Summary
Chemistry
이 메타패키지는 화학과 관련된 데비안 과학 패키지를 설치할 것 입니다. 사용자는 또한 field::chemistry debtag와, 사용자의 관심에 따라, education-chemistry 메타패키지에 관심있을 수도 있습니다.
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 Debian Science
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Science mailing list
Links to other tasks
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Debian Science Chemistry packages
Official Debian packages with high relevance
adun.app
Molecular Simulator for GNUstep (GUI)
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Versions of package adun.app |
Release | Version | Architectures |
jessie | 0.81-6 | amd64,armel,armhf,i386 |
bookworm | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.81-13 | amd64,arm64,armhf,i386 |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package adun.app: |
field | biology, biology:structural |
interface | x11 |
role | program |
scope | application |
suite | gnustep |
uitoolkit | gnustep |
use | analysing, organizing, viewing |
works-with | 3dmodel, db |
x11 | application |
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License: DFSG free
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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.
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apbs
Adaptive Poisson Boltzmann Solver
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Versions of package apbs |
Release | Version | Architectures |
sid | 3.4.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.4.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4-1 | amd64,arm64,armhf,i386 |
stretch | 1.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.4-1 | amd64,armel,armhf,i386 |
trixie | 3.4.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.0.0+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package apbs: |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
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License: DFSG free
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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.
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atomes
atomic-scale 3D modeling toolbox
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Versions of package atomes |
Release | Version | Architectures |
sid | 1.1.15-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm-backports | 1.1.14-1.1~bpo12+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.15-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
The package is enhanced by the following packages:
atomes-data
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avogadro
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Versions of package avogadro |
Release | Version | Architectures |
bookworm | 1.97.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.93.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.0-4 | amd64,arm64,armhf,i386 |
jessie | 1.0.3-10.1 | amd64,armel,armhf,i386 |
Debtags of package avogadro: |
field | chemistry |
role | program |
uitoolkit | qt |
use | viewing |
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License: DFSG free
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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.
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bkchem
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Versions of package bkchem |
Release | Version | Architectures |
buster | 0.13.0-6 | all |
jessie | 0.13.0-4 | all |
sid | 0.14.0~pre4+git20211228-5 | all |
trixie | 0.14.0~pre4+git20211228-5 | all |
bookworm | 0.14.0~pre4+git20211228-3 | all |
stretch | 0.13.0-5 | all |
Debtags of package bkchem: |
field | chemistry |
role | program |
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License: DFSG free
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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)
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bodr
Blue Obelisk Data Repository
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Versions of package bodr |
Release | Version | Architectures |
buster | 10-1 | all |
sid | 10-3 | all |
trixie | 10-3 | all |
bookworm | 10-2 | all |
bullseye | 10-2 | all |
stretch | 10-1 | all |
jessie | 10-1 | all |
Debtags of package bodr: |
role | app-data |
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License: DFSG free
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Common repository of chemical and physical facts that aim
to increase interoperability between chemistry programs.
https://dx.doi.org/10.1021/ci050400b
Please cite:
Peter Murray-Rust:
The Blue Obelisk
(eprint)
CDK News
2(2):43-46
(2005)
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chemeq
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Versions of package chemeq |
Release | Version | Architectures |
sid | 3.6-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.6-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.23-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.19-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.18-1 | amd64,arm64,armhf,i386 |
stretch | 2.12-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.12-1 | amd64,armel,armhf,i386 |
Debtags of package chemeq: |
devel | interpreter |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
use | calculating, learning, text-formatting, typesetting |
works-with | text |
works-with-format | tex |
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License: DFSG free
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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
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chemical-mime-data
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Versions of package chemical-mime-data |
Release | Version | Architectures |
jessie | 0.1.94-6 | all |
sid | 0.1.94-7.2 | all |
trixie | 0.1.94-7.2 | all |
bookworm | 0.1.94-7.2 | all |
bullseye | 0.1.94-7.1 | all |
buster | 0.1.94-7 | all |
stretch | 0.1.94-6 | all |
Debtags of package chemical-mime-data: |
field | biology, chemistry |
role | app-data |
use | organizing |
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License: DFSG free
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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.
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chemical-structures
web service providing molecular structures in open formats
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Versions of package chemical-structures |
Release | Version | Architectures |
sid | 2.2.dfsg.0-20 | all |
trixie | 2.2.dfsg.0-20 | all |
bookworm | 2.2.dfsg.0-20 | all |
bullseye | 2.2.dfsg.0-18 | all |
buster | 2.2.dfsg.0-13 | all |
stretch | 2.2.dfsg.0-12 | all |
jessie | 2.2.dfsg.0-12 | all |
Debtags of package chemical-structures: |
field | biology, biology:bioinformatics, chemistry |
interface | commandline, web |
role | data, program |
science | visualisation |
use | comparing, converting, learning, viewing |
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License: DFSG free
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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.
