Debian Science Chemistry packages

Adun ist ein Simulator für Biomoleküle, der zusätzlich die Fähigkeiten für Datenverwaltung und -analyse mitbringt. Adun wurde am »Computational Biophysics and Biochemistry Laboratory«, einem Teil der »Research Unit on Biomedical Informatics« der UPF entwickelt.

Dieses Paket enthält die grafische Adun-Oberfläche UL.

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 ist ein System für Molekülgrafiken und -modellierung, das für Moleküle und Biomoleküle gedacht ist. Es kann Eigenschaften wie Molekülorbitale oder elektrostatische Potentiale visualisieren und enthält einen intuitiven Moleküleditor.

Es verfügt über die folgenden Fähigkeiten:

• Molekülmodellierer mit automatischer kraftfeldbasierter Geometrie-Optimierung
• Molekülmechanik einschließlich der Suche mit Bedingungen und Conformern
• Visualisierung von Molekülorbitalen und allgemeinen Isoflächen
• Visualisierung von Schwingungen und Darstellung von Schwingungsspektren
• Unterstützung von kristallografischen Einheitszellen
• Eingabeerzeugung für die quantenchemischen Pakete Gaussian, GAMESS und MOLPRO
• Flexible Erweiterungsarchitektur und Python-Skripting

Avogadro kann die Dateiformate PDB, XYZ, CML, CIF und Molden sowie die Ausgabe von Gaussian, GAMESS und MOLPRO lesen.

BKchem ist ein freies Chemie-Zeichenprogramm, das in Python geschrieben ist.

Einige Eigenschaften, die Sie erwarten können:

• Zeichnen (Zeichnen von Bindung zu Bindung; Vorlagen für gebräuchliche Ringstrukturen; Expansion gebräuchlicher Gruppen; Zeichnen von Radikalen, Ladungen, Pfeilen; Unterstützung von Farben ...)
• Bearbeiten (unbegrenztes Rückgängig machen und Wiederherstellen; Ausrichten; Skalieren; Rotation (2D, 3D) ...)
• Export/Import (vollständige Unterstützung von SVG-, OpenOffice.org-Draw-, EPS-Export; grundlegende Unterstützung von CML1- und CML2-Im- und Export)

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

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

chemeq ist ein in C, Flex und Bison geschriebener eigenständiger Filter. Er verarbeitet Zeilen wie

       2H2 + O2 ---> 2 H2O
und gibt LaTeX-Code und Mitteilungen über das Gleichgewicht der chemischen

Reaktion aus.

Beispiel:/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 is a GTK+ based 2D chemical structure editor for X11. It supports many bond styles, most forms of text needed for chemical typesetting and splines/arcs/curved arrows.

Drawings can be exported to MOL and PDB format, SVG or XFig format for further annotation, as a PiCTeX drawing, as a bitmap or as Postscript files (several of these through XFig's companion program fig2dev).

The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file. Cht can either be called directly by Chemtool or on the console.

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 ist ein Programm, welches Ihnen hilft, hochqualitative Diagramme von Molekülen und zweidimensionale chemische Formeln zu erstellen, welche nach PDF, PS, LaTeX und fig exportiert werden können.

EasyChem wurde ursprünglich entwickelt, um Diagramme für Chemiebücher zu erstellen, und wird mittlerweile für kommerzielle und nichtkommerzielle Chemiebücher eingesetzt.

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 ist ein wissenschaftlicher Taschenrechner. Er unterstützt verschiedene Basen für Zahlen (DEC/HEX/OCT/BIN) und Winkel (DEC/RAD/GRAD). Zurzeit wird eine große Menge mathematischer (grundlegende arithmetische Operationen, trigonometrische Funktionen etc.) und anderer nützlicher Funktionen (Speicher etc.) unterstützt. galculator kann im algebraischen Modus sowie mit Umgekehrter Polnischer Notation verwendet werden.

General Atomistic Modelling Graphic Interface (GAMGI) bietet eine grafische Oberfläche, um atomare Strukturen zu erstellen, zu betrachten und zu analysieren. Das Programm ist für die Wissenschaftsgemeinschaft gedacht und bietet eine grafische Oberfläche an, um atomare Strukturen zu betrachten und Bilder für Präsentationen zu erstellen. Außerdem hilft es beim Lehren der atomaren Struktur der Materie.

