calculate-contacts

This is a simple program to calculate the contacts in a single PDB file with multiple chains written in Rust.

Installation

Compile it with cargo

$ cargo build --release
    Finished release [optimized] target(s) in 0.00s

Copy the binary to wherever you need it

$ cp target/release/calculate-contacts $HOME/bin # or anywhere else

Usage

calculate-contacts <input.pdb> <cutoff>

Example:

Download some PDB and calculate all the contacts in it

$ wget https://files.rcsb.org/view/2OOB.pdb
$ ./calculate-contacts 2OOB.pdb 5.0
GLN N B 49 PHE CG A 946 4.702
GLN N B 49 PHE CD1 A 946 4.434
GLN N B 49 PHE CD2 A 946 4.496
GLN N B 49 PHE CE1 A 946 3.915
GLN N B 49 PHE CE2 A 946 3.986
GLN N B 49 PHE CZ A 946 3.662
GLN CA B 49 PHE CG A 946 4.785
GLN CA B 49 PHE CD1 A 946 4.636
GLN CA B 49 PHE CD2 A 946 4.836
GLN CA B 49 PHE CE1 A 946 4.52
# ...

Troubleshoot

Running in old CentOS 7

If you are trying to use the compiled binary in an old CentOS7 machine, you might encounter GLIBC issues such as:

./calculate-contacts: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by ./calculate-contacts)
./calculate-contacts: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by ./calculate-contacts)

There is no easy way around it, the "simplest" solution is to use musl to compile a static binary. There is an amazing rust-musl-cross docker image that can make this very simple:

$ alias rust-musl-builder='docker run --rm -it -v "$(pwd)":/home/rust/src messense/rust-musl-cross:armv7-musleabihf'
$ rust-musl-builder cargo build --release

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