Debian Science Chemistry packages

Adun is a biomolecular simulator that also includes data management and analysis capabilities. It was developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF.

This package contains UL, the Adun GUI frontend.

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.

Avogadro는 분자 및 생체분자를 대상으로 하는 분자 그래픽 및 모델링 시스템입 니다. 분자 궤도 및 정전기 전위와 같은 특성을 시각화할 수 있으며 직관적인 분 자 빌더를 특징으로 합니다.

특징은 아래와 같습니다:

• 자동 force-field 기반에 지오메트리 최적화 기능을 갖춘 분자 모델러
• 제약 조건 및 이형태체 검색을 포함하는 분자 역학
• 분자 궤도 및 일반 등밀도면 시각화
• 진동의 시각화 및 진동 스펙트럼 플로팅
• 결정학상의 단위 세포 지원
• Gaussian, GAMESS 및 MOLPRO 양자 화학 패키지를 위한 입력 생성
• 유연한 플러그인 아키텍쳐 및 파이썬 스크립팅

Avogadro가 읽을 수 있는 파일 형식은 PDB, XYZ, CML, CIF, Molden 및 Gaussian, GAMESS, MOLPRO 출력입니다.

BKchem은 파이썬으로 작성된 화학 드로잉 오픈 프로그램입니다.

기대할 수 있는 일부 기능은은 아래와 같습니다:

• 드로잉 (bond-by-bond 드로잉; 일반 링을 위한 템플릿; 일반 그룹 확장; 라디칼, charges, 화살표 그리기; 색상 지원...)
• 편집 (무제한 실행 취소 및 다시 실행 기능; 정렬; 크기 조정; 회전 (2D, 3D)...)
• 내보내기/가져오기 (SVG-, OpenOffice.org-Draw-, EPS-export 완벽 지원; CML1 및 CML2 가져오기/내보내기 기본 지원)

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

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

chemeq는 C, flex, 그리고 bison으로 만들어진 기본적인 독립형 필터입니다. 이 프로그램은 아래와 같은 입력 문자열을 받습니다.

 2H2 + O2 ---> 2 H2O
그리고 화학 반응의 평형에 대한 LaTeX 코드와 메시지를 출력합니다.

예: ~/src$ echo "2H2 + O2 ---> 2 H2O" | chemeq -lc 2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O OK

기존의 MIME 타입에 1996년 Henry Rzepa, Peter-Murray Rust 및 Benjamin Whitaker는 화학 미디어 타입 및 여러 하위 타입을 추가로 제안했습니다. 제안은 이어지지 못했지만 여러 어플리케이션에서 이러한 MIME/파일 타입을 사용합니다. 이 패키지는 chemical/* 미디어 타입 파일을 감지하고 인식하기 위해 리눅스 데스크톱에 대한 지원을 추가합니다.

http://www.ch.ic.ac.uk/chemime/ 도 보십시오.

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).

DRAWxtl은 단위 셀 파라미터, 공간 그룹, 원자 좌표, 온도 매개 변수 또는 푸리 에 맵을 포함하는 크리스탈 구조의 기본적인 설명을 읽고, 다면체, 평면, 고립 전자쌍 콘, 구 또는 타원체, 결합, iso-surface 푸리에 윤곽, 및 단위 셀 경계를 포함하는 기하학적 객체를 출력합니다.

네개의 그래픽 형식을 만듭니다:

• 바로 볼 수 있는 OpenGL 윈도우
• 출판물 품질의 그림을 위한 비전 레이 추적기의 지속성 (Persistence of Vision Ray Tracer/POV-RAY) 장면 언어
• 인터넷을 통해 제공되는 가상 현실 모델링 언어 (Virtual Reality Modeling Language/VRML)
• 고품질 출력을 원하지만 POV-RAY는 설치되지 않은 사람들을 위한 OpenGL 윈도우의 포스트스크립트 랜더링.

파일 형식 DRAWxtl은 CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS, WIEN2k들을 읽을 수 있습니다.

EasyChem은 PDF, PS, LaTeX, fig로 저장할 수 있는 분자 고품질 다이어그램 및 2D 화학식 생성을 도와주는 프로그램입니다.

EasyChem은 원래 화학 책에 대한 다이어그램을 작성하기 위해 개발되었으며, 지 금은 상용 및 비상용 화학 관련 책을 위해 사용됩니다.

