Molck - the Molecular Checker binary (deprecated)¶
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 atoms not following
the nomenclature
Default: hyd
--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. Delault: auto
--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.