Database files

The connection table of the query object (similarity probe) is processed to obtain the set of atom pairs, and then the database file is scanned to evaluate the similarity between the query and each of the database structures. The maximum number of structures that the program will select is specified, as well as the minimum similarity score that a database compoimd must show to be selected. Within these limits, the program will select from the database the structures that are most similar (with the highest similarity value) to the query and will create an output file of compoimd numbers and similarity values, sorted by decreasing similarity, for the selected compounds. 

Size of the database industry can be measured in terms of the number of database records, databases, database entries in CRDB, database producers, database vendors, or online searches. Growth in number of database entries, databases, producers, and vendors is plotted in Figure 1. The slowest growth is at the vendor level, the fastest growth is in database files. 

I aniily Copy - copies database files between families. Select the family to he copied from, ilicn choose the Family Copy button to specify an empty recipient. 

Load and Extract - converts information to/from the generic output found in the Models and Results Database (MAR-D) file format to/from the SAPHIRE database file. 

So, back then to aspirin. Very often, X-ray data is available for the molecule of interest or related molecules. The lingua franca for molecular modelling purposes is a file of Cartesian coordinates such as the following. pdb (Protein Database) file. Figure 1.13, for aspirin. 

Exposure Levels in Humans. Although some data on the levels of americium in human tissues exposed to natural background levels (food, water, and air) are available, few measurements have been made on the americium content in human tissues. The principal source of information about occupationally exposed individuals is the U.S. Transuranium and Uranium Registries (USTUR) Tissue Program and database, established to document levels and distribution of uranium and transuranium isotopes in human tissues for occupationally exposed workers (USTUR 1999). Several major database files are available. 

Your dm.xls Excel file is then created. The process of exporting a Microsoft Access database file is just as easy, requiring only a few clicks of the mouse. 

The initial recording of research ideas and data is most always private and takes the form of laboratory notebooks and database files. The first communication of research data and ideas may or may not be private. Oral and informal written communication occurs between research colleagues and teams. In the era of e-mail and listserves, these initial written communications may also be public in that they exist on the Internet. If there is a financial or proprietary interest in the research, the first communication may be in the form of a patent application. 

First create a new data base using the option "New Database" (File menu) or open a pre-existing data base using the option "Open Database" (File menu). 

On entering the program (by a double click on its icon), the only thing you will see is the menu bar. To begin work, you must bring up on screen the window corresponding to a data base by going to the options "New Database" or "Open Database" File menu). 

Go to the option "Open Database" File menu), which will bring up a dialog box. Locate the file you desire to open and double click on its name or, with the file highlighted in black, click "Open". 

Fig. 11.7. Random section of the COSMO frag database file five-digit atom word are separated by blanks. The first 8 words are the atom similarity codes of order 0 to 7, followed by 2 by-codes containing additional information. At the end of each line the molecule of each atom is marked, using a nine-letter unique name constructed from the molecule identity index, followed by information on the neighbor atoms and implicit hydrogens. In this section all atoms are identical up to the second order, while atoms 5 and 6 are the most identical (up to fifth order).

To export data files into a database program, a database file format called. DB2 was developed in an early PC database, dBase II. Databases are made up of files, which could be compared to a Rolodex file box full of cards, all containing the same type of information. The Rolodex card would be equivalent to a database record. Each record has on it a series of entries, fields, in the same place on each card. To import data into a database record, all the entries in the report must be matched up with existing fields in the database s format. Most software that uses database formats has export/import subprograms that allow you to align fields between the two formats and allow you to select various ways of determining coding for end-of-file and end-of-record terminators. 

Public patent information can be accessed through the USPTO s website. If a patent application issues or is published and you know the application number, patent number, or U.S. publication number, you can look up the file history of the application in the Public PAIR section of the website (http //portal.uspto.gov/external/portal/pair). Most of the information is available as PDFs that can be viewed one page at a time. Before the advent of the Public PAIR database, file histories were available only as hard copies and tended to be very expensive to obtain. With Public PAIR, one can see much of the correspondence between a patent applicant and the USPTO. This is particularly useful when you are interested in learning more about another party s patent application status. 

To build database file (table), activate Table tab, then ... 

The database file as a table object can be opened from the activated Table tab for manipulation. For examples, fields (columns) can be added from the Datasheet view by clicking the right edge of the existing column and then selecting Column from Insert menu. This brings a new column (labeled Field 1) or columns (repeated selection of Column option). Double click the new column to enter the field name. Records (rows) can be added also from the Datasheet view after clicking New record button on the tool bar. 

