Pyadmin: 2 revisions

2014-03-28T01:19:59Z

2 revisions

Speleo3: untar only plugins

2012-05-30T11:29:55Z

untar only plugins

Speleo3: created

2012-05-30T11:22:16Z

created

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Patching the PyMOL source with the latest VMD plugins.

== Procedure ==

1) Download [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD] to <code>/tmp</code>.

2) Save the [[#Required Files]] to <code>/tmp</code>

3) Run in a shell:

<syntaxhighlight lang="bash">
cd /tmp
tar xzf vmd-1.9.1.src.tar.gz
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
cd /tmp/pymol
python /tmp/vmd_plugins_update.py /tmp/plugins
patch -p0 -i /tmp/setup.patch
</syntaxhighlight>

4) Continue with [[Linux_Install#Compile_and_install]]

== Required Files ==

=== setup.patch ===

<syntaxhighlight lang="diff">
--- setup.py (revision 3998)
+++ setup.py (working copy)
@@ -265,6 +265,16 @@
"-g" ]
ext_link_args = []

+with_vmd_plugins = 1
+if with_vmd_plugins:
+ try:
+ from setup_vmd_plugins import vmd_plugins_dirs, vmd_plugins_files
+ except ImportError:
+ raise SystemExit('please run vmd_plugins_update.py first')
+ inc_dirs += vmd_plugins_dirs
+ def_macros += [ ("_PYMOL_VMD_PLUGINS", None) ]
+else:
+ vmd_plugins_files = []

distribution = setup ( # Distribution meta-data
name = "pymol",
@@ -420,6 +430,7 @@
"layer5/TestPyMOL.c",
"layer5/main.c"
# VMD plugin support
+ ] + vmd_plugins_files + [
# switch the 0 to 1 to activate the additional source code
] + 0 * [
# (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
</syntaxhighlight>

=== vmd_plugins_update.py ===

<syntaxhighlight lang="python">
'''
Convert VMD plugin source files for PyMOL.
(Modified version of "contrib/uiuc/plugins/molfile_plugin/update.py")

Please download and unpack the VMD source code from:

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Then run this script from the PyMOL source root and point it to the "plugins"
directory from the VMD source tree. Example:

cd /tmp
tar xzf vmd-1.9.1.src.tar.gz
cd /tmp/pymol
python vmd_plugins_update.py /tmp/plugins

You can enable/disable particular plugins from the "src_list" variable in
this file.
'''

import os
import sys
from glob import glob
from distutils import file_util, dir_util

src_list = [
# 'avsplugin',
# 'babelplugin', # requires openbabel
# 'basissetplugin', #
# 'bgfplugin',
# 'binposplugin',
# 'biomoccaplugin',
# 'brixplugin',
# 'carplugin',
# 'ccp4plugin',
# 'cdfplugin', # requires netcdf
# 'corplugin',
# 'cpmdlogplugin', #
# 'cpmdplugin',
'crdplugin',
# 'cubeplugin',
'dcdplugin',
# 'dlpolyplugin',
# 'dsn6plugin',
# 'dtrplugin', #
# 'dxplugin',
# 'edmplugin',
# 'fs4plugin',
# 'gamessplugin',
# 'gaussianplugin', #
# 'graspplugin',
# 'grdplugin',
# 'gridplugin',
'gromacsplugin',
# 'hoomdplugin', # requires expat
# 'jsplugin', #
# 'lammpsplugin', # requires gz
# 'maeffplugin', #
# 'mapplugin',
# 'mdfplugin',
# 'mmcif', #
# 'mol2plugin',
# 'moldenplugin',
# 'mrcplugin', # gone?
# 'msmsplugin',
# 'namdbinplugin',
# 'netcdfplugin', # requires netcdf
# 'parm7plugin',
# 'parmplugin',
# 'pbeqplugin', #
# 'pdbplugin',
# 'phiplugin',
# 'pltplugin',
# 'pqrplugin',
# 'psfplugin',
# 'raster3dplugin',
# 'rst7plugin',
# 'situsplugin',
# 'spiderplugin',
# 'stlplugin',
# 'tinkerplugin',
# 'uhbdplugin',
# 'vaspchgcarplugin', #
# 'vaspoutcarplugin', #
# 'vaspparchgplugin', #
# 'vaspposcarplugin', #
# 'vaspxdatcarplugin', #
# 'vaspxmlplugin', #
# 'vtfplugin', #
# 'webpdbplugin', # tcl dependent
# 'xbgfplugin',
# 'xsfplugin',
# 'xyzplugin',
]

