Re: [Open Babel] Atom numbers again, this time from python

2013-06-05 Thread Dimitri Maziuk
On 06/05/2013 03:50 PM, Maciek Wójcikowski wrote: ... although I believe that 'b' : None should be 'b' : '' if you > wish to pass empty value, since None is reserved for options without value. Hehe. I wanted "b" : "none", actually (Geoff was right) and I didn't even notice myself until the pictur

Re: [Open Babel] Atom numbers again, this time from python

2013-06-05 Thread Dimitri Maziuk
On 06/05/2013 03:50 PM, Maciek Wójcikowski wrote: > There is an undocumented option in molecule.write() and .readfile() which > allows of passing options to reading/writing. You must pass opt with > dictionary of options. For line you gave: opt = {'b' : None, 'i' : None, > 'a' : None} although I be

Re: [Open Babel] Atom numbers again, this time from python

2013-06-05 Thread Geoffrey Hutchison
> All I can see in TFM is pybel.Molecule.addh() for "-h" -- is there way > to get to the rest? Specifically, "-xa" and "-xi", as I can > post-process the SVG to change the size and the background. These are output options in the Python openbabel module (not accessible from pybel, IIRC) conv = ob

Re: [Open Babel] Atom numbers again, this time from python

2013-06-05 Thread Maciek Wójcikowski
There is an undocumented option in molecule.write() and .readfile() which allows of passing options to reading/writing. You must pass opt with dictionary of options. For line you gave: opt = {'b' : None, 'i' : None, 'a' : None} although I believe that 'b' : None should be 'b' : '' if you wish to pa

[Open Babel] Atom numbers again, this time from python

2013-06-05 Thread Dimitri Maziuk
Hi everyone, one more python question: I'm trying to do obabel -h --canonical -xb none -xi -xa -xP1000 -osvg ... All I can see in TFM is pybel.Molecule.addh() for "-h" -- is there way to get to the rest? Specifically, "-xa" and "-xi", as I can post-process the SVG to change the size and the back

Re: [Open Babel] Atom numbers

2013-04-26 Thread Dimitri Maziuk
On 4/26/2013 2:49 AM, Chris Morley wrote: > It's hardwired in line 247 in src/depict/depict.cpp if you are in a > position to recompile. I'll change it to "teal" for the future. I can, however, a) I'm not yet sure I need to and b) I can also post-process the svg. Dima (I'd change it to '-xi [co

Re: [Open Babel] Atom numbers

2013-04-26 Thread Chris Morley
On 25/04/2013 23:39, Dimitri Maziuk wrote: > On 04/25/2013 05:00 PM, Chris Morley wrote: >> On 25/04/2013 21:52, Dimitri Maziuk wrote: >> >>> is there an option to display atom numbers on 2D drawing (png or svg, >>> using sdf for input)? E.g. MarvinView has a checkbox under View - Misc. >>> >>> Spe

Re: [Open Babel] Atom numbers

2013-04-25 Thread Dimitri Maziuk
On 04/25/2013 05:00 PM, Chris Morley wrote: > On 25/04/2013 21:52, Dimitri Maziuk wrote: > >> is there an option to display atom numbers on 2D drawing (png or svg, >> using sdf for input)? E.g. MarvinView has a checkbox under View - Misc. >> >> Specifically, as a command line switch to [o]babel or

Re: [Open Babel] Atom numbers

2013-04-25 Thread Chris Morley
On 25/04/2013 21:52, Dimitri Maziuk wrote: > is there an option to display atom numbers on 2D drawing (png or svg, > using sdf for input)? E.g. MarvinView has a checkbox under View - Misc. > > Specifically, as a command line switch to [o]babel or pybel api call? There is for svg: use the -xi opti

[Open Babel] Atom numbers

2013-04-25 Thread Dimitri Maziuk
Hi everyone, is there an option to display atom numbers on 2D drawing (png or svg, using sdf for input)? E.g. MarvinView has a checkbox under View - Misc. Specifically, as a command line switch to [o]babel or pybel api call? TIA -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison --