Utils

cli_align_pdb()

Command-line interface for aligning PDB file.

cli_filter_pdb()

Command-line interface for filtering PDB file lines

cli_merge_pdbs()

Command-line interface for merging PDB files

cli_write_pdb()

Command-line interface for writing PDB from topology and coordinate files.

keep_lines(lines, record_types=('ATOM', 'HETATM', 'TER', 'END'))

Filter PDB lines to keep in file.

PARAMETER	DESCRIPTION
lines	List of lines in the PDB file. TYPE: Iterable[str]
record_types	Records to keep in the PDB file. TYPE: tuple[str, ...] DEFAULT: ('ATOM', 'HETATM', 'TER', 'END')

RETURNS	DESCRIPTION
list[str]	Filtered lines.

parse_atomname(line)

Gets the atom name from a line.

PARAMETER	DESCRIPTION
line	Line of a PDB file that starts with ATOM or HETATM. TYPE: str

RETURNS	DESCRIPTION
str	Atom name.

parse_resid(line)

Gets the residue ID from a line.

PARAMETER	DESCRIPTION
line	Line of a PDB file that starts with ATOM or HETATM. TYPE: str

RETURNS	DESCRIPTION
str	Residue ID.

parse_resname(line)

Gets the residue name from a line.

PARAMETER	DESCRIPTION
line	Line of a PDB file that starts with ATOM or HETATM. TYPE: str

RETURNS	DESCRIPTION
str	Residue ID.

replace_in_pdb_line(line, orig, new, start, stop)

General function to replace parts of a PDB line.

PARAMETER	DESCRIPTION
line	PDB line. TYPE: str
orig	Original value to check if it exists. TYPE: str
new	If orig is in line, replace it with this value. This must be formatted for all columns, not just the value with no spaces. For example, " 42" not "42". TYPE: str
start	Slice the line starting here to replace. TYPE: int | None
stop	Slice the line stopping here to replace. TYPE: int | None

run_align_pdb(pdb_path, out_path, selection_str=None)

Align structure in PDB file.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file. TYPE: str
out_path	Path to write aligned PDB file. TYPE: str
selection_str	Selection string for MDAnalysis universe. TYPE: str | None DEFAULT: None

run_filter_pdb(pdb_path, output_path=None, record_types=None)

Only keep PDB lines that contain specified record types.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file. TYPE: str
output_path	Path to save new PDB file. If None, then no file is written. TYPE: str | None DEFAULT: None
record_types	Records to keep in the PDB file. Defaults to ("ATOM", "HETATM", "TER", "END"). TYPE: tuple[str, ...] | None DEFAULT: None

RETURNS	DESCRIPTION
list[str]	PDB file lines.

run_merge_pdbs(*pdb_paths, output_path=None)

Merge PDB files. No atoms are removed, only added.

PARAMETER	DESCRIPTION
*pdb_paths	Paths to PDB files in order of decreasing precedence. We assume the residue indices are consistent across PDB files. TYPE: str DEFAULT: ()

run_write_pdb(file_paths, output_path, selection_str=None, stride=1)

Write PDB file from file paths.

PARAMETER	DESCRIPTION
file_paths	Paths of files to load into MDAnalysis. TYPE: Iterable[str]
output_path	Path to save PDB file. TYPE: str
selection_str	Selection string for MDAnalysis universe. TYPE: str | None DEFAULT: None