Alphabetical list of 3D data formats

Alphabetical list of 3D API specifications and data formats

http://local.wasp.uwa.edu.au/~pbourke/dataformats/

3D2	Stereo CAD-3D object format
3DML	Flatland 3DML language
AC3D	AC3D
3DS ASE ASC	3D-Studio File Format 3D Studio Max Ascii Export Format 3D Studio Ascii Format
ALC	Alchemy III molecule file format
AL2	Alchemy 2000 molecule file format
BMF	BMF by David Farrell, exported from 3dStudio by "view3ds'.
CDF	Cyberspace Description Format
CGM	Computer Graphics Metafile (ISO/IEC standardfor vector graphics)
cinema4d	Cinema4d file format from "Maxon Computer"
COB	Calgari trueSpace2 File Format
DAE	Sony / Khronos Collada
cube	Gaussian cube file format for volumetric data
DF3	Povray DF3 density (volumetric) format
Direct-X	Microsofts answer to QuickDraw3D and OpenGL
DMO	Duke Nukem 3D or Redneck Rampage
DWF	Format used by AutoDesks attempt at an internet format for it's models, used by the WHIP viewer.
DXF2000 Release 14 Release 12 Release 10	DXF, AutoDesk/AutoCAD interchange format in the various format versions that have appeared over the years.
Minimal 3D DXF	The minimal requirements to represent 3D geometry in DXF, useful for creating geometry for commercial packages from your own software.
EGDR	MOLA Experiment Gridded Data Record
FACT	From ElectricImage
FBX	Autodesk FBX
FFIVW	File Format for the Interchange of Virtual Worlds
fld	AVS Field format.
FLT	OpenFlight format by MulitGen Inc
GEO	Videoscape geo an early Amiga 3D animation program written by Allen Hastings.
Geom	Geom format as used by "Stereo", an OpenGL interactive stereo pair package.
GLF	3D font format for the GLF library
GOCAD	GOCAD ascii data format
HIV	HyperChem molecular format
HPGL	Hewlett Packard Graphics Language for platters
hf	Hyperfun: Language for F-rep Geometric Modelling
IGES	Initial Graphics Exchange Specification by the National Bureau of Standards
ILDA	International Laser Display Association
Infini3D	Infini3D internal format
Inventor	Inventor ASCII format from SGI
IRIT	IRIT interchange format by Gershon Elber
LWOB Lightwave 5.x	LightWave Object File format Importing geometry into Lightwave 5.x
MDL	From Cornell University and Indiana University
MGF	Materials and Geometry format originally appearing as part of the Radiance package. By Greg Ward, Lawrence Berkeley Laboratory.
MI	Mental Images, as used by Mental Ray, SoftImage, and others
MOL2	Tripos mol2 molecule format
MovieBYU	Format from Birmingham Young University to represent polygons, originally designed for FORTRAN file IO.
MS3D	MilkShape 3D format
MSLD	Manchester Scene Description Language
MTL	Lightwave / OBJ material file
NDO	NENDO by Izware
nff	For Eric Haines' SPD package
nff	Neutral ASCII File Format
enff	Extensions to Neutral File Format
NUAGES	Format for the NUAGES software, a tool for 3D reconstruction from parallel cross-sections
OBJ	Wavefront .obj file format specification for the Advanced Visualizer software.
OFF	OFF format as used by the Geometry Center