Garlic is written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. This version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.

It only depends on the X libraries, no other libraries are needed.

Features include:

• The slab position and thickness are visible in a small window.
• Atomic bonds as well as atoms are treated as independent drawable objects.
• The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
• Capable to display stereo image.
• Capable to display other geometric objects, like membrane.
• Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
• Capable to load more than one structure.
• Capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity and hydrophobic moment plot.
• The command prompt is available at the bottom of the main window. It is able to display one error message and one command string.

Gaussum wertet die Ausgabedateien von ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar und PC GAMESS aus, um nützliche Informationen zu extrahieren.

Gaussum stellt mit GNUPlot den Verlauf von geometrischen Optimierungen, Zustandsdichteverteilungen, UV-VIS-Spektren, IR-Spektren, Raman-Spektren und Elektronendichteunterschiedskarten dar. Es kann auch alle Zeilen, die einen beliebigen Ausdruck enthalten, darstellen, und vieles mehr.

GChemPaint ist ein Editor für chemische 2D-Strukturen mit einer Schnittstelle für mehrere Dokumente. Gezeichnete Moleküle können im NIST Webbook und in PubChem gesucht werden.

GNOME Crystal ist ein ressourcenschonender Betrachter für Kristallstrukturen. Er basiert auf den GNOME Chemistry Utils und nutzt OpenGL. Das Programm sollte Modelle aller Arten mikroskopischer Kristallstrukturen darstellen können.

The GNOME Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They will be used in future versions of both gcrystal and gchempaint.

This package provides 4 applications:

• a molecular structures viewer (GChem3D)
• a molar mass calculator (GChemCalc)
• a periodic table of the elements (GChemTable)
• a spectra viewer (GSpectrum)

Ein auf GTK beruhendes Programm für die Anzeige und Manipulation von isolierten Molekülen, des Periodensystems und der Beschaffenheit von Kristallen. Es wird noch entwickelt, ist aber dennoch recht gut benutzbar. Es bietet die folgenden Fähigkeiten:

• Unterstützung für mehrere Dateitypen (CIF, BIOSYM, XYZ, XTL, MARVIN und GULP)
• Ein einfaches Werkzeug zur Erzeugung und Manipulation von Molekülen
• Ein Dialog für die Erstellung von Anfangskonfigurationen für Molekulardynamik-Simulationen
• Diverse Werkzeuge für die Visualisierung (geometrische Informationen, Hervorhebung von Regionen usw.)
• Animation von BIOSYM-Dateien (auch gerenderten Animationen, siehe unten)

Mit Hilfe anderer Pakete kann GDIS auch die folgenden Aufgaben ausführen:

• Darstellung von Modellen (Hilfestellung durch Povray)
• Energieminimierung (Hilfestellung durch GULP)
• Berechnung der Molekülgestalt (Hilfestellung durch CDD)
• Verarbeitung räumlicher Gruppen (Hilfestellung durch SgInfo)
• Betrachtung des Periodensystems (Hilfestellung durch GPeriodic)
• Lesen zusätzlicher Dateitypen, wie PDB (Hilfestellung durch Babel)

gpdc ist ein grafisches Programm zur Visualisierung von Ausgabedaten aus Molekulardynamik-Simulationen. Es verwendet sowohl das Standarddateiformat xyz als auch andere gebräuchliche Formate als Eingabe. Bilder jedes Frames können im JPG- oder im PNG-Format ausgegeben werden.

gElemental ist ein GTK+ Betrachter für das Periodensystem mit detaillierten Informationen über die chemischen Elemente.

Es bietet eine tabellarische Ansicht mit der Möglichkeit, die Elemente thematisch nach verschiedenen Eigenschaften einzufärben; eine sortierbare Listenansicht und Fenster, welche eine Vielzahl an Informationen über ein Element anzeigen, einschließlich historischer, thermodynamischer, elektrochemischer und kristallographischer Eigenschaften.

Dieses Paket enthält die Hauptanwendung.

Ghemical ist ein Paket für die rechnergestützte Chemie, das in C++ geschrieben wurde. Es hat eine grafische Benutzeroberfläche und es unterstützt sowohl quantenmechanische (semi-empirische) als auch molekularmechanische Modelle. Zurzeit bietet es geometrische Optimierungen, molekulare Dynamik und eine große Menge an Visualisierungswerkzeugen, die OpenGL benutzen.

