This chapter seeks to give a general overview of the major design decisions behind OEChem TK. The reader should have an understanding of the basic OEChem TK objects and functions. The reader should also be familiar with the basics of object oriented programming.
Throughout this manual, the OEMol, OEGraphMol, and OEQMol are the concrete classes which handle most molecular representation in OEChem TK. The OEGraphMol API is defined in the OEMolBase abstract base-class, the OEMol API is defined by the OEMolBase and OEMCMolBase abstract base-classes, and the OEQMol API is defined by the OEMolBase and OEQMolBase abstract base-classes. The OEMCMolBase class publicly inherits from the OEMolBase class, which in turn inherits from the OEBase class. Similarly, the OEQMolBase class publicly inherits from the OEMolBase class, which again inherits from the OEBase class. An OEGraphMol, can be passed to any function which takes an OEMolBase argument. An OEMol can be passed to any function which takes an OEMCMolBase or OEMolBase argument, and an OEQMol can be passed to any function which takes an OEQMolBase or OEMolBase argument. Figure: Hierarchy A represents the OEChem TK molecule hierarchy described in this paragraph.
The most important data types in the OEChem TK library are OEMolBase, OEAtomBase, and OEBondBase. These three classes describe the behaviors of molecules, atoms, and bonds respectively. However, these types are abstract classes, describing the methods and semantics of molecules, atoms and bonds, but without defining an actual implementation. (See Figure: Hierarchy B)
Hiding the implementation of these types is very important to the longevity of OEChem TK. It avoids the problem of the leaky abstraction. If code was written that was expecting a certain behavior from the implementation it would be fragile to arbitrary changes in implementation. Therefore, these abstract base-classes are considered stable, with a guarantee that they will not change from version to version.
Since OEAtomBase, OEBondBase, and OEConfBase can only be accessed through their parent molecules, there is no need for concrete instances of these classes. In OEChem TK, these three classes are accessed via references to their respective base-classes, or through the iterator interface discussed in the Atom and Bond Traversal chapter.
It is standard practice when working with abstract base-classes, such as the OEMolBase, to define a function which returns a pointer to one of these objects. These functions, called factories, give library users access to concrete objects even when only the abstract base-class is exposed in the public API. The following factory functions are provided to create molecule objects in OEChem TK. The associated symbolic namespace is used to control what type of molecule implementation is returned.
|Factory Function||Symbolic Namespace|
The problem with factory functions is that they require the user to manage the object’s memory. When the factory function returns a pointer to an abstract base-class, it also passes ownership of the memory to the programmer. To alleviate the problems associated with memory management introduced by factories, the smart-pointer idiom is often used. Simply put, a smart-pointer holds a real pointer to an object, and deallocates the pointer’s memory when the smart-pointer goes out of scope (e.g. in its destructor). In OEChem TK, OEGraphMols, OEMols, and OEQMols fulfill the function of both factories and smart-pointers. This gives the user access to multiple implementations without the need of worrying about memory management. The constructors allow the user to specify which implementation they would like using the associated symbolic namespace described in the previous table. Then the objects themselves act as smart-pointers, cleaning up the implementation pointers when the molecules go out of scope.
Listing 1 demonstrates how to specify an alternative molecule implementation. A SMILES string is then read into different implementation. This demonstrates how implementations that adhere to the OEMolBase interface can reuse existing algorithms written towards it.
Listing 1: Using an alternative molecule implementation
from __future__ import print_function from openeye import oechem mol = oechem.OEGraphMol(oechem.OEMolBaseType_OEMiniMol) oechem.OESmilesToMol(mol, "C1=CC=CC=C1") print("Canonical isomeric SMILES is", oechem.OEMolToSmiles(mol))
It is not uncommon in chemical informatics to consider the equivalence of the graph which represents a molecule and the graph which represents a substructure query. Indeed the simplest of queries are molecules themselves. If one considers each node (or atom) as a potentially complex atom query, even highly complex queries can be represented as molecules.
