Other Software

[*] ADAPT (Automated Data Analysis using Pattern Recognition Toolkit) is a software system designed to allow the user to develop structure-activity relationships (SARs) or structure-property relationships (SPRs). ADAPT provides facilities for graphical entry and storage of molecular structures and their associated data, generation of 3-D molecular models, molecular descriptor calculation and analysis of the descriptors using multivariate statistical, pattern recognition, or neural network methods to build predictive equations. In addition, it can import structures as molfiles and 3-D coordinates. ADAPT has a large selection of molecular descriptor generation routines (topological, geometrical, electronic and physicochemical) and the ability to generate hybrid descriptions that combine features. Statistical approaches supported include multiple linear regression, clustering, discriminant analysis and neural networks. ADAPT runs on Sun workstations under the UNIX operating system. License fee: Call Contacts: Peter Jurs, 152 Davey Laboratory, Chemistry Department, Pennsylvania State University, University Park, PA 16802 USA, 814-865-3739, 814-865-3314 (F)
[*] ASAD (A Self-contained Atmospheric chemistry coDe) is a package that has been developed for integrating chemical schemes in atmospheric models.
[*] New! BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. This will include objects for manipulating sequences, file parsers, CORBA interoperability, access to ACeDB, dynamic programming, and simple statistical routines.
[*] ChemApp. is a programmable thermodynamic calculation interface. A light version could be realeased for free; if you are interested read this! ChemApp consists of an interface containing a library of FORTRAN subroutines that link to the data-handling and phase equilibrium calculation modules of ChemSage. It opens up new horizons for the use of thermochemical calculations across a wide spectrum of applications. Furthermore, with GTT's access to appropriate algorithms and kinetic data, it is also possible to apply the routine to develop programs for time-dependent (dynamic) applications.
Keywords: thermodynamics, thermochemistry, process simulation, chemical engineering, free energy minimizer.
[GPL] New! ChemCalc is intended to be a calculator oriented towards chemistry. What is being implemented at this point is a set of prompts to take information from the user to calculate certain values dependent on the particular scientific law you specify.
[GPL] New! Chemeq is a basic standalone filter written in C, flex, and bison. It inputs strings that represent chemical equations, like "2H2 + O2 ---> 2 H2O", and outputs LaTeX code and a message about the equilibrium of a chemical reaction.
[*] New! ChemSol is designed for the calculations of solvation free energies using the Langevin Dipoles (LD) solvation model, in which the solvent is approximated by polarizable dipoles fixed on a cubic grid.
[*] New! CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical-user interface (GUI). At present, CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.
[GPL] GPeriodic acts as a periodic table reference and allows you to browse through the table of elements, and view detailed information on each of the elements. 118 elements are currently listed.
[*] kc (Kinetic Compiler) is a program which is able to transform chemical equations into simulation programs. That is, kc transform a chemical/kinetic model into one or more subroutines used by an integrator. The integrator can be a continuation program or a dynamical simulator.
[*] KMol calculates elemental compositon and molecular weight of compounds from their chemical formula. KMol supports user defined groups and elements, unlimited nesting of subgroups, multicomponent compounds, global and per-user symbol definitions. It runs under Linux, and is designed to be used with the KDE.
[*] Linux Lab Project The Linux Lab Project is intended to help people with development of data collection and process control software for LINUX. It should be in understood as software and knowledge pool for interested people and application developers dealing with this stuff in educational or industrial environment. Everything that has to do with data aquisition, process control, laboratory automation and data analysis is welcome as contribution to this project.
[*] OPIUM is a console based program for the analysis of solution equilibria, determination of chemical model, determination of equilibrium (stability, formation, protonation, dissociation, association) constants using potentiometry, UV/VIS spectrophotometry, NMR spectroscopy, polarography, capillary zone electrophoresis and other useful methods. The data are processed by means of the generalized nonlinear least squares method.
[*] PALLAS Software predicting pKa,logP, logD values and metabolites based on structural formulae of compounds. In the field of industrial pharmacy perhaps the most important physicochemical characteristics of drugs and excipients are their acidity or basicity (expressed by their pKa value), their hydrophobicity and it's dependence on pH (expressed by their logP and logD values respectively). Whether in research and development or in drug quality control, these values can be used in a variety of situations. To determine precision values of pKa, logP or logD presents a great deal of work. Thus the use of computers is giving great progress to the practice. The profile in reaction kinetics depends closely on pKa values (1,2,3). In preparative chemistry, pKa values of the reaction products can be used to select conditions for synthesis. The knowledge of the pKa values of intermediate products is also important, although they are often very difficult to measure. In many cases the chemist can save much time and cost using predicted pKa values.
[*] POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases). POLYRATE--version 7.8.1 is an enhanced version of POLYRATE with improved capabilities for direct dynamics and curvilinear coordinates. The methods used are variational or conventional transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. Generalized transition state theory calculations may be carried out using either rectilinear coordinates, non-redundant curvilinear coordinates, or redundant curvilinear coordinates. Zero-curvature, centrifugal-dominant small-curvature, and large-curvature-version 3 (LC3) tunneling methods are included, including tunneling into excited states in the LC3 model, and optimized multidimensional tunneling is also included.
[*] QCPE for Linux (Quantum Chemistry Program Exchange) has made a collection of Fortran software. Have a look of the main QCPE page too!
[*] RdLength calculates the Radiation Length of a single molecule based on its empirical formula. The unit used is g/cm2 (gram/centimeter square). The method used is the one proposed by Tsai. Y.S., on Rev. Mod. Physics, 46, p.815, 1974. It is the same method used by the Particle Physics Booklet. The program also displays the formula needed to calculate the Radiation Length of a multi-molecular material.
[*] Remote Microscope The Rem ote Microscope system allows users to access and control an optical microscope over the Internet using a Java applet
[*] Steric is a program for the calculation of molecular steric parameters. Angular calculations include the Tolman cone angle and both numerical and semi-analytical solid angles, including conformer averages and angular and radial profiles. Orthogonal calculations include numerical volumes of molecules and cavities in crystals, and molecular areas projected onto planes, as well projected areas of molecular overlap.
[*] SYNGEN (Automatic Synthesis Design System) is a unique program for automatic generation of the shortest, most economic organic synthesis routes for a given target compound.
[CM] Thermo Calc is a powerful and flexible software for all kinds of thermodynamic and phase diagram calculations. It is specially designed for systems with strongly non-ideal phases. Thermo-Calc has been developed since 1981 and gained worldwide reputation as the best system for calculation of multicomponent phase diagrams and there are more than 100 installations all over the world today. It is the only software which can calculate arbitrary phase diagram sections with up to five independent variables in multicomponent systems. There are also facilities to calculate many other types of diagrams for example CVD depositions, Scheil-Gulliver solidification simulations, partial pressures in gases etc.
[*] Xelem displays a "hypertext" periodic table. Each element, when clicked upon, displays a window with selected data on this element. The data values can be selected and pasted into other applications.
The standard Tk convention of dragging the middle mouse button allows scrolling material that overflows its display window.