OFF	OFF format specification originally developed by WSE.
OOGL	As used by GeomView
PEDR	MOLA Precision Experiment Data Records from NASA
PDB (V2.1)	Protein Data Base (Atomic Coordinate File)
PHD	PolyHedra Database (NetLib)
PI	Format for the polyray raytracer by Alexander Enzmann
PLG, FIG, WLD	Virtual World formats as used in Gossamer, Rend386, and others.
PLY	Polygon File Format also known as the Stanford Triangle Format.
Poly	Another Polygon Format from the University of Iowa, Image Analysis Facility
PS	Introduction to Postscript
POVRAY (v3.6)	Scene format for the Persistence Of Vision RAYtracer (and derivatves).
PVL	Processed VoLume (and other RAW formats) as used by the Drishti volume rendering software.
Macperspective	Translator for this undocumented format.
PowerFlip	Data format (SGI)
PRT	PRT raytracer format by Kory Hamzeh
PRT	Unigraphics "parts" file format.
q3o	Quick3D Object File and Scene file format (.q3s)
QuickDraw3D Primitive summary	Apple's Quickdraw 3D meta format
radio	Radio format by Anthony D'Agostino
RAD V3.1 RAD V2.5 ArchiCAD -> Radiance StrataStudio -> Radiance	Radiance scene description by Greg Ward. ArchiCAD to Radiance converter StrataStudio to Radiance converter
RAW	PovRay raw triangle format
RAY RAY summary	RayShade scene description format, a solid modelling by Craig Kolb.
RIB	Pixar RenderMan scene description (RenderMan Interface Bytestream)
Rotater	Macintosh interactive line and point viewer by Craig Kloeden.
rsd	Playstation
SAT	ACIS 3D format for viewing and transferring solid information
SCENE	A proposed format for 3D geometry
SCN	SCeNe format designed to replace SFF for the Rtrace ray-tracer.
SDML Old SDML	Spatial Data Modelling Language
SHP	ERSI Shapefile
SLC	SLiCe format
STL	Industry standard format for stereoLithography.
STP	SteinLib format
STEP	Standard for exchange of product model
Super3D	Text export format used by the Macintosh modeller Super3D.
SURF	Export format from 3D-XplorMath
Tachyon	Preliminary scene format for tachyon by John E. Stone
FORM TDDD	By Impulse's Turbo Silver for Sense8's WorldToolKit Neutral File Format specification
tet	Format for tetrahedra, originating at the Computer Science department of Williams College.
TIN	Triangular Irregular Network
TM	LONI triangle surface model format to represent surface models.
TP	TecPlot file format
TRI	Triangle format
U3D	Universal 3D
UNREAL	UNREAL File Format
V	VIVID file format by Stephen Coy
VEF	Vertex - Edge - Face format
Vision3D	Text format for the Macintosh Vision3D modeller
VLA	Digistar II VLA format
vmd	VMD - WinOSi (XOSi, MacOSi) raytacer by Michael Granz.
vol	Paul Bourke volumetric data format
VRI	Virtual Reality Interchange Language
WLD	Morfit's WorldBuilder format
WRM	World Reference Model by Multigen Inc.
VRML V1.0 VRML 97	The Virtual Reality Modelling Language
WMF	Windows Metafile Format
x3d	WEB3D consortium
XYZ	XYZ molecular format
YASRT	YASRT - Yet Another Simple Ray Tracer
YAODL	SGI PowerFlip format