The form is saved and appended to the database file dbname.mdb. Similar steps are followed to create a report after invoking Report Wizard option from the activated Report tab. The Wizard provides options for grouping level, sorting order, layout, and style. 

Save the query hie which is appended to database file and can be retrieved (opened) from Query tab. 

Another option of dBASE is that one can sort the.contents of a database file. This means that, depending on the type of the field you w ant to sort on, a new database file is created in which the records are reordered in an alphabetical, chronological... 

Until now we have used the database for a very simple purpose, namely to extract information from a single file. However, it is also possible to connect several files. Let us suppose that we want to use dBASE for the following problem. In atomic absorption spectroscopy (AAS), one has to choose between the flame and the (flameless) graphite tube methods. The flame methods does not have such a low detection limit as the graphite tube, but it is easier to handle, less prone to interferences and more robust. For that reason the user s strategy will often be to apply the flame method above a certain concentration limit and the flameless method below it. The flame method has its own experimental characteristics and we suppose that we have another database file in which the characteristics for flame methods are given per element. In that case, we would like the consultation to go like this ... 

The first command use opens on disk drive A the database file flame which contains the characteristics for the flame method. Then the element Tl and the concentration (0.02 micro g/ml) one wants to analyze are stored in two memory variables melem and mconc , respectively. 

Before one can examine whether or not the detection limit is reached one has to move the record pointer to the record for thallium, which is done with the locate command. dBASE compares whether the concentration one wants to analyze is lower than the determination limit for the element (which is stored in concen , a field of the flame database file). dBASE then checks whether the equation (the last statement in the above set of commands) is. T. (True) or. F. (False). In case it is False, the concentration to be analyzed exceeds the determination limit and one can obtain the conditions for the flame method by typing the command display. However, if the concentration is lower than specified, the flameless method must be used. To obtain the conditions for the flameless method, one then has to open the database file containing the characteristics for the flameless method and use the display command. 

Journaling is the writing of all before and after images of modifications of the database to a journal file as well as to the database file. The journal device should be a device other than that used to store the database in case of failure. Database Operator utilities (DBO) are provided to specify the after image journal device (DBO/ AFTER-JOURNAL), make backup copies of the database (DBO/BACKUP), restore the corrupted database with the backup (DBO/RESTORE), and reapply all changes since the last backup from the after-image journal to the backup database (DBO/RECOVER). 

The data sets WATEQ4F.dat, MINTEQ.dat, PHREEQC.dat and LLNL.dat are automatically installed with the program PHREEQC and can be chosen from the menu item Calculations/File under Database File. The internal structure of these thermodynamic data sets has already been explained in great detail in chapter... 

Software module/unit data (i.e., databases, files, records, data)... 

A second smaller source of data on software usage is another database file available from the Chemical Abstracts Service. The file CJWILEY covers the full text of polymer journals (Table 3) published by John Wiley Sons. CJWILEY lists 8775 articles published in the seven-year period 1987—1993. Unfortunately, CJWILEY does not include Wiley s Journal of Computational Chemistry. By comparing findings from CJWILEY to the CJACS results, however, one can ascertain whether there are different patterns for modeling polymers versus modeling molecules in general. 

Figure 2 Number of papers added each year to the CJACS (Current Journals of the American Chemical Society) database file of the Chemical Abstracts Service. This file contains full text of each paper published. For purposes of this figure, computational chemistry papers are counted based on any mention of at least one of the 60 or so programs covered in this chapter. Among these programs are many of those most widely used, as well as a sampling of additional computational chemistry programs. The numbers of computational chemistry papers in this plot are lower bounds to the true numbers, however, because there are thousands of other programs in use.

Figure 23 Total number of times three general purpose molecular modeling packages were mentioned in the CJACS and CJWILEY database files during the years 1987—1993. A logarithmic scale is used, to increase the visibility of the bars for the smaller data set.

Relatively simple database files can be constructed within the more advanced spreadsheets using the columns and rows as fields and records respectively. These are capable of limited sorting and searching operations and are probably sufficient for the types of databases you are likely to require as an undergraduate. You may also make use of a bibliography database especially constructed for that purpose. 

The true business value of an EDMS is realized to the extent that it serves as more than just the terminus for document-related activities in an enterprise. To fully realize its goals, an enterprise paperless documentation system will perform functions across the entire document life-cycle. In addition to the storage of existing documents, users with appropriate system privileges must be able to create new electronic documents from within the electronic document management system. The system must explicitly support the file formats used by the business, which typically include word processing, spreadsheet, graphics, and database files. 

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