DebiChem Project
Summary
Input preparation and output processing
DebiChem input preparation and output processing

This metapackage will install graphical frontends and input generators/output processors for computational chemistry packages which might be useful for chemists.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

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DebiChem Input preparation and output processing packages

Official Debian packages with high relevance

Ase
Atomic Simulation Environment
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ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomic simulations. ASE is part of CAMPOS, the CAMP Open Source project.

ASE contains Python interfaces to several different electronic structure codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA.

This package provides the executable scripts.

Avogadro
분자 그래픽 및 모델링 시스템
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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.

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
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Ballview
자유 분자 모델링 및 분자 그래픽 도구
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BALLView는 분자 구조, 분자 역학 방법 (최소화, AMBER, CHARMM, 및 MMF94 힘의 장을 사용하는 MD 시뮬레이션), 정전 속성 (FDPB) 및 분자 편집 기능의 계산 및 시각화에 대한 빠른 OpenGL 기반의 시각화를 제공합니다.

BALLView는 특히 단백질 화학자와 생물 물리학자의 가장 일반적인 요구 사항에 초점을 맞춘 BALL (Biochemical Algorithms Library)에 기반한 그래픽 사용자 인 터페이스로 간주될 수 있습니다. Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany)와 Oliver Kohlbacher (University of Tuebingen, Germany) 그룹에서 개발되었습니다. BALL은 분자 모델링및 전산 분자 생물학의 신속한 소프트웨어 개발을 위해 특별히 지속적으로 설계된 C++의 어플리케이션 프레임워크입니다. 분자 역학, 향상된 용매 화법, 단백질 구조의 비교 및 분석, 파일 import/export, 시각화를 위한 광범위한 데이타 구조와 클래스를 제공합니다.

Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)
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Cclib
Parsers and algorithms for computational chemistry
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A Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.

This package contains helper scripts for end users.

If you are looking for the unit tests and data files managed by cclib, they are distributed separately as in non-free package cclib-data.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. (eprint) J. Comp. Chem. 29(5):839-845 (2008)
Gabedit
Ab Initio 패키지에 대한 그래픽 사용자 인터페이스
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Gabedit는 아래의 계산 화익 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)에 서 실행됩니다. Gabedit는 대부분의 주요 분자 파일 형식을 포함하는 다양한 계 산 결과를 표시할 수 있습니다. 발전되 "분자 빌더"는 분자에서 빠른 스케치와 3D로 그것들을 실험할 수 있도록 합니다. 그래픽은 애니메이션을 포함한 다양한 형식으로 익스포트될 수 있습니다.

Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
Gausssum
Gaussian, GAMESS 및 기타 출력을 파싱하고 출력
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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.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. J. Comp. Chem. 29(5):839-845 (2008)
Jmol
분자 뷰어
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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.

Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)
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Travis
trajectory analyzer and visualizer
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TRAVIS (Trajectory Analyzer and Visualizer) is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. The aim of TRAVIS is to collect as many analyses as possible in one program, creating a powerful tool and making it unnecessary to use many different programs for evaluating simulations. This should greatly rationalize and simplify the workflow of analyzing trajectories. The following analysis functions are available:

Static (time independent) Functions:

  • Radial, Angular, Dihedreal or Combined Distribution Function
  • Point-Plane or Point-Line Distance Distribution
  • Plane Projection Distribution
  • Fixed Plane Density Profile
  • Density, Spatial or Dipole Distribution Function

Dynamic (time dependent) Functions:

  • Velocity Distribution Function
  • Mean Square Displacement / Diffusion Coefficients
  • Velocity Autocorrelation Functions
  • Vector Reorientation Dynamics
  • Van Hove Correlation Function
  • Aggregation Functions (DACF, DLDF, DDisp)

Spectroscopic Functions:

  • Calculate Power Spectrum
  • Calculate IR Spectrum
  • Calculate Raman Spectrum

TRAVIS can read trajectory files in XYZ, PDB, LAMMPS or DLPOLY format.

Please cite: Martin Brehm and Barbara Kirchner: TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories. (eprint) J. Chem. Inf. Model. 51(8):2007-2023 (2011)
Viewmol
graphical front end for computational chemistry programs
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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.

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Xcrysden
Crystalline and Molecular Structure Visualizer
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XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.

XCrySDen allows for real-time capture of display. Several movie encoders are supported, in particular for Animated-GIF convert (imagemagick), gifsicle, or whirlgif are necessary. For AVI/MPEG mencoder or ppmtompeg (netpbm) is required. For window dumps either imagemagick or xwd (x11-apps) needs to be present.

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