Typing every time your molecules and system is not fun nor efficient, for this reason chemlab provides ready-to-use database utilities.
Databases in chemlab can store arbitrary data, that can be retrieved by using the get method. The following is an example retrieving a molecular structure from CIR http://cactus.nci.nih.gov/chemical/structure , the chemical resolve identifier website:
from chemlab.db.cirdb import CirDB
mol = CirDB().get("molecule", "aspirine")
Note
CirDB uses internally the CirPy wrapper https://github.com/mcs07/CIRpy , all credits go to the author.
Chemlab includes also his own database for data as well as some molecules. For example to get the vdw radii (the data was taken from OpenBabel) you can:
from chemlab.db import ChemlabDB
cdb = ChemlabDB()
vdw = cdb.get("data", "vdwdict")
vdw['He']
For more information refer to the chemlab.db.ChemlabDB documentation.
See also
It may happen that you have your most-frequently used collection of molecules and systems. Chemlab provides a serialization system that let you easily dump your objects in a directory and retrieve them by using a local database.
This is achieved by the class chemlab.db.LocalDB:
from chemlab.db import LocalDB
ldb = LocalDB('/path/to/yourdb')
# Generate/retrieve some molecule
ldb.store('molecule', 'examplemol', mol)
ldb.store('system', 'examplesys', sys)
The method chemlab.db.LocalDB.store() takes a first argument that can be ither molecule or system, as a second argument the key used to store/retrieve the entry and finally the object to store.
You can, at a later time retrieve the entries in this way:
from chemlab.db import LocalDB
ldb = LocalDB('/path/to/yourdb')
mol = ldb.get('molecule', 'examplemol')
s = ldb.get('system', 'examplesys')
The molecules files are serialized using the json format and stored in a very simple directory structure. For the previous example, the database directory would look like this:
/path/to/yourdb/
- molecule/
- examplemol.json
- system/
- examplesys.json
The reason for such a simple structure is that in the future it will be easy to define custom-made remote database, for example you could have a community mantained github repo with commonly used molecules and data, that can be directly accessed by chemlab (everybody is welcome to develop such an extension). On top of that, you can copy-paste json molecule files without having to do any migration.
See also