{"category":{"categoryid":416,"name":"sci-chemistry","summary":"The sci-chemistry category contains software that can be used in chemistral scientific environments."},"packages":[{"categoryid":416,"description":"Python framework for Gromacs","firstseen":"2013-03-23T14:36:09.782010","maintainer":"alexxy@gentoo.org","maintainername":"Alexey Shvetsov","name":"GromacsWrapper","packageid":60581},{"categoryid":416,"description":"A python library to analyze and manipulate molecular dynamics trajectories","firstseen":"2018-06-28T12:50:09.365176","name":"MDAnalysis","packageid":69239},{"categoryid":416,"description":"Parameter and topology file editor and molecular mechanical simulator engine","firstseen":"2022-02-16T13:38:20.457240","name":"ParmEd","packageid":74444},{"categoryid":416,"description":"A suite of automated docking tools","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"autodock","packageid":50485},{"categoryid":416,"description":"Program for drug discovery, molecular docking and virtual screening","firstseen":"2010-05-19T00:31:14.093199","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"autodock_vina","packageid":55781,"summary":"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"},{"categoryid":416,"description":"Advanced molecule editor and visualizer 2","firstseen":"2015-12-29T14:39:31.689058","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"avogadro2","packageid":64815},{"categoryid":416,"description":"The Blue Obelisk Data Repository listing element and isotope properties","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"bodr","packageid":53774,"summary":"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."},{"categoryid":416,"description":"Analysis of NMR spectra and Computer Aided Resonance Assignment","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"cara-bin","packageid":50090},{"categoryid":416,"description":"Program to fit chemical exchange induced shift and relaxation data","firstseen":"2018-05-02T20:16:22.140643","name":"chemex","packageid":69111},{"categoryid":416,"description":"A collection of data files to add support for chemical MIME types","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"chemical-mime-data","packageid":43855},{"categoryid":416,"description":"A GTK program for drawing organic molecules","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"chemtool","packageid":44694},{"categoryid":416,"description":"Build lists of van der Waals clashes from an input PDB file","firstseen":"2010-07-19T14:36:00.880923","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"clashlist","packageid":56069,"summary":"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."},{"categoryid":416,"description":"Build lists of collections of interacting items","firstseen":"2010-07-18T14:35:32.459536","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"cluster","packageid":56062,"summary":"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."},{"categoryid":416,"description":"The protein secondary structure standard","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"dssp","packageid":44107},{"categoryid":416,"description":"Chemical structure drawing program - focused on presentation","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"easychem","packageid":49566,"summary":"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."},{"categoryid":416,"description":"periodic table of the elements","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"elem","packageid":54847},{"categoryid":416,"description":"Periodic table viewer with detailed information on the chemical elements","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"gelemental","packageid":53664},{"categoryid":416,"description":"Programs and library containing GTK widgets and C++ classes related to chemistry","firstseen":"2020-03-01T16:59:22.409529","name":"gnome-chemistry-utils","packageid":70878},{"categoryid":416,"description":"Periodic table application for Linux","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"gperiodic","packageid":44587,"summary":"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."},{"categoryid":416,"description":"The ultimate molecular dynamics simulation package","firstseen":"2010-05-04T00:54:45.661860","maintainer":"ottxor@gentoo.org","maintainername":"Christoph Junghans","name":"gromacs","packageid":45952},{"categoryid":416,"description":"An open source implementation of sci-chemistry\/dssp","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"ksdssp","packageid":49437},{"categoryid":416,"description":"Homology or comparative modeling of protein three-dimensional structures","firstseen":"2020-12-02T12:42:00.053196","name":"modeller","packageid":72238},{"categoryid":416,"description":"Molecular dynamics simulations platform","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"moldy","packageid":48187},{"categoryid":416,"description":"Abstract, manage and coordinate execution of tasks","firstseen":"2013-07-19T13:36:30.549347","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"molequeue","packageid":61029,"summary":"MoleQueue is an open-source, cross-platform, system-tray resident desktop application for abstracting, managing, and coordinating the execution of tasks both locally and on remote computational resources. It is built and tested and Linux, Mac OS X, and Windows, with nightly binaries currently available for Mac OS X and Windows. Users can set up local and remote queues that describe where the task will be executed. Each queue can have programs, with templates to facilitate the execution of the program. Input files can be staged, and output files collected using a standard interface."