<jupyter_start><jupyter_text>Introduction to Biopython I. Testing modules in jupyter  a) Testing Biopython<jupyter_code># check your Biopython installation
import Bio
Bio.__version__<jupyter_output><empty_output><jupyter_text>b) Testing NumPy-based Bio module<jupyter_code># import NumPy based module
from Bio import PDB

# get information about the module
help(PDB)<jupyter_output>Help on package Bio.PDB in Bio:

NAME
    Bio.PDB - Classes that deal with macromolecular crystal structures.

DESCRIPTION
    Includes: PDB and mmCIF parsers, a Structure class, a module to keep a local
    copy of the PDB up-to-date, selective IO of PDB files, etc.
    
    Author: <NAME>.  Additional code by <NAME>.

PACKAGE CONTENTS
    AbstractPropertyMap
    Atom
    Chain
    DSSP
    Dice
    Entity
    FragmentMapper
    HSExposure
    MMCIF2Dict
    MMCIFParser
    Model
    NACCESS
    NeighborSearch
    PDBExceptions
    PDBIO
    PDBList
    PDBParser
    PSEA
    Polypeptide
    QCPSuperimposer (package)
    Residue
    ResidueDepth
    Selection
    Structure
    StructureAlignment
    StructureBuilder
    Superimposer
    Vector
    kdtrees
    mmcifio
    mmtf (package)
    parse_pdb_header
    vectors

DATA
    protein_letters_3to1 = {'00C': 'C', '01W': 'X', '02K': 'A', '03Y': 'C'...
    standard_aa_names = ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY',[...]<jupyter_text>c) Testing matplotlib module<jupyter_code># check matplotlib
import matplotlib.pyplot as plt
import math

# fill a list
x = [math.sin(i * 2 * math.pi/100.) for i in range(100)]
plt.plot(x)
plt.show()<jupyter_output><empty_output>
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