Standard file structures

Data may be organized by type of data, such as adverse events, laboratory data, demography, physical exam, etc. Since many of these categories of data exist across clinical trials, standard file structures can be designed and implemented. This standardization allows for the reuse of validated software as well as facilitates the pooling of data across studies for use in project safety summaries and other data reporting across studies. 

As many different file formats have been developed since the early 1970s, the need for a standard chemical structure format has been increasingly felt. Various attempts have been made by different groups of the chemical commimity to define and push such a format, but none has achieved unanimous acceptance. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

When the button "submit smiles is pressed, the SMILES string is sent to the web server of Molsoft, converted to 3D, and the 3D structure is displayed in a java molecule viewer on an automatically created web page (see Figure 2-139). Unfortunately, the Molsoft server does not support downloading of the 3D structures in a standard file format. 

M D Lmolfile Standardized file format for chemical structures including substructure query features (initially defined by Molecular Design Ltd)... 

Another way to get a structure into the computer is to import (read) a molecule file containing the atomic co-ordinates (and perhaps other atomic and molecular information) into your program. Unfortunately, there is no single standard file format that all programs use. However, some of the commonly encountered formats include those of SYBYL MOL2 files and Protein Data Bank (PDB) files. There are also free programs available for download from the World Wide Web that can interconvert the numerous file formats still in use. 

The chemical business rules of a compound registration solution define the individual identities of chemical structure representations in order to meaningfully assign a unique corporate ID to each unique structure. After applying these rules, standardized parent structures are stored in a main structure table. The (structure) records from the original compound library data file entering the system are saved into a batch table on which each batch entry is associated with its unique parent structure. All data relating to the physical compound sample remain uniquely associated with this batch entry and thus are also associated with one unique parent structure. 

VT105 in that it is a richer command set and is a simple ASCII stream, it can be easily read with out resorting to decoding the bit patterns of characters. Graphics figures can be stored as simple sequential files, edited with a standard editor and transported between system (ours or other vendors) without worrying about the oddities of binary file structures and data being interpreted as control codes. ... 

Every project should indicate the mandatory documented program coding standards, directory structure standards, file naming conventions, and configuration management processes that are expected to be undertaken for all coding output. AU of these documents should be readily available, either in electronic or hard copy, for all staff to consult as necessary. 

Brown, I. D. The standard crystallographic file structure. Acta Cryst. A39, 216-224 (1985). 

Brown, I. D. Standard crystallographic file structure — 84. Acta Cryst. A41, 399 (1983). 

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. 

Searching for structures or reactions in an external repository is an alternative to entering the structure directly into the scientific document. This is especially helpful if the structure is complex and not easy to author. Another application is the search for structures stored in an external system — for instance, to find already performed identical or similar reactions. The search query is typically entered via commonly used structure editors that provide the required standard file format. The search query can be performed on individual databases or on all connected databases, including the internal one, at the same time. 

This is all the information about the hydrogen bonds you can get from a standard crystal structure. The only thing left to do is the refinement of the weighting scheme to convergence. This has been done in the file hbond-05.res. Figure 3.6 shows the final model with some symmetry equivalent molecules and all hydrogen bonds. 

Application Configuration Specification. The Application Configuration Specification (ACS) documents the application configuration required to meet the URS. The ACS records system setup parameters, process configuration, database configuration, file structures and so on required to implement the specific business implementation of the system. Where a standard implementation of the core product is adopted, this will be the only custom specification delivered to the pharmaceutical organization, accompanied by standard technical and user manuals. 

Each facility should set up a standard file strucmre on the company network that is accessible to all authorized persons, and that is consistent across different investigations. The structure shown in Table 11.11 can be used as a go by. 

Diffraction Standards, File No. 78-0428). It can also be seen from fig. 10.1 that there are some relatively weak and broad peaks before 20 = 30° that arise from the diffraction of modification layer on the coated nanoparticles. Thus, it is concluded that the Cu nanoparticles with fee structure were successfully prepared and that there are some oxides on its surface. 

ODB-I-+ uses a standard file system structure. ODB-1--1- denotes a job using a simple directory tree that can be transferred between systems with no loss of data (see Fig. 18.16). 

Brown, I.D. Standard Crystallographic File Structure . Acta Crystallogr 1983, A39, 216-224. 

Screen search identifies the file structures that contain at least the set of screens present in the query structure. Tl e process consists of a standard inverted file search in which the search terms consist of screens generated from the query structure. The. results are a set of candidate file structures that have satisfied the screen logic expression. This candidate set is then passed to the iterative search phase. Thus, screen search provides a rapid reduction of the databa structures to those that are likely to match the query structure so that the computer intensive iterative search need only be performed on this smaller set of file strucfures. 

Proposals for a standard file format were advanced separately by DeLos F. DeTar and by T. J. O Donnell and John S. Garavelli at the Gordon Conference on Computational Chemistry in July 1988. Both these proposals were advanced to address problems confronting molecular modelers. The proposal of DeTar provided for representation of force field data as well as molecular structure information. O Donnell and Garavelli presented several general formats including an alternative to fixed column, record oriented formats. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

An alternative and much more flexible approach is represented hy the STAR file format [L48, 149, which can be used for building self-describing data files. Additionally, special dictionaries can be constructed, which specify more precisely the contents of the eorresponding data files. The two most widely used such dictionaries (and file formats) arc the CIF (Crystallographic Information File) file format [150] - the International Union of Crystallography s standard for representation of small molecules - and mmCIF [151], which is intended as a replacement for the PDB format for the representation of macromolecular structures,... 

HyperChem contains a database of amino and nucleic acid residues so you can quickly build polymers con laining these subunits. You can also read in structures in files from standard databases, such as the Brookhaven Protein Data Bank (see the HyperChem Reference Manual). 

The molecular structure input requires atom types to be assigned, which are not the same from one force field to the next. The input also includes a list of bonds in the molecule. There is not a module to automatically assign atom types. Most of the modules use a Cartesian coordinate molecular structure, except for a few that work with torsional space. The same keyword file is read by all the executables. A little bit of input is obtained by the program either interactively or from an ASCII file piped to standard input, which makes for a somewhat cryptic input file. This system of common input files and the user choosing which executables to run give TINKER the ability to run very sophisticated simulations while keeping the input required for simple calculations fairly minimal within the limitations mentioned here. 

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