The [Chemical Component Dictionary](http://www.wwpdb.org/ccd.html) is an external reference file describing all residue and small molecule components found in PDB entries. This dictionary contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules.

By default BioJava ships with a minimal representation of standard amino acids, which is useful when you just want to work with atoms and a basic data representation. However if you want to work with a correct representation (e.g. distinguish ligands from the polypeptide chain, correctly resolve chemically modified residues), it is good to tell the library to either

1. Fetch missing **Chemical Component Definitions** on the fly (small download and parsing delays every time a new chemical compound is found), or

2. Load all **Chemical Component Definitions** at startup (slow startup, but then no further delays later on, requires more memory)

You can enable the first behaviour by doing using the [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/FileParsingParameters.html) class:

AtomCache cache = new AtomCache();

// by default all files are stored at a temporary location.

// you can set this either via at startup with -DPDB_DIR=/path/to/files/

// or hard code it this way:

cache.setPath("/tmp/");

FileParsingParameters params = new FileParsingParameters();

params.setLoadChemCompInfo(true);

cache.setFileParsingParams(params);

StructureIO.setAtomCache(cache);

Structure structure = StructureIO.getStructure(...);

If you want to enable the second behaviour (slow loading of all chem comps at startup, but no further small delays later on) you can use the same code but change the behaviour by switching the [ChemCompProvider](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/ChemCompProvider.html) implementation in the [ChemCompGroupFactory](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.html)