In OEChem TK, this concept of a query as a molecule is represented by the OEQMolBase abstract base-class. An OEQMolBase contains OEQAtomBase and OEQBondBase atom and bond representations. These versions of OEChem TK atoms and bonds manage the atom and bond expressions which comprise the query.
OEChem TK defines the concrete OEQMol class which provides a programmer access to the API defined by the OEQMolBase class. This is analogous to the way an OEGraphMol provides concrete access to OEMolBase API. Figure: Hierarchy C represents the OEChem TK query molecule hierarchy.
This abstraction allows OEChem TK to treat separate query mechanisms to work similarly. This is similar to how OEChem TK can represent any molecular file format through a single OEMolBase interface. For example, SMARTS can be parsed into an OEQMolBase using the OEParseSmarts function. Also, MDL Queries can be parsed into an OEQMolBase using the OEReadMDLQueryFile file.
Pattern Matching for a general discussion of OEChem TK pattern matching facilities.
OEChem TK is an object-oriented library. However, the design philosophy is that molecule objects are primarily data containers with data access member functions. Most powerful data analysis and manipulation routines in OEChem TK are implemented as free functions rather than member functions. This decision is based on the realization that the abstraction of a molecule can be neither stable nor consistent. To one programmer, a molecule should describe and perceive the space group of organometallic complexes, while to another a molecule should describe the residues and secondary structure of a macromolecule. Both of these perspectives are reasonable and should be supported. Further, a nearly infinite additional list of molecule designs can be imagined and should be supported. In order to do this, the OEChem TK molecule must be extensible, light-weight, and easily re-implemented. Thus, major changes to the OEChem TK molecules can be made, without need to re-implement more than a handful of functions. Conversely, an entire new area of chemistry can be added to the OEChem TK repertoire through free-functions without needing to implement the function in multiple molecules. We have used namespaces extensively to keep the free-functions from cluttering the global namespace.
The OEChem Functions API section for a complete listing of all of OEChem TK‘s free-functions.
Programming Layers: The Deep and Twisted Path¶
OEChem TK was designed to provide a library which puts powerful algorithms in the hands of novice users without hand-cuffing the expert. For this reason, OEChem TK can at the same time seem trivial and overwhelming. There are often several ways to carry out certain tasks in OEChem TK each with its subtle advantages, which can benefit an experienced user. There are very few algorithms we have shied away from including in OEChem TK, and many of the methods are new, unique and powerful. This gives OEChem TK a very rich interface, yet to gain this efficiency and power OEChem TK may force the user to think about problems in ways they are not accustomed to doing. The hope is that the user can benefit from the experience.
OEChem TK has several layers of interfaces to most of its functionality. There are “high-level” interfaces, which provide the user with an enormous amount of power with minimal code. This level is exemplified by the OEReadMolecule and OEWriteMolecule functions. With these functions the functionality of the babel file-format conversion program is trivial. While this is trivial to write and understand (maybe after understanding this manual), it should not belie the fact that OEChem TK is carrying out an enormous amount of work under the surface.
A perhaps “mid-level” interface in OEChem TK is the ability to fine tune molecule file-formats using flavors described in Flavored Input and Output section. Flavors are most useful when file-formats are being used for more than they were originally intended, for example, PDB files. While this functionality is perhaps not for the first-day user, it certainly doesn’t require a stout heart.
Finally, for advanced programmers, OEChem TK provides access to nearly all of the details. OEChem TK molecules have a simple API which can be used to derived custom molecule implementations. The free-function heavy API lets the user apply OEChem TK’s powerful algorithms on custom data structures. Similarly, many of the functions that are wrapped in high level functions (like the molecule readers and writers) are also available directly to the user at the low level. For instance, OEWritePDBFile allows the user to write out a PDB file with a very specific flavor without any normalization that OEWriteMolecule may perform.
OEChem TK is a still a live moving software project. If a roadblock is found a particular level, dig deeper into the next level. Often, the functionality is already present.