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

Gabedit는 아래의 컴퓨터 화학 패키지에 대한 그래픽 사용자 인터페이스입니다:

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

Ab Initio 소프트웨어 패키지는 내부 또는 외부 서버 (FTP, RSH, SSH를 지원)에서 실행됩니다. Gabedit는 대부분의 주요 분자 파일 형식을 포함하는 다양한 계산 결과를 표시할 수 있습니다. 발전된 "분자 빌더"는 분자에서 빠른 스케치와 3D로 그것들을 실험할 수 있도록 합니다. 그래픽은 애니메이션을 포함한 다양한 형식으로 익스포트될 수 있습니다.

slurm-wlm-torque 및 gridengine-client는 PBS 명령을 위한 래퍼를 제공하는 워크로드 매니저입니다. Gabedit를 사용하면 다른 워크로드 매니저에 대해서도 구성할 수 있습니다.

galculator는 공학용 계산기입니다. 이 프로그램은 여러 진법(DEC/HEX/OCT/BIN) 과 각도 계산(DEG/RAD/GRAD) 그리고 넓은 범위의 수학 계산(기본적인 산술계산 처리, 삼각법 함수)을 처리 할 수 있습니다. 현재 이 프로그램은 여러가지 유용 한 기능 (memory 등등)을 지원합니다. Reverse Polish Notation(역 폴리쉬 기법 /RPN)과 마찬가지로 galculator는 대수학 모드를 사용할 수도 있습니다.

General Atomistic Modelling Graphic Interface (GAMGI)는 원자 구조를 빌드하 고, 보고, 분석하기 위한 그래픽 인터페이스를 제공합니다. 이 프로그램은 과학 커뮤니티를 목적으로 하며, 원자 구조를 연구하고 프리젠테이션을 위해 이미지를 준비하고 물질의 원자 구조를 가르치는 그래픽 인터페이스를 제공합니다.

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.

GaussSum은 ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar 및 PC HAMESS 계산의 출 력 파일에서 유용한 정보를 추출하기 위해 파싱합니다.

GaussSum은 기하학 최적화, 상태 밀도, UV-VIS 스펙트럼, IR 스펙트럼, 라만 스 펙트럼, 및 선형 밀도 차이등 맵의 진행 상황을 표시하기 위해 GNUPlot을 사용합 니다. 또한 임의 문장을 포함하는 모든 라인을 표시하고 그 이상을 표시합니다.

GChemPaint는 다중 문서 인터페이스를 갖는 2D 화학 구조를 위한 편집기입니다. 추출된 분자는 NIST Webbook 및 PubChem에서 검색할 수 있습니다.

GNOME Crystal은 결정 구조에 대한 경량 모델 시각화입니다. 이 프로그램은 그놈 화학 유틸에 기반하며 OpenGL을 사용하여 모든 종류의 결정 미세 구조 모델을 표 시해야 합니다.

그놈 화학 유틸 (GNOME Chemistry Utils)는 화학과 관련된 C++ 클래스와 Gtk+-2 위젯을 제공합니다. 이들은 gcrystal 및 gchempaint의 미래 버전에서도 사용될 수 있을것입니다.

이 패키지는 네개의 어플리케이션을 제공합니다:

• 분자 구조 뷰어 (GChem3D)
• 몰 질량 계산기 (GChemCalc)
• 주기율표 (GchemTable)
• 스펙트럼 뷰어 (GSpectrum)

분리된 분자, 주기 시스템 및 결정 습관을 표시하고 조작하기 위한 GTK+ 기반 프로그램. 개발 중이지만 그럼에도 상당한 기능을 가지고 있습니다. 아래와 같은 기능을 포함합니다:

• 여러 파일 형식 지원 (CIF, BIOSYM, XYZ, XTL, MARVIN, GULP)
• 간단한 분자 생성 및 조작 도구
• 분자 역학 시뮬레이션을 위해 시작 구성을 생성하는 대화 상자
• 시각화를 위한 다양한 도구 (기하학적 정보, 영역 강조 표시등)
• BIOSYM 파일 애니메이션 (렌더링된 애니메이션도 있음, 아래 참조)

GDIS를 사용하면 다른 패키지들을 통해 다음 기능을 수행할 수 있습니다:

• 모델 렌더링 (POVRay 제공)
• 에너지 최소화 (GULP 제공)
• 형태 계산 (cdd 제공)
• 공간 그룹 처리 (SgInfo 제공)
• 주기율표 보기 (GPeriodic 제공)
• PDB와 같은, 추가 파일 시스템 로드 (Babel 제공)

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.

gElemental은 화학원소에 대한 자세한 정보를 제공하는 GTK+ 주기율표 뷰어입니다.

