Re: [PyMOL] echo colour
Hi Joel, the color is stored as a numeric atom property, you can use iterate to get it. PyMOL> iterate (first objX), print color If you need the name of the color, get the index to name mapping as a dictionary from PyMOL like this: PyMOL> stored.cn = dict((i,c) for (c,i) in cmd.get_color_indices()) PyMOL> iterate (first objX), print stored.cn[color] Last but not least, there is the psico.querying.get_color function in the PSICO module :) Cheers, Thomas Joel Tyndall wrote, On 01/23/13 02:04: > Hi list, > > With the myriad of colours in Pymol, I tend to forget which shade of > what I have used. Is there a way/command to print the colour I have used > to colour object X? > > Cheers > > Joel > _ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > > Skype: jtyndall > > Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How do I get current selection name from python?
It prints the selection all right. Why then save wouldn't save it: def bk_saves_unique_pdb(Selection = None): """Takes current selection (or "all" -- if nothing selected) and saves it as a uniquetly named pdb file (Frame_Selection_RandomString.pdb) in the current working directory.""" if not Selection: Selection = cmd.get_names('selections', 1) if Selection: Selection = Selection[0] # it was a list else: Selection = 'all' tempFile = tempfile.NamedTemporaryFile(dir=os.curdir, prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(), sel=Selection) , suffix=".pdb") print tempFile.name, Selection # prints righteous file name and selection name (though not in quotes) cmd.save(tempFile.name, Selection) # but still saves nothing cmd.extend("bk_saves_unique_pdb", bk_saves_unique_pdb) On Tue, Jan 22, 2013 at 10:49 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Boris, > > this will give you the list of active selections, which has by default > only one entry (or zero, if no selection is enabled). > > active_selections = cmd.get_names('selections', 1) > > Hope that helps. > > Cheers, > Thomas > > On Jan 22, 2013, at 2:08 PM, Boris Kheyfets wrote: > > I want to save current selection as a uniquetly-named pdb file. So I > need tempfile of python. > > > > So I write def, and I want it have current selection as default one (not > the '(all)'). How do I do that? > > > > I think it will be somewhere under > > cmd.get_session() > > > > I read the sources, but couldn't find a single instance where current > selection would be a default one. > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How do I get current selection name from python?
http://docs.python.org/2/library/tempfile.html#tempfile.NamedTemporaryFile Quote: "If delete is true (the default), the file is deleted as soon as it is closed." Cheers, Thomas Boris Kheyfets wrote, On 01/23/13 14:47: > It prints the selection all right. Why then save wouldn't save it: > > > def bk_saves_unique_pdb(Selection = None): > """Takes current selection (or "all" -- if nothing selected) and saves it > as a uniquetly named pdb file (Frame_Selection_RandomString.pdb) in the > current working directory.""" > if not Selection: > Selection = cmd.get_names('selections', 1) > if Selection: > Selection = Selection[0] # it was a list > else: > Selection = 'all' > tempFile = tempfile.NamedTemporaryFile(dir=os.curdir, > prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(), sel=Selection) , > suffix=".pdb") > print tempFile.name, Selection # prints righteous file name and selection > name (though not in quotes) > cmd.save(tempFile.name, Selection) # but still saves nothing > cmd.extend("bk_saves_unique_pdb", bk_saves_unique_pdb) -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] echo colour
Thanks Thomas, seems to work. -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Wednesday, 23 January 2013 10:47 p.m. To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] echo colour Hi Joel, the color is stored as a numeric atom property, you can use iterate to get it. PyMOL> iterate (first objX), print color If you need the name of the color, get the index to name mapping as a dictionary from PyMOL like this: PyMOL> stored.cn = dict((i,c) for (c,i) in cmd.get_color_indices()) PyMOL> iterate (first objX), print stored.cn[color] Last but not least, there is the psico.querying.get_color function in the PSICO module :) Cheers, Thomas Joel Tyndall wrote, On 01/23/13 02:04: > Hi list, > > With the myriad of colours in Pymol, I tend to forget which shade of > what I have used. Is there a way/command to print the colour I have > used to colour object X? > > Cheers > > Joel > _ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry National School of Pharmacy > University of Otago PO Box 56 Dunedin 9054 New Zealand > > Skype: jtyndall > > Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net