Structure generation commands

To address these issues regarding adequate structural searching in CHIRBASE, some facilities have been recently added to the user interface. The result is the automatic generation and search of strategic 2D query structures defined with the help of the following commands (Fig. 4-5) ... 

The result of any retrieval command in MAECIS is a set of chemical structures which is referred to as the "current set". If a second retrieval is made, the current set is moved into another internal storage area and is referred to as the "prior set". In this way, MAECIS automatically keeps track of at least two retrievals for the user. However, it is often necessary to establish several sets of molecules during a single computer session. In MAECIS, any number of sets can be retained using a SAVE command which allows the user to name and save any set of molecules created by a retrieval command. Any stored set in MAECIS can also be referenced in a subsequent FIND command. Thus, new sets can be generated from old sets through the find command s boolean operations. Sets retained with the SAVE command are in temporary memory. To make them permanent, the STORE and RESTORE commands are available to move sets to and from permanent disk files. 

Once the lattice is created, the bonds are randomly destroyed in a proportion specified at the command line. There is a linked list of sheets in the structure, and each sheet involves a linked list of bonds thus, all bonds are processed using a double nested loop. For each bond, a random number between 0 and 1 is generated and compared to the specified probability (which is also between 0 and 1) if the random number is smaller, the bond is deleted. When a bond is deleted, it acquires the property deleted , which is used later in the program. 

Loops and acquisition commands are often related. Two typical applications of loops are the execution of a time averaging experiment and the measurement of a series of spectra to generate a two dimensional matrix during a 2D experiment. Both examples implement data acquisition and data storage in a specific way. The acquisition commands used in NMR-SIM pulse programs have to be structured to be consistent with the pulse programs used on BRUKER NMR spectrometers. 

With the help of SAME, the geometry of two or more groups of atoms can be restrained to be similar. This can be convenient when a structure contains several crystal-lographically independent but geometrically equivalent molecules or ligands. The SAME command generates the necessary SADI restraints with appropriate standard uncertainties (0.02 A for 1,2-distances and 0.04 A for 1,3-distances) for equivalent molecules or parts of molecules. It is a very powerful restraint but particularly error-prone, since it requires both the atoms named with the restraint and the atoms following the SAME command in the. ins file to be in the correct order. The syntax as well as the benefits and pitfalls of SAME are explained in Chapter 5. 

Manipulating Structures. Table III shows that all of the programs offer the standard features necessary to arrange structures on the screen. ChemBase, however, is the only program which offers a very powerful "Clean" command which takes a poorly drawn structure and generates a "clean", chemically correct version. 

Support of personal computers with graphics systems will include the development of new software for generating a metafile from the vector data which can be interpreted by the PC graphics packages. So far, there is no general metafile standard, but we hope that the GKS (8,9) metafile will cover most future metafile structures. Further plans relate to a special command in STN for ordering off-line prints of patent drawings. 

The skeletomotor system provides the structure and drives to move the body and Kmbs relative to the surroundings and to maintain the posture in space. The motor systems act on the environment by transforming neural information and metabolic energy into movement. Changes in external events or in the internal environment, signaled by the sensory systems, set up commands that are transmitted to the skeletal muscles by nerve impulses. The muscles convert the neural information into a command that transforms chemical into mechanical energy by generating a contractile force. 

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