$aminoAcidCodes
$aminoAcidCodes : array
3-letter to 1-letter amino acid code table, for turning SEQRES residues into a usable protein sequence. Unknown residues (including HETATM-only ones) map to "X".
Class ParsePdbManager PDB structure files describe 3D atomic coordinates, not GenBank/EMBL-style annotated sequences, so this parser does not reuse the Sequence/Feature entities of ParseDbAbstractManager - it exposes its own plain Domain\Parser\Entity objects instead.
Only the fields most commonly used in structural bioinformatics are covered (identification, sequence per chain, secondary structure, atomic coordinates); the many rarely-used PDB record types (CONECT, ANISOU, MASTER, ...) are left out, matching what Legacy/pdb.inc.php itself had actually implemented.
parseDataFile(array $aFlines) : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence
Parses a PDB data file and populates this manager's fields and model objects.
| array | $aFlines | The lines the script has to parse |
$oSequence
parseSpecificationList(string $sText) : array
Parses a COMPND or SOURCE record, both written in what the PDB format calls a specification list : "TOKEN: value;" pairs where each MOL_ID opens the block of one molecule. Keeping the blocks apart is what ties a chain to the molecule it belongs to, so a structure holding several molecules yields several blocks. Records of files older than the specification are free text carrying no token, and stay plain strings.
| string | $sText |
parseHelix(string $sLine) : \Amelaye\BioPHP\Domain\Parser\Interfaces\PdbHelixInterface
Parses one HELIX line.
Columns : 12-14 helixID, 16-18 initResName, 20 initChainID, 22-25 initSeqNum, 28-30 endResName, 32 endChainID, 34-37 endSeqNum, 39-40 helixClass, 72-76 length.
| string | $sLine |
parseSheet(string $sLine) : \Amelaye\BioPHP\Domain\Parser\Interfaces\PdbSheetInterface
Parses one SHEET line.
Columns : 8-10 strand, 12-14 sheetID, 18-20 initResName, 22 initChainID, 23-26 initSeqNum, 29-31 endResName, 33 endChainID, 34-37 endSeqNum.
| string | $sLine |
parseAtom(string $sLine) : \Amelaye\BioPHP\Domain\Parser\Interfaces\PdbAtomInterface
Parses one ATOM or HETATM line.
Columns : 7-11 serial, 13-16 name, 17 altLoc, 18-20 resName, 22 chainID, 23-26 resSeq, 31-38 x, 39-46 y, 47-54 z, 55-60 occupancy, 61-66 tempFactor, 77-78 element.
| string | $sLine |