Debian Science Chemistry packages

Adun je simulátor biomolekúl s možnosťou správy dát a analýzy. Vyvinuli ho v Computational Biophysics and Biochemistry Laboratory, čo je časť Research Unit on Biomedical Informatics v rámci UPF.

Tento balík obsahuje UL, grafické používateľské rozhranie pre Adun.

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

• simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
• implicit solvent molecular dynamics of biomolecules ,
• solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
• and biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

This package contains the apbs program and utilities.

Atomes is a tool box to analyze (physico-chemical properties calculations), visualize (atoms, bonds, colormaps, measurements, coordination polyedra ...) create (crystal builder, molecular library, surface creation and passivation ...) 3D atomistic models. Atomes offers a workspace capable of handling many projects opened simultaneously. The different projects in the workspace can exchange data: analysis results, atomic coordinates... Atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: Classical MD: DLPOLY and LAMMPS

• ab-initio MD: CPMD and CP2K
• QM-MM MD: CPMD and CP2K To prepare the input files for these calculations is likely to be the key, and most complicated step towards MD simulations. Atomes offers a user-friendly assistant to help and guide the scientist step by step to achieve this crucial step.

This package provides the binaries.

Avogadro je systém molekulárnej grafiky a modelovania cielený na molekuly a biomolekuly. Dokáže vizualizovať vlastnosti ako molekulárne orbitály alebo elektrostatické potenciály a obsahuje inovatívny nástroj na tvorbu molekúl.

Medzi jeho vlastnosti patrí:

• modelovač molekúl s automatickou optimalizáciou geometrie založenou na silovom poli
• molekulárna mechanika vrátane obmedzení a hľadaní vyhovujúcich
• vizualizácia molekulárnych orbitálov a všeobecných isopovrchov
• vizualizácia vibrácií a kreslenie vibračného spektra
• podpora jednotiek kryštalografických buniek
• generovanie vstupu pre balíky kvantovej chémie Gaussian, GAMESS a MOLPRO
• flexibilná architektúra zásuvných modulov a skriptovanie v Pythone

Avogadro dokáže čítať súborové formáty PDB, XYZ, CML, CIF, Molden a tiež zapisovať výstup do Gaussian, GAMESS a MOLPRO.

BKchem is a free chemical drawing program, which is written in Python.

Some of the features, you can expect:

• Drawing (bond-by-bond drawing; templates for common rings; expanding of common-groups; draws radicals, charges, arrows; color support ...)
• Editing (unlimited undo and redo capabilities; aligning; scaling; rotation (2D, 3D) ...)
• Export/Import (fully supported SVG-, OpenOffice.org-Draw-, EPS-export; basic support for CML1 and CML2 import and export)

Common repository of chemical and physical facts that aim to increase interoperability between chemistry programs.

https://dx.doi.org/10.1021/ci050400b

chemeq je jednoduchý samostatný filter napísaný v jazykoch C, Flex a Bison. Z reťazca na vstupe v tvare

 2H2 + O2 ---> 2 H2O
vyprodukuje kód v LaTeXu a správy o rovnosti chemickej reakcie.
 priklad:~/src$ echo "2H2 + O2 ---> 2 H2O" | chemeq -lc
 2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O
 OK

The chemical media type and various subtypes have been proposed by Henry Rzepa, Peter-Murray Rust and Benjamin Whitaker in 1996 as an addition to the existing MIME types. The proposal didn't succeed but various applications make use of these MIME/file types. This package adds support to Linux desktops to detect and recognize files of the chemical/* media type.

See also for http://www.ch.ic.ac.uk/chemime/.

This web service allows one to browse a rich set of molecular structures provided by the package chemical-structures-data, and eventually have them translated to other open formats, thanks to openbabel.

Chemtool je editor chemických štruktúr pre X11 založený na GTK+. Podporuje mnohé štýly väzieb, väčšinu tvarov textu potrebných na písanie chemických textov a krivky/oblúky/zakrivené šípky.

