Properties molfile

Create Type frowns. named j roperty As (name Text, value Text) Create Or Replace Function frowns.molfile properties(molfile Text) Returns Setof f rowns. named j roperty As EOPY from frowns import MDL import StringlO... 

Create Or Replace Function openbabel.molfile properties(molfil Text) Returns Setof openbabel.named property As EOPY import pybel... 

A molecule editor can draw a chemical structure and save it, for example as a Molfile. Although it is possible to include stereochemical properties in the drawing as wedges and hashed bonds, or even to assign a stereocenter/stereogroup with its identifiers R/S or E/Z), the connection table of the Molfile only represents the constitution (topology) of the molecule. 

Suppose we want to develop a module that represents the chemical structure of compounds. A structure is the signature of a compound that, in most cases, uniquely defines all chemical properties of the compound such as mol-weight, molformula, stereo chemistry, pKa, and logP. Suppose a structure can be represented in many different formats—Molfile, Chime, Smiles. The algorithms of calculating the chemical properties are different depending on the structure format, and our application has to support all of them. A naive solution is to develop a class for each structure format and repeat every common attribute and method in all of them. 

The same approach can be used for property calculations, because you may have multiple choices and each one has different APIs. It is possible that today you choose one vendor solution to do the work. Some time in the future you may switch to a different vendor for the purpose of cost savings, better algorithm, performance, or reliability. Or you may face a harder choice—the vendor you chose in the past is going out of business. The solution we described above for Molfile-Smiles conversion keeps your system closed for... 

Structure registration is the process of entering structural information in a centralized repository, usually a structure database. These repositories serve as a pool for providing structure information that has been created in other departments of a company. Structure databases are set up according to the individual needs of a department or company. They consist of a common representation of a structure in a standardized file format, such as MolFile, SDF, reaction (RXN) (MDL), JCAMP (International Union of Pure and Applied Chemistry), or simplified molecular input line entry specification. Any additional data can be stored with the structure depending on the context typical examples are structure properties, reaction conditions, and literature references. 

The recommendation here is to use SMILES to store molecular structure itself. If other features of the molecule or atoms need to be stored, other data types and columns can be added to the row describing the molecule. It is the "SQL way" to not encode a lot of information into one data type. When using a molfile as the structural data type, too much data is encoded in a single data type. The individual data items must be parsed and validated. Errors creep into the data, due to missing, extra, or invalid portions of the molfile. Ways of storing atomic coordinates, atom types, and molecular properties are discussed Chapter 11. 

The molfile or sdf file format is a very common way to store molecular structures. This can be considered as an external representation of a molecular structure data type. There are many other common file formats in use and only the essential features common to all of them will be considered here. The essential aspects of molecular structure contained in these files are atomic number or atomic symbol, formal atomic charge, bonded atom pairs, and bond orders. These are the minimum attributes necessary to define an unambiguous valence bond molecular structure. Other atom properties, such as atom types might also occur in these files, but these are specific to particular modeling programs and will not be discussed here. Sometimes molecular properties are also stored in these files. A way to store these properties in relational tables is discussed. 

The column structure.id is a unique integer relating the structure, sdf and property tables. The sdf.molfile column contains the molfile for each structure as defined by the vendor. The structure.name and structure.cansmiles columns contain the name and canonical smiles parsed and computed from the molfile. The structure.coord column will contain an array of atomic coordinates. The structure, atom column will contain an array of atom numbers from the file in canonical order to correspond to the atom order in the canonical SMILES. The OpenBabel/plpythonu extension functions molfile mol and molfile properties will be used to parse the vendor SDF molfiles and populate these tables. The molfile column of the sdf table is first populated from the SDF file, using the following perl script. 

At this point, the vla4.sdf table has been created in the database named mydb. The molfile column contains the molfile for each structure in the sdf file. The sdf. id column contains a unique integer that can be used to relate the vla4.property table. Notice the use of the default value nextval( vla4.structure id sql ) in the SQL statement that creates the vla4. sdf table. This causes the sdf. id column to contain... 

Finally, any properties contained in the molfile will be stored in a separate table containing the text value copied from the file as well as a numeric value for the property, if that is appropriate for the property. There will be a one-to-many relationship between the structure and property table, allowing any number of properties to be stored for each structure. The function openbabel.molfile properties is shown in the Appendix. It expects a molfile and returns a composite data type, defined as follows. 

The following SQL is used to parse the molfile column from the vla4.structure table using the openbabel.molfile properties function. The name and value fields of the composite data type are inserted into the vla4. property table, along with the appropriate id selected from the vla4.structure table along with the molfile column. 

Select id, (molfile properties).name, (molfile properties).value From (Select id, opeiibabel. molf ile properties (molf ile) From vla4.sdf) atmp... 

This insert statement is a bit more complex than the one that inserted rows into the vla4.structure table. In that table, only one row was returned from the mol file mol function. The mol file properties function returns multiple rows for each molfile, when there are multiple properties for each molfile. The second select statement above (the one in parentheses and identified with the name atmp) selects all the rows for each molfile. The first select statement selects all the columns from each returned row from molfile properties. These are then inserted into the vla4. property table. 

Consolidated chemical catalogs from various suppliers provides physical properties and safety data links to molfiles and MSDS Chemical directory, with links to several property databases... 

SDF created by MDL is a chemical data file format and displays information on chemical stractuie [55]. SDF is an extension (additional infomiation) of MDL Molfile. The first portion of the SDF file is the same as the MDL Molfile, and the second half contains additional information related to some molecnlar property. Delimiter is a set of specific characters nsed to segregate mnltiple compounds (Fig. 1.18). 

---