Analysis software - Revision history

Oliver: /* MD Analysis libraries */

2011-04-21T01:08:19Z

MD Analysis libraries

← Older revision		Revision as of 01:08, 21 April 2011
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	== MD Analysis libraries ==		== MD Analysis libraries ==

	;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze ~~dcd~~ trajectories (~~in conjunction with a psf~~)		;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze a range of trajectories (e.g. DCD, XTC, TRR, XYZ) and single frames (PDB, GRO, CRD, PQR).

	;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.		;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

Agrossfield: /* MD Analysis libraries -- updated link for LOOS to point to the distribution web page on sourceforge*/

2010-08-16T18:17:27Z

MD Analysis libraries -- updated link for LOOS to point to the distribution web page on sourceforge

← Older revision		Revision as of 18:17, 16 August 2010
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	;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.		;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

	;[http://~~membrane~~.~~urmc~~.~~rochester.edu/Software/LOOS/Docs/main.html~~ LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out.		;[http://loos.sourceforge.net LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out.

	== Specialized tools ==		== Specialized tools ==

Oliver: /* Specialized tools */

2009-02-07T14:09:24Z

Specialized tools

← Older revision		Revision as of 14:09, 7 February 2009
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	== Specialized tools ==		== Specialized tools ==

	;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances.		;[http://hole.biop.ox.ac.uk/hole HOLE]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances.

	;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations.		;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations.

Oliver: /* MD Analysis libraries */

2009-02-07T14:07:57Z

MD Analysis libraries

← Older revision		Revision as of 14:07, 7 February 2009
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	== MD Analysis libraries ==		== MD Analysis libraries ==

	;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf)		;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze dcd trajectories (in conjunction with a psf)

	;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.		;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

Oliver: /* MD Analysis libraries */

2009-02-07T14:07:29Z

MD Analysis libraries

← Older revision		Revision as of 14:07, 7 February 2009
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	;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.		;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

	;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS}: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out.		;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out.

	== Specialized tools ==		== Specialized tools ==

Oliver: /* MD Analysis libraries */ LOOS

2009-02-07T14:07:06Z

MD Analysis libraries: LOOS

← Older revision		Revision as of 14:07, 7 February 2009
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	;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.		;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

			;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS}: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out.

	== Specialized tools ==		== Specialized tools ==

Oliver: categories

2008-06-30T15:49:00Z

Oliver at 15:48, 30 June 2008

2008-06-30T15:48:23Z

← Older revision		Revision as of 15:48, 30 June 2008
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	;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform		;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform

	;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect		;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect

	;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve		;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve

	;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]]		;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]]

			;Amber/[[ptraj]]: command-line based analysis

	== MD Analysis libraries ==		== MD Analysis libraries ==

	;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf)		;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf)
	~~;Amber/[[ptraj]]: command-line based analysis~~

	;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.		;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

Oliver: basic analysis list (Woolf Wiki + changes)

2008-06-30T15:47:39Z

basic analysis list (Woolf Wiki + changes)

New page

Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done".

== "Native" tools ==
Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools.

;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform
;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect
;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve
;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]]

== MD Analysis libraries ==

;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf)
;Amber/[[ptraj]]: command-line based analysis

;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use.

== Specialized tools ==

;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances.

;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations.

;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times.

; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences.

;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles.

== General purpose mathematical packages ==
;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities
;[[matlab]]:
;[[Mathematica]]:
;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

← Older revision		Revision as of 15:49, 30 June 2008
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	;[[Mathematica]]:		;[[Mathematica]]:
	;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.		;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.


			[[Category:Analysis]]
			[[Category:Software]]