New in version 0.8.
This topology parser uses a PDB file to build a minimum internal structure representation (list of atoms). The only difference from PrimitivePDBParser is that this parser reads a non-standard PDB-like format in which residue numbers can be five digits instead of four.
The topology reader reads a PDB file line by line and ignores atom numbers but reads residue numbers up to 99,999 correctly. If you have systems containing at least 100,000 residues then you need to use a different file format that can handle such residue numbers.
Note
The parser processes atoms and their names. Masses are guessed and set to 0 if unknown. Partial charges are not set. Bond connectivity can be guessed if the bonds=True keyword is set for Universe.
See also
Parser that obtains a list of atoms from an non-standard “extended” PDB file.
Extended PDB files (MDAnalysis format specifier XPDB) may contain residue sequence numbers up to 99,999 by utilizing the insertion character field of the PDB standard.
See also
MDAnalysis.coordinates.PDB.ExtendedPDBReader
New in version 0.8.