Re: [Open Babel] Atom numbering unification

2010-09-24 Thread Dmitry Osolodkin
Thank you Tim, works fine now. Best regards, Dmitry. On 09/24/2010 04:58 PM, Tim Vandermeersch wrote: > 2010/9/24 Dmitry Osolodkin : >> On 09/24/2010 04:08 PM, Tim Vandermeersch wrote: > babel --canonical somefile.mol2 somefile_can.mol2 It doesn't work. Atom order remains the same a

Re: [Open Babel] Atom numbering unification

2010-09-24 Thread Tim Vandermeersch
2010/9/24 Dmitry Osolodkin : > On 09/24/2010 04:08 PM, Tim Vandermeersch wrote: babel --canonical somefile.mol2 somefile_can.mol2 >>> >>> It doesn't work. Atom order remains the same as in input files. Using >>> the latest development version or stable 2.2.3 -- no difference. >> >> Make sure t

Re: [Open Babel] Atom numbering unification

2010-09-24 Thread Dmitry Osolodkin
On 09/24/2010 04:08 PM, Tim Vandermeersch wrote: >>> babel --canonical somefile.mol2 somefile_can.mol2 >> >> It doesn't work. Atom order remains the same as in input files. Using >> the latest development version or stable 2.2.3 -- no difference. > > Make sure to run make install or use ./bin/babe

Re: [Open Babel] Atom numbering unification

2010-09-24 Thread Tim Vandermeersch
2010/9/24 Dmitry Osolodkin : > Hi Tim, > > On 09/24/2010 02:20 PM, Tim Vandermeersch wrote: >> If you are willing to try the development version, you can >> canonicalize the atom order for any format using: >> >> babel --canonical somefile.mol2 somefile_can.mol2 > > It doesn't work. Atom order rema

Re: [Open Babel] Atom numbering unification

2010-09-24 Thread Dmitry Osolodkin
Hi Tim, On 09/24/2010 02:20 PM, Tim Vandermeersch wrote: > If you are willing to try the development version, you can > canonicalize the atom order for any format using: > > babel --canonical somefile.mol2 somefile_can.mol2 It doesn't work. Atom order remains the same as in input files. Using th

Re: [Open Babel] Atom numbering unification

2010-09-24 Thread Tim Vandermeersch
Hi, 2010/9/23 Dmitry Osolodkin : > Hello OpenBabel developers and users, > > probably you could help me with a simple problem. I have two molecules > (attached) to compute all-atom RMSD between them; they are same at all > except the position in the space (docking result and a cocrystal > structur

[Open Babel] Atom numbering unification

2010-09-23 Thread Dmitry Osolodkin
Hello OpenBabel developers and users, probably you could help me with a simple problem. I have two molecules (attached) to compute all-atom RMSD between them; they are same at all except the position in the space (docking result and a cocrystal structure). The only problem is that they have differ