Tool Wrappers (modelarchive.tool)

I.O.U. a nice introduction.

MAXIT (modelarchive.tools.maxit)

MAXIT from RCSB converts coordinate files in PDB legacy format to CIF and CIF files to mmCIF. This module also adds functionality to turn a PDB file into a (minimalist) ModelCIF file. But don’t get too excited - none of the functionality will turn a PDB file into a fully annotated ModelCIF file. It just makes sure the starting point is of valid CIF syntax. Extra data still need to be added…

MAXIT is not bundled with this module. The source code can be downloaded here. Installation instructions are available, and here is a TL;DR how to compile on macOS and most Linux distributions:

# cd into the unpacked source directory first
export RCSBROOT=$(pwd)
make
make binary
# binaries are found in bin/
# RCSBROOT needs to point at data/ when running maxit

modelarchive.tools.maxit.MAXIT_BINARY = 'maxit'

Path to the maxit binary, defaults to maxit from $PATH.

Can be overridden by setting the MAXIT_BINARY environment variable before import, or by assigning directly in a function call.

modelarchive.tools.maxit.cif2mmcif(infile, outfile)

Convert a CIF file to mmCIF using MAXIT.

Only returns log messages upon failure.

Parameters:

• infile (Path | str) – Input CIF file.

• outfile (Path | str) – Output mmCIF file.

Returns:

MAXIT log messages on failure, empty list on success.

Return type:

list[str]

Raises:

RuntimeError – If RCSBROOT environment variable is not set.

modelarchive.tools.maxit.fixing_pdb2mmcif(pdb_as_string, outfile)

Convert a PDB legacy format string to mmCIF, fixing known issues.

Adds missing chain names if necessary before conversion. Only returns log messages upon failure.

Parameters:

• pdb_as_string (str) – Input file content in PDB legacy format.

• outfile (Path | str) – Output mmCIF file.

Returns:

MAXIT log messages on failure, empty list on success.

Return type:

list[str]

Raises:

RuntimeError – If RCSBROOT environment variable is not set.

modelarchive.tools.maxit.main()

Entry point for the ma-maxit command line tool.

modelarchive.tools.maxit.pdb2cif(infile, outfile)

Convert a PDB legacy format file to CIF using MAXIT.

Only returns log messages upon failure.

Parameters:

• infile (Path | str) – Input file in PDB legacy format.

• outfile (Path | str) – Output CIF file.

Returns:

MAXIT log messages on failure, empty list on success.

Return type:

list[str]

Raises:

RuntimeError – If RCSBROOT environment variable is not set.

modelarchive.tools.maxit.pdb2mmcif(infile, outfile)

Convert a PDB legacy format file to mmCIF using MAXIT.

Runs MAXIT first in PDB to CIF mode, then converts the result to mmCIF. Only returns log messages upon failure.

Parameters:

• infile (Path | str) – Input file in PDB legacy format.

• outfile (Path | str) – Output mmCIF file.

Returns:

MAXIT log messages on failure, empty list on success.

On failure, the first element indicates which conversion step failed.

Return type:

list[str]

Raises:

RuntimeError – If RCSBROOT environment variable is not set.

modelarchive.tools.maxit.run_maxit(infile, outfile, mode, logfile=None)

Run MAXIT without checks, mode-preselection, or cleanup.

Parameters:

• infile (Path | str) – Input file. Either PDB legacy format or CIF.

• outfile (Path | str) – Output file.

• mode (str) – MAXIT operation mode. Use "1" for PDB to CIF, "2" for CIF to PDB, "8" for CIF to mmCIF.

• logfile (Path | str, optional) – File for MAXIT log messages.

Returns:

Result of the MAXIT run.

Return type:

subprocess.CompletedProcess

modelarchive.tools.maxit.run_maxit_log2list(infile, outfile, mode)

Run MAXIT and return the log file content as a list.

Parameters:

• infile (Path | str) – Input file. Either PDB legacy format or CIF.

• outfile (Path | str) – Output file.

• mode (str) – MAXIT operation mode. Use "1" for PDB to CIF, "2" for CIF to PDB, "8" for CIF to mmCIF.

Returns:

A tuple of the log file content as a list of strings and the MAXIT exit status.

Return type:

tuple[list[str], int]