file format surf

*.surf

http://filext.com/file-extension/SURF

3D Scanner File

http://local.wasp.uwa.edu.au/~pbourke/dataformats/surf/

QuteMol

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers 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.

• Real Time Ambient Occlusion
• Depth Aware Silhouette Enhancement
• Ball and Sticks, Space-Fill and Liquorice visualization modes
• High resolution antialiased snapshots for creating publication quality renderings
• Automatic generation of animated gifs of rotating molecules for web pages animations
• Real-time rendering of large molecules and protein (>100k atoms)
• Standard PDB input
• Quick installers for Win and Mac OS X (intel) (new!)
• Support as a plugins of the NanoEngineer-1 the modeling and simulation program for nano-composites (new!)

FSL library of analysis tools for FMRI, MRI and DTI brain imaging data.

http://www.fmrib.ox.ac.uk/fsl/index.html

Introduction
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK. FSL runs on Apple, PCs (Linux and Windows) and Sun, and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces).

Referencing
To quote the relevant references for FSL tools you should look in the individual tool's manual page (or the Analysis Group publications page), and also the FSL overview paper:
S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004

Next - see the list of tools in FSL.

ParaSolid, geometric modeling kernel, modeleur géométrique

file extension .x_t

There are two main suppliers of kernel software in the market, who provide the basic routines that are used by the overwhelming majority of application software packages. Spatial's ASIC is used to provide the guts for AutoCAD and one or two other packages, while Parasolid, developed by Unigraphics Solutions, is used by most mid-range CAD application developers, such Solid Edge, Solid Works, MicroStation Modeller, Top Solid, etc. Parasolid is also claimed to be the only kernel that is used in high-end 3D modelling systems.

Parasolid is a geometric modeling kernel originally developed by ShapeData, now owned by "Siemens Automation & Drives" former UGS Corp., that can be licensed by other companies for use in their 3D computer graphics software products. It is used in many Computer-aided design (CAD), Computer-aided manufacturing (CAM), Computer-aided engineering (CAE), Product visualization, and CAD data exchange packages, for example: NX (Unigraphics), SolidWorks, SolidEdge, Powershape, T-FLEX CAD, MasterCAM, OneCNC, Virtual Gibbs, DesignFlow, DesignSpace, Renishaw Productivity+, STAR-Design, and Moldflow.

When exported from the parent software package, a Parasolid commonly has the file extension .x_t. Most Parasolid files can communicate and migrate only 3D solids and/or surface data - Parasolid files currently cannot communicate and migrate 2D data such as lines and arcs.

Exemple:

TopSolid est un logiciel de conception assistée par ordinateur conçu et réalisé par Missler Software. Apparu en 1987 sous le nom commercial TopCAD, il était alors l'un des premiers logiciels de CAO volumique fonctionnant sur micro-ordinateur, ce qui lui avait valu la dénomination de "Catia sur micro". Il utilisait alors un modeleur polyédrique c'est-à-dire approximant les formes géométriques par des polyèdres (à facettes planes). TopSolid est donc une CFAO, qui utilise le modeleur géométrique exact ParaSolid, et qui est capable de lire et écrire dans tous les formats ouverts du marché, ainsi que dans quelques formats propriétaires, comme CATIA ou ParaSolid. TopSolid est aujourd'hui diffusé dans le monde entier, et revendique la seconde place française des logiciels de CFAO, derrière Dassault Systèmes avec les logiciels CATIA et Solidworks. Il est même le premier en FAO pure. Il est aussi dans les dix premiers mondiaux.

comsol finite element CAD import module

Getting your CAD geometries ready for FEA modeling is easier than ever with the CAD Import Module. It facilitates the reading of industry-standard formats such as STEP, IGES, ACIS® (SAT®) or Parasolid®. Extra add-ons support file formats for packages that have their own geometry kernel.

The CAD Import Module goes beyond just the reading of file formats. The interactive repair feature assures that imported geometries are mathematically correct for FEA modeling. And, in order to cut down on unnecessary details in your CAD geometries, defeaturing tools that remove fillets, small faces, sliver faces, as well as spikes or short edges are included.

The CAD Import Module also provides a bidirectional interface to SolidWorks® that maintains associativity with the CAD system. This means that parameters can be changed in COMSOL models, which result in automatically updating the CAD geometry in SolidWorks that then updates the COMSOL geometry for a new model.

File formats supported by COMSOL products

Product	File format (file extensions)	Supported versions
COMSOL Multiphysics	STL (.stl)
	VRML (.wrl, .wml)	1.0
	DXF (.dxf)	up to R14
	GDS (.gds)¹	2
CAD Import Module	Parasolid (.x_t, .x_b)	up to V18
	SAT (.sat, .sab)	up to R17
	STEP (.step, .stp)	AP203, AP214
	IGES (.igs, .iges)	up to 5.3
CATIA V4 Import Module	CATIA V4 (.model)	4.1.9 to 4.2.4
CATIA V5 Import Module	CATIA V5 (.CATPart, .CATProduct)	R2 to R17
Inventor Import Module	Autodesk Inventor (.ipt)²	6 to 11
Pro/E Import Module	Pro/Engineer (.prt, .asm)	16 to Wildfire 3
VDA-FS Import Module	VDA-FS (.vda)	1 and 2

¹ GDS Import requires COMSOL Script.
² Only import of parts is supported.