Ghemical benötigt externen Code, um quantenmechanische Berechnungen durchführen zu können. Semi-empirische Funktionen MNDO, MINDO/3, AM1 und PM3 werden vom MOPAC7-Paket (Public Domain) erbracht und sind in diesem Paket enthalten. Das MPQC-Paket wird verwendet, um ab-initio-Methoden zur Verfügung zu stellen. Die Methoden, die auf der Hartree-Fock-Theorie basieren, werden im Moment mit Basissätzen von STO-3G bis 6-31G** unterstützt.

GPeriodic ist ein kleines X/GTK+-basiertes Programm, welches das Periodensystem der Elemente darstellt und auch ausführlichere Informationen zu jedem Element liefert. Es umfasst z.Z. 118 Elemente.

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 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 MPICH (v3) interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines.

GROMACS ist ein vielseitiges Paket, um Molekulardynamik anzuwenden, z.B. um die Newtonschen Bewegungsgleichungen für Systeme mit Hunderten bis zu Millionen von Teilchen zu simulieren.

Es wurde primär für biochemische Moleküle wie Proteine und Fette entworfen, die eine Vielzahl von komplizierten kovalenten Wechselwirkungen aufweisen. Da aber GROMACS die nicht-kovalenten Interaktionen (welche in Simulationen dominieren) extrem schnell berechnen kann, nutzen viele Gruppen es auch für Forschungen an nicht-biologischen Systemen, z.B. an Polymeren.

Dieses Paket enthält nur das eigentliche Simulationsprogramm, das über die OpenMPI-Schnittstelle Parallelisierung unterstützt. Es eignet sich für die Knoten eines Clusters oder für Multiprozessor-Maschinen.

Jmol ist ein Java-Programm zur Darstellung von dreidimensionalen chemischen Strukturen auf Molekülebene. Es kann eine Vielzahl von Dateitypen und Ausgaben von Programmen der Quantenchemie lesen sowie Multiframe-Dateien und berechnete Normalmodi von Quantenprogrammen animieren. Es kann Chemikalien, Kristalle, Materialien und Biomoleküle anzeigen. Jmol kann für Studenten, Lehrende und Forscher in der Chemie und Biochemie nützlich sein.

Jmol kann unter anderem folgende Dateiformate lesen: PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton und VASP.

Kalzium ist eine voll funktionsfähige Chemieanwendung. Sie beinhaltet ein Periodensystem der Elemente, Chemie-Referenzen, einen Löser für chemische Gleichungen und einen Betrachter für 3D-Moleküle.

Dieses Paket ist Teil des KDE-Bildungsmoduls.

Im Rätselspiel KAtomic verschiebt der Spieler Atome auf einem Brett, um Moleküle zusammenzubauen.

Dieses Paket ist Teil des KDE-Spielemoduls.

Das CDK ist eine Bibliothek von Java-Klassen, welche in der computergestützten Chemie, in Chemo- und Bioinformatik angewendet wird. Sie beinhaltet Programme zur Bildsynthese, Dateiein- und -ausgabe, Erzeugung und Analyse von SMILES- Daten, Algorithmen für größte gemeinsame Substrukturen, »DNA fingerprinting« und vieles, vieles mehr.

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 stellt Verfahren auf halbempirischem Niveau zur Ermittlung der Elektronenkonfiguration von Molekülen zur Verfügung. Zu den verfügbaren Methoden gehören MNDO, MINDO/3, AM1 und PM3.

Dieses Paket enthält die MOPAC7-Binärdateien.

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 bedeutet Massively Parallel Quantum Chemistry Program. Es ist ein ab- initio Quantenchemieprogramm und wurde speziell entwickelt, um Moleküle auf hoch parallele Weise zu berechnen.

Dieses Paket enthält Perlmodule zur Analyse der Ausgabe, Betriebsarten für Emacs zur Bearbeitung von mpqc-Dateien und molrender, ein Programm, um Moleküle im OOGL-Format auszugeben.