# check command line argument
if len(sys.argv) < 2 or sys.argv[1] in ('-h', '--help'):
print __doc__.strip()
sys.exit(1)

# paths
vmd_plugins_path = sys.argv[1]
molfile_src_path = os.path.join(vmd_plugins_path, 'molfile_plugin', 'src')
molfile_dst_path = os.path.join('contrib', 'uiuc_molfile_plugin')

# copy required files
dir_util.mkpath(molfile_dst_path)
for f in [os.path.join(molfile_src_path, 'hash.c')] + \
glob(os.path.join(molfile_src_path, '*.h*')) + \
glob(os.path.join(vmd_plugins_path, 'include', '*.h')):
file_util.copy_file(f, molfile_dst_path)

# prepare setup_vmd_plugins.py
setup_out = open('setup_vmd_plugins.py', 'w')
setup_out.write('vmd_plugins_dirs = [ %s ]\n' % repr(molfile_dst_path))
setup_out.write('vmd_plugins_files = [\n')
for f in ['PlugIOManagerInit.c', 'hash.c']:
out_file = os.path.join(molfile_dst_path, f)
setup_out.write(repr(out_file) + ',\n')

# patch and copy desired plugin source files
for pref in src_list:
try:
in_file = glob(molfile_src_path + "/" + pref + ".[cC]*")[0]
except KeyError:
print 'MISSING:', pref
continue

out_file = os.path.join(molfile_dst_path, pref + '.c')
content = open(in_file).read()
content.replace('(vmdplugin_t *)', '(vmdplugin_t *)(void*)')

# c++
if in_file[-2:] == '.C' or in_file[-4:] == '.cxx':
out_file += 'pp'
content = content.replace('VMDPLUGIN_API', 'VMDPLUGIN_EXTERN')

print in_file, '->', out_file
setup_out.write(repr(out_file) + ',\n')

with open(out_file, 'w') as g:
g.write("/* MACHINE GENERATED FILE, DO NOT EDIT! */\n\n")
g.write("#define VMDPLUGIN molfile_%s\n" % pref)
g.write("#define STATIC_PLUGIN 1\n\n")
g.write(content)

setup_out.write(']\n')
setup_out.close()

# PlugIO init file
with open(os.path.join(molfile_dst_path, 'PlugIOManagerInit.c'), 'w') as g:
g.write('''
/* MACHINE GENERATED FILE, DO NOT EDIT! */
#include "vmdplugin.h"
typedef struct _PyMOLGlobals PyMOLGlobals;
int PlugIOManagerRegister(PyMOLGlobals *G, vmdplugin_t *);
''')

# prototypes
for pref in src_list:
g.write('''
int molfile_%s_init(void);
int molfile_%s_register(void *, vmdplugin_register_cb);
int molfile_%s_fini(void);
''' % (pref, pref, pref))

g.write('''
int PlugIOManagerInitAll(PyMOLGlobals *G) {
int ok = 1 \\
''')

# init
for pref in src_list:
g.write('''
&& (molfile_%s_init() == VMDPLUGIN_SUCCESS)''' % pref)

# register
for pref in src_list:
g.write('''
&& (molfile_%s_register(G, (vmdplugin_register_cb)PlugIOManagerRegister) == VMDPLUGIN_SUCCESS)''' % pref)

g.write(''';

return ok;
}

int PlugIOManagerFreeAll(void) {
int ok = 1 \\
''')

# fini
for pref in src_list:
g.write('''
&& (molfile_%s_fini() == VMDPLUGIN_SUCCESS)''' % pref)

g.write(''';

return ok;
}
''')
</syntaxhighlight>

← Older revision	Revision as of 01:19, 28 March 2014
(No difference)

@@ Line 11: / Line 11: @@
 <syntaxhighlight lang="bash">
 cd /tmp
-tar xzf vmd-1.9.1.src.tar.gz
+tar xzf vmd-1.9.1.src.tar.gz plugins
 svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
 cd /tmp/pymol

User:Speleo3/VMD plugins - Revision history

Pyadmin: 2 revisions

Speleo3: untar only plugins

Speleo3: created