다양한 속성, 정렬가능한 리스트 뷰, 요소 특성 대화 상자를 통해서 화학 요소들 을 테마별 색상으로 정리하는 테이블 뷰를 특징하며, 히스토리, 열역학, 전기 화 학, 결정 화학적 속정을 포함하는 다양한 정보를 표시합니다.

이 패키지는 주요 어플리케이션을 포함합니다.

Ghemical은 C++로 작성된 계산 화학 소프트웨어 패키지입니다. Ghemical은 그래 피컬 사용자 인터페이스를 가지고 있으며, 양자 역학 (반경험적) 모델과 분자 역 학 모델 양쪽을 모두 지원합니다. 구조 최적화, 분자 동력학 그리고 OpenGL을 사 용하는 여러가지 시각화 도구등이 현재 사용할 수 있습니다.

Ghemical은 양자 역학 계산을 제공하는 외부 코드에 의존합니다. 반경험적 방법 MNDO, MINDO/3, AM1 그리고 PM3은 MoPAC7 (퍼블릭 도메인)패키지에서 가져왔으 며, 이 패키지에 포함되어 있습니다. MPQC 패키지는 순이론 방법을 제공하기 위 해서 사용되고 있습니다: Hartree-Fock 이론에 근거한 이 방법은 현재 STO-3G 에 서 6-31G** 까지 범위를 기본 세트로 함께 지원됩니다.

GPeriodic은 화학 원소의 주기율표를 통해 검색하고, 각 요소의 자세한 정보를 볼 수 있도록 하는 작은 X/GTK+ 기반 프로그램입니다. 118 요소는 현재 리스트되어 있습니다.

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 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.

Jmol은 3차원 화학 구조를 위한 Java 분자 뷰어입니다. 특징으로 다양한 파일 타 입을 읽어 양자 화학 프로그램에서 출력하고, 멀티 프레임 파일 및 양자 프로그 램에서 계산된 일반 모드의 애니메이션을 포함합니다. 화학 물질, 결정체, 자료, 생체 분자에 대한 기능을 포함합니다. Jmol은 화학 및 생화학 분야에 학생, 교육 자 및 연구원에게 유용할 수 있습니다.

Jmol이 읽는 파일 형식으로는 PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton 및 VASP가 있습니다.

Kalzium is a full-featured chemistry application, including a Periodic Table of Elements, chemical reference, chemical equation solver, and 3D molecule viewer.

This package is part of the KDE education module.

KAtomic is a puzzle game in which the player slides atoms around the board to assemble a molecule.

This package is part of the KDE games module.

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).

MPQC는 ab-inito 양자 화학 프로그램입니다. 이 프로그램은 특히 높은 병렬 방식 에 미분자 계산을 위해 설계되었습니다.

이 패키지에는 출력을 해석하기 위한 펄 모듈, mpqc 편집을 도와주는 Emacs- modes 그리고 OOGL 포맷으로 분자를 출력하는 프로그램이 들어있습니다.

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

PSI3은 제1원리 계산 프로그램입니다. 이 프로그램은 특히 고도로 연관된 기술을 사용하여 중간 분자에 대한 작은 성질을 정밀하게 계산하도록 설계되었습니다.

