Re: [Open Babel] Y-help

2012-10-17 Thread qiancheng shen
That's easy. Step one: babel xxx.smi xxx.fpt -xh -xfFP2 [Step two: convert hex in xxx.fpt to an int (in python, we can use "int(each_byte,16)") Step three: int to binary] Or just hex to binary 2012/10/17 Chris Morley > On 17/10/2012 02:32, 蓝鱼在嘴里 wrote: > > Hi,all, > > I know openbabel can gen

Re: [Open Babel] babel segvs on certain gaussian log files

2012-10-17 Thread Reinis Danne
On Wed, Oct 17, 2012 at 09:36:40PM +0200, David van der Spoel wrote: > > How can I contribute a feature to extract the G2 etc. Energies? There is a patch tracker [1], you can post it there I think that is the most appropriate. We are in process to migrate to Git, so after that also git format-pat

Re: [Open Babel] babel segvs on certain gaussian log files

2012-10-17 Thread David van der Spoel
On 17 okt 2012, at 21:30, Chris Morley wrote: > On 17/10/2012 14:46, David van der Spoel wrote: >> On 2012-10-17 15:15, David van der Spoel wrote: >>> Hi, >>> >>> I've done some G2 calculations on small molecules using Gaussian, and >>> each of these files contains 7 calculations. Babel crashe

Re: [Open Babel] babel segvs on certain gaussian log files

2012-10-17 Thread Chris Morley
On 17/10/2012 14:46, David van der Spoel wrote: > On 2012-10-17 15:15, David van der Spoel wrote: >> Hi, >> >> I've done some G2 calculations on small molecules using Gaussian, and >> each of these files contains 7 calculations. Babel crashes when trying >> to read this: >> >> % curl http://folding

Re: [Open Babel] installing perl and python bindings on mac

2012-10-17 Thread Reinis Danne
On Wed, Oct 17, 2012 at 06:24:06PM +0200, KC soh wrote: > Hi > > I'm using Mac 10.6 and i tried to install the perl and python bindings but > i ran into this problem. I copied the Eigen folder into /usr/local/include > > XXXmac2:build kc$ cmake ../openbabel-2.3.1 -DPYTHON_BINDINGS=ON > -DPERL_BIN

[Open Babel] installing perl and python bindings on mac

2012-10-17 Thread KC soh
Hi I'm using Mac 10.6 and i tried to install the perl and python bindings but i ran into this problem. I copied the Eigen folder into /usr/local/include XXXmac2:build kc$ cmake ../openbabel-2.3.1 -DPYTHON_BINDINGS=ON -DPERL_BINDINGS=ON -DEIGEN2_INCLUDE_DIR=/usr/local/include/ -- Using included in

Re: [Open Babel] SMARTS output format

2012-10-17 Thread Tim Vandermeersch
Hi, On Wed, Oct 17, 2012 at 12:57 PM, Reinis Danne wrote: > On Wed, Oct 17, 2012 at 11:04:55AM +0200, Fredrik Wallner wrote: >> If you build up the molecule from within OpenBabel, chances >> are that that molecule will be possible to describe as a >> SMILES string which is valid SMARTS. > > This,

Re: [Open Babel] babel segvs on certain gaussian log files

2012-10-17 Thread David van der Spoel
On 2012-10-17 15:15, David van der Spoel wrote: > Hi, > > I've done some G2 calculations on small molecules using Gaussian, and > each of these files contains 7 calculations. Babel crashes when trying > to read this: > > % curl http://folding.bmc.uu.se/222-trichloroethanol-g2.log > > 222-trichloroe

[Open Babel] babel segvs on certain gaussian log files

2012-10-17 Thread David van der Spoel
Hi, I've done some G2 calculations on small molecules using Gaussian, and each of these files contains 7 calculations. Babel crashes when trying to read this: % curl http://folding.bmc.uu.se/222-trichloroethanol-g2.log > 222-trichloroethanol-g2.log % babel -ig09 222-trichloroethanol-g2.log -o

Re: [Open Babel] SMARTS output format

2012-10-17 Thread Reinis Danne
On Wed, Oct 17, 2012 at 11:04:55AM +0200, Fredrik Wallner wrote: > If you build up the molecule from within OpenBabel, chances > are that that molecule will be possible to describe as a > SMILES string which is valid SMARTS. This, and also look at the thread "[OpenBabel-scripting] text representa

Re: [Open Babel] SMARTS output format

2012-10-17 Thread Fredrik Wallner
If you build up the molecule from within OpenBabel, chances are that that molecule will be possible to describe as a SMILES string which is valid SMARTS. Kind regards, Fredrik 16 okt 2012 kl. 20:35 skrev J Birch : > `If I am reading the code correctly, it looks like support for parsing SMARTS

Re: [Open Babel] Y-help

2012-10-17 Thread Chris Morley
On 17/10/2012 02:32, 蓝鱼在嘴里 wrote: > Hi,all, > I know openbabel can generate four kinds of fingerprints,each has an > original > fragement library.If I just want to code a molecule's fingerprint use 0 > or 1 bit to > represent a fragament exist in the molecule or not,how can I do this? Is > there >

Re: [Open Babel] OBAlign() error

2012-10-17 Thread Scott McKechnie
Excellent, working perfectly now, many thanks. I used your calcrmsd.py script from an earlier thread as a starting point for my scripts, so to avoid any future problems a simple canonical conversion of the conformers can be added in? This might be repetitive if done already but it would save any po