[PyMOL] Expose PyMOL API
Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from
outside of PyMOL? An example, the below is a script (inspired by Thomas
Holder) which saves down to disk all amino acids of a protein structure
into separate PDB files.
# *
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *
def seq(state, selection=name ca or resn hoh or resn lig):
print Generating seqs.
cmd.select(prot, selection)
while cmd.pop(_tmp, prot):
cmd.iterate(_tmp, stored.x=(resn,resv))
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(),
stored.x[1], state)
cmd.save(filename, byres _tmp)
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -
Is it possible to somehow include this in a Python script, and running
it from the command line? If not, why?
Thanks for any feedback.
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
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Re: [PyMOL] Expose PyMOL API
Hi Martin,
the recommended way is to use PyMOL as your python interpreter, so
instead of:
python file.py
do this:
pymol -cqr file.py
However, launching a PyMOL process from a python terminal as you
suggested is also possible. Have a look at Example 2 of
http://pymolwiki.org/index.php/Launching_From_a_Script , the important
lines are those:
import pymol
pymol.pymol_argv = ['pymol','-qc']
pymol.finish_launching()
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 09:26:
Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from
outside of PyMOL? An example, the below is a script (inspired by Thomas
Holder) which saves down to disk all amino acids of a protein structure
into separate PDB files.
# *
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *
def seq(state, selection=name ca or resn hoh or resn lig):
print Generating seqs.
cmd.select(prot, selection)
while cmd.pop(_tmp, prot):
cmd.iterate(_tmp, stored.x=(resn,resv))
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(),
stored.x[1], state)
cmd.save(filename, byres _tmp)
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -
Is it possible to somehow include this in a Python script, and running
it from the command line? If not, why?
Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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Re: [PyMOL] Expose PyMOL API
Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
Launching_From_a_Script examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 13:14:
Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
me @ ~/PROG_TEST $ python
Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type help, copyright, credits or license for more information.
imported numpy
from PyQt4.QtGui imported *
from PyQt4.QtCore imported *
import os, sys
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
sys.path.insert(0, moddir)
os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
import pymol
Traceback (most recent call last):
File stdin, line 1, inmodule
File
/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py, line
472, inmodule
import _cmd
ImportError: No module named _cmd
import pymol
What could be the problem? Could it be that the 'pymol/pymol_path' call
is not exactly right? In the modules/pymol directory, there is a module
'pymol/launch_pymol', but I have a similar error (No module named
_cmd) when I try to import it.
Martin
Am 22.11.11 09:47, schrieb Thomas Holder:
Hi Martin,
the recommended way is to use PyMOL as your python interpreter, so
instead of:
python file.py
do this:
pymol -cqr file.py
However, launching a PyMOL process from a python terminal as you
suggested is also possible. Have a look at Example 2 of
http://pymolwiki.org/index.php/Launching_From_a_Script , the important
lines are those:
import pymol
pymol.pymol_argv = ['pymol','-qc']
pymol.finish_launching()
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 09:26:
Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features
from outside of PyMOL? An example, the below is a script (inspired by
Thomas Holder) which saves down to disk all amino acids of a protein
structure into separate PDB files.
# *
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *
def seq(state, selection=name ca or resn hoh or resn lig):
print Generating seqs.
cmd.select(prot, selection)
while cmd.pop(_tmp, prot):
cmd.iterate(_tmp, stored.x=(resn,resv))
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' %
(one_letter[stored.x[0]].lower(), stored.x[1], state)
cmd.save(filename, byres _tmp)
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -
Is it possible to somehow include this in a Python script, and
running it from the command line? If not, why?
Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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] Expose PyMOL API
Martin,
The _cmd module is indeed statically linked into MacPyMOL. But, if you
built from open-source it's dumped into site-packages/pymol. Also,
view the files inside pymol/examples/launching. There are plenty of
examples. If you're using a pre-built package from elsewhere, then
please contact the package maintainer to see how it's built.