이 프로그램은 다음과 같은 방법을 위해 에너지와 변화도를 계산할 수 있습니다:

• 닫힌 쉘과 일반적으로 제한된 열린 쉘 하트리-폭 (RHF/ROHF) (RHF에 대한 분석 헤센 포함)
• 폐각 Moeller-Plesset pertubation 이론 (MP2)
• 완전한 활동 공간 SCF (CASSCF)
• Coupled-cluster singles doubles (CCSD)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (오직 제한되지 않는 (UHF) 참조 파동 함수를 위해)

추가로, 이 프로그램은 다음과 같은 방법을 위해 에너지를 계산할 수 있습니다:

• 무제한 열린 쉘 하트리-폭 (UHF)
• 닫힌/열린 쉘 Moeller-Plesset의 pertubation 이론 (MP2)
• 폐각 명시적 상관 관계 MP2 이론 (MP2-R12) 및 스핀 구성 요소 확장 MP2 이론 (SCS-MP2)
• 다중 참조 구성 상호 작용 (MRCI)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T))
• 2/3차 근사 coupled-cluster singles doubles (CC2/CC3)
• 다중 참조 coupled-cluster singles doubles (MRCCSD)
• 닫힌 쉘과 일반적으로 제한된 열린 쉘 운동 방정식 coupled-cluster singles doubles (EOM-CCSD)

추가적인 기능으로 다음을 포함합니다:

• 유연하고, 모듈형이며 그리고 사용자 정의가 가능한 입력 형식
• CC2/CC3, EOM-CCSD, CASSCF and MRCI 및 MRCCSD 방법을 통한 흥분 상태 계산
• 내부 좌표 기하학 최적화
• 고주파 주파수 계산
• 쌍극자 / 사극자 능률, 자연 궤도, 정전기 전위, 미세 커플링 상수 또는 스핀 밀도와 같은 1 전자 특성
• 효율성을 높이기 위한 분자 포인트 그룹 대칭의 활용

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 is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

• Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
• Molecular builder and sculptor
• Internal raytracer and movie generator
• Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and 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.

RasMol은 단백질, 핵산, 작은 분자의 시각화를 위한 분자 그래프 프로그램입니다. 이 프로그램의 목적은 출판물 품질 이미지의 표시, 교육, 생성입니다.

이 프로그램은 분자 좌표 파일을 읽어서 대화식으로 분자를 다양한 색 구성과 분자 표현으로 화면에 표시합니다. 현재 사용 가능한 표현으로는 depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and sticky, Solid and strand biomolecular ribbons, atom labels, dot surfaces를 포함합니다.

지원되는 입력 파일 형식으로는 Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format을 포함합니다.

이 패키지는 두개의 RasMol 버젼을 설치합니다. rasmol-gtk는 현대적 GTK 기반의 사용자 인터페이스를 가지고 있으며 rasmol-classic은 오래된 Xlib GUI 버젼입니다.

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_Sim은 결정, 입자 경계, 분자등과 같은 원자 구조를 시각화합니다 (이진 형식 또는 일반 텍스트 형식).

렌더링은 구 (원자) 또는 화살표 (회전)를 사용하여 의사 3D로 수행됩니다. 사용자는 보기 선택, 바인딩 설정, 절단면 그리기, 스칼라 필드에서 표면 계산, 노드 복제, 형상 측정과 같은 여러 기능을 통해 상호작용 할 수 있습니다. 또한 V_Sim은 뷰를 PNG, JPG, PDF (bitmap), SVG (스키마) 및 기타형식의 이미지로 내보낼 수 있습니다. 몇몇 도구들은 데이타 값에서 원자를 색상화 하거나 또는 화면상에 많은 위치 파일을 애니메이션화하는데 사용할 수 도 있습니다.

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

XMakemol은 원자 및 기타 화학 시스템을 보고 조작하기 위해, LessTif 위젯 세트를 사용해서 개발된, 마우스 기반 프로그램입니다. XYZ 입력을 읽어서 원자, 결합, 수소 결합을 렌더링합니다.

아래 기능들을 포함합니다.

• 멀티 프레임 파일 애니메이션
• 결합 길이, 결합 각도 및 비틀림 각도의 대화식 측정
• 원자/결합 크기 제어
• Xpm, 캡슐화된 PostScript 및 XYZ 형식으로 내보내기
• 원자 그룹의 가시성 전환
• 원자 하위 집합의 위치 편집

이 패키지는 OpenGL이 활성화된 XMakemol 패키지입니다. 이미지는 실제 3D 그래픽 기본 요소를 사용해서 렌더링되며 Xpm 형식을 사용해서 내보낼 수 있습니다; 빨강/파랑 스테레오 이미지도 생성할 수 있습니다. OpenGL 패키지는 벡터 표시에 대한 더 좋은 지원과 함께 더 많은 디스플레이 옵션을 제공합니다. 타원도 렌더링 할 수 있습니다.

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.