• CAD Import Modules Platform Support
• CAD Import Specifications (PDF)
• SolidWorks Live Interface

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autres formats:

http://www.spinfire-fr.com/SpinFireProfessionnel/FormatsCAODAO/tabid/56/Default.aspx

Spartan Mac OSX intel

Wavefunction is pleased to announce the release of Spartan'06 for Macintosh – Molecular Modeling for Intel-based Mac's with support for OS X 10.5 (Leopard). This new suite of software is designed to provide Macintosh users with easy to use modeling tools across a wide range of computational chemistry tasks, including conformational searching, calculation of structure, energies, and properties, and quantifying 3-D molecular similarity.

http://www.wavefun.com/products/macintosh/Spartan06/mac_spartan_pricing.html

Spartan'06 is the release of Wavefunction's flagship Spartan line. In addition to the performance, stability, and functionality provided by more than 15 years of professional software development, the following New Features have been added.

---------

chapter 15

This chapter describes functions available under the Setup menu.
Calculations is used to specify molecular mechanics calculations,
semi-empirical calculations, Hartree-Fock molecular orbital
calculations, and correlated calculations, including local density
calculations, density functional calculations, Møller-Plesset
calculations, coupled cluster calculations and quadratic configuration
interaction calculations for ground-state species, and configuration
interaction calculations, local density calculations and (time
dependent) density functional calculations for excited-state species.
Tasks include calculation of energy, equilibrium structure and
conformation, transition-state structure and constructing energy
profiles, although not all tasks are available for some methods. A
wide variety of all-electron Gaussian basis sets are supported for
Hartree-Fock and correlated calculations as are pseudopotentials
for calculations on molecules incorporating heavy elements. Also
provided are a number of thermochemical recipes, including G3 and
G3(MP2), as well as a new (and more economical) parameterized
scheme. Calculations also requests IR, NMR and UV/visible spectra,
and calculation and printing of a variety of molecular properties.
Finally, Calculations identifies libraries and specifies conditions for
identifying similar molecules, based either on molecular structure or
chemical functionality, as well as for identifying molecules that are
compatible with a pharmacophore.
----------

Spartan'06 can retrieve and plot experimental IR (~ 14,000 molecules) and UV/Vis (~ 1,500) spectra from the NIST Chemistry Webbook.

---------

Vertical excitation spectra based using either CIS/CIS(D) or Time Dependent DFT models is provided.

---------

Click here for itemized New Feature List (pdf file)

	Graphical User Interface Features: (RED items not available in Spartan'06 Essential)
	Substituent Builder for construction of substituted molecules / virtual libraries
	Assignment of Chemical Function Descriptors
	Experimental IR and UV/vis spectra available from NIST (on-line) database

Molpro quantum chemistry package

Molpro is a complete system of ab initio programs for molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Using recently developed integral-direct local electron correlation methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

uv-vis prediction

----------

Molpro benchmarks

The timings for the standard Molpro benchmark suite:

Version 2006.3

• macpro_intel_4cpu

Molpro: Secondary platforms

MOLPRO is not tested regularly on the following machines, but has worked on them in the past..

Machine name	Hardware and operating system	Integer bytes	Other information	Known problems
apple-intel	i386-apple-darwin	4	Intel Fortran 9.0

Computational Methods and Tools

http://www.chem.ucsb.edu/~kalju/comp_tools.html

Computational Biochemistry is Not a Set of Black Box Techniques

A good part of gas phase organic and inorganic chemistry can be described well using standard methods of quantum chemistry and statistical mechanics. There are two fundamental reasons why quantum chemistry and statistical mechanics are so successful in describing the chemistry and thermodynamics of molecules in the gas phase chemistry. First, the molecules of interest to the gas phase chemistry are typically small, and thus amenable to highly accurate quantum chemical calculations. Second, isolated molecules or molecular complex in the gas phase have only a few energetically accessible states, and statistical averaging over these states is often feasible. The situation is very different in biochemistry, where one typically studies heterogeneous polymers, such as proteins or nucleic acids, that interact with other molecules in aqueous environment via multitude of weak interactions. Such molecules and molecular complexes are often too large for quantitative description by even the crudest quantum chemical methods, and possess so many energetically accessible states that their complete enumeration is prohibitive. It is clear that research problems in computational biochemistry cannot be solved by simply applying "black box" techniques that have been so successful in characterizing the gas phase chemistry.

