mctc-rmsd.1.adoc

mctc-rmsd(1)

Name

mctc-rmsd - Structure comparison by root mean square deviation

Synopsis

mctc-rmsd [options ] _file file…​

Description

Requires at least two input files. Supported formats are: - xyz, mol, sdf, coord (0D), gen ©, pdb

Configuration data is read from [rmsd] table in mctc.toml. Just place the configuration file mctc.toml (or .mctc.toml) in your home directory. Example:

[rmsd]
unit = "AA"
[rmsd.filter]
heavy.exclude = [ "H", "h" ]

Options

--filter name

Use name filter from configuration data to apply mask

--rc

Check configuration data and print it to standard out

--version

Print program version and exit

--help

Show this help message

Filter

Filters can be defined in the [rmsd.filter] section, they take a list of atomic numbers and/or element symbols to define the allow-/deny-list. For example, to only check all carbon, nitrogen and oxygen atoms create a filter named organic with:

organic.include = [6, 7, 8]

Similarly, to create a filter for all heavy elements, effectively just excluding hydrogen with standard symbols, use:

heavy.exclude = ["H", "h"]

Note that this approach will still consider deuterium labeled as D, which would be excluded as well when using the atomic number instead.

To create a PDB specific filter use the four character PDB identifier of the atoms and enable the PDB functionality. To match only the proteine backbone use

backbone.include = [" CA ", " N  ", " C  ", " O  "]
backbone.pdb = true

Atomic numbers and element symbols can be included here as well.