Kresby možno exportovať do formátov MOL a PDB, SVG alebo XFig na ďalšie pridanie poznámok, ako kresbu PiCTeX, ako bitmapu alebo ako PostScriptový súbor (niekoľko z nich pomocou transfig - sprievodného programu fig2dev).

Balík tiež obsahuje pomocný program cht na výpočet sumárneho vzorca a (presnej) molekulárnej hmotnosti zo súboru kresby chemtool. Cht je možné volať buď priamo z Chemtool alebo z konzoly.

CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics (AIMD) simulations.

CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian calculations as well. Features include:

Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:

• Density-Functional Theory (DFT) energies and forces
• Hartree-Fock (HF) energies and forces
• Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
• Random Phase Approximation (RPA) energies
• Gas phase or Periodic boundary conditions (PBC)
• Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave approach (GPW/GAPW)
• Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core corrected (NLCC) pseudopotentials, or all-electron calculations
• Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE
• Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS
• Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3
• Double-hybrid XC functionals including B2PLYP and B2GPPLYP
• Additional XC functionals via LibXC
• Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
• Non-local van der Waals corrections for XC functionals including B88-vdW, PBE-vdW and B97X-D
• DFT+U (Hubbard) correction
• Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and for MP2/RPA via Resolution-of-identity (RI)
• Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation
• Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer
• Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
• Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear scaling of molecular systems
• Excited states via time-dependent density-functional perturbation theory (TDDFPT)

Ab-initio Molecular Dynamics:

• Born-Oppenheimer Molecular Dynamics (BOMD)
• Ehrenfest Molecular Dynamics (EMD)
• PS extrapolation of initial wavefunction
• Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
• Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics (Second-Generation Car-Parrinello Molecular Dynamics (SGCP))

Mixed quantum-classical (QM/MM) simulations:

• Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part
• Linear-scaling electrostatic coupling treating of periodic boundary conditions
• Adaptive QM/MM

Further Features include:

• Single-point energies, geometry optimizations and frequency calculations
• Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations
• Global optimization of geometries
• Solvation via the Self-Consistent Continuum Solvation (SCCS) model
• Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations, density-functional tight-binding (DFTB) and self-consistent-polarization tight-binding (SCP-TB), with or without periodic boundary conditions
• Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats
• Metadynamics including well-tempered Metadynamics for Free Energy calculations
• Classical Force-Field (MM) simulations
• Monte-Carlo (MC) KS-DFT simulations
• Static (e.g. spectra) and dynamical (e.g. diffusion) properties
• ATOM code for pseudopotential generation
• Integrated molecular basis set optimization

CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).

DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

• an OpenGL window for immediate viewing
• the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
• the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
• a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

EasyChem je program, ktorý vám pomáha tvoriť diagramy molekúl a 2D chemických vzorcov vo vysokej kvalite, ktoré je možné exportovať do PDF, PS, LaTeX a fig.

EasyChem bol pôvodne vyvinutý na tvorbu diagramov do chemických kníh a dnes sa často na tento účel používa v komerčných aj nekomerčných chemických knihách.

The feff85exafs project aims to provide high quality theoretical standards for EXAFS analysis within an open source, freely re-distributable framework.

Gabedit is a graphical user interface to computational chemistry packages like:

• MPQC
• GAMESS-US
• Gaussian
• Molcas
• Molpro
• Q-Chem

These Ab Initio software packages might run locally or on a remote server (supporting FTP, RSH and SSH). Gabedit can display a variety of calculation results including most major molecular file formats. The advanced "Molecule Builder" allows one to rapidly sketch in molecules and examine them in 3D. Graphics can further be exported to various formats, including animations.

slurm-wlm-torque and gridengine-client are workload managers which provide wrappers for PBS commands. Gabedit also allows one to configure it for any other workload manager.

galculator je vedecká kalkulačka. Momentálne podporuje rozličné číselné sústavy (10/16/8/2) jednotky uhlov (deg/rad/graf) a širokú škálu matematických (základné aritmetické operácie, trigonometrické funkcie) a ďalších užitočných funkcií (pamäť atď.). galculator je možné používať v algebraickom režime a tiež v reverznej poľskej notácii (RPN).

