Hi Andreas,
this error was introduced in the open-source tree with the updates from
PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I
got it to work:
Download the latest VMD source code and unpack it:
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
In the PyMOL source tree, edit the file
contrib/uiuc/plugins/molfile_plugin/update.py
and point "molfile_src_path" to the correct path in the VMD source tree.
Then run "python update.py".
In setup.py, comment out "cpmdlogplugin.c", "cpmdplugin.c" and
"gaussianplugin.c" (they are commented out in update.py as well). You
may use the attached patch.
Cheers,
Thomas
On 02/28/2012 11:36 AM, Andreas Förster wrote:
Dear all,
driven beyond the reach of sanity by VMD, I've tried to enable the
loading of DCD trajectories (from NAMD2 molecular dynamics simulations)
in PyMOL. I followed the instructions given on this mailing list a few
weeks back, specifically (setup.py):
- uncommenting "contrib/uiuc/plugins/include",
"contrib/uiuc/plugins/molfile_plugin/src",
("_PYMOL_VMD_PLUGINS",None),
- changing the line underneath
# VMD plugin support
# switch the 0 to 1 to activate the additional source code
from ] + 0 * [
to ] + 1 * [
Compilation (python setup.py build install) crashes because of an error
in the molfile plugin:
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
‘read_basis_metadata’:
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error:
‘molfile_qm_metadata_t’ has no member named ‘have_esp’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error:
‘molfile_qm_metadata_t’ has no member named ‘have_npa’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error:
‘molfile_qm_metadata_t’ has no member named ‘have_internals’
error: command 'gcc' failed with exit status 1
Have others encountered that? Is there a solution or work-around?
Thanks.
Andreas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Index: setup.py
===================================================================
--- setup.py (revision 3983)
+++ setup.py (working copy)
@@ -9,6 +9,8 @@
from distutils.core import setup, Extension
import sys, os
+with_vmd_plugins = 0
+
#============================================================================
if sys.platform=='win32':
# NOTE: this branch not tested in years and may not work...
@@ -265,6 +267,11 @@
"-g" ]
ext_link_args = []
+ with_vmd_plugins = 1
+ if with_vmd_plugins:
+ inc_dirs += [ "contrib/uiuc/plugins/include",
+ "contrib/uiuc/plugins/molfile_plugin/src"]
+ def_macros += [ ("_PYMOL_VMD_PLUGINS", None) ]
distribution = setup ( # Distribution meta-data
name = "pymol",
@@ -420,7 +427,7 @@
"layer5/main.c"
# VMD plugin support
# switch the 0 to 1 to activate the additional source code
- ] + 0 * [
+ ] + (1 if with_vmd_plugins else 0) * [
# (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
@@ -432,8 +439,8 @@
'contrib/uiuc/plugins/molfile_plugin/src/carplugin.c',
'contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp',
'contrib/uiuc/plugins/molfile_plugin/src/corplugin.c',
- 'contrib/uiuc/plugins/molfile_plugin/src/cpmdlogplugin.c',
- 'contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c',
+# 'contrib/uiuc/plugins/molfile_plugin/src/cpmdlogplugin.c',
+# 'contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c',
'contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c',
'contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp',
'contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c',
@@ -444,7 +451,7 @@
'contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp',
'contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp',
'contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c',
- 'contrib/uiuc/plugins/molfile_plugin/src/gaussianplugin.c',
+# 'contrib/uiuc/plugins/molfile_plugin/src/gaussianplugin.c',
'contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp',
'contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp',
'contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp',
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