Names

structure.pdb.names.cli_replace_resnames()

Command-line interface for renaming residues.

structure.pdb.names.cli_unify_water_labels()

Command-line interface for unifying water residue and atom names.

structure.pdb.names.modify_lines(pdb_lines, fn_process, fn_args, fn_filter=None, include=None, exclude=None)

structure.pdb.names.replace_atom_names(pdb_lines, orig_atom_name, new_atom_name)

Replace all atom names with another.

PARAMETER	DESCRIPTION
pdb_lines	List of lines in the PDB file. TYPE: Iterable[str]
orig_atom_name	Original atom name to replace. TYPE: str
new_atom_name	New atom name. TYPE: str

RETURNS	DESCRIPTION
list[str]	PDB lines with replace atom names.

structure.pdb.names.replace_residue_names(pdb_lines, orig_resname, new_resname, fn_filter=None, include=None, exclude=None)

Replace all instances of residue names with another.

PARAMETER	DESCRIPTION
pdb_lines	List of lines in the PDB file. TYPE: Iterable[str]
orig_resname	Original residue name to replace. TYPE: str
new_resname	New residue name. TYPE: str
fn_filter	Filter function to parse part of a line to see if it is in include or exclude. TYPE: Callable[[str], str] | None DEFAULT: None
include	Only process lines where the result of fn_filter is in this list. TYPE: list[str] | None DEFAULT: None
exclude	Do not process lines where the result of fn_filter is in this list. TYPE: list[str] | None DEFAULT: None

RETURNS	DESCRIPTION
list[str]	PDB lines with replace residue names.

structure.pdb.names.run_replace_resnames(pdb_path, resname_map, output_path=None, fn_filter=None, include=None, exclude=None)

Replace residue names.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file. TYPE: str
resname_map	Original (key) and new (value) mapping of residue names to change. TYPE: dict[str, str]
output_path	Path to save new PDB file. If None, then no file is written. TYPE: str | None DEFAULT: None
fn_filter	Filter function to parse part of a line to see if it is in include or exclude. TYPE: Callable[[str], str] | None DEFAULT: None
include	Only process lines where the result of fn_filter is in this list. TYPE: list[str] | None DEFAULT: None
exclude	Do not process lines where the result of fn_filter is in this list. TYPE: list[str] | None DEFAULT: None

RETURNS	DESCRIPTION
list[str]	PDB lines with changed residues.

structure.pdb.names.run_unify_water_labels(pdb_path, atom_map=None, water_resname='WAT', water_atomnames=None, output_path=None)

Ensure that water molecule atom names are O, H1, and H2.

Warning

This has not been tested yet.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file. TYPE: str
atom_map	Water atom mappings for O, H1, and H2. H1 and H2 are the first and second hydrogen atoms after O in the PDB file, respectively. If None, then we default to O, H1, and H2. TYPE: dict[str, str] | None DEFAULT: None
water_atomnames	Specifies what water atom names are eligible for replacement. If None, then we default to {"O": ["OW"], "H": ["HW"]}. TYPE: dict[str, Iterable[str]] | None DEFAULT: None
water_resname	Residue name of the water molecules. TYPE: str DEFAULT: 'WAT'
output_path	Path to save new PDB file. If None, then no file is written. TYPE: str | None DEFAULT: None

RETURNS	DESCRIPTION
Iterable[str]	PDB lines with changed residues.