The General Atomistic Modelling Graphic Interface (GAMGI) provides a graphical interface to build, view and analyze atomic structures. The program is aimed at the scientific community and provides a graphical interface to study atomic structures and to prepare images for presentations, and for teaching the atomic structure of matter.

Garlic je napísaný na vyšetrovanie membránových bielkovín. Je možné ho použiť na vizualizáciu iných bielkovín a tiež niektorých geometrických objektov. Táto verzia Garlic pozná formát PDB verzie 2.1. Garlic je možné použiť na analýzu bielkovinových sekvencií.

Závisí iba od knižníc X, nie sú potrebné žiadne iné knižnice.

Medzi jeho vlastnosti patria:

• Pozícia a hrúbka platničiek (slab) sú viditeľné v malom okne.

• Atómové väzby a farby väzieb v závislosti od polohy. Je dostupných päť režimov mapovania (ako pri platničkách).

• Schopný zobraziť stereoskopický obraz.

• Schopný zobraziť iné geometrické objekty ako membrány.

• Atómové informácie sú dostupné pre atóm, na ktorom sa nachádza kurzor myši. Nie je potrebné klikať, len presunúť kurzor nad štruktúru.

• Schopný načítať viac ako jednu štruktúru.

• Schopný nakresliť Ramachandranov diagram, závitnicové koleso, Vennov diagram, spriemerovanú hydrofóbnosť a hydrofobický moment.

• Naspodku hlavného okna je k dispozícii príkazový riadok. Dokáže zobraziť jednu chybovú správu a jeden reťazec príkazov.

GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information.

GaussSum uses GNUPlot to display the progress of geometry optimisations, density of states spectrum, UV-VIS spectra, IR spectra, Raman spectra, and electron density difference maps. It can also display all lines containing an arbitrary phrase and more.

GChemPaint is an editor for 2D chemical structures with a multiple document interface. Drawn molecules can be searched at NIST Webbook and PubChem.

GNOME Crystal je odľahčený vizualizátor modelov kryštálových štruktúr. Je založený na Chemických nástrojoch GNOME a mal by zobrazovať modely všetkých druhov kryštálových mikroskopických štruktúr pomocou OpenGL.

Chemické nástroje GNOME poskytujú triedy C++ a ovládacie prvky Gtk+-2 týkajúce sa chémie. Budú použité v budúcich verziách gcrystal a gchempaint.

Tento balík poskytuje 4 aplikácie:

• zobrazovač molekulárnych štruktúr (GChem3D)
• kalkulačku molárnej hmotnosti (GChemCalc)
• periodickú tabuľku prvkov (GChemTable)
• spektrálny prehliadač (GSpectrum)

Program založený na GTK+ na zobrazovanie a manipuláciu s izolovanými molekulami, periodickými systémami a kryštalickými štruktúrami. Program je síce vo vývoji, ale dostatočne použiteľný. Má nasledovné rysy:

• Podpora viacerých typov súborov (CIF, BIOSYM, XYZ, XTL, MARVIN a GULP)
• Nástroj na jednoduchú tvorbu a manipuláciu s molekulami
• Dialóg na tvorbu štartovacích konfigurácií pre molekulárne dynamické simulácie
• Rôzne nástroje na vizualizáciu (informácia o geometrii, zvýrazňovanie oblastí, atď.)
• Animácie BIOSYM súborov (tiež vykresľované animácie, pozri ďalej)

GDIS taktiež umožňuje vykonávať nasledujúce funkcie pomocou ďalších balíkov:

• Vykresľovanie modelov (vďaka POVRay)
• Minimalizácia energie (vďaka GULP)
• Kalkulácia morfológie (vďaka cdd)
• Spracovanie priestorových grúp (vďaka SgInfo)
• Zobrazenie Periodickej tabuľky (vďaka GPeriodic)
• Načítanie prídavných typov súborov, ako napríklad PDB (vďaka Babel)

gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

gElemental je prehliadač periodickej tabuľky pre GTK+, ktorý poskytuje podrobné informácie o chemických prvkoch.

