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Features
The features given below for Brabosphere and CrdView always pertain to the latest development version published on SourceForge. The latest stable version may subsequently miss some of them.
Common
- Free OpenSource software released under the GNU General Public License.
- Run on a large number of platforms using the native look 'n' feel of each platform.
- Can read a large number of coordinate file formats. The size of the molecular systems that can be read, is only limited by RAM (tested up to 1 million atoms!). There is, however, a limit for reading file formats provided by Open Babel. That library is limited to around 65000 atoms.
- Molecules are visualised in 3D using the high-performance OpenGL library utilising the hardware acceleration capabilities of current videocards. This also enables the applications to run over the network using X- or VNC-servers that support the protocol (Cygwin for example).
- All manipulations of the molecules are done using the mouse (or keyboard) and modifier keys, disabling the need for akward 'states' and the need for remembering the current state.
- The 3D scene can be exported as an image in several formats.
Brabosphere
- Molecule builder:
- Atoms can be added and positioned using absolute or relative cartesian coordinates and internal coordinates.
- They can, of course, also be deleted
- Atoms or groups of atoms can be moved using mouse/keyboard or by giving the exact values.
- Groups of atoms can be rotated around their center of mass.
- Bonds, valence angles and torsion angles can be altered using the mouse/keyboard. Calculating torsion potentials has never been easier!
- The following properties can be visualised in the 3D windows:
- Element type and index
- Mulliken or stockholder's charges
- Atomic forces
- An unlimited number of 3D density isosurfaces with different colors and transparency settings
- Calculations are saved in the Chemical Markup Language (CML) format, the XML-based chemistry format of the future.
- The following types of BRABO calculations can be set up:
- Single point energy
- Energy and forces
- Geometry optimization
- The calculation settings can be changed in extreme detail with an interface allowing the addition of new keywords and options. Generated input files can be reviewed before execution.
- An easy interface is provided for showing all output files created by a calculation.
- 2D electron density map files created by BRABO's Potdicht program can be visualized in high quality in a variety of ways. Regions can be analyzed for extrema in the density.
- 3D hydrogen-like orbitals can be calculated analytically for all elements and visualized using isodensity and scatter plots.
- MDI: Brabosphere can open an unlimited number of calculations and present them in the native Multiple Document Interface of each platform. One can switch between the Windows MDI mode, the UNIX Toplevel mode and the tabpage mode, even while the application is running.
CrdView
- Small and lightweight molecule viewer.
- Multiple instances can be opened to view multiple molecules at once.
- Command line file format conversion allows batch conversions to be carried out.
File formats
Brabosphere and CrdView can read the following file formats (depending on the version of Open Babel):
- Alchemy (alc)
- MSI BGF (bgf)
- Dock 3.5 (box)
- Ball & Stick (bs)
- Chem3D (c3d1, c3d2)
- Cacao (caccrt)
- Accelrys/MSI Biosym/Insight II (car)
- CCC (ccc)
- Chemical Markup Language (cml, cmlr)
- BRABO (crd, c00, ncr, crdcrd)
- Chemical Resource Kit (crk2d, crk3d)
- ChemDraw (ct)
- DMol3 (dmol)
- Gaussian checkpoint (fchk)
- Feature (feat)
- Free Form Fractional (fract)
- FastSearching (fs)
- Gaussian G98/03 output (g98, g03)
- GAMESS (gam, gamout)
- Ghemical (gpr, mm1gp, qm1gp)
- Hyperchem (hin)
- ShelX (ins, res)
- Jaguar (jout)
- MMADS (mmads)
- MDL Molfile (mdl, mol)
- MacroModel (mmod, out, dat)
- Sybyl (mol2)
- MOPAC (mopcrt, mopout)
- MPQC (mpqc)
- NWChem (nwo)
- PubChem (pc)
- PCModel (pcm)
- Protein Data Bank (pdb, ent)
- Parallel Quantum Solutions (pqs)
- Amber (prep)
- Q-Chem (qcout)
- MDL RXN (rxn)
- MDL Isis (sdf, sd)
- SMILES (smi)
- TurboMole (tmol)
- OpenEye (bin)
- Unichem (unixyz)
- ViewMol (vmol)
- General XML (xml)
- XYZ (xyz)
- Yasara.org (yob)
This is the list of export formats:
- Alchemy (alc)
- MSI BGF (bgf)
- OpenEye (bin)
- Dock 3.5 (box)
- Ball & Stick (bs)
- Chem3D (c3d1, c3d2)
- Cacao (caccrt, cacint)
- CAChe (cache)
- MSI Biosym/Insight II (car)
- Chemtool (cht)
- Chemical Markup Language (cml, cmlr)
- Gaussian 98/03 input (com, gau)
- BRABO (crd)
- Chemical Resource Kit (crk2d, crk3d)
- Accelrys/MSI Quanta (csr)
- CSD (cssr)
- ChemDraw (ct)
- DMol3 (dmol)
- Feature (feat)
- Fenske-Hall Z-Matrix (fh)
- Fingerprint (fpt)
- Free Form Fractional (fract)
- FastSearching (fs)
- GAMESS (gamin, inp)
- Ghemical (gpr)
- GROMOS (gr96a, gr96n)
- Hyperchem (hin)
- InchI (inchi)
- Jaguar (jin)
- MDL Molfile (mdl, mol)
- MMADS (mmads)
- MacroModel (mmod, out, dat)
- Sybyl (mol2, mpd)
- MOPAC (mopcrt)
- MPQC (mpqcin)
- NWChem (nw)
- PCModel (pcm)
- Protein Data Bank (pdb, ent)
- POV-Ray (pov)
- Parallel Quantum Solutions (pqs)
- Q-Chem (qcin)
- Open Babel Report (report)
- MDL RXN (rxn)
- MDL Isis (sdf, sd)
- SMILES (smi, fix)
- TurboMole (tmol)
- Titles (txt)
- Tinker (txyz)
- Unichem (unixyz)
- ViewMol (vmol)
- XED (xed)
- XYZ (xyz)
- Yasara.org (yob)
- ZINDO (zin)
Platforms
Brabosphere and CrdView should run on the following platforms (tested where noted):
- AIX (4.1 or later)
- BSD/OS (2.0 or later)
- DG/UX
- FreeBSD (2.1 or later)
- HP-UX (10.20 or later)
- IRIX (6.x)
- Linux → tested SuSE 9.2 64bit and Kubuntu 5.10 32bit
- MacOS X
- NetBSD
- OpenBSD
- OpenServer
- QNX
- Reliant UNIX
- Solaris (2.5.1 or later)
- Tru64 UNIX (4.0 or later)
- UnixWare
- Windows (95, 98, Me)
- Windows (NT4, 2000, XP) → tested 2000 and XP
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