RE: [PyMOL] Using PyMol as a library - no GUI
Truls, That looks to me like a crash where the PyMOL API was somehow called before PyMOL was initialized...how and why this could happen is a mystery to me though -- that's what pymol.finish_launching() is supposed to prevent -- but there may be some flaw in the logic. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Debian Chooser [mailto:ker...@herocamp.org] On Behalf Of Truls A. Tangstad Sent: Friday, October 17, 2003 3:18 PM To: Warren L. DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Using PyMol as a library - no GUI On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote: Truls A. Tangstad wrote: I'm very interested in using alot of the functionality that PyMol offers programmatically from Python, i.e. without using a GUI at all. The chempy package seems to cover alot of my needs, loading different file formats etc. even though it doesn't seem to be documented. Is it also possible to use the rest of the functionality in PyMol from other Python scripts? Right now, just importing the pymol package seems to force the GUI to open. If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a pymol_argv list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Thanks, seems to work like a charm in scripts after adding the assignment operator: __main__.pymol_argv = ['pymol', '-qc'] # adding miss Somehow it segfaults when trying the same thing in an interactive python interpreter though, right after importing pymol. This might be due to a shoddy install on my part, but I'm including a gdb backtrace: #0 0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #1 0x41d7c683 in SettingGet () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #2 0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #3 0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site- packages/pymol/_cmd.so #4 0x4006d74d in PyCFunction_Call () from /usr/lib/libpython2.3.so.1.0 #5 0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #6 0x400a2a4a in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.3.so.1.0 #7 0x4000 in PyFile_WriteObject () from /usr/lib/libpython2.3.so.1.0 #8 0x400556e6 in PyFile_WriteString () from /usr/lib/libpython2.3.so.1.0 #9 0x400d56b6 in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #10 0x400d4b2c in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0 #12 0x40101043 in _PyUnicode_TypeRecords () from /usr/lib/libpython2.3.so.1.0 Any idea why it shouldn't work interactively? I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable. -- Truls - kerfue+pymol-us...@herocamp.org
RE: [PyMOL] Using PyMol as a library - no GUI
If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a pymol_argv list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Truls A. Tangstad Sent: Friday, October 17, 2003 4:48 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Using PyMol as a library - no GUI I'm very interested in using alot of the functionality that PyMol offers programmatically from Python, i.e. without using a GUI at all. The chempy package seems to cover alot of my needs, loading different file formats etc. even though it doesn't seem to be documented. Is it also possible to use the rest of the functionality in PyMol from other Python scripts? Right now, just importing the pymol package seems to force the GUI to open. -- Truls - kerfue+pymol-us...@herocamp.org --- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Using PyMol as a library - no GUI
On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote: Truls A. Tangstad wrote: I'm very interested in using alot of the functionality that PyMol offers programmatically from Python, i.e. without using a GUI at all. The chempy package seems to cover alot of my needs, loading different file formats etc. even though it doesn't seem to be documented. Is it also possible to use the rest of the functionality in PyMol from other Python scripts? Right now, just importing the pymol package seems to force the GUI to open. If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a pymol_argv list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Thanks, seems to work like a charm in scripts after adding the assignment operator: __main__.pymol_argv = ['pymol', '-qc'] # adding miss Somehow it segfaults when trying the same thing in an interactive python interpreter though, right after importing pymol. This might be due to a shoddy install on my part, but I'm including a gdb backtrace: #0 0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #1 0x41d7c683 in SettingGet () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #2 0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #3 0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #4 0x4006d74d in PyCFunction_Call () from /usr/lib/libpython2.3.so.1.0 #5 0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #6 0x400a2a4a in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.3.so.1.0 #7 0x4000 in PyFile_WriteObject () from /usr/lib/libpython2.3.so.1.0 #8 0x400556e6 in PyFile_WriteString () from /usr/lib/libpython2.3.so.1.0 #9 0x400d56b6 in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #10 0x400d4b2c in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0 #12 0x40101043 in _PyUnicode_TypeRecords () from /usr/lib/libpython2.3.so.1.0 Any idea why it shouldn't work interactively? I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable. -- Truls - kerfue+pymol-us...@herocamp.org