Obsahuje zobrazenie tabuľky, ktoré umožňuje tematické zafarbenie prvkov podľa niekoľkých vlastností, zobrazenie zoznamu, ktoré možno zoradiť a dialóg vlastností prvku s rozličnými informáciami vrátane historických, termodynamických, elektrochemických a kryštalografických vlastností.

Tento balík obsahuje hlavnú aplikáciu.

Ghemical je balík softvéru na výpočtovú chémiu napísaný v C++. Má grafické používateľské prostredie a podporuje modely kvantovej mechaniky (semi-empirické) aj modely molekulárnej mechaniky. Momentálne sú dostupné funkcie optimalizácie geometrie, dynamiky molekúl a veľká množina vizualizačných nástrojov používajúcich OpenGL.

Ghemical využíva na kvantovo-mechanické výpočty externý kód. Semi-empirické metódy MNDO, MINDO/3, AM1 a PM3 pochádzajú z balíka MOPAC7 (voľné dielo) a sú súčasťou balíka. Balík MPQC poskytuje metódy ab initio: metódy založené na teórii Hartree-Fock sú momentálne podporované so základnými sadami od STO-3G do 6-31G**.

GPeriodic je malý program založený na X/GTK+, ktorý vám umožňuje prehliadať periodickú tabuľku chemických prvkov a zobrazovať pomerne podrobné informácie o každom z prvkov. Momentálne obsahuje 118 prvkov.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains variants both for execution on a single machine, and using the MPI interface across multiple machines.

GROMACS je všestranný balík na simuláciu dynamiky molekúl, t.j. Newtonovských pohybových rovníc systémov so stovkami až miliónmi častíc.

Je primárne určený na biochemické molekuly ako sú bielkoviny a tuky, ktoré majú množstvo komplikovaných väzbových interakcií, ale keďže GROMACS dokáže veľmi rýchlo počítať neväzbové interakcie (ktoré v simuláciách väčšinou prevažujú), mnohé výskumné skupiny ho môžu využiť aj pri výskume nebiologických systémov, napr. polymérov.

Tento balík obsahuje iba základné simulačné jadro s podporou paralelizácie pomocou rozhrania MPICH (v3). Je vhodný pre uzly vy výpočtovom klastri alebo na viacprocesorových počítačoch.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains only the core simulation engine with parallel support using the OpenMPI interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines.

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry.

File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP.

Kalzium je plnohodnotná chemická aplikácia vrátane periodickej tabuľky prvkov, chemickej referenčnej tabuľky, riešenia chemických rovníc a 3D prehliadača molekúl.

Tento balík je súčasťou modulu Vzdelávanie KDE.

KAtomic je logická hra, v ktorej je cieľom zložiť molekulu posúvaním jej atómov po hernej ploche.

Tento balík je súčasťou modulu Hry KDE.

The CDK is a library of Java classes used in computational and information chemistry and in bioinformatics. It includes renderers, file IO, SMILES generation/parsing, maximal common substructure algorithms, fingerprinting and much, much more.

mMass is a free mass spectrum viewer/analyzer in which the following proteomics-related tasks can be performed:

• Open raw text, mzXML and mzData mass spectra;
• Define peak lists;
• Powerful mass spectrum viewer (zoom, cursor...);
• Data recalibration;
• Protein-only simulations;
• Online Mascot searches.

The software can be easily extended by additional Python modules. This package contains the platform-independent parts of the software.

mMass is a free mass spectrum viewer/analyzer in which the following proteomics-related tasks can be performed:

• Open raw text, mzXML and mzData mass spectra;
• Define peak lists;
• Powerful mass spectrum viewer (zoom, cursor...);
• Data recalibration;
• Protein-only simulations;
• Online Mascot searches.

The software can be easily extended by additional Python modules. This package contains the platform-dependent parts of the software.

MOPAC provides routines to solve the electronic structure of molecules on a semi-empirical level. Available methods include MNDO, MINDO/3, AM1 and PM3.

This package contains the MOPAC7 binaries.

MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

It can compute energies and gradients for the following methods:

• Closed shell and general restricted open shell Hartree-Fock (HF)
• Density Functional Theory (DFT)
• Closed shell second-order Moeller-Plesset perturbation theory (MP2)

Additionally, it can compute energies for the following methods:

• Open shell MP2 and closed shell explicitly correlated MP2 theory (MP2-R12)
• Second order open shell pertubation theory (OPT2[2])
• Z-averaged pertubation theory (ZAPT2)

It also includes an internal coordinate geometry optimizer.

MPQC is built upon the Scientific Computing Toolkit (SC).

MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

This package includes Perl modules to parse the output, Emacs-modes to facilitate editing mpqc files and molrender, a program to output the molecules in OOGL-format.

msXpertSuite provides programs to model linear (bio-) polymer chemistries, simulate mass spectral data, analyse and data-mine mass. It is the successor of GNU polyXmass, first, and then of massXpert.

The massXpert and mineXpert programs allow the following:

massXpert:

• making brand new polymer chemistry definitions;
• using the definitions to perform easy calculations in a desktop calculator-like manner;
• performing sophisticated polymer sequence editing and simulations;

• perform m/z list comparisons;

  Chemical simulations encompass cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence, cross-linking of monomers in the sequence, arbitrary mass searches, calculation of the isotopic pattern...

mineXpert:

• Open mass spectrometry data files (mzML, mzXML, asc, xy, ...);
• Calculate and display the TIC chromatogram;
• For mobility data, calculate and display a mz=f(dt) color map;
• Integrate the data from the TIC chromatogram or color map
• to mass spectrum;
• to drift spectrum;
• back to TIC chromatogram (XIC chromatogram);
• reverse operations;
• to single TIC intensity value (for mass spectral intensity comparisons);
• Model centroids peaks into mass spectra using either the Gaussian model or the Lorentzian model;
• Export the data to text files;
• Slice a big initial file into smaller chunks for easier mining;
• Define how mining activity is recorded on disk for later use;
• Convert mzML files into a private (albeit open) mass spectrometry format that allows better performance (based on SQLite3).

This package depends on both massXpert and mineXpert packages and thus will install both of them. To install only one of the packages, install the corresponding msxpertsuite-massxpert or msxpertsuite-minexpert package.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

• obabel: Convert between various chemical file formats
• obenergy: Calculate the energy for a molecule
• obminimize: Optimize the geometry, minimize the energy for a molecule
• obgrep: Molecular search program using SMARTS pattern
• obgen: Generate 3D coordinates for a molecule
• obprop: Print standard molecular properties
• obfit: Superimpose two molecules based on a pattern
• obrotamer: Generate conformer/rotamer coordinates
• obconformer: Generate low-energy conformers
• obchiral: Print molecular chirality information
• obrotate: Rotate dihedral angle of molecules in batch mode
• obprobe: Create electrostatic probe grid

OpenFOAM is the free, open source CFD software released and developed primarily by OpenCFD Ltd since 2004. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Package contains binaries.

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include:

• Adding a limited number of missing heavy atoms to biomolecular structures
• Determining side-chain pKas
• Placing missing hydrogens
• Optimizing the protein for favorable hydrogen bonding
• Assigning charge and radius parameters from a variety of force fields

PSI3 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques.

It can compute energies and gradients for the following methods:

• Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF) (including analytical hessians for RHF)
• Closed shell Moeller-Plesset pertubation theory (MP2)
• Complete active space SCF (CASSCF)
• Coupled-cluster singles doubles (CCSD)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions)

Additionally, it can compute energies for the following methods:

• Unrestricted open shell Hartree-Fock (UHF)
• Closed/open shell Moeller-Plesset pertubation theory (MP2)
• Closed shell explicitly correlated MP2 theory (MP2-R12) and spin-component scaled MP2 theory (SCS-MP2)
• Multireference configuration-interaction (MRCI)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T))
• Second/third-order approximate coupled-cluster singles doubles (CC2/CC3)
• Multireference coupled-cluster singles doubles (MRCCSD)
• Closed shell and general restricted open shell equation-of-motion coupled- cluster singles doubles (EOM-CCSD)

Further features include:

• Flexible, modular and customizable input format
• Excited state calculations with the CC2/CC3, EOM-CCSD, CASSCF, MRCI and MRCCSD methods
• Internal coordinate geometry optimizer
• Harmonic frequencies calculations
• One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
• Utilization of molecular point-group symmetry to increase efficiency

PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

PyMOL je systém na vykresľovanie molekúl cielený na stredné až veľké biomolekuly ako sú bielkoviny. Dokáže tvoriť obrázky a animácie molekúl vo vysokej, produkčnej kvalite.

