 3
#    ss_key = string.replace(ss_key, 'G', 'H')
#    ss_key = string.replace(ss_key, 'B', 'C')
#    ss_key = string.replace(ss_key, 'I', 'C')
#    ss_key = string.replace(ss_key, 'T', 'C')
#    ss_key = string.replace(ss_key, 'S', 'C')
#Scheme 4
#    ss_key = string.replace(ss_key, 'B', 'E')
#    ss_key = string.replace(ss_key, 'G', 'C')
#    ss_key = string.replace(ss_key, 'I', 'C')
#    ss_key = string.replace(ss_key, 'T', 'C')
#ss_key = string.replace(ss_key, 'S', 'C')
#Scheme 5
#    ss_key = string.replace(ss_key, 'G', 'C')
#    ss_key = string.replace(ss_key, 'B', 'C')
#    ss_key = string.replace(ss_key, 'I', 'C')
#    ss_key = string.replace(ss_key, 'T', 'C')
#    ss_key = string.replace(ss_key, 'S', 'C')

    print(aa_key)
    print(ss_key)

else:
    parser.error(
        '\n\n !!! Input file "%s" does not exist !!!\n' %
        args.input_file)