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chemtool
chemical structures drawing program
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Versions of package chemtool |
Release | Version | Architectures |
bookworm | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.6.14-1 | amd64,armel,armhf,i386 |
stretch | 1.6.14-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.6.14-3 | amd64,arm64,armhf,i386 |
bullseye | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package chemtool: |
field | chemistry |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | editing, learning |
works-with | image, image:vector |
works-with-format | svg |
x11 | application |
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License: DFSG free
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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.
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cp2k
Ab Initio Molecular Dynamics
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Versions of package cp2k |
Release | Version | Architectures |
sid | 2023.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
buster | 6.1-2 | amd64,arm64,armhf,i386 |
bullseye | 8.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2023.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2024.3 |
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License: DFSG free
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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).
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drawxtl
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Versions of package drawxtl |
Release | Version | Architectures |
jessie | 5.5-3 | amd64,armel,armhf,i386 |
buster | 5.5-3 | amd64,arm64,armhf,i386 |
stretch | 5.5-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 5.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.5-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package drawxtl: |
interface | x11 |
role | program |
uitoolkit | glut |
x11 | application |
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License: DFSG free
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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.
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easychem
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Versions of package easychem |
Release | Version | Architectures |
bookworm | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.6-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.6-8 | amd64,armel,armhf,i386 |
bullseye | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.6-8 | amd64,arm64,armhf,i386 |
trixie | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package easychem: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
x11 | application |
|
License: DFSG free
|
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.
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feff85exafs
Open Source theoretical EXAFS calculations
|
Versions of package feff85exafs |
Release | Version | Architectures |
sid | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
The feff85exafs project aims to provide high quality theoretical standards for
EXAFS analysis within an open source, freely re-distributable framework.
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gabedit
Ab Initio 패키지에 대한 그래픽 사용자 인터페이스
|
Versions of package gabedit |
Release | Version | Architectures |
bullseye | 2.5.1~20200828-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.8-1 | amd64,armel,armhf,i386 |
stretch | 2.4.8-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.8-3 | amd64,arm64,armhf,i386 |
Debtags of package gabedit: |
field | chemistry |
role | program |
uitoolkit | gtk |
|
License: DFSG free
|
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.
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galculator
|
Versions of package galculator |
Release | Version | Architectures |
buster | 2.1.4-1 | amd64,arm64,armhf,i386 |
bullseye | 2.1.4-1.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.3-1 | amd64,armel,armhf,i386 |
stretch | 2.1.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.4-1.2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package galculator: |
field | mathematics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
x11 | application |
|
License: DFSG free
|
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.
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gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
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Versions of package gamgi |
Release | Version | Architectures |
stretch | 0.17.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.17.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.17.3-2 | amd64,arm64,armhf,i386 |
jessie | 0.17.1-1 | amd64,armel,armhf,i386 |
Debtags of package gamgi: |
role | program |
uitoolkit | gtk |
|
License: DFSG free
|
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.
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garlic
visualization program for biomolecules
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Versions of package garlic |
Release | Version | Architectures |
buster | 1.6-3 | amd64,arm64,armhf,i386 |
bookworm | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.6-1.1 | amd64,armel,armhf,i386 |
stretch | 1.6-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package garlic: |
field | biology, chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | xlib |
use | viewing |
x11 | application |
|
License: DFSG free
|
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.
Please cite:
Damir Zucic and Davor Juretic:
Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program
(eprint)
Croatica Chemica Acta
77(1-2):397-401
(2004)
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gausssum
Gaussian, GAMESS 및 기타 출력을 파싱하고 출력
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Versions of package gausssum |
Release | Version | Architectures |
sid | 3.0.2-2 | all |
stretch | 3.0.1.1-1 | all |
bookworm | 3.0.2-2 | all |
bullseye | 3.0.2-2 | all |
jessie | 2.2.6.1-1 | all |
buster | 3.0.2-1 | all |
trixie | 3.0.2-2 | all |
Debtags of package gausssum: |
field | chemistry |
role | program |
|
License: DFSG free
|
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.
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gchempaint
GNOME2 데스크탑을 위한 2D 화학 구조 편집기
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Versions of package gchempaint |
Release | Version | Architectures |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gchempaint: |
field | chemistry |
interface | x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning |
x11 | application |
|
License: DFSG free
|
GChemPaint는 다중 문서 인터페이스를 갖는 2D 화학 구조를 위한 편집기입니다.