Medzi jeho vlastnosti patria:

• vizualizácia molekúl, trajektórií molekúl a povrchov kryštalografických dát alebo orbitálov
• zostavovanie a úprava molekúl
• interný raytracing a generátor videoklipov
• úplná rozšíriteľnosť a skriptovateľnosť pomocou rozhrania pre Python

Medzi formátu súborov, s ktorými PyMOL dokáže pracovať patria: PDB, XYZ, CIF, MDL Molfile, ChemDraw, mapy CCP4, mapy XPLOR a mapy Gaussian cube.

GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package contains the Python binding.

python-pymzml (pymzML) is an extension to Python that offers:

• easy access to mass spectrometry (MS) data that allows the rapid development of tools;
• a very fast parser for mzML data, the standard in mass spectrometry data format;
• a set of functions to compare or handle spectra.

This package contains python-pymzml for Python 3.

QuteMol is an interactive, high quality molecular visualization system. It exploits the current GPU capabilities through OpenGL shaders to offer an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

Qutemol uses advanced OpenGL techniques and might not work correctly with all video cards and drivers.

Features QuteMol offers include:

• Real time ambient occlusion
• Depth aware silhouette enhancement
• Ball-and-stick, space-filling and liquorice visualization modes
• High resolution antialiased snapshots for creating publication quality renderings
• Automatic generation of animated gifs of rotating molecules for web page animations
• Interactive rendering of macromolecules (>100k atoms)

QuteMol reads PDB files as input.

RasMol je program na molekulárnu grafiku s účelom vizualizácie proteínov, nukleových kyselín a malých molekúl. Program je určený na zobrazovanie, výuku a tvorbu obrázkov v tlačovej kvalite.

Program načíta súbor so súradnicami molekúl a interaktívne zobrazuje molekulu na obrazovke v rozličných farebných schémach a reprezentáciách molekúl. Medzi momentálne dostupné reprezentácie patria hĺbkové drôtené modely, „Dreidingove“ paličky, gule vypĺňajúce priestor (CPK), gule a paličky, pevné a zreťazené biomolekulárne reťazce, označenia atómov a bodové povrchy.

Medzi podporované vstupné formáty patria Protein Data Bank (PDB), formáty Alchemy od Tripos Associates a Sybyl Mol2, formát (MDL) Mol od Molecular Design Limited, XYZ (XMol) od Minnesota Supercomputer Center (MSC), formát CHARMm, formát CIF a formát mmCIF.

Tento balík nainštaluje dve verzie RasMol, rasmol-gtk s moderným používateľským rozhraním založeným na GTK a rasmol-classic so starým rozhraním Xlib.

X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification.

This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at http://www.thegpm.org/docs/X_series_output_form.pdf.

Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.

V_Sim visualizes atomic structures such as crystals, grain boundaries, molecules and so on (either in binary format, or in plain text format).

The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins). The user can interact through many functions to choose the view, set the bindings, draw cutting planes, compute surfaces from scalar fields, duplicate nodes, measure geometry... Moreover V_Sim allows one to export the view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats. Some tools are also available to colorize atoms from data values or to animate on screen many position files.

Viewmol is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

At present Viewmol includes input filters for Discover, DMol3, Gamess, Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as for PDB files. Structures can be saved as Accelrys' car-files, MDL files, and Turbomole coordinate files. Viewmol can generate input files for Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that OpenBabel can serve as an input as well as an output filter for coordinates.

xbs ball-and-sticks plotting program can create still and moving three dimensional models of molecules. X11 and PostScript output are available. Models can be rotated, scaled, etc. Various labeling, shading, lighting, coloring options are available.