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 ist eine Python-Bibliothek für die azimuthale Integration. Sie ermöglicht die Umwandlung von Beugungsbildern, die mit 2D-Detektoren wie CCD-Kameras aufgenommen werden, in Röntgenpulvermuster, die von anderen Softwarewerkzeugen wie beispielsweise zur Rietveld-Veredelung (z.B. FullProf), Phasenanalyse oder Texturanalyse verwendet werden können.

Da PyFAI eine Bibliothek ist, ist ihr Hauptziel die Integration in andere Werkzeuge wie PyMca, LiMa oder EDNA. Um eine Online-Datenanalyse durchführen zu können, muss die genaue Beschreibung des Versuchsaufbaus bekannt sein. Aus diesem Grund enthält PyFAI auch Code zur Optimierung von Geometrie an »Puderringen« von Referenzproben. Alternativ kann PyFAI auch Geometrien importieren, die mit anderen Werkzeugen wie Fit2D angepasst wurden.

PyFAI wurde entwickelt, um mit jeder Art von Detektor mit jeder Geometrie (Übertragung, Reflexion, Off-Axis, …) zu arbeiten. Die Software verwendet die Python-Bibliothek FabIO, um die meisten Bilder zu lesen, die von Diffraktometern aufgenommen wurden.

PyMOL ist ein Grafiksystem für Moleküle, ausgerichtet auf mittelgroße bis große Biomoleküle wie Proteine. Es kann qualitativ hochwertige, den Anforderungen einer Publikation genügende Molekülgrafiken als Bilder oder Animationen erstellen.

Zu den Funktionen zählen:

• Visualisierung von Molekülen, molekularen Bahnen und Oberflächen von Kristallografiedaten oder Orbitalen
• Manuelle und automatisierte Erstellung von Molekülen
• Interner Raytracer und Filmerzeuger
• Voll erweiterbar und programmierbar durch eine Python-Schnittstelle

PyMOL kann unter anderem folgende Dateiformate lesen: PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 Maps, XPLOR Maps und Gaussian Cube Maps.

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 ist ein Grafikprogramm zur Moleküldarstellung, das die dreidimensionale Anordnung von Proteinen, Nukleinsäuren und beliebigen kleinen Molekülen visualisiert. Hierbei wird auf die Verwendbarkeit in der Forschung und Lehre Wert gelegt und auch auf eine druckreife Qualität der Darstellungen.

Das Programm liest eine Datei mit Koordinaten ein und zeigt das Molekül interaktiv am Bildschirm an, mit der Möglichkeit zur Veränderung von Farben und der Gestalt der Atome. Derzeit verfügbare Abbildungen sind »depth-cued«-Drahtmodelle, »Dreiding«-Sticks, raumfüllende (CPK-)Kugeln, Stäbchenmodell, sekundäre Strukturen wie Faltblätter und Helices, Atombeschriftungen und Punktoberflächen.

Unterstützt werden Dateien aus der Protein Data Bank (PDB), Tripos Associates' Alchemy und Sybyl-Mol2-Formate, Molecular Design Limiteds (MDL) Mol-Dateiformat, Minnesota Supercomputer Centers (MSC) XYZ- (XMol-)Format, CHARMm-Format, CIF-Format und mmCIF formatierte Dateien.

Dieses Paket installiert zwei Versionen von RasMol, rasmol-gtk hat eine moderne GTK-basierte Bedienoberfläche und rasmol-classic die Xlib-GUI.

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 visualisiert Atomstrukturen wie Kristalle, Korngrenzen, Moleküle und so weiter (sowohl im binären Format oder auch im Textformat ASCII).

Die Darstellung erfolgt in »pseudo-3D« mit Kugeln (Atome) oder Pfeilen (Spins). Der Benutzer kann durch viele Funktionen eingreifen, um die Ansicht oder die Bindungen zu ändern, die Schnittebenen darzustellen, Oberflächen aus skalaren Feldern zu erstellen, Knoten zu duplizieren, die Geometrie zu vermessen… Mehr noch, V_Sim ermöglicht das Exportieren der Ansichten als Bild im PNG-, JPG-, PDF-Format (Bitmap), als SVG (Entwurf) und in andere Formate. Es sind auch einige Werkzeuge zum Einfärben von Atomen mittels Datenwerten oder zur Animation vieler Positionsdateien auf dem Bildschirm vorhanden.

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.