추출된 분자는 NIST Webbook 및 PubChem에서 검색할 수 있습니다.
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gcrystal
|
Versions of package gcrystal |
Release | Version | Architectures |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gcrystal: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
x11 | application |
|
License: DFSG free
|
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.
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gcu-bin
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Versions of package gcu-bin |
Release | Version | Architectures |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package gcu-bin: |
role | program |
uitoolkit | gtk |
|
License: DFSG free
|
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)
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gcu-plugin
??? missing short description for package gcu-plugin :-(
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Versions of package gcu-plugin |
Release | Version | Architectures |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
Debtags of package gcu-plugin: |
field | chemistry |
role | plugin |
uitoolkit | gtk |
|
License: DFSG free
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gdis
|
Versions of package gdis |
Release | Version | Architectures |
sid | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.90-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.90-5 | amd64,armel,armhf,i386 |
buster | 0.90-5 | amd64,arm64,armhf,i386 |
bookworm | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gdis: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
|
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)
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gdpc
visualiser of molecular dynamic simulations
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Versions of package gdpc |
Release | Version | Architectures |
buster | 2.2.5-9 | amd64,arm64,armhf,i386 |
stretch | 2.2.5-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.5-3 | amd64,armel,armhf,i386 |
sid | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.2.5-15 | amd64,arm64,mips64el,ppc64el |
bullseye | 2.2.5-14 | amd64,arm64,mips64el,ppc64el |
Debtags of package gdpc: |
field | biology, biology:structural, chemistry, physics |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | viewing |
works-with | 3dmodel, image, video |
works-with-format | jpg, png |
x11 | application |
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License: DFSG free
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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.
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gelemental
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Versions of package gelemental |
Release | Version | Architectures |
buster | 1.2.0-12 | amd64,arm64,armhf,i386 |
jessie | 1.2.0-9 | amd64,armel,armhf,i386 |
bullseye | 2.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.0.2-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.0.2-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2.0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package gelemental: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
use | viewing |
x11 | application |
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License: DFSG free
|
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.
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ghemical
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Versions of package ghemical |
Release | Version | Architectures |
stretch | 3.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.0-4 | amd64,arm64,armhf,i386 |
bullseye | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
Debtags of package ghemical: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
|
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.
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gperiodic
|
Versions of package gperiodic |
Release | Version | Architectures |
trixie | 3.0.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.0.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.0.3-1 | amd64,arm64,armhf,i386 |
bullseye | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.0.10-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0.10-7 | amd64,armel,armhf,i386 |
Debtags of package gperiodic: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
|
License: DFSG free
|
GPeriodic은 화학 원소의 주기율표를 통해 검색하고, 각 요소의 자세한 정보를
볼 수 있도록 하는 작은 X/GTK+ 기반 프로그램입니다.
118 요소는 현재 리스트되어 있습니다.
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gromacs
Molecular dynamics simulator, with building and analysis tools
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Versions of package gromacs |
Release | Version | Architectures |
bookworm | 2022.5-2 | amd64,arm64,mips64el,ppc64el,s390x |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
experimental | 2025.0~beta-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
trixie | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2025.0~beta |
Debtags of package gromacs: |
field | biology, biology:structural, chemistry |
interface | commandline, x11 |
role | program |
uitoolkit | xlib |
x11 | application |
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License: DFSG free
|
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.
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gromacs-mpich
Molecular dynamics sim, binaries for MPICH parallelization
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Versions of package gromacs-mpich |
Release | Version | Architectures |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
upstream | 2025.0~beta |
Debtags of package gromacs-mpich: |
devel | lang:c, library |
field | biology, chemistry |
interface | commandline |
role | devel-lib, program |
scope | utility |
works-with | software:package |
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License: DFSG free
|
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.
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gromacs-openmpi
Molecular dynamics sim, binaries for OpenMPI parallelization
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Versions of package gromacs-openmpi |
Release | Version | Architectures |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
upstream | 2025.0~beta |
Debtags of package gromacs-openmpi: |
devel | lang:c, library |
field | biology, chemistry |
interface | commandline |
role | devel-lib, program |
scope | utility |
works-with | software:package |
|
License: DFSG free
|
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.
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jmol
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Versions of package jmol |
Release | Version | Architectures |
bullseye | 14.6.4+2016.11.05+dfsg1-4 | all |
stretch | 14.6.4+2016.11.05+dfsg1-3 | all |
jessie | 12.2.32+dfsg2-1 | all |
bookworm | 14.32.83+dfsg-2 | all |
trixie | 16.2.33+dfsg-1 | all |
sid | 16.2.33+dfsg-1 | all |
buster | 14.6.4+2016.11.05+dfsg1-4 | all |
upstream | 16.2.37 |
Debtags of package jmol: |
field | chemistry |
role | program |
scope | utility |
use | viewing |
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License: DFSG free
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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.
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kalzium
periodic table and chemistry tools
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Versions of package kalzium |
Release | Version | Architectures |
buster | 17.08.3-1 | amd64,arm64,armhf,i386 |
stretch | 16.08.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.14.2-1 | amd64,armel,armhf,i386 |
experimental | 24.08.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 20.12.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 24.12.0 |
Debtags of package kalzium: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | browsing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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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.
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katomic
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Versions of package katomic |
Release | Version | Architectures |
bullseye | 20.12.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.12.4-1 | amd64,armel,armhf,i386 |
stretch | 16.08.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
experimental | 24.08.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 18.04.1-1 | amd64,arm64,armhf,i386 |
upstream | 24.12.0 |
Debtags of package katomic: |
game | puzzle |
interface | x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | gameplaying |
x11 | application |
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License: DFSG free
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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.
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libcdk-java
Chemistry Development Kit (CDK) Java libraries
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Versions of package libcdk-java |
Release | Version | Architectures |
bookworm | 2.8-2 | all |
trixie | 2.9-2 | all |
sid | 2.9-2 | all |
jessie | 1.2.10-6 | all |
stretch | 1.2.10-6 | all |
buster | 1.2.10-7 | all |
bullseye | 2.3.134.g1bb9a64587-2 | all |
Debtags of package libcdk-java: |
devel | lang:java, library |
field | chemistry |
role | devel-lib |
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License: DFSG free
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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.
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mmass
Mass spectrometry tool for proteomics
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Versions of package mmass |
Release | Version | Architectures |
jessie | 5.5.0-4 | all |
buster | 5.5.0-5 | all |
stretch | 5.5.0-5 | all |
Debtags of package mmass: |
field | biology, chemistry |
interface | x11 |
role | program |
science | plotting, visualisation |
scope | application |
uitoolkit | gtk, wxwidgets |
use | analysing |
works-with | biological-sequence, db |
works-with-format | xml |
x11 | application |
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License: DFSG free
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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.
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mmass-modules
Mass spectrometry tool for proteomics - extension modules
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Versions of package mmass-modules |
Release | Version | Architectures |
jessie | 5.5.0-4 | amd64,armel,armhf,i386 |
buster | 5.5.0-5 | amd64,arm64,armhf,i386 |
stretch | 5.5.0-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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mopac7-bin
Semi-empirical Quantum Chemistry Library (binaries)
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Versions of package mopac7-bin |
Release | Version | Architectures |
sid | 1.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.15-6 | amd64,armel,armhf,i386 |
stretch | 1.15-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.15-6 | amd64,arm64,armhf,i386 |
bullseye | 1.15-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.15-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package mopac7-bin: |
field | chemistry |
role | program |
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License: DFSG free
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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.
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mpqc
Massively Parallel Quantum Chemistry Program
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Versions of package mpqc |
Release | Version | Architectures |
bullseye | 2.3.1-21 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.1-19 | amd64,arm64,armhf,i386 |
bookworm | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.3.1-18+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.1-16 | amd64,armel,armhf,i386 |
sid | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package mpqc: |
field | chemistry, physics |
interface | commandline, x11 |
role | program |
scope | utility |
uitoolkit | gtk |
x11 | application |
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License: DFSG free
|
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).
Please cite:
The Massively Parallel Quantum Chemistry Program (MPQC), Version 2.3.1, Curtis L. Janssen, Ida B. Nielsen, Matt L. Leininger, Edward F. Valeev, Joseph P. Kenny, Edward T. Seidl, Sandia National Laboratories, Livermore, CA.
(2008)
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mpqc-support
Massively Parallel Quantum Chemistry 프로그램 (지원 도구)
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Versions of package mpqc-support |
Release | Version | Architectures |
bookworm | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.1-16 | amd64,armel,armhf,i386 |
stretch | 2.3.1-18+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.1-19 | amd64,arm64,armhf,i386 |
bullseye | 2.3.1-21 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package mpqc-support: |
field | chemistry, physics |
interface | commandline, x11 |
role | program |
scope | utility |
suite | emacs |
uitoolkit | tk |
x11 | application |
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License: DFSG free
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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.
Please cite:
The Massively Parallel Quantum Chemistry Program (MPQC), Version 2.3.1, Curtis L. Janssen, Ida B. Nielsen, Matt L. Leininger, Edward F. Valeev, Joseph P. Kenny, Edward T. Seidl, Sandia National Laboratories, Livermore, CA.
(2008)
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msxpertsuite
mass spectrometry software suite - metapackage
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Versions of package msxpertsuite |
Release | Version | Architectures |
bullseye | 5.8.9-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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openbabel
Chemical toolbox utilities (cli)
|
Versions of package openbabel |
Release | Version | Architectures |
bullseye | 3.1.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.1.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1+dfsg-3 | amd64,arm64,armhf,i386 |
jessie | 2.3.2+dfsg-2 | amd64,armel,armhf,i386 |
trixie | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.3.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package openbabel: |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
use | converting |
|
License: DFSG free
|
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
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openfoam
Open source toolbox for Computational Fluid Dynamics (CFD) - binaries
|
Versions of package openfoam |
Release | Version | Architectures |
buster | 1812+dfsg1-2 | amd64,arm64,armhf,i386 |
bookworm | 1912.200626-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1912.200626-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
stretch | 4.1+dfsg1-1 | amd64,arm64,armhf,i386,ppc64el,s390x |
sid | 1912.200626-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bullseye | 1912.200626-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2406 |
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License: DFSG free
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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.
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pdb2pqr
Preparation of protein structures for electrostatics calculations
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Versions of package pdb2pqr |
Release | Version | Architectures |
stretch | 2.1.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.1.1+dfsg-5 | amd64,arm64,armhf,i386 |
bullseye | 2.1.1+dfsg-7+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.5.2+dfsg-3 | all |
jessie | 1.9.0+dfsg-1 | amd64,armel,armhf,i386 |
trixie | 3.6.1+dfsg-1 | all |
sid | 3.6.1+dfsg-1 | all |
upstream | 3.6.2 |
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License: DFSG free
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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
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psi3
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Versions of package psi3 |
Release | Version | Architectures |
stretch | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.4.0-5 | amd64,armel,armhf,i386 |
bookworm | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.4.0-6 | amd64,arm64,armhf,i386 |
Debtags of package psi3: |
field | chemistry, physics |
interface | commandline |
role | program |
science | calculation |
scope | suite |
use | calculating |
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License: DFSG free
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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
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pyfai
Fast Azimuthal Integration scripts
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Versions of package pyfai |
Release | Version | Architectures |
sid | 2024.05-3 | all |
stretch-backports | 0.15.0+dfsg1-1~bpo9+1 | all |
buster | 0.17.0+dfsg1-3 | all |
bookworm-backports | 2023.9.0-1~bpo12+1 | all |
stretch | 0.13.0+dfsg-1 | all |
jessie | 0.10.2-1 | amd64,armel,armhf,i386 |
bookworm | 0.21.3+dfsg1-4 | all |
bullseye | 0.20.0+dfsg1-3 | all |
buster-backports | 0.19.0+dfsg1-3~bpo10+1 | all |
trixie | 2024.05-3 | all |
upstream | 2024.09 |
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License: DFSG free
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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.
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pymol
Molecular Graphics System
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Versions of package pymol |
Release | Version | Architectures |
bookworm | 2.5.0+dfsg-1 | all |
buster | 2.2.0+dfsg-4 | all |
sid | 3.0.0+dfsg-1 | all |
trixie | 3.0.0+dfsg-1 | all |
bullseye | 2.4.0+dfsg-2 | all |
stretch | 1.8.4.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.7.2.1-1 | amd64,armel,armhf,i386 |
Debtags of package pymol: |
field | biology:structural, chemistry |
interface | 3d, x11 |
role | program |
scope | utility |
uitoolkit | tk |
use | learning, viewing |
works-with | image |
x11 | application |
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License: DFSG free
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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.
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python3-mpiplus
Python GPU framework for alchemical free energy calculations (Python 3)
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Versions of package python3-mpiplus |
Release | Version | Architectures |
trixie | 0.0.2+ds-1 | all |
sid | 0.0.2+ds-1 | all |
bookworm | 0.0.1-2 | all |
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License: DFSG free
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GPU-accelerated Python framework for exploring algorithms for alchemical free
energy calculations.
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python3-openbabel
Chemical toolbox library (Python bindings)
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Versions of package python3-openbabel |
Release | Version | Architectures |
bookworm | 3.1.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.1.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
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Versions of package python3-pymzml |
Release | Version | Architectures |
bookworm | 2.5.2+repack1-1 | all |
stretch | 0.7.6-dfsg-4 | all |
bullseye | 2.4.7-3 | all |
sid | 2.5.10+repack1-1 | all |
trixie | 2.5.10+repack1-1 | all |
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License: DFSG free
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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.
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qutemol
interactive visualization of macromolecules
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Versions of package qutemol |
Release | Version | Architectures |
bullseye | 0.4.1~cvs20081111-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.4.1~cvs20081111-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.4.1~cvs20081111-3.2 | amd64,armel,armhf,i386 |
trixie | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.4.1~cvs20081111-12 | amd64,arm64,armhf,i386 |
Debtags of package qutemol: |
interface | x11 |
role | program |
uitoolkit | glut, wxwidgets |
x11 | application |
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License: DFSG free
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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.
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rasmol
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Versions of package rasmol |
Release | Version | Architectures |
trixie | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.7.6.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.7.6.0-1 | amd64,arm64,armhf,i386 |
stretch | 2.7.5.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x |
jessie | 2.7.5.2-2 | amd64,armel,armhf,i386 |
Debtags of package rasmol: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
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License: DFSG free
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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.
The package is enhanced by the following packages:
rasmol-doc
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tandem-mass
mass spectrometry software for protein identification
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Versions of package tandem-mass |
Release | Version | Architectures |
trixie | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2013.09.01-2 | amd64,armel,armhf,i386 |
bookworm | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 201702011-1 | amd64,arm64,armhf,i386 |
stretch | 20151215-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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v-sim
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Versions of package v-sim |
Release | Version | Architectures |
sid | 3.7.2-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.7.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.7.2-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.7.2-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package v-sim: |
field | chemistry, physics |
interface | x11 |
role | program |
science | visualisation |
scope | application |
uitoolkit | gtk |
use | viewing |
x11 | application |
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License: DFSG free
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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.
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viewmol
graphical front end for computational chemistry programs
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Versions of package viewmol |
Release | Version | Architectures |
stretch | 2.4.1-24 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.1-22 | amd64,armel,armhf,i386 |
buster | 2.4.1-25 | amd64,arm64,armhf,i386 |
Debtags of package viewmol: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | motif |
use | learning, viewing |
x11 | application |
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License: DFSG free
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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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xbs
3-d models and movies of molecules
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Versions of package xbs |
Release | Version | Architectures |
bullseye | 0-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0-10 | amd64,arm64,armhf,i386 |
stretch | 0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0-8 | amd64,armel,armhf,i386 |
Debtags of package xbs: |
field | chemistry |
interface | 3d |
role | program |
scope | application |
uitoolkit | xlib |
use | printing, viewing |
works-with | text |
works-with-format | postscript |
x11 | application |
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License: DFSG free
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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.
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xdrawchem
Chemical structures and reactions editor
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Versions of package xdrawchem |
Release | Version | Architectures |
bullseye | 1.11.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.11.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.11.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.11.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.0-3 | amd64,armel,armhf,i386 |
stretch | 2.0-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.10.2.1-2 | amd64,arm64,armhf,i386 |
Debtags of package xdrawchem: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | qt |
use | editing, learning, viewing |
x11 | application |
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License: DFSG free
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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.
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xmakemol
program for visualizing atomic and molecular systems
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Versions of package xmakemol |
Release | Version | Architectures |
sid | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 5.16-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 5.16-9 | amd64,arm64,armhf,i386 |
bullseye | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 5.16-7 | amd64,armel,armhf,i386 |
Debtags of package xmakemol: |
field | chemistry |
hardware | input, input:mouse |
interface | x11 |
role | program |
scope | application |
uitoolkit | motif |
use | editing, viewing |
x11 | application |
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License: DFSG free
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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
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xmakemol-gl
원자 및 분자 시스템 (OpenGL) 시각화 프로그램
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Versions of package xmakemol-gl |
Release | Version | Architectures |
sid | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 5.16-7 | amd64,armel,armhf,i386 |
stretch | 5.16-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 5.16-9 | amd64,arm64,armhf,i386 |
Debtags of package xmakemol-gl: |
uitoolkit | motif |
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License: DFSG free
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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.
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Official Debian packages with lower relevance
gdpc-examples
example files for the gdpc program
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Versions of package gdpc-examples |
Release | Version | Architectures |
bookworm | 2.2.5-15 | all |
sid | 2.2.5-16 | all |
trixie | 2.2.5-16 | all |
jessie | 2.2.5-3 | all |
bullseye | 2.2.5-14 | all |
buster | 2.2.5-9 | all |
stretch | 2.2.5-6 | all |
Debtags of package gdpc-examples: |
field | biology, biology:structural, chemistry, physics |
role | documentation |
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License: DFSG free
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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.
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libcoordgen-dev
2D coordinate generation for chemical compounds - header files
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Versions of package libcoordgen-dev |
Release | Version | Architectures |
bookworm | 3.0.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.4.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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libmaeparser-dev
Development files to parse Schrödinger Maestro files
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Versions of package libmaeparser-dev |
Release | Version | Architectures |
trixie | 1.3.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.3.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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This package provides header files to develop one's own software
that uses a library wth an Open Source parser for Maestro (.mae)
files.
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libschroedinger-coordgenlibs-dev
2D coordinate generation for chemical compounds - header files
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Versions of package libschroedinger-coordgenlibs-dev |
Release | Version | Architectures |
buster | 1.1-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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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.
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python-pymzml-doc
mzML mass spectrometric data parsing - documentation
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Versions of package python-pymzml-doc |
Release | Version | Architectures |
bookworm | 2.5.2+repack1-1 | all |
stretch | 0.7.6-dfsg-4 | all |
sid | 2.5.10+repack1-1 | all |
bullseye | 2.4.7-3 | all |
trixie | 2.5.10+repack1-1 | all |
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License: DFSG free
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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).
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python3-amp
Atomistic Machine-learning Package (python 3)
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Versions of package python3-amp |
Release | Version | Architectures |
bookworm | 0.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.6.1-1 | amd64,arm64,armhf,i386 |
bullseye | 0.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 4878fc892f2cbc5cd9f29f7a367d7b05bdeb6ee9 |
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License: DFSG free
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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.
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python3-periodictable
Extensible periodic table of the elements (Python 3)
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Versions of package python3-periodictable |
Release | Version | Architectures |
trixie | 2.0.1-1 | all |
bookworm | 1.6.0-1 | all |
sid | 2.0.1-1 | all |
bullseye | 1.5.3-1 | all |
buster | 1.5.0-7 | all |
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License: DFSG free
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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.
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refmac-dictionary
dictionary for macromolecular refinement and model building
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Versions of package refmac-dictionary |
Release | Version | Architectures |
trixie | 5.41-3 | all |
bookworm | 5.41-2 | all |
bullseye | 5.41-2 | all |
buster | 5.41-1 | all |
sid | 5.41-3 | all |
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License: DFSG free
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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.
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Packaging has started and developers might try the packaging code in VCS
fdmnes
calculates spectra of different spectroscopies
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Versions of package fdmnes |
Release | Version | Architectures |
VCS | 0.0.20120607-1 | all |
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License: To-be-clarified
Version: 0.0.20120607-1
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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.
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molden
processing program of molecular and electronic structure
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Versions of package molden |
Release | Version | Architectures |
VCS | 5.2-1 | all |
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License: non-free
Debian package not available
Version: 5.2-1
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MOLDEN is a package for displaying Molecular Density from the Ab
Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the
Semi-Empirical packages Mopac/Ampac, it also supports a number of
other programs via the MOLDEN Format. MOLDEN reads all the required
information from the GAMESS / GAUSSIAN outputfile. MOLDEN is capable
of displaying Molecular Orbitals, the electron density and the
Molecular minus Atomic density. Either the spherically averaged
atomic density or the oriented ground state atomic density can be
subtracted for a number of standard basis sets. MOLDEN supports
contour plots, 3-d grid plots with hidden lines and a combination of
both. It can write a variety of graphics instructions; postscript, X,
VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The X
version of MOLDEN is also capable of importing and displaying of
chemx, PDB, and a variety of mopac/ampac files and lots of other
formats. It also can animate reaction paths and molecular
vibrations. It can calculate and display the true or Multipole
Derived Electrostatic Potential and atomic charges can be fitted to
the Electrostatic Potential calculated on a Connolly surface. MOLDEN
has a powerful Z-matrix editor which give full control over the
geometry and allows you to build molecules from scratch, including
polypeptides. MOLDEN was also submitted to the QCPE (QCPE619),
allthough the X version is considerably running behind on the current
one.
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molekel
Advanced Interactive 3D-Graphics for Molecular Sciences
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Versions of package molekel |
Release | Version | Architectures |
VCS | 5.4-1 | all |
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License: free
Debian package not available
Version: 5.4-1
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Molekel is an open-source multi-platform molecular visualization program.
Some of the features are:
- Different methods to speed-up rendering of molecules with support
for billboards and view-dependent level of detail techniques
- Programmable shaders; standard shaders to enhance rendering quality,
outline contours and perform sketch-like renderings are provided
- Visualization of residues (ribbon or schematic)
- Complete control over the generation of molecular surfaces (bounding
box and resolution)
- Visualization of the following surfaces:
- Orbitals
- Iso-surface from density matrix
- Iso-surface from Gaussian cube grid data
- SAS
- SES
- Van der Waals
- Animation of molecular surfaces
- Animation of vibrational modes
- Export high resolution images for 300+ DPI printing
- Export to PostScript and PDF
- Export animation
- Plane widget to visualize a scalar field: the plane can be freely
moved in 3d space and the points on the plane surface will be colored
according to the value of the scalar field: a cursor can be moved on
the plane surface to show the exact value of the field at a specific
point in space.
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tinker
Software Tools for Molecular Design
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Versions of package tinker |
Release | Version | Architectures |
VCS | 4.2-5~dev | all |
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License: free
Debian package not available
Version: 4.2-5~dev
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The TINKER molecular modeling software is a complete and general
package for molecular mechanics and dynamics, with some special
features for biopolymers. TINKER has the ability to use any of
several common parameter sets, such as Amber (ff94, ff96, ff98 and
ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS
(OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials,
and our own AMOEBA polarizable atomic multipole force
field. Parameter sets for other standard force fields such as GROMOS,
UFF, ENCAD and MM4 are under consideration for future releases.
The TINKER package includes a variety of novel algorithms such as a
new distance geometry metrization method that has greater speed and
better sampling than standard methods, Elber's reaction path methods,
several of our Potential Smoothing and Search (PSS) methods for
global optimization, an efficient potential surface scanning
procedure, a flexible implementation of atomic multipole-based
electrostatics with explicit dipole polarizability, a selection of
continuum solvation treatments including several variants of the
generalized Born (GB/SA) model, an efficient truncated Newton (TNCG)
local optimizer, surface areas and volumes with derivatives, a simple
free energy perturbation facility, normal mode analysis, minimization
in Cartesian, torsional or rigid body space, velocity Verlet
stochastic dynamics, an improved spherical energy cutoff method,
Particle Mesh Ewald summation for partial charges and regular Ewald
for polarizable multipoles, a novel reaction field treatment of long
range electrostatics, and more....
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No known packages available but some record of interest (WNPP bug)
rational protein design library
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License: LGPL
Debian package not available
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The EGAD Library is a modular, object oriented approach to rational protein
design. It is platform-independent, written in C++ and, most importantly,
free. Its raison d'etre is to serve as a tool for building protein design
applications. It can also be used as a test-bed for the comparison of
different energy functions and minimization algorithms under the same physical
model.
Citations of EGAD Library should reference the paper in the Journal of
Computational Chemistry. doi:10.1002/jcc.20727
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Evaluate the integrals in modern atomic and molecular theory
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License: GPL
Debian package not available
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Libint library is used to evaluate the traditional (electron repulsion)
and certain novel two-body matrix elements (integrals) over Cartesian
Gaussian functions used in modern atomic and molecular theory. The idea
of the library is to let computer write optimized code for computing
such integrals. There are two primary advantages to this: much less
human effort is required to write code for computing new integrals, and
code can be optimized specifically for a particular computer
architecture (e.g., vector processor).
Libint has been utilized to implement methods such as Hartree-Fock (HF)
and Kohn-Sham density functional theory (KS DFT), second-order
Moller-Plesset perturbation theory (MP2), coupled cluster singles and
doubles (CCSD) method, as well as explicitly correlated R12 methods.
The following software packages use Libint:
Improves mpqc (#409025) and psi3.
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No known packages available
openchrom
process chromatographic and mass spectrometric data
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License: EPL
Debian package not available
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OpenChrom is an open source software for chromatography based on the
Eclipse Rich Client Platform (RCP). Its focus is to handle mass
spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files
natively. OpenChrom is able to import binary and textual chromatographic
data files, such as *.D chromatograms from Agilent Technologies or
NetCDF. Moreover, it offers a nice graphical user interface and is
available for various operating systems, e.g. Windows, Linux, Solaris
and Mac OSX. A basis set of methods to detect baselines, peaks and to
integrate peaks in a chromatogram are implemented. Preprocessing steps,
e.g. to remove certain mass fragments (m/z) such as nitrogen (28) or
water (18), are supported by applying filter on the chromatogram or mass
spectrum. Extensions are welcome, as OpenChrom is open source and uses a
flexible approach, which allows others to implement their own methods,
algorithms, filters, detectors or integrators. Therefore, OpenChrom
shall be an efficiently system to process chromatographic and mass
spectrometric data using an extensible and flexible plugin approach.
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