biophysics provides a library for parsing protein-files and a set of command-line tools for common protein manipulation operations.
It has been developed by Andreas Füglistaler at the Laboratory of Protein and Cell Engineering, EPFL (https://www.epfl.ch/labs/barth-lab/).
The biophysics library and tools have been developed in D (https://dlang.org). A D-compiler and the package/build manager dub are needed to install the tools (https://dlang.org/download.html).
Get a local copy of biophysics
$ git clone https://github.com/glis-glis/biophysics.git
Install the binaries
$ cd biophysics $ ./install
Run tests
$ ./test
The source files of the library are in the src/biophysics folder, the source files of the tools in the tools folder. The shared library will be installed in the lib folder and the binaries in the bin folder.
Each tool has a help, which can be evoked with the command-line
option --help. The tools take a protein-file as input, and write
the result to the standard output. This allows chaining different
tools using pipes. For example, extracting chains A and C, renaming
them to A and B, and calculating all contacts between the two
chains can be done as follows:
$ extract -c BD my.pdb | renumber -r | contacts -c B
Example usage of all tools is shown in the file examples/run_examples.
align | Align pdb-file to another one |
contacts | Find contacting residues |
extract | Extract chains and/or residues |
fasta | Get sequence of protein |
geometry | Center of Mass, Eigenvalues and Eigenvectors |
insert | Insert missing residues |
loops | Print loop residues, not in secondary structure |
missing | Print all missing residues-numbers of fasta-file |
parse | Parse and correct pdb-files |
pdb_info | Information of pdb-file |
remove | Remove residues from pdb-file |
renumber | Renumber residues and/or chains |
rmsd | Root-mean-square deviation between pdb-files |
rotate | Rotate around major axis (eigenvectors) |
split_pdb | Split pdb-file into chains by distance or residue-number |
thread | Thread sequence onto pdb-file |
translate | Translate chain(s) of pdb-file in x-, y- and z-direction |
within | List residues within distance of chain |
Each tool can only do one thing, but does it very fast. Tools can be piped together to achieve more complicated operations.
The D programming language (https://dlang.org) is still rather unknown, but presents many upsides. It combines the speed of compiled programming languages such as C/C++ or FOTRAN with the ease of use and productivity of interpreted languages such as Python or R. It is a safe language, detecting out of bounce arrays, and handles memory allocations through garbage collection.
D allows the fast development of quick tools. To appreciate its
speed, consider that parsing a normal-length pdb-file is more than
an order of magnitude faster running import numpy on Python!
The biophysics tools transform input data into output data. Therefore, a data-driven approach is chosen. Most tools are line-oriented, using basic operations (map, filter, reduce) on each ATOM-line of a pdb-file.
Even though a protein can be viewed as a tree (a protein consists of chains, a chain consists of residues, a residue consists of atoms), the internal representation is a flat table of atoms. This helps for data locality and makes lazy data easier.
Data is handled lazily, that is, it is only evaluated when needed, for example when printing. This prevents unnecessary and time-consuming conversions from strings to numbers and back.