Last, I prefer the newer pymol2 strategy where you get a handle to a
PyMOL cmd instance:
from pymol2 import PyMOL
cmd=PyMOL().cmd
Cheers,
-- Jason
On Tue, Nov 22, 2011 at 8:19 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
Launching_From_a_Script examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 13:14:
Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
me @ ~/PROG_TEST $ python
Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type help, copyright, credits or license for more information.
imported numpy
from PyQt4.QtGui imported *
from PyQt4.QtCore imported *
import os, sys
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
sys.path.insert(0, moddir)
os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
import pymol
Traceback (most recent call last):
File stdin, line 1, inmodule
File
/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py, line
472, inmodule
import _cmd
ImportError: No module named _cmd
import pymol
What could be the problem? Could it be that the 'pymol/pymol_path' call
is not exactly right? In the modules/pymol directory, there is a module
'pymol/launch_pymol', but I have a similar error (No module named
_cmd) when I try to import it.
Martin
Am 22.11.11 09:47, schrieb Thomas Holder:
Hi Martin,
the recommended way is to use PyMOL as your python interpreter, so
instead of:
python file.py
do this:
pymol -cqr file.py
However, launching a PyMOL process from a python terminal as you
suggested is also possible. Have a look at Example 2 of
http://pymolwiki.org/index.php/Launching_From_a_Script , the important
lines are those:
import pymol
pymol.pymol_argv = ['pymol','-qc']
pymol.finish_launching()
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 09:26:
Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features
from outside of PyMOL? An example, the below is a script (inspired by
Thomas Holder) which saves down to disk all amino acids of a protein
structure into separate PDB files.
# *
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *
def seq(state, selection=name ca or resn hoh or resn lig):
print Generating seqs.
cmd.select(prot, selection)
while cmd.pop(_tmp, prot):
cmd.iterate(_tmp, stored.x=(resn,resv))
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' %
(one_letter[stored.x[0]].lower(), stored.x[1], state)
cmd.save(filename, byres _tmp)
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -
Is it possible to somehow include this in a Python script, and
running it from the command line? If not, why?
Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
All the data continuously generated
Re: [PyMOL] Expose PyMOL API
Thanks for the answers. I'll be trying to get it compile on a linux box,
if I could access some of the PyMOL features there, that's fine as well.
A friend tried to compile PyMOL on Mac and had quite some trouble, so
I'll be first trying the Linux option.
Martin
Am 22.11.11 15:56, schrieb Jason Vertrees:
Martin,
The _cmd module is indeed statically linked into MacPyMOL. But, if you
built from open-source it's dumped into site-packages/pymol. Also,
view the files inside pymol/examples/launching. There are plenty of
examples. If you're using a pre-built package from elsewhere, then
please contact the package maintainer to see how it's built.
Last, I prefer the newer pymol2 strategy where you get a handle to a
PyMOL cmd instance:
from pymol2 import PyMOL
cmd=PyMOL().cmd
Cheers,
-- Jason
On Tue, Nov 22, 2011 at 8:19 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
Launching_From_a_Script examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 13:14:
Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
me @ ~/PROG_TEST $ python
Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type help, copyright, credits or license for more information.
imported numpy
from PyQt4.QtGui imported *
from PyQt4.QtCore imported *
import os, sys
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
sys.path.insert(0, moddir)
os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
import pymol
Traceback (most recent call last):
File stdin, line 1, inmodule
File
/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py, line
472, inmodule
import _cmd
ImportError: No module named _cmd
import pymol
What could be the problem? Could it be that the 'pymol/pymol_path' call
is not exactly right? In the modules/pymol directory, there is a module
'pymol/launch_pymol', but I have a similar error (No module named
_cmd) when I try to import it.
Martin
Am 22.11.11 09:47, schrieb Thomas Holder:
Hi Martin,
the recommended way is to use PyMOL as your python interpreter, so
instead of:
python file.py
do this:
pymol -cqr file.py
However, launching a PyMOL process from a python terminal as you
suggested is also possible. Have a look at Example 2 of
http://pymolwiki.org/index.php/Launching_From_a_Script , the important
lines are those:
import pymol
pymol.pymol_argv = ['pymol','-qc']
pymol.finish_launching()
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 09:26:
Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features
from outside of PyMOL? An example, the below is a script (inspired by
Thomas Holder) which saves down to disk all amino acids of a protein
structure into separate PDB files.
# *
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *
def seq(state, selection=name ca or resn hoh or resn lig):
print Generating seqs.
cmd.select(prot, selection)
while cmd.pop(_tmp, prot):
cmd.iterate(_tmp, stored.x=(resn,resv))
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' %
(one_letter[stored.x[0]].lower(), stored.x[1], state)
cmd.save(filename, byres _tmp)
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -
Is it possible to somehow include this in a Python script, and
running it from the command line? If not, why?
Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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