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Software

In this page you can find some of the computer programs that we have developed in our Laboratory for educational purposes or to solve certain technical problems of research, etc. There are also a few games that can be instructive simple examples for beginners who are interested in learning computer programming.

In the first part are the programs already compiled and ready to install and run in computers with WINDOWS 95, 98 or NT. All the programs have educational purposes and there is no commercial interest involved. We would only appreciate to receive, if the reader is willing to send, comments and suggestions of constructive intent (send to mgconsta@usp.br).

1) Programs to run directly in WINDOWS (95, 98, NT).

Just copy the file to your computer, extract to a temporary directory and click in Setup.exe. Then just follow instructions.

bulletDisplay mmx 2011 with examples.
bullet FOMSC3_rm (2011) with examples.
bullet Read_NMR (2011) with examples.
bulletMS Analyzer - This program is intended to help research chemists to process the required operations for the analysis of a mass spectrum (MS). With this program you can calculate molecular weights, you can get information about isotopes and fragments, you can calculate the formulas corresponding to a certain molecular weight, etc. The program has also some graphical resources to trace spectra from data tables, to copy the spectra to other programs, etc. After extracting and installing, copy the file "Examples" to the same directory to which the program was installed. There is also a Manual[ Manual (*.zip, Word document, 49 KB), or Manual (*.pdf, 99 KB)].
bulletChemSeeker - This program, developed by Adilson Beatriz, is meant to elaborate a file of chemicals of a certain laboratory and provide simple and fast access to the informations contained in the file. Running the program you can remove items from the file (a file containing a few items as an example is enclosed in the program pack), add items corresponding to the chemicals of your laboratory (together with several informations such as molecular formula, storing place, vendor, etc.), modify informations, and so on, thus elaborating your own file. Then you can quicly find any desired product through its name, molecular formula or, a particularly useful feature, through a part of its name. Typing "bromo", for instance, the program will give a list of all chemicals containing "bromo" in their names; try to type "acid", or "acet", or "ol", or "ene", and then you will have an idea of how useful is this feature.
bulletRead_IR2 (Subst. Read_IR3) - Program to read infrared files from Perkin-Elmer spectrometers (only *.sp files). The original file has the spectral data in binary form; these data cannot be read by the common programs to plot graphs. With Read_IR2 it is possible to copy the read data and paste them in several other programs such as Word, Excel, Origin, Notebook and so on. The data can also be saved as *.txt files. The program also offers some graphical resources to plot the spectrum (with horizontal scale in microns or in cm-1), label peaks, expanding, etc. The spectrum can be printed directly or can be copied and pasted in Word, for preparing reports.
bulletFirst Order Multiplet Simulator/Checker (FOMSC) - This program is an improved version of FOMS 2 (below). Try it, it can now open an experimental spectrum ("1r" already processed spectra by Bruker spectrometers only) and display it together with the simulation, to enable close visual comparison. Several examples are built in.
bulletFirst Order Multiplet Simulator  (Subst. FOMS_2) (see also FOMSC above) - Program that can be used to show the supposable appearance of a multiplet, in an 1H NMR spectrum, when we know all the involved coupling constants; in the case of a multiplet involving more than 1 hydrogen, we need to know also the chemical shift of each one.

Commonly the modern NMR equipment give spectra in which the hydrogen signals of a molecule are all separated from each other, resulting in many multiplets that, even being essentially of first order, have no easily recognizable appearance to the chemist. One of such cases is shown when the program is opened; it corresponds to a hydrogen of a natural product, 15-Deoxygoyazensolide: its appearance vaguely resembles a sextet, but it is an extremely complex signal, involving six different values of coupling constants, that were measured by several different means. It would be extremely hard to the chemist to obtain a confirmation that this splitting, with these J values, would produce a multiplet with that appearance; in this program, we just have to enter the chemical shift of the hydrogen (the center of the multiplet) and the J values, and instantly we can see, in the screen, a picture that is, essentially, identical to the actual spectrum, including the position of the peaks maxima, that differ from actual values by only 0.1 or 0.2 Hz. This provides a very convincing confirmation of the measured J values.

Besides that, the program draws (by itself) the corresponding splitting diagram (or splitting tree), and the whole picture shown in the screen can be copied and pasted in text programs such as Word. The graphical tools ensure a reasonable flexibility: it is possible to stretch or compress the graph, and remove from the picture the undesired information (splitting diagram, J values, individual peaks, histogram, and so on). The plotted curves can be Gaussian or Lorentzian, or even a combination of these. By modifying the value of the “Width at half height”, we can obtain pictures similar to actual spectra that were obtained with different resolution; the value named “Resolution” in the program refers to the limit at which the lines of the histogram are fused together; we can use “zero” for this value, and no change in the Gaussian envelope will occur (only the histogram and the individual peaks change appearance).