Quantum Chemistry of Biomolecules

One powerful research strategy to make computational analysis of biomacromolecules feasible involves the combination of reductionism and systems approach. In the first, reductionist stage, a necessary description of components of a biological macromolecule is obtained using quantum mechanics. Then, during the systems approach stage, molecular simulation techniques based on a simplified Hamiltonian are used to describe the structure, motions, and thermodynamics of the whole system. For example, quantum chemistry allows determination of charges, dispersion coefficients (van der Waals parameters), and barriers for torsional motion (flexibility) of components of macromolecules. Quantum chemistry also provides information about the structure, reactivity, and spectroscopic properties of biological molecules. Such information may be needed as input when applying molecular simulation techniques. In summary, quantum chemistry provides an excellent starting point in understanding many biochemical phenomena.

A large number of powerful quantum chemistry programs are available. Below is a list of some quantum chemistry programs that I find useful in my research:

• Dalton
  
  • Molecular polarizabilities
  • Dispersion coefficients (van der Waals parameters)
  
  
• DIRCCR12
  
  • Explicitly correlated calculations
  • Highly accurate energies
  
  
• Gaussian
  
  • All the usual: geometries, isotope effects, conformational search, reaction paths, solvation
  • Trickier things: QM/MM via ONIOM, NMR properties, UV-vis
  
  
• Gamess
  
  • Environment description via effective fragment potentials
  • Renormalized coupled cluster energies
  
  
• Jaguar
  
  • Conformational analysis
  • Solvation free energies
  
  
• SAPT
  
  • Intermolecular forces
  • Dispersion interactions
  
  
• Molpro
  
  • Multireference systems
  • Prediction of UV-Vis spectra
  
  
• Spartan
  
  • Electronic structures, conformational analysis
  • Visualization of molecular properties
  
  

Molecular Simulations

Description of the dynamic behavior and thermodynamic properties of biological macromolecules molecules in solution requires application of molecular simulation techniques. Simulation techniques such as molecular dynamics and Monte Carlo sampling are well established for description of physical properties of fluids. Molecular dynamics simulations have been employed also to describe dynamical structure of proteins, nucleic acids, and their complexes. Free energy simulations provide a theoretically rigorous way to evaluate binding free energies, opening up possibilities to predict efficacy and safety of potential drug candidates.

The field of molecular simulations is plagued by its own problems. For example, it is unlikely that molecular dynamics simulations with currently accessible timescales in the order of 10-100 ns can capture the full dynamics of biological macromolecules. Similarly, it is not clear if currently available molecular mechanics force fields and sampling methods are sufficient for reliable description of binding affinities in novel systems.

Despite these problems, molecular simulations have been proven valuable in understanding chemical reactivity in condensed media and appear promising in understanding the mechanism of enzyme action. Some of the molecular simulation programs that I have used are:

• BOSS
  
  • Parameterization of OPLS-AA force field and conformational analysis
  • Monte Carlo simulations of pure liquids, calculation of free energies of solvation
  
  
• CHARMM
  
  • Protein structure and dynamics
  • Correlation of atomic motions in enzymes
  
  
• MCPro
  
  • Monte Carlo simulations of proteins
  • Free energies of binding of drug candidates
  
  
• NAMD
  
  • Protein structure and dynamics
  • Conformational free energies
  
  
• TINKER
  
  • Reaction free energies via thermodynamic cycles
  • Parameterization of polarizable force fields
  
  

