Jared -
Many thanks for the quick reply. I think you and I found the same thing at
the same time.
I noticed in the keyboard.py file that there was a "get_ctsh" section.
Which I assumed (and it is) equivalent to "Ctrl-Shift".
Also under the "get_ctsh" section there was no definition for
"Ctrl-Shift-M":
'm' : [ editor.attach_amino_acid, ("pk1","methane"), {}],
So I added it and it works.
Now you can type on the command line.
for aa in "M": cmd._ctsh(string.lower(aa))
and get a methane molecule.
Thanks for the help and guidance.
Ben
On Wed, May 20, 2015 at 12:49 PM, Sampson, Jared <jared.samp...@nyumc.org>
wrote:
> Hi Ben -
>
> Try this:
>
> editor.attach_fragment("pk1", "methane", 1, 0)
>
> Here's how I tracked this down, not having known about this function
> before your email. cmd._alt() and likewise cmd._ctrl() are functions (you
> can see for yourself in the source code in pymol/modules/pymol/cmd.py), and
> they are basically wrappers (via internal.py and back through cmd.py again)
> for functions in keyboard.py called keyboard.get_alt() and
> keyboard.get_ctrl(), which each return a dictionary list of commands to run
> for each shortcut key. For example:
>
> def get_alt(self_cmd=cmd):
> return {
> '1' : [ editor.attach_fragment , ("pk1","formamide",5,0), {}],
> '2' : [ editor.attach_fragment , ("pk1","formamide",4,0), {}],
> '3' : [ editor.attach_fragment , ("pk1","sulfone",3,1), {}],
> '4' : [ editor.attach_fragment , ("pk1","cyclobutane",4,0), {}],
> '5' : [ editor.attach_fragment , ("pk1","cyclopentane",5,0), {}],
> '6' : [ editor.attach_fragment , ("pk1","cyclohexane",7,0), {}],
> '7' : [ editor.attach_fragment , ("pk1","cycloheptane",8,0), {}],
> '8' : [ editor.attach_fragment , ("pk1","cyclopentadiene",5,0),
> {}],
> '9' : [ editor.attach_fragment , ("pk1","benzene",6,0), {}],
> '0' : [ editor.attach_fragment , ("pk1","formaldehyde",2,0), {}],
> 'a' : [ editor.attach_amino_acid, ("pk1","ala"), {}],
> 'b' : [ editor.attach_amino_acid, ("pk1","ace"), {}],
>
> 'c' : [ editor.attach_amino_acid, ("pk1","cys"), {}],
> 'd' : [ editor.attach_amino_acid, ("pk1","asp"), {}],
> 'e' : [ editor.attach_amino_acid, ("pk1","glu"), {}],
> 'f' : [ editor.attach_amino_acid, ("pk1","phe"), {}],
> ...etc
> }
>
> So to add a methyl group, just model it after the cyclobutane example,
> and just run the editor.attach_fragment command (which you can explore in
> pymol/modules/pymol/editor.py) for methane. A little more info from the
> editor.attach_fragment() docstring:
>
> def attach_fragment(selection,fragment,hydrogen,anchor,_self=cmd):
> '''
> ARGUMENTS
>
> selection = str: must be "pk1"
>
> fragment = str: fragment name to load from fragment library
>
> hydrogen = int: hydrogen atom ID in fragment to fuse
>
> anchor = int: none-hydrogen atom ID in fragment to fuse
> '''
>
> You can also define custom fragments
> <http://www.pymolwiki.org/index.php?title=Modeling_and_Editing_Structures#Adding_and_using_your_own_fragments>
> .
>
> Also, in case you didn't know about it, an easier way to create your
> peptide might be the `fab` function (so long as you don't need to continue
> editing it afterward):
>
> fab GTHYRD, my_peptide
>
> Hope that helps!
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
> On May 20, 2015, at 8:43 AM, Benjamin Bobay <bgbo...@ncsu.edu> wrote:
>
> H
> i All,
>
> I was wondering if someone could point me to the correct notation for
> something.
>
> When making a peptide from the command line one could type:
>
> for aa in "GTHYRD":cmd._alt(string.lower(aa))
>
> Let's say that I want to add a methane. The key code is CTRL+SHIFT+M
>
> I was wondering how to alter the "cmd.
> _
> alt" to be CTRL-SHIFT.
>
> I've tried
> "cmd._ctrl+_shift"
> "cmd._ctrl and _shift"
> "cmd.(_ctrl and _shift)"
> "cmd._ctrl._shift"
>
> Nothing has worked. I searched the list serve but came up empty on how
> to combine two keys to the "cmd'.
>
> Any help would be greatly appreciated!
>
> Thanks
> Ben
>
> --
> ____________________________________________
> Research Assistant Professor
> North Carolina State University
> Department of Molecular and Structural Biochemistry
> 128 Polk Hall
> Campus Box 7622
> Raleigh, NC 27695
> Phone: (919)-513-0698
> Fax: (919)-515-2047
> http://biochem.ncsu.edu/
> http://biochem.ncsu.edu/faculty/bobay/bobaypage.php
> http://biochem.ncsu.edu/faculty/bobay/index.php
> http://biochem.ncsu.edu/NMR
> ____________________________________________
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--
____________________________________________
Research Assistant Professor
North Carolina State University
Department of Molecular and Structural Biochemistry
128 Polk Hall
Campus Box 7622
Raleigh, NC 27695
Phone: (919)-513-0698
Fax: (919)-515-2047
http://biochem.ncsu.edu/
http://biochem.ncsu.edu/faculty/bobay/bobaypage.php
http://biochem.ncsu.edu/faculty/bobay/index.php
http://biochem.ncsu.edu/NMR
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