a fast method of reading data from PDB files

Version (2.39 KB) by Evan
This file is a blazingly fast method of reading PDB files


Updated 26 Jun 2012

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This is the fastest way I know to read in a PDB. Strings are conveniently stored as cell variables, and numbers are stored as matrices. Unfortunately there is no faster way that I am aware of to convert text to numbers, so there is an upper limit in matlab for reading a PDB.

To speed up the program, comment out any lines for data not being used. Commenting one line that converts numeric data speeds the program up by roughly 7-8%.

example usage : this plots the atoms of 3IJU.pdb

atoms = fastPDBRead('3IJU.pdb')
plot3(atoms.X, atoms.Y, atoms.Z, '.');

Cite As

Evan (2023). a fast method of reading data from PDB files (https://www.mathworks.com/matlabcentral/fileexchange/35009-a-fast-method-of-reading-data-from-pdb-files), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2010a
Compatible with any release
Platform Compatibility
Windows macOS Linux

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Version Published Release Notes

very small and silly tweak to make it read a wider variety of files

I revised the previous version so that it reads any atomtype for any file, and it reads the comment section at the end of each line (in charmm this is the chain name, in Avogadro this is the element symbol, and so on)