Molecular Visualization

Biological macromolecules are a lot more complex than typical organic molecules. The complexity arises from the large number of atoms in a biological macromolecule, and from the possibility of relatively free rotation around many covalent bonds in a macromolecule. The low rotational barriers give macromolecules flexibility and high conformational complexity. The number of theoretically possible three-dimensional structures that any macromolecule can take is enormous. However, each biological macromolecule adopts a distinct three-dimensional conformation, called the native conformation. Prediction of the native conformation of a unique biomacromolecule based on its covalent structure is a challenging problem, and most information about macromolecular structures is obtained from analysis of X-ray diffraction data from single crystals or from analysis on NMR data of dissolved macromolecules. Further analysis of these structures can be performed using molecular simulation techniques. For example, molecular dynamics simulations allow studying enzyme-substrate complexes, which cannot be studied experimentally due to rapid catalytic turnover under experimental conditions. Visualization tools are indispensable for analysis and presentation of macromolecular structures. Some that I find most useful in my research are:

• PyMol
  
  • Raytraced publication-quality images and movies
  • Complex scenes thanks to a powerful command language
  
  
• gOpenMol
  
  • Analysis of molecular dynamics trajectories
  • Visualization and analysis of macromolecular structures
  
  
• MOLDEN
  
  • Creation and editing of coordinate files
  • Analysis of outputs from quantum chemistry programs
  
  
• VMD
  
  • Analysis of molecular dynamics trajectories
  • Interactive molecular dynamics
  
  
• MOLEKEL
  
  • Visualization and analysis of macromolecular structures
  • Visualization of molecular properties from quantum chemistry programs
  
  

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matlab mac os -or octave

Installation of matlab on linux or macOSX is not so easy.

First the same 3disks but it is different: Mac OS X does not have a Linux kernel and its Darwin kernel is based on FreeBSD and Mach technologies.

Matlab linux macOSX R14 after the name has changed 2007a, 2008 etc...

remarks:

CD2 and CD3 content ureadable data

It works well with mount -o loop .iso /mnt/

For a open source alternative to this, you should check out "octave". It is mostly compatible with matlab.

http://www.gnu.org/software/octave/

i

Starting Installation:

see http://linuxexpert.wordpress.com/2007/06/18/how-to-install-matlab-7-r14-for-linux/

you need your disks

it’s 3 cd’s collection as ISO images with totally 1.11 GB.

You need 3 files:

-----------

license.dat
license.lic
readme_lic.txt

------------

1. you have to copy license.dat to the installation folder; ~/$MATLAB/.

2. you have to initiate this command from the $MATLAB not from CD.

sudo sh /media/cdrom/install



if you are tired from writing cp command for copying files u can initiate the file manager in the root permissions, i do it for ubuntu with Gnome file manager “Nautilus”.

sudo cp /media/ramy/license.dat /media/ramy/matlab/etc/
# you can do it in windows-like way
sudo nautilus


3. Welcome Screen as usual, press OK.



4. License Agreement, press OK.

5. u can note that installation directory is the same that you initiate the installer from by the command in step 2, you have to put the license.dat there because the installer test if it’s there then it moves it to ~/$MATLAB/etc. press OK.

6. I’m not sure about this message, so proceed and press OK.



7. Also continue, by pressing OK.



8. I’m already chosen all the packages and toolboxes with matlab, press OK.



9. press the button beside “Create symbolic…”, then press OK.



10. press OK.



11. You are asked to put the two other CD’s, press OK.



12. Installation Complete, but the story does not complete :P.

13. You have to open the “license.lic” file and replace the string “your_host_name” with the hostname of the computer where Matlab is being installed, ok if u don’t know what’s the host name go System->Administration->System Monitor-> System tab. In my system it’s ramy-desktop.



14.Copy the edited “license.lic” file to “$MATLAB/etc/”.

15. copy the matlab script file from $MATLAB/bin/scripts to $MATLAB/bin.

16. in the Matlab folder you have install_matlab shell script file, you have to initiate that script you can use this command.

sudo sh install_matlab

then , u will have a wizard in the terminal, ok it’s sth long, if you are not interested in any modification by accepting the default configurations. i’m a big YES MAN so accepting all of them. if you forget this last step u will have only the matlab running without any functionality because this step makes the required default path configuration and library path configuration.