Molecular Checker (Molck)¶

The Molecular Checker (Molck) is a tool for cleaning up molecular structures and making them conform to the compound library.

Molck removes any residues and atoms that are not defined in the compound library. This means that if the structure contains residues or atoms that are not part of the compound library, they will be removed during the cleaning process.

Caution

Do not use Molck if you need to preserve residues or atoms that are not defined in the compound library. For example, if your structure contains ligands or other custom molecules that are not in the compound library, using Molck would not preserve these components.

Programmatic usage¶

Molecular Checker (Molck) could be called directly from the code using Molck function:

#! /bin/env python

"""Run Molck with Python API.


This is an exemplary procedure on how to run Molck using Python API which is
equivalent to the command line:

molck <PDB PATH> --rm=hyd,oxt,nonstd,unk \
                 --fix-ele --out=<OUTPUT PATH> \
                 --complib=<PATH TO compounds.chemlib>
"""

from ost.io import LoadPDB, SavePDB
from ost.mol.alg import MolckSettings, Molck

from ost.conop import CompoundLib


pdbid = "<PDB PATH>"
lib = CompoundLib.Load("<PATH TO compounds.chemlib>")

# Using Molck function
ent = LoadPDB(pdbid)
ms = MolckSettings(rm_unk_atoms=True,
                   rm_non_std=True,
                   rm_hyd_atoms=True,
                   rm_oxt_atoms=True,
                   rm_zero_occ_atoms=False,
                   colored=False,
                   map_nonstd_res=False,
                   assign_elem=True)
Molck(ent, lib, ms)
SavePDB(ent, "<OUTPUT PATH>")

It can also be split into subsequent commands for greater controll:

#! /bin/env python

"""Run Molck with Python API.


This is an exemplary procedure on how to run Molck using Python API which is
equivalent to the command line:

molck <PDB PATH> --rm=hyd,oxt,nonstd,unk \
                 --fix-ele --out=<OUTPUT PATH> \
                 --complib=<PATH TO compounds.chemlib>
"""

from ost.io import LoadPDB, SavePDB
from ost.mol.alg import (RemoveAtoms, MapNonStandardResidues,
                         CleanUpElementColumn)
from ost.conop import CompoundLib


pdbid = "<PDB PATH>"
lib = CompoundLib.Load("<PATH TO compounds.chemlib>")
map_nonstd = False

# Using function chain
ent = LoadPDB(pdbid)
if map_nonstd:
    MapNonStandardResidues(lib=lib, ent=ent)

RemoveAtoms(lib=lib,
            ent=ent,
            rm_unk_atoms=True,
            rm_non_std=True,
            rm_hyd_atoms=True,
            rm_oxt_atoms=True,
            rm_zero_occ_atoms=False,
            colored=False)

CleanUpElementColumn(lib=lib, ent=ent)
SavePDB(ent, "<OUTPUT PATH>")

API¶

class MolckSettings(rm_unk_atoms=True, rm_non_std=False, rm_hyd_atoms=True, rm_oxt_atoms=False, rm_zero_occ_atoms=False, colored=False, map_nonstd_res=True, assign_elem=True)¶

Stores settings used for Molecular Checker.

Parameters:

rm_unk_atoms – Sets rm_unk_atoms.
rm_non_std – Sets rm_non_std.
rm_hyd_atoms – Sets rm_hyd_atoms.
rm_oxt_atoms – Sets rm_oxt_atoms.
rm_zero_occ_atoms – Sets rm_zero_occ_atoms.
colored – Sets colored.
map_nonstd_res – Sets map_nonstd_res.
assign_elem – Sets assign_elem.

rm_unk_atoms¶

Tip

This flag should always be set to True. Other flags will behave unexpectedly otherwise.

Remove unknown atoms. That is 1) any atom from residues that are not present in the compound library (provided at Molck call) and 2) any atom with a name that is not present in the respective entries of the compound library.

Type:: bool

rm_non_std¶

Remove all residues not one of the 20 standard amino acids. This removes all other residues including unknown residues, ligands, saccharides and nucleotides (including the 4 standard nucleotides).

Type:: bool

rm_hyd_atoms¶

Remove hydrogen atoms. That’s all atoms with element specified as H or D in the respective entries of the compound library (provided at Molck call). Unknown atoms (see rm_unk_atoms) are not removed by this flag. If you really want to get rid of every hydrogen, you need to combine it with rm_unk_atoms.

Type:: bool

rm_oxt_atoms¶

Remove all atoms with name “OXT”. That’s typically terminal oxygens in protein chains, but this might remove arbitrary atoms in other molecules. You should only use this flag in combination with rm_non_std.

Type:: bool

rm_zero_occ_atoms¶

Remove atoms with zero occupancy.

Type:: bool

colored¶

Whether output should be colored.

Type:: bool

map_nonstd_res¶

Maps modified residues back to the parent amino acid, for example MSE -> MET, SEP -> SER.

Type:: bool

assign_elem¶

Assigns elements as defined in the respective entries of the compound library (provided at Molck call). For unknown atoms (see definition in rm_unk_atoms), the element is set to an empty string. To avoid empty strings as elements, this property should only be applied in combination with rm_unk_atoms.

Type:: bool

ToString()¶

Returns:: String representation of the MolckSettings.
Return type:: str

Warning

The API here is set such that the functions modify the passed structure ent in-place. If this is not ok, please work on a copy of the structure.

Molck(ent, lib, settings[, prune=True])¶

Runs Molck on provided entity. Reprocesses ent with ost.conop.HeuristicProcessor and given lib once done.

Parameters:

ent (EntityHandle) – Structure to check
lib (CompoundLib) – Compound library
settings (MolckSettings) – Molck settings
prune (bool) – Whether to remove residues/chains that don’t contain atoms anymore after Molck cleanup

MapNonStandardResidues(ent, lib, reprocess=True)¶

Maps modified residues back to the parent amino acid, for example MSE -> MET.

Parameters:

ent (EntityHandle) – Structure to check
lib (CompoundLib) – Compound library
reprocess – The function generates a deep copy of ent. Highly recommended to enable reprocess that runs ost.conop.HeuristicProcessor with given lib. If set to False, you’ll have no connectivity etc. after calling this function.

RemoveAtoms(ent, lib, rm_unk_atoms=True, rm_non_std=False, rm_hyd_atoms=True, rm_oxt_atoms=False, rm_zero_occ_atoms=False, colored=False,

reprocess=True)

Removes atoms and residues according to some criteria.

Parameters:

ent (EntityHandle) – Structure to check
lib (CompoundLib) – Compound library
rm_unk_atoms – See MolckSettings.rm_unk_atoms
rm_non_std – See MolckSettings.rm_non_std
rm_hyd_atoms – See MolckSettings.rm_hyd_atoms
rm_oxt_atoms – See MolckSettings.rm_oxt_atoms
rm_zero_occ_atoms – See MolckSettings.rm_zero_occ_atoms
colored – See MolckSettings.colored
reprocess – Removing atoms may impact certain annotations on the structure (chem class etc.) which are set by ost.conop.Processor. If set to True, a ost.conop.HeuristicProcessor with given lib reprocesses ent.

CleanUpElementColumn(ent, lib)¶

Assigns elements as defined in the respective entries of the compound library as described in MolckSettings.assign_elem. This should only be called after RemoveAtoms() with rm_unk_atoms set to True.

Parameters:

ent (EntityHandle) – Structure to check
lib (CompoundLib) – Compound library

Molecular Checker (Molck)¶

Programmatic usage¶

API¶

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