from icolos.core.workflow_steps.pmx.base import StepPMXBase
from pydantic import BaseModel
[docs]class StepPMXgenlib(StepPMXBase, BaseModel):
"""Generate pmx ff library."""
def __init__(self, **data):
super().__init__(**data)
[docs] def execute(self):
pass
help_string = """
pmx genlib -h
usage: pmx [-h] [-f1 ipdb1] [-f2 ipdb2] [-o1 opdb1] [-o2 opdb2]
[--ffpath ffpath] [--fatp fatp] [--fnb fnb] [--moltype moltype]
[--noalign] [--cbeta] [--noH2Heavy] [--log log]
The script creates hybrid structure and topology database entries (mtp and rtp)
in order to generate a pmx alchemical force field library.
The easiest way to generate the library is to call this script from within
the folder of the force field you are interested in.
If two pdb files (aligned on the backbone) are provided, the hybrid pdb, mtp,
and rtp files are written to file. If no pdb input file is provided,
the script uses pregenerated residues in order to build hybrid pdb, mtp, and
rtp files for all possible residue pairs, thus preparing the whole pmx ff
library.
In addition, atomtype (-fatp) and non-bonded parameter (-fnm) files for the
introduced dummy atoms are generated. By default, these point towards the
files already present in the forcefield. In this way, the additional parameters
for the dummies are appended to the existing ff file, rather than being
written to new files.
optional arguments:
-h, --help show this help message and exit
-f1 ipdb1 First input PDB file. Default is none provided.
-f2 ipdb2 Second input PDB file. Default is none provided.
-o1 opdb1 First output PDB file. Default is none provided.
-o2 opdb2 Second output PDB file. Default is none provided.
--ffpath ffpath Path to mutation forcefield. Default is current folder.
--fatp fatp Atom types (atp) file. If the file is
present, data is appended to it, otherwise a new
file is created. Default is "atomtypes.atp".
--fnb fnb Non-bonded (nb) types file. If the file is
present, data is appended to it, otherwise a new
file is created. Default is "ffnonbonded.itp".
--moltype moltype The type of molecule for which the library is
being built. Available options are "protein", "dna",
or "rna". Default is "protein".
--noalign Whether to align the sidechains of the two
input PDB files provided. Default it True; this flag
sets it to False.
--cbeta Whether to morph sidechain between the two
residues or to use dummy atoms to (de)couple the
whole sidechain. By default, sidechain atoms are
morphed so to minimise the size of the perturbation.
With this flag set, whole sidechains are (de)coupled
instead; i.e. all atoms after C-beta are not mapped
between the two residues.
--noH2Heavy Whether to allow hydrogen to/from heavy atoms
morphing. Default is True, this flag sets it to False.
--log log Logging level. Either "info" or "debug". Default is "info".
"""