Ports Search

Tinker is a set of small programs for doing general purpose molecular modeling calculations. Tools are included for energy minimizations, geometry calculations, simulated annealing, molecular dynamics, and molecular analysis calculations. Tools for converting coordinate sets are also provided. Tinker employs several force fields and minimization techniques. This port sets the maxatm value to 2500 atoms. This should be sufficient for most molecular systems. Should you need to work with larger systems you can set the maxatm parameter in the sizes.i file located in the tinker/source directory and recompile. Note that if it is set too large that tinker programs will abort and core dump. For more information about Tinker see:

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.

Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.

ADMS is a code generator that converts electrical compact device models specified in high-level description language into ready-to-compile C code for the API of spice simulators.

BrickUtils is a simple utility for builders that use LEGO Digital Designer or LDraw-compatible CAD for designing models.

The goals of the FreeHDL project are to develop a VHDL simulator that has a graphical waveform viewer and a source level debugger. It also aims at VHDL-93 compliancy. The project is at a very early development stage.

This is GDT (graphics data text) format translator written in C/C++ that converts a binary gdsii file to a text format that is compact and easy to parse.

Gerber Viewer (gerbv) is a viewer for Gerber files. Gerber files are generated from PCB CAD system and sent to PCB manufacturers as basis for the manufacturing process. The standard supported by gerbv is RS-274X. The basic difference between RS-274D (the old standard) and RS-274X is basically the addition of apertures in RS-274X. It might be possible to make an RS-274X file out of an RS-274D file and an aperture list. gerbv also supports drill files. The format supported are known under names as NC-drill or Excellon. The format is a bit undefined and different EDA-vendors implement it different. But basically you need to have the tools definition in the file, then the parser is quite tolerant. The different holes are shown as dots in the (scaled) correct size. The different layers of the PCB are separated into different files. gerbv can load all files at the same time and display them "on top of each other". You can independently turn them on and off.

This is Gmsh with support of OpenCascade. Gmsh is an automatic 3D finite element mesh generator (primarily Delaunay) with build-in CAD and post-processing facilities. Its primal design goal is to provide a simple meshing tool for academic test cases with parametric input and up to date visualization capabilities. One of its strengths is the ability to respect a characteristic length field for the generation of adapted meshes on lines, surfaces and volumes, and to mix these meshes with simple structured grids. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.

Impact is an explicit Finite Element Program which simulates dynamic impact events. It has a range of elements, contact handling and different material laws. Models can be created and viewed with external programs or the included postprocessor.