Io

write_pdbs

A class for converting numpy arrays into PDB-formatted strings.

__create_pdb_line(numpy_array, index, resname, letter)

Create a string formatted according to the PDB standard.

PARAMETER	DESCRIPTION
numpy_array	A 1x3 np.array representing a 3D point.
index	An integer, the atom index to use in the string.
resname	A string, the RESNAME to use.
letter	A string, the atom name/chain/etc to use for the output.

RETURNS	DESCRIPTION
	A string, formatted according to the PDB standard.

numpy_to_pdb(narray, letter, resname='')

Create a string formatted according to the PDB standard.

Args: narray: A nx3 np.array representing a 3D point. letter: A string, the atom name/chain/etc to use for the output. resname: An optional string, the RESNAME to use for the output.

Returns: A string, formatted according to the PDB standard.

create_pdb_line(numpy_array, index, resname, letter)

Create a string formatted according to the PDB standard.

PARAMETER	DESCRIPTION
numpy_array	A 1x3 np.array representing a 3D point.
letter	A string, the atom name/chain/etc to use for the output.

RETURNS	DESCRIPTION
	A string, formatted according to the PDB standard.

dx_freq(freq_mat, output_prefix, config)

Generates a DX file that records the frequency that a volume element is open.

PARAMETER	DESCRIPTION
freq_mat	a Nx4 matrix, where the first 3 columns are the x,y,z coords of the point, and the 4th column is the frequency of emptiness for that point in space TYPE: NDArray[float64]

fix_filename(path, must_exist=True)

Returns a standardized Path object, handling both Windows and Unix-formatted paths.

PARAMETER	DESCRIPTION
path	The file path to standardize. TYPE: str
must_exist	If True, verifies that the path exists. TYPE: bool DEFAULT: True

RAISES	DESCRIPTION
FileNotFoundError	If the path does not exist and must_exist is True.
ValueError	If the path format is invalid.

RETURNS	DESCRIPTION
Path	A pathlib.Path object representing the standardized path. TYPE: Path

gzopenfile(path, mode='r')

Opens a gz compressed file, regardless of whether unix or windows formatted path.

PARAMETER	DESCRIPTION
path	A string, the path.
mode	A string, the file mode. Defaults to "r". DEFAULT: 'r'

RETURNS	DESCRIPTION
	The file object.

numpy_to_pdb(narray, letter, resname='')

Create a string formatted according to the PDB standard.

PARAMETER	DESCRIPTION
narray	A nx3 np.array representing a 3D point.
letter	A string, the atom name/chain/etc to use for the output.

RETURNS	DESCRIPTION
	A string, formatted according to the PDB standard.

openfile(path, mode='r')

Opens a file, regardless of whether unix or windows formatted path.

PARAMETER	DESCRIPTION
path	A string, the path.
mode	A string, the file mode. Defaults to "r". DEFAULT: 'r'

RETURNS	DESCRIPTION
	The file object.

write_to_file(fo, s, encode=True)

Writes to a file, encoding if necessary.

PARAMETER	DESCRIPTION
fo	The file object.
s	The string to write.
encode	Whether to encode the file before writing. Defaults to True. TYPE: bool DEFAULT: True