Editing

Implementation for editing protein structures using MDAnalysis.

convert_cif2pdb(file_path, write_path)

Convert CIT file to PDB file

PARAMETER	DESCRIPTION
file_path	Path to cif file.
write_path	Path to write PDB file.

filter_hetatoms(mda_univ, keep_het_chain=None)

Filter hetero atoms.

PARAMETER	DESCRIPTION
mda_univ	MDAnalysis universe to process.
keep_het_chain	Chains to keep their HETATM and remove other HETATMs. Default is None.

Returns: MDAnalysis universe with filtered hetero atoms.

find_common_atoms(mda_univ1, mda_univ2)

Find common atoms between two MDAnalysis universes.

PARAMETER	DESCRIPTION
mda_univ1	MDAnalysis universe to process.
mda_univ	MDAnalysis universe to process.

Returns: List of common atoms.

get_mda_universe(pdb)

Prepare MDAnalysis universe Args: pdb : Path to PDB file. Returns: MDAnalysis universe for this pdb.

merge_universes(mda_univs)

Merge multiple MDAnalysis universes.

PARAMETER	DESCRIPTION
mda_univs	list of MDAnalysis universes to merge.

Returns: Merged MDAnalysis universe.

read_cif(file_path)

Read CIF file.

PARAMETER	DESCRIPTION
file_path	Path to CIF file.

RETURNS	DESCRIPTION
Structure	Structure object.

remove_hetatoms(mda_univ)

Remove hetero atoms.

PARAMETER	DESCRIPTION
mda_univ	MDAnalysis universe to process.

Returns: MDAnalysis universe with hetero atoms removed.

remove_residues(mda_univ, residues)

Remove residues from structure.

PARAMETER	DESCRIPTION
u	MDAnalysis universe to process.
residues	types of residues to remove.

Returns: MDAnalysis universe for the structure without the specified residues.

select_chains(mda_univ, chains=None)

Select specific chains.

PARAMETER	DESCRIPTION
u	MDAnalysis universe to process.
chains	Chains to keep if None then select chain A. Default is None.

select_common_atoms(mda_univ, common_atoms)

Select common atoms.

PARAMETER	DESCRIPTION
mda_univ	MDAnalysis universe to process.
common_atoms	types of atoms to select.

Returns: MDAnalysis universe for the selected atoms in the structure.

select_residues(mda_univ, residues)

Select residues from structure.

PARAMETER	DESCRIPTION
mda_univ	MDAnalysis universe to process.
residues	types of residues or the residues id to select.

Returns: MDAnalysis universe for the selected residues.

select_water(pdb, water_selection, ligand, water_distance=3.6)

Select specific water molecules from the structure.

PARAMETER	DESCRIPTION
pdb	MDAnalysis universe to process or path to PDB file.
water_selection	Selection of water molecules to keep. surface: Water molecules on the second hydration shell. i.e 3.6 A from the ligand but not in direct contact with the protein. interfacial: Water molecules on the first hydration shell. i.e 3.6 A from the ligand and in direct contact with the protein.
ligand	Ligand to calculate the distance from.
water_distance	Distance to select water molecules. Default is 3.6 A.

Returns: MDAnalysis universe with selected water molecules.

validate_chains(mda_univ, chains)

Validate chains.

PARAMETER	DESCRIPTION
u	MDAnalysis universe to process.
chains	Chains to validate.

Returns: True if chains are present in the structure.

write_mda_universe(mda_univ, file_path)

Write MDAnalysis universe to file.

PARAMETER	DESCRIPTION
mda_univ	MDAnalysis universe to process.
file_path	File to write to.