},{"categoryid":416,"description":"Publication-quality molecular visualization package","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"molmol","packageid":50319},{"categoryid":416,"description":"A drawing tool for 2D molecular structures","firstseen":"2010-11-02T14:34:07.577095","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"molsketch","packageid":56464,"summary":"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."},{"categoryid":416,"description":"The Massively Parallel Quantum Chemistry Program","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"mpqc","packageid":43617},{"categoryid":416,"description":"MSMS very efficiently computes triangulations of Solvent Excluded Surfaces","firstseen":"2010-10-31T14:36:36.232433","maintainer":"alexxy@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"msms-bin","packageid":56456},{"categoryid":416,"description":"MUltiple STructural AligNment AlGorithm","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"mustang","packageid":50255},{"categoryid":416,"description":"Interconverts file formats used in molecular modeling","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"openbabel","packageid":48429,"summary":"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."},{"categoryid":416,"description":"Manipulate and process PDB files using tools such as Perl, awk, etc","firstseen":"2012-10-12T13:40:19.750796","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"pdbcat","packageid":59882,"summary":"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'."},{"categoryid":416,"description":"Convert atom names for amino acids\/nucleic acid bases between PDB and CNS format","firstseen":"2012-03-02T14:36:00.095771","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"pdbcns","packageid":58971},{"categoryid":416,"description":"Calculate Tirion's model from pdb structures","firstseen":"2012-03-22T15:06:18.781906","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"pdbmat","packageid":59046,"summary":"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)."},{"categoryid":416,"description":"Evaluates atomic packing within or between molecules","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"probe","packageid":46267},{"categoryid":416,"description":"pKa-value prediction of ionizable groups in protein and protein-ligand complexes","firstseen":"2014-05-11T13:38:29.489302","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"propka","packageid":62187},{"categoryid":416,"description":"Suite for ab initio quantum chemistry computing various molecular properties","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"psi","packageid":46065},{"categoryid":416,"description":"A Python-extensible molecular graphics system","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"pymol","packageid":47100},{"categoryid":416,"description":"Generation high quality raster images of proteins or other molecules","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"raster3d","packageid":50341},{"categoryid":416,"description":"The ROC RNA Ontology nomenclature and conformer-list development","firstseen":"2010-07-15T14:36:18.300391","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"suitename","packageid":56046,"summary":"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."},{"categoryid":416,"description":"Solvent accesible Surface calculator","firstseen":"2011-03-22T14:41:03.308363","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"surf","packageid":57127},{"categoryid":416,"description":"Maximum likelihood superpositioning and analysis of macromolecular structures","firstseen":"2012-03-21T20:52:40.034466","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"theseus","packageid":59040},{"categoryid":416,"description":"3V: Voss Volume Voxelator","firstseen":"2010-10-31T14:36:36.232433","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"threeV","packageid":56458},{"categoryid":416,"description":"Molecular modeling package that includes force fields, such as AMBER and CHARMM","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"tinker","packageid":44363},{"categoryid":416,"description":"Quick & Accurate Structural Alignment","firstseen":"2012-03-21T20:52:40.034466","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"tm-align","packageid":59041,"summary":"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."},{"categoryid":416,"description":"Visual Molecular Dynamics","firstseen":"2010-05-04T00:54:45.661860","maintainer":"alexxy@gentoo.org","maintainername":"Alexey Shvetsov","name":"vmd","packageid":48144},{"categoryid":416,"description":"Versatile Object-oriented Toolkit for Coarse-graining Applications","firstseen":"2021-12-17T03:35:36.039626","name":"votca","packageid":73759},{"categoryid":416,"description":"Chemical 3D graphics program with GAMESS input builder","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"wxmacmolplt","packageid":55600,"summary":"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."},{"categoryid":416,"description":"Software for processing single-crystal X-ray monochromatic diffraction data","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"xds-bin","packageid":45741}]}