Another possible use of the program is didactic: it is easy to verify, for instance, how many and which possible appearances can have a triplet and a quartet that are partially overlapped, or two triplets, and so on. We can also use it just to obtain a certain splitting diagram, which is usually a very hard task in normal drawing programs, particularly when several J values are involved.
bullet(go to Pentomino page)
bulletTicTacToe. TicTacToe_2011.
bulletFFT SpecMusEV
bulletFFT SpecEV
bulletFFT MusEV
bulletReadPCM
bulletBoltz. New version, developed with Visual Basic 2005 (Express): Boltz_2005
bulletFFTMus2. Slightly modified new version of FFT Mus. wavExamples; More Examples.

 

2) Programs in Visual Basic.

In order to run the programs offered here, you must have Microsoft Visual Basic 5.0 installed in your computer. In this way, besides running the programs, you will be able to read the codes, modify them according to your preferences, use routines to your own programs, etc. Of course, you can also compile the program and use it as a *.exe file.

Click here to read instructions to install the programs.

bullet Display mmx 2011 (VB 2010)
bullet FOMSC3_rm (VB 2010)
bullet Read_NMR (VB 2010)
bulletTicTacToe - The popular game, to be played by human against computer.
bullet TicTacToe (VB 2008)
bulletPrograms about Fast Fourier Transform (FFT) (English)
In all these programs the routine to effect the Fourier Transform calculations is the one described in "Numerical Recipes", translated to Basic and slightly modified to suit the requirements for each program. We thank Professor Léo Degrève for valuable suggestions.
bulletFFT SpecMusEV - With this program the user can generate (in graphical form or as a table of points) several periodic functions, both simple and composed (including sin x, cos x, square wave, triangular wave, etc.), and then calculate the Fourier transform of this function. It is also possible to calculate the Fourier transform of data from a *.raw file (three *.raw files are enclosed as examples, short passages from Glenn Miller's "Moonlight Serenade" and from Beethoven's "Symphony n° 5"). The Fourier transform is shown as a linear graph (vector, real and/or imaginary parts, etc.), or as a graph with a logarithmic scale, which is suitable for musical analysis (a mute piano keyboard drawn below the graph helps to identify the musical note).

Another operation that the user can perform is the recovery of the original function from the data of the Fourier transform. This reverse calculation gives the results as a graph and as a table of points, permitting easy comparison of original and recovered data.

It is also possible to print a report containing data from the original function and from the Fourier transform, to print graphs, save graphs as *.bmp files, etc.
bulletFFT SpecEV - This program shows how the Fourier transform can be used to process the data obtained from a nuclear magnetic resonance spectrometer, transforming the "fid" curve from the spectrometer in a NMR spectrum. This is a simple program, elaborated with the sole purpose of illustrating the processes. The spectrometers come already with much more elaborated programs, but the user cannot know what he is doing, because the program as a *.exe file cannot be interpreted; our program in Visual Basic, on the other hand, can have all routines unraveled to satisfy any kind of curiosity, and can be used as a starting point for the elaboration of more complex programs.

There are routines for calculating the Fourier transform, to display graphs of vector, real and imaginary parts separately, to "adjust the phase" (which means to combine real and imaginary parts in a peculiar way), to correct the effects of the "Bruker" filter, to display, format and print the spectrum, etc.

Of course, due to the simplicity of the program, it can read "fid" files only from the Bruker spectrometer. Some few files are given to be used as examples.
bulletFFT MusEV - A program that shows how the Fourier transform can be used to analyze a complex musical sound (recorded in a *.wav file), determining which musical notes (frequencies) are present in a certain passage, how is the harmonics composition of a certain musical instrument, etc.

The file *.wav to be analyzed is shown as a graph; the sound corresponding to the whole graph or to a selected part of it can be heard as wished, thus permitting to choose the passage containing the desired sound.
The Fourier transform is shown as a graph with a logarithmic scale; below the graph is displayed an active piano keyboard that can produce sounds of several instruments, permitting a very instructive analysis of the graph.

Several short *.wav files are enclosed. Other files, longer than these, are in "wavExtraFiles" (see below). The reader can record his own *.wav files from a common CD or from a microphone, using the programs that come together with the multimedia kits.
bulletwavExtraFiles - this file is NOT a program, but a collection of *.wav files that the reader can use together with the FFT MusEV program above. As already noted, it is easy to record your own *.wav files, there is no need to copy these files or to remain limited to them.
bulletRead PCM - Program that can be used to read files from programs such as PC Model and GMMX. When one of these files (*.mmx, *.sst, etc.) is opened, a figure of the corresponding molecular model is displayed. This figure can be in several different modes, including frozen or in random movement, in perspective, in "mono" or "stereo", etc. To observe the figure in "stereo" mode it is convenient to use a stereoscope such as the one described by M. G. Constantino, G. V. J. da Silva and M. M. M. Pelisson in Química Nova 21, 337-340 (1998). The program also calculates all dihedral (torsion) angles of the molecule; the values are displayed in a table. There are no routines for printing or for saving files, thus this is a safe program. No harm can arise from trying all the menu commands and buttons. Several files are offered as examples, including some molecules synthesized in our laboratory.
bulletBoltz - This program can be used to calculate the Boltzmann distribution of several (up to 10) conformers, according to their ground state energy (in kcal/mol), as a function of temperature.
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This page was last updated on 12/14/11

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