diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 842c5a8d8334aa99c997ccb66658018bdcc63b4b..1816100c024249600998e0aae690dc8d9e25e072 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -1249,3 +1249,178 @@ to standard amino acids.
whether the Cbeta atom was inserted into the ``dst_res``.
+Molecular Checker (Molck)
+--------------------------------------------------------------------------------
+
+Programmatic usage
+##################
+
+Molecular Checker (Molck) could be called directly from the code using Molck
+function:
+
+.. code-block:: python
+
+ #! /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>", profile="SLOPPY")
+
+It can also be split into subsequent commands for greater controll:
+
+.. code-block:: python
+
+ #! /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>", profile="SLOPPY")
+
+API
+###
+
+
+.. class:: MolckSettings
+
+ Stores settings used for Molecular Checker.
+
+ .. method:: __init__(rm_unk_atoms=False,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)
+
+ Initializes MolckSettings.
+
+ :param rm_unk_atoms: Remove unknown and atoms not following the nomenclature
+ :type rm_unk_atoms: :class:`bool`
+ :param rm_non_std: Remove all residues not one of the 20 standard amino acids
+ :type rm_non_std: :class:`bool`
+ :param rm_hyd_atoms: Remove hydrogen atoms
+ :type rm_hyd_atoms: :class:`bool`
+ :param rm_oxt_atoms: Remove terminal oxygens
+ :type rm_oxt_atoms: :class:`bool`
+ :param rm_zero_occ_atoms: Remove atoms with zero occupancy
+ :type rm_zero_occ_atoms: :class:`bool`
+ :param colored: Whether output should be colored
+ :type colored: :class:`bool`
+ :param map_nonstd_res: Maps modified residues back to the parent amino acid, for example
+ MSE -> MET, SEP -> SER
+ :type map_nonstd_res: :class:`bool`
+ :param assign_elem: Clean up element column
+ :type assign_elem: :class:`bool`
+
+ .. method:: ToString()
+
+ String representation of the MolckSettings.
+
+
+.. function:: Molck(ent, lib, settings)
+
+ Runs Molck on provided entity.
+
+ :param ent: Structure to check
+ :type ent: :class:`~ost.mol.EntityHandle`
+ :param lib: Compound library
+ :type lib: :class:`~ost.conop.CompoundLib`
+ :param settings: Molck settings
+ :type settings: :class:`MolckSettings`
+
+
+.. function:: MapNonStandardResidues(ent, lib)
+
+ Maps modified residues back to the parent amino acid, for example MSE -> MET.
+
+ :param ent: Structure to check
+ :type ent: :class:`~ost.mol.EntityHandle`
+ :param lib: Compound library
+ :type lib: :class:`~ost.conop.CompoundLib`
+
+.. function:: RemoveAtoms(ent,lib,rm_unk_atoms=False,rm_non_std=False,rm_hyd_atoms=True,rm_oxt_atoms=False,rm_zero_occ_atoms=False,colored=False)
+
+ Removes atoms and residues according to some criteria.
+
+ :param ent: Structure to check
+ :type ent: :class:`~ost.mol.EntityHandle`
+ :param lib: Compound library
+ :type lib: :class:`~ost.conop.CompoundLib`
+ :param rm_unk_atoms: Remove unknown and atoms not following the nomenclature
+ :type rm_unk_atoms: :class:`bool`
+ :param rm_non_std: Remove all residues not one of the 20 standard amino acids
+ :type rm_non_std: :class:`bool`
+ :param rm_hyd_atoms: Remove hydrogen atoms
+ :type rm_hyd_atoms: :class:`bool`
+ :param rm_oxt_atoms: Remove terminal oxygens
+ :type rm_oxt_atoms: :class:`bool`
+ :param rm_zero_occ_atoms: Remove atoms with zero occupancy
+ :type rm_zero_occ_atoms: :class:`bool`
+ :param colored: Whether output should be colored
+ :type colored: :class:`bool`
+
+.. function:: CleanUpElementColumn(ent, lib)
+
+ Clean up element column.
+
+ :param ent: Structure to check
+ :type ent: :class:`~ost.mol.EntityHandle`
+ :param lib: Compound library
+ :type lib: :class:`~ost.conop.CompoundLib`
\ No newline at end of file
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8dd1d1f39ed9ae3ebb1c8bba5126701c58f85476
--- /dev/null
+++ b/modules/mol/alg/doc/molck.rst
@@ -0,0 +1,59 @@
+=========================
+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:
+
+.. code-block:: bash
+
+ molck --complib <PATH TO COMPOUND LIB> struc1.pdb
+
+The checked and cleaned file will be saved by default ad struc1-molck.pdb.
+
+Similarly it is possible to check a list of PDB files:
+
+.. code-block:: bash
+
+ 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:
+
+.. code-block:: bash
+
+ 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.
\ No newline at end of file