Xdrawchem is a 2D editor for chemical structures and reactions. It mirrors the abilities of the commercial ChemDraw suite and has file compatibility with it as well as other chemical formats through OpenBabel.

This packaged version comes from a fork available at https://gitlab.com/yamanq/xdrawchem, as the previous version was no longer actively maintained. More information about it in the copyright file.

XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

• Animating multiple frame files
• Interactive measurement of bond lengths, bond angles and torsion angles
• Control over atom/bond sizes
• Exporting to Xpm, Encapsulated PostScript and XYZ formats
• Toggling the visibility of groups of atoms
• Editing the positions of subsets of atoms

XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

• Animating multiple frame files
• Interactive measurement of bond lengths, bond angles and torsion angles
• Control over atom/bond sizes
• Exporting to Xpm, Encapsulated PostScript and XYZ formats
• Toggling the visibility of groups of atoms
• Editing the positions of subsets of atoms

This is the OpenGL-enabled XMakemol package. The images are rendered using true 3D graphics primitives, and can be exported using the Xpm format; red/blue stereo images can also be produced. The OpenGL package provides more display options, along with better support for displaying vectors. Ellipses can also be rendered.

gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

This package contains examples to be used by the gdpc program.

This package provides the Open Source release of Schroedinger's routines for the 2D coordinate representation of chemical compounds.

This package provides header files for developing against the API of that library.

This package provides header files to develop one's own software that uses a library wth an Open Source parser for Maestro (.mae) files.

This package provides the Open Source release of Schroedinger's routines for the 2D coordinate representation of chemical compounds.

This package provides header files for developing against the API of that library.

python-pymzml (pymzML) is an extension to Python that offers:

• easy access to mass spectrometry (MS) data that allows the rapid development of tools;
• a very fast parser for mzML data, the standard in mass spectrometry data format;
• a set of functions to compare or handle spectra.

This package contains the documentation in PDF and HTML format, along with the text sources (processed with sphinx).

Amp is an open-source package designed to easily bring machine-learning to atomistic calculations. This project is being developed at Brown University in the School of Engineering, primarily by Andrew Peterson and Alireza Khorshidi, and is released under the GNU General Public License. Amp allows for the modular representation of the potential energy surface, allowing the user to specify or create descriptor and regression methods.

Amp is designed to integrate closely with the Atomic Simulation Environment (ASE). As such, the interface is in pure python, although several compute-heavy parts of the underlying code also have fortran versions to accelerate the calculations. The close integration with ASE means that any calculator that works with ASE ─ including EMT, GPAW, DACAPO, VASP, NWChem, and Gaussian ─ can easily be used as the parent method.

This package provides the python 3 modules.

This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.

Masses, densities and natural abundances come from the NIST Physics Laboratory, but do not represent a critical evaluation by NIST scientists.

Neutron scattering calculations use values collected by the Atomic Institute of the Austrian Universities. These values do corresponding to those from other packages, though there are some differences depending to the tables used. Bound coherent neutron scattering for gold in particular is significantly different from older value: 7.63(6) as measured in 1974 compared to 7.90(7) as measured in 1990.

X-ray scattering calculations use a combination of empirical and theoretical values from the LBL Center for X-ray Optics. These values differ from those given in other sources such as the International Tables for Crystallography, Volume C, and so may give different results from other packages.

This package installs the library for Python 3.

Dictionary of ligands and constituent blocks (e.g. amino acids, nucleic acids, sugars) contains necessary stereochemical information (e.g. bond lengths, angles, torsion angles) about small molecules used in refinement and model building. Values in the dictionary are for an abstract form of monomers, i.e there is no conformational/configurational or environment dependence.

FDMNES calculates the spectra of different spectroscopies related to the real or virtual absorption of x-ray in material. It gives the absorption cross sections of photons around the ionization edge, that is in the energy range of XANES in the EXAFS. The calculation is performed with all conditions of rectilinear or circular polarization. In the same way, it calculates the structure factors and intensities of anomalous or resonant diffraction spectra (DAFS or RXD). FDMNES also allows the comparison of the simulated spectra to experimental ones with the help of objective criteria.