diff --git a/pymolfile/__init__.py b/pymolfile/__init__.py
index 0e4f244a9fecb0fa27699383764a33f9bd9b22cf..2c2eb8483d30419664826a7c3a7842d633c5bdad 100644
--- a/pymolfile/__init__.py
+++ b/pymolfile/__init__.py
@@ -1,11 +1,14 @@
from __future__ import absolute_import
+import warnings
+try:
+ from .molfile import libpymolfile
+except ImportError:
+ warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
+
+from . import plugin_list
from . import pymolfile
__all__ = [ "pymolfile" ]
-MAX_NUM_PLUGINS = 200
-C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
-MOLFILE_PLUGINS = pymolfile.plugins()
-
diff --git a/pymolfile/__init__.pyc b/pymolfile/__init__.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..db20cea1fbf7e49adc459293f5aed9592e6b1e5b
Binary files /dev/null and b/pymolfile/__init__.pyc differ
diff --git a/pymolfile/__pycache__/__init__.cpython-36.pyc b/pymolfile/__pycache__/__init__.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..63924f642961ed427b9c7f4fb811158d1fbc4432
Binary files /dev/null and b/pymolfile/__pycache__/__init__.cpython-36.pyc differ
diff --git a/pymolfile/__pycache__/plugin_list.cpython-36.pyc b/pymolfile/__pycache__/plugin_list.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..5083ef19e1fb1d757a92f41b3057ff13fa8093c2
Binary files /dev/null and b/pymolfile/__pycache__/plugin_list.cpython-36.pyc differ
diff --git a/pymolfile/__pycache__/pymolfile.cpython-36.pyc b/pymolfile/__pycache__/pymolfile.cpython-36.pyc
index 1e19a06a51bf6003652eb8cfb19bc4b9a0a26c52..54786c87e0e5f0ff6aaaaacaaec9edcfe4107478 100644
Binary files a/pymolfile/__pycache__/pymolfile.cpython-36.pyc and b/pymolfile/__pycache__/pymolfile.cpython-36.pyc differ
diff --git a/pymolfile/molfile/__init__.py b/pymolfile/molfile/__init__.py
index 2fa350890c2794810c7356d8e44d2271788527c6..7d9a865f6f70451bcb9b0efc731be5bb612b7db6 100644
--- a/pymolfile/molfile/__init__.py
+++ b/pymolfile/molfile/__init__.py
@@ -1,7 +1,7 @@
-# Stand-alone python bindings for libvmdmolfile
+# Stand-alone python bindings for libpymolfile
# Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
-# Published under the BSD LICENSE
+# Published under the UIUC OpenSource LICENSE
"""libpymolfile library.
"""
diff --git a/pymolfile/molfile/__init__.pyc b/pymolfile/molfile/__init__.pyc
index abcb6018cc59e2cabc6876c73bafec8ec6bfa898..c7f427c1eb27c1e30e6a82be67f5fe5f3031bc4d 100644
Binary files a/pymolfile/molfile/__init__.pyc and b/pymolfile/molfile/__init__.pyc differ
diff --git a/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc b/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc
index 3aaa7daa4aa032356318545e3c703ed00ac0ac6e..f4bafae7c67b6c6045648c7b759850b862012a34 100644
Binary files a/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc and b/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc differ
diff --git a/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc b/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc
index bc43e9aae4503301f6e3a92af0ca934b25c01e4b..8dd9e9273c607b9be2faa81535ac9f264641d5af 100644
Binary files a/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc and b/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc differ
diff --git a/pymolfile/molfile/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so
index fdfdcc550fe4a6a7dba7e86c38a4b9974d2da208..c2d0abc0cc6df354db0bd7aab872dd1cc619cbdb 100755
Binary files a/pymolfile/molfile/_libpymolfile.so and b/pymolfile/molfile/_libpymolfile.so differ
diff --git a/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so
index a0b3a8c49d4db6f95fffdd9921c301f5d99e2fdd..e04a1213f814adef895c7fc7f017a6c7929ca7ae 100644
Binary files a/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so and b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so differ
diff --git a/pymolfile/molfile/compile-without-tng.sh b/pymolfile/molfile/compile-without-tng.sh
