Aplikasi Kimia di Ubuntu

Kembali otak-atik Ubuntu Linux. Fokusnya adalah optimalisasi kemampuan ubuntu untuk pengajaran kimia dan ilmu kimia sendiri. Dari list synatic package manager (SPM) ubuntu cukup banyak aplikasi terkait kimia yang memungkinkan digunakan dalam mendukung pembelajaran kimia di sekolah.
Beberapa deskripsi aplikasi-aplikasi tersebut sebagai berikut:
Xdrawchem (Chemical structures and reactions editor)
Xdrawchem adalah editor 2D untuk struktur dan reaksi kimia. Kemampuannya merupakan bayangan program komersial ChemDraw, terutama untuk 2D-nya.
GChempaint (2D chemical structures editor for the GNOME2 desktop)
GChempait adalah aplikasi yg mirip dengan Xdrawchem, namun ditambah dengan kemampuannya membuat dokumen dengan berbagai interface. Gambar berbagai molekul hasil GChempaint ini dapat disearch pada NIST Webbook and PubChem.
Chemtool (Chemical structures drawing program)

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 transfig).
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.
Openbabel (Chemical toolbox utilities)
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows 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:
* babel: 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
* obprop: Print standard molecular properties
* obfit: Superimpose two molecules based on a pattern
* obrotamer: Generate conformer/rotamer coordinates
* obchiral: Print molecular chirality information
* obrotate: Rotate dihedral angle of molecules in batch mode
Chemeq (Parser for chemical formula and equilibria)
Chemeq is a basic standalone filter written in C language, flex and bison. It inputs strings like:
2H2 + O2 —> 2 H2O
then it outputs LaTeX code and messages about the equilibrium of a chemical reaction.
example:~/src$ echo “2H2 + O2 —> 2 H2O” | chemeq -lc
2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O
OK
Easychem (Draw high-quality molecules and 2D chemical formulas)
EasyChem is a program that helps you creating high quality diagrams of molecules and 2D chemical formulas that can be exported to PDF, PS, LaTeX and fig.
EasyChem was originally developed to create diagrams for chemistry books and is now frequently used for this purpose in commercial and non-commercial chemistry-related books.
Bkchem (Python based chemical structures editor)
BKchem is a free chemical drawing program, which is written in Python.
Some of the features, you can expect:
* Drawing (bond-by-bond drawing; templates for common rings; expanding of common-groups; draws radicals, charges, arrows; color support …)
* Editing (unlimited undo and redo capabilities; aligning; scaling; rotation (2D, 3D) …)
* Export/Import (fully supported SVG-, OpenOffice.org-Draw-, EPS-export; basic support for CML1 and CML2 import and export)
Autodock (analysis of ligand binding to protein structure)
AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account.
The AutoDock program performs the docking of the ligand to a set of grids describing the target protein. AutoGrid pre-calculates these grids.
Gperiodic (periodic table application)
GPeriodic is a small X/GTK+-based program which allows you to browse through a periodic table of chemical elements, and view somewhat detailed information on each of the elements. 118 elements are currently listed.
gElemental (Periodic Table viewer)
gElemental is a GTK+ periodic table viewer that provides detailed information about chemical elements.
It features a table view which allows the elements to be coloured thematically by several properties, a sortable list view and an element properties dialog, displaying a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties.
xmakemol (A program for visualizing atomic and molecular systems)
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
horae (interactive graphical processing and analysis of EXAFS data)
ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest, including deglitching, aligning, merging, background removal, and Fourier transforms.
ARTEMIS is an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis.
HEPHAESTUS is a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data.
PSI3 (Quantum Chemical Program Suite)
PSI3 is an ab-inito quantum chemistry program.  It is especially designed to compute properties of small to medium molecules using high-level ab initio techniques.
It can compute energies and gradients for the following methods:
* Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF)
* Complete active space SCF (CASSCF)
* Coupled-cluster singles doubles (CCSD)
Additionally, it can compute energies for the following methods:
* Unrestricted open shell Hartree-Fock (UHF)
* Closed/open shell Moeller-Plesset pertubation theory (MP2)
* Closed shell linear R12 Moeller-Plesset pertubation theory (MP2-R12)
* Configuration-interaction (CI)
* Multireference configuration-interaction (MRCI)
* Coupled-cluster singles doubles with pertubative triples (CCSD(T))
* Closed shell and general restricted open shell equation-of-motion CCSD
It also includes an internal coordinate geometry optimizer.










