Protein-class

Protein Class used to Define Protein Objects of S3 and S4 Types.
Currently still in development, Integrity checks still need to be added.

Read Protein Data Bank (PDB) files, performs its analysis, and
presents the result using different visualization types including 3D. The
package also has additional capability for handling Virus Report data from
the National Center for Biotechnology Information (NCBI) database.
Nature Structural Biology 10, 980 (2003) <doi:10.1038/nsb1203-980>.
US National Library of Medicine (2021) <https://www.ncbi.nlm.nih.gov/datasets/docs/reference-docs/data-reports/virus/>.

Simon Liles

protein8k

Perform Analysis and Create Visualizations of Proteins

Protein-class function

Breakdown of a Protein Object's structure:<ul>
<li>header: List of 2, Header Line and Title <ul>
<li>header_line: List of 3, Classification, depDate, and idCode <ul>
<li>classifiation: Classification of the Protein in the PDB</li>
<li>depDat: Date the PDB was deposited or created</li>
<li>idCode: 4 digit identifier for the PDB. Always unique.</li>
</ul></li>
<li>title: The title of the PDB.</li>
</ul></li>
<li>structure: Dataframe of 16 variables <ol>
<li>record_type:Type of record in this section. Generally ATOM or HETATM</li>
<li>serial_num: The serial number for the position of the atom in the sequence</li>
<li>atom_name: A name to identify the atom in a structure</li>
<li>alt_location_id:</li>
<li>residue_name: 3 character identifier for a residue</li>
<li>chain_id:</li>
<li>residue_seq_num: Number representing where in the sequence a residue is.</li>
<li>insert_residue_code:</li>
<li>x_ortho_coord: X coordinate in &lt;U+00C5&gt;ngstroms on an orthogonal plane</li>
<li>y_ortho_coord: Y coordinate in &lt;U+00C5&gt;ngstroms on an orthogonal plane</li>
<li>z_ortho_coord: Z coordinate in &lt;U+00C5&gt;ngstroms on an orthogonal plane</li>
<li>occupancy:</li>
<li>temp_factor: The amount of overall error in the measurement of an atom.</li>
<li>segment_id:</li>
<li>element_symbol: Periodic symbol representing an atom.</li>
<li>charge: Charge of the given atom. Can be +, -, or none at all</li>
</ol></li>
</ul>

Protein-class: Protein Class Definitions

Description

Arguments

Format