- <init>
- getAcceptedAtomNames
By default the parser will read in all atoms (unless using the CAonly switch).
This allows to specif
- getAtomCaThreshold
The maximum number of atoms that will be parsed before the parser switches to a
CA-only representati
- getMaxAtoms
The maximum numbers of atoms to load in a protein structure (prevents memory
overflows)
- isAlignSeqRes
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
- isHeaderOnly
Parse only the PDB file header out of the files
- isParseBioAssembly
Should the biological assembly info (REMARK 350) be parsed from the PDB file?
- isParseCAOnly
The flag if only the C-alpha atoms of the structure should be parsed.
- isParseSecStruc
Is secondary structure assignment being parsed from the file? default is null
- setAlignSeqRes
Define if the SEQRES in the structure should be aligned with the ATOM records if
yes, the AminoAcids
- setCreateAtomBonds
Should we create bonds between atoms when parsing a file. Will create
intra-group bonds from informa
- setParseBioAssembly
Should the biological assembly info (REMARK 350) be parsed from the PDB file?