new file mode 100644
index 0000000000000000000000000000000000000000..3f2ddc97294adb3c692ed46004874d49ea7dfb1b
--- /dev/null
+++ b/pymolfile/molfile/compile-without-tng.sh
@@ -0,0 +1,20 @@
+echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
+swig -py3 -Wall -c++ -python libpymolfile.i
+echo "'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'"
+g++-7 -fPIC -Wall -Wextra -shared -g -Wunused-function -Wunused-parameter \
+ -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ \
+ -I./include \
+ -I./include/molfile_plugin/include \
+ -I./lib/molfile_plugin/lib \
+ -I./include/plugin_src/include \
+ -I./include/netcdf/include \
+ -I./include/expat/include \
+ -I./include/tng/include \
+ libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so -L. \
+ -L./lib/molfile_plugin/lib \
+ -L./lib/netcdf/lib \
+ -L./lib/expat/lib \
+ -L./lib/tng/lib \
+ lib/molfile_plugin/lib/libmolfile_plugin.a -I/labEnv3/include/python3.6m/ \
+ -L/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib \
+ -lpython3.6 -lnetcdf
diff --git a/pymolfile/molfile/compile27.sh b/pymolfile/molfile/compile27.sh
new file mode 100644
index 0000000000000000000000000000000000000000..5863c883f775c4e6a1ec560c4a11a330b2a22bef
--- /dev/null
+++ b/pymolfile/molfile/compile27.sh
@@ -0,0 +1,22 @@
+echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
+#swig -py3 -Wall -c++ -python libpymolfile.i
+swig -Wall -c++ -python libpymolfile.i
+echo "'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'"
+g++-7 -fPIC -Wall -Wextra -Xlinker -export-dynamic -shared -g -Wunused-function -Wunused-parameter \
+ -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/ \
+ -I./include \
+ -I./include/molfile_plugin/include \
+ -I./lib/molfile_plugin/lib \
+ -I./include/plugin_src/include \
+ -I./include/netcdf/include \
+ -I./include/expat/include \
+ -I./include/tng/include \
+ libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so -L. \
+ -L./lib/molfile_plugin/lib \
+ -L./lib/netcdf/lib \
+ -L./lib/expat/lib \
+ -L./lib/tng/lib \
+ lib/molfile_plugin/lib/libmolfile_plugin.a \
+ -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/include/python2.7/ \
+ -L/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib \
+ -lpython2.7 -ltng_io -lnetcdf -lexpat
diff --git a/pymolfile/molfile/libpymolfile.i b/pymolfile/molfile/libpymolfile.i
index 4531072d9c1840d9e5080f4ec2a81303a30575ea..ff8fdad9ef1b08e1308ea58093ad82ca8a8ea1fa 100644
--- a/pymolfile/molfile/libpymolfile.i
+++ b/pymolfile/molfile/libpymolfile.i
@@ -165,9 +165,10 @@ PyObject * my_close_file_read(PyObject* molpack) {
plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
- plugin->close_file_read(file_handle);
+ Py_INCREF(plugin_handle);
+ plugin->close_file_read(file_handle);
Py_DECREF(plugin_handle);
- Py_DECREF(molpack);
+ /*Py_DECREF(molpack);*/
Py_RETURN_NONE;
}
%}
diff --git a/pymolfile/molfile/libpymolfile_wrap.cxx b/pymolfile/molfile/libpymolfile_wrap.cxx
index 533687b00f09f7f7734804817b5a34f0917f375f..41187236a0516f0d7f6db83ce2865f0fc727bb7a 100644
--- a/pymolfile/molfile/libpymolfile_wrap.cxx
+++ b/pymolfile/molfile/libpymolfile_wrap.cxx
@@ -3445,9 +3445,10 @@ PyObject * my_close_file_read(PyObject* molpack) {
plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
- plugin->close_file_read(file_handle);
+ Py_INCREF(plugin_handle);
+ plugin->close_file_read(file_handle);
Py_DECREF(plugin_handle);
- Py_DECREF(molpack);
+ /*Py_DECREF(molpack);*/
Py_RETURN_NONE;
}
diff --git a/pymolfile/molfile/pymolfile.h b/pymolfile/molfile/pymolfile.h
index 94a0b42d5dcb259684cb942600e482c97e5ed797..14b925546ef5d974e1cb0182bef4dc1e9ff2baeb 100644
--- a/pymolfile/molfile/pymolfile.h
+++ b/pymolfile/molfile/pymolfile.h
@@ -61,7 +61,7 @@ void del_molfile_plugin_list(PyObject* molcapsule);
static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
{
- void *ret = PyCapsule_GetPointer(obj, NULL);
+ void *ret = PