mofbuilder.io.PdbReader

class mofbuilder.io.PdbReader(comm=None, ostream=None, filepath=None)

Bases: object

Class for reading and processing atomic coordinates from PDB files.

Parameters:

• comm (Any | None)

• ostream (veloxchem.outputstream.OutputStream | None)

• filepath (str | None)

comm

MPI communicator.

Type:

MPI.Comm

rank

MPI rank of current process.

Type:

int

nodes

Total number of MPI processes.

Type:

int

ostream

Output stream for logging.

Type:

OutputStream

filepath

Path to the PDB file.

Type:

str | Path | None

com_target_type

Atom type used for center-of-mass calculation.

Type:

str

data

Parsed atom data as array; see row format below.

Type:

np.ndarray | None

X_data

Rows corresponding to atom type “X”.

Type:

np.ndarray | None

node_atoms

Atom types and labels for processed nodes.

Type:

np.ndarray | None

node_ccoords

Coordinates for all node atoms, recentered.

Type:

np.ndarray | None

node_x_ccoords

Coordinates for atoms of type “X”, recentered.

Type:

np.ndarray | None

_debug

Toggle debug-level logging.

Type:

bool

read_pdb()

Reads the PDB file and extracts atom data.

Parameters:

• filepath (str | None)

• recenter (bool)

• com_type (str | None)

Return type:

None

expand_arr2data()

Converts an array of atom records into the library’s standard format.

Parameters:

arr (ndarray | None)

Return type:

Tuple[ndarray | None, ndarray | None]

process_node_pdb()

Specialized recentering and extraction for node atoms.

Return type:

None

read_pdb(filepath=None, recenter=True, com_type=None)

Read a PDB file, extract atoms, and optionally recenter coordinates.

Populates self.data with shape (N, 11): [atom_type, atom_label, atom_number, residue_name, residue_number, value_x, value_y, value_z, occupancy, b_factor, note].

Parameters:

• filepath (str, optional) – Path to the PDB file. Overrides instance filepath if given.

• recenter (bool, optional) – If True (default), recenter coordinates to center-of-mass.

• com_type (str, optional) – Atom type for COM; if None, uses all atoms.

Raises:

AssertionError – If file does not exist.

Return type:

None

Note

Only ATOM/HETATM records are parsed; format assumes canonical PDB column mapping.

expand_arr2data(arr)

Convert array of minimal records to standard data format.

Parameters:

arr (np.ndarray | list) – Array/list of [atom_type, atom_label, x, y, z].

Returns:

All parsed data (as for self.data), and extracted rows where note is ‘X’.

Return type:

Tuple[np.ndarray | None, np.ndarray | None]

Example

data, x_data = pdb_reader.expand_arr2data([[“Fe”, “Fe”, 0.0, 0.0, 0.0]])

process_node_pdb()

Read the PDB and prepare node-centered atom sets.

Parses self.data, recenters coordinates for self.com_target_type (default ‘X’), and stores node atoms, coordinates, and “X” atoms.

Note

Intended for node PDB files (metal nodes) in the MOF framework.

Populates:

• self.node_atoms: [atom_type, atom_label] for all atoms

• self.node_ccoords: centered coordinates for all atoms

• self.node_x_ccoords: centered coordinates for “X” atoms

Return type:

None