qp.manager.charge_embedding

Generate charge embedding ptchrges.xyz file for TeraChem input.

By default, partial charges are taken from the built-in AMBER ff14SB dictionary. Users can supply a custom JSON file of charges via the charge_embedding_charges configuration option to support other force fields.

Functions

calculate_centroid	Calculate the geometric centroid of a set of coordinates.
get_charges	Generate the MM point charge embedding file (ptchrges.xyz).
load_custom_charges	Load custom partial charges from a JSON file.
parse_pdb	Write ff14SB partial charges into the B-factor column of a PDB file.
parse_pdb_to_xyz	Convert PDB with charges to TeraChem point charge XYZ format.
read_pdb	Read a PDB file and extract ATOM record lines.
read_xyz	Read an XYZ file and extract atomic coordinates.
remove_atoms_from_pdb	Filter PDB lines to remove atoms close to XYZ coordinates.
remove_qm_atoms	Remove QM cluster atoms from a PDB file based on coordinate matching.
rename_and_clean_resnames	Rename histidine residues for ff14SB compatibility and convert HETATM to ATOM.
write_pdb	Write PDB lines to a file.