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Molecular Checker (Molck)

Where can I find the Molck executable?

The Molck executable can be found at <YOUR-OST-STAGE-DIR>/bin

Basic Usage

To check one PDB file (struc1.pdb) with Molck, use the following command:

molck --complib <PATH TO COMPOUND LIB> struc1.pdb

The checked and cleaned file will be saved by default ad struc1-molcked.pdb.

Similarly it is possible to check a list of PDB files:

molck --complib <PATH TO COMPOUND LIB> struc1.pdb struc2.pdb struc3.pdb

All Options

The molck executable supports several other command line options, please find them following:

usage: molck [options] file1.pdb [file2.pdb [...]]
options
  --complib=path       location of the compound library file. If not provided, the
                       following locations are searched in this order:
                           1. Working directory,
                           2. OpenStructure standard library location (if the
                              executable is part of a standard OpenStructure installation)
  --rm=<a>,<b>         remove atoms and residues matching some criteria:
                            - zeroocc - Remove atoms with zero occupancy
                            - hyd - Remove hydrogen atoms
                            - oxt - Remove terminal oxygens
                            - nonstd - Remove all residues not one of the 20 standard amino acids
                            - unk - Remove unknown and atoms not following the nomenclature
  --fix-ele            clean up element column
  --stdout             write cleaned file(s) to stdout
  --out=filename       write cleaned file(s) to disk. % characters in the filename are
                       replaced with the basename of the input file without extension.
                       Default: %-molcked.pdb
  --color=auto|on|off  whether output should be colored
  --map-nonstd         maps modified residues back to the parent amino acid, for example
                       MSE -> MET, SEP -> SER.

Molck Python API

Within OST, one can also call the Molck() function directly on entities to get the same effect as with the binary.

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