https://packages.gentoo.org/ 2026-03-09T00:16:33Z Gentoo Packages for search query: sci-chemistry/votca-csg Gentoo Packages Database 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/gnome-chemistry-utils unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/votca unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/chemex unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/chemtool unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/chemical-mime-data unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/easychem

EasyChem is a program designed to draw chemical molecules, written under Linux using Gtk+ 2.4. It is implemented with a strong focus on producing press quality molecules. Easychem can be a little more difficult to learn to use, but when mastered it can be very fast and powerful. It can draw ornaments easily, and exports to EPS with LaTeX fonts among other things.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/clashlist

Clashlist is a simple UNIX script which uses the awk facility along with the programs Probe and Cluster to build lists of van der Waals clashes from an input PDB-format molecular data file (with H atoms). These lists are organized such that collections of interacting residues are grouped together, sorted by the worst clash. For the purposes of this analysis, a clash is defined as a van der Waals overlap >= 0.4 A.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/vmd unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/surf unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/cluster

Cluster is a simple UNIX C++ program to build lists of collections of interacting items from records containing interacting pairs and larger fragments. It reads in lines consisting of two or more names and output connected clusters of names. Each line of output is prefixed with a cluster number, the size of the cluster and an optional name string.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/cara-bin unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/suitename

Suitename is a new C program that supports the ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development (see our RNA backbone rotamer section. From dihedral-angle input for a specific RNA structure (usually from Dangle), Suitename categorizes the RNA backbone geometry of each suite (the sugar-to-sugar version of a residue) either as an outlier ("!!") or as belonging to one of the 53 defined conformer bins. The output is either a one-line-per-suite report, or a linear conformer string (as shown below the image here) in one of several variant formats. Suitename is built into MolProbity, producing entries in the multi-criterion chart for an RNA model and also a suitestring file. The Suitename code is made available here for bulk or individual command-line use.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/autodock_vina

AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. [1] AutoDock Vina has been designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. If you used AutoDock Vina in your work, please cite: O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading Journal of Computational Chemistry 31 (2010) 455-461

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/probe unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/bodr

Blue Obelisk Data Repository (BODR) is a shared data repository. It lists many important chemoinformatics data such as elemental properties, atomic radii, etc. including references to original literature. Software developers can use this repository on online webpages or in chemistry software for free.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/raster3d unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/propka unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/ksdssp unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/gromacs unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/moldy unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/dssp unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/pdbcns unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/pymol unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/xds-bin unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/wxmacmolplt

wxMacMolPlt is a program for plotting 3D molecular structures and normal modes (vibrations), various orbitals and electron density maps. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations. It has a simple GAMESS input (.inp) builder and a primitive molecule builder.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/tinker unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/mpqc unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/molmol unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/autodock unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/gperiodic

GPeriodic is a program for looking up various data about elements from the periodic table, based on the GTK2 toolkit. It also features a command line interface.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/gelemental unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/theseus unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/pdbcat

The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column based format. This is designed to be read easily read by FORTRAN programs. Indeed, if you get the format description (from anonymous ftp to ftp.pdb.bnl.gov, the file /pub/format.desc.ps) they show the single input line needed to read each record type. However, I am a C/C++ programmer in the Unix environment. It is a easier for me to deal with field based input than column based ones. If the fields are white space delimited I can easily use awk and perl to manipulate the coordinate information. So I needed some way to convert the ATOM and HETATM records of PDB files from the standard column based format to a field based one and back again. It needed to denote missing fields if they exist. That converter is `pdbcat'.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/MDAnalysis unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/mustang unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/psi unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/tm-align

TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. The value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller 0.2 indicates that there is no similarity between two structures; a TM-score greater 0.5 means the structures share the same fold. What is the difference between TM-score and TM-align? The TM-score program is to compare two models based on their given and known residue equivalency. It is usually NOT applied to compare two proteins of different sequences. The TM-align is a structural alignment program for comparing two proteins whose sequences can be different. The TM-align will first find the best equivalent residues of two proteins based on the structure similarity and then output a TM-score. The TM-score values in both programs have the same definition.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/mdtraj unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/GromacsWrapper unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/ParmEd unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/elem unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/molsketch

Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/msms-bin unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/threeV unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/pdbmat

A fortran program in which Tirion's model (also called the Elastic Network Model) is implemented. Within the frame of this model, atoms (particles) less than cutoff (angstroms) away from each others are linked by springs of same strength. Alternatively, a list of interacting atoms can be given to the program. Requirements: a file with the coordinates of the system, in PDB (Protein Data Bank) or "x y z mass" format. Output: the hessian (the mass-weighted second derivatives of energy matrix), in the "i j non-zero-ij-matrix-element" format. Diagstd, a fortran program with a standard diagonalization routine, can next be used in order to obtain the corresponding normal modes of the system. If the system is large, the RTB approximation can prove usefull (see below).

unknown 2026-03-09T00:16:33Z tag:packages.gentoo.org,2026-03-09:/package/sci-chemistry/avogadro2 unknown