Aplikasi Kimia di Ubuntu
Kembali otak-atik Ubuntu Linux. Fokusnya adalah optimalisasi kemampuan ubuntu untuk pengajaran kimia dan ilmu kimia sendiri. Dari list synatic package manager (SPM) ubuntu cukup banyak aplikasi terkait kimia yang memungkinkan digunakan dalam mendukung pembelajaran kimia di sekolah.
Beberapa deskripsi aplikasi-aplikasi tersebut sebagai berikut:
Xdrawchem (Chemical structures and reactions editor)
Xdrawchem adalah editor 2D untuk struktur dan reaksi kimia. Kemampuannya merupakan bayangan program komersial ChemDraw, terutama untuk 2D-nya.
GChempaint (2D chemical structures editor for the GNOME2 desktop)
GChempait adalah aplikasi yg mirip dengan Xdrawchem, namun ditambah dengan kemampuannya membuat dokumen dengan berbagai interface. Gambar berbagai molekul hasil GChempaint ini dapat disearch pada NIST Webbook and PubChem.
Chemtool (Chemical structures drawing program)
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 transfig).
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.
Openbabel (Chemical toolbox utilities)
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows 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:
* babel: 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
* obprop: Print standard molecular properties
* obfit: Superimpose two molecules based on a pattern
* obrotamer: Generate conformer/rotamer coordinates
* obchiral: Print molecular chirality information
* obrotate: Rotate dihedral angle of molecules in batch mode
Chemeq (Parser for chemical formula and equilibria)
Chemeq is a basic standalone filter written in C language, flex and bison. It inputs strings like:
2H2 + O2 —> 2 H2O
then it outputs LaTeX code and messages about the equilibrium of a chemical reaction.
example:~/src$ echo “2H2 + O2 —> 2 H2O” | chemeq -lc
2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O
OK
Easychem (Draw high-quality molecules and 2D chemical formulas)
EasyChem is a program that helps you creating high quality diagrams of molecules and 2D chemical formulas that can be exported to PDF, PS, LaTeX and fig.
EasyChem was originally developed to create diagrams for chemistry books and is now frequently used for this purpose in commercial and non-commercial chemistry-related books.
Bkchem (Python based chemical structures editor)
BKchem is a free chemical drawing program, which is written in Python.
Some of the features, you can expect:
* Drawing (bond-by-bond drawing; templates for common rings; expanding of common-groups; draws radicals, charges, arrows; color support …)
* Editing (unlimited undo and redo capabilities; aligning; scaling; rotation (2D, 3D) …)
* Export/Import (fully supported SVG-, OpenOffice.org-Draw-, EPS-export; basic support for CML1 and CML2 import and export)
Autodock (analysis of ligand binding to protein structure)
AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account.
The AutoDock program performs the docking of the ligand to a set of grids describing the target protein. AutoGrid pre-calculates these grids.
Gperiodic (periodic table application)
GPeriodic is a small X/GTK+-based program which allows you to browse through a periodic table of chemical elements, and view somewhat detailed information on each of the elements. 118 elements are currently listed.
gElemental (Periodic Table viewer)
gElemental is a GTK+ periodic table viewer that provides detailed information about chemical elements.
It features a table view which allows the elements to be coloured thematically by several properties, a sortable list view and an element properties dialog, displaying a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties.
xmakemol (A program for visualizing atomic and molecular systems)
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
horae (interactive graphical processing and analysis of EXAFS data)
ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest, including deglitching, aligning, merging, background removal, and Fourier transforms.
ARTEMIS is an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis.
HEPHAESTUS is a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data.
PSI3 (Quantum Chemical Program Suite)
PSI3 is an ab-inito quantum chemistry program.  It is especially designed to compute properties of small to medium molecules using high-level ab initio techniques.
It can compute energies and gradients for the following methods:
* Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF)
* Complete active space SCF (CASSCF)
* Coupled-cluster singles doubles (CCSD)
Additionally, it can compute energies for the following methods:
* Unrestricted open shell Hartree-Fock (UHF)
* Closed/open shell Moeller-Plesset pertubation theory (MP2)
* Closed shell linear R12 Moeller-Plesset pertubation theory (MP2-R12)
* Configuration-interaction (CI)
* Multireference configuration-interaction (MRCI)
* Coupled-cluster singles doubles with pertubative triples (CCSD(T))
* Closed shell and general restricted open shell equation-of-motion CCSD
It also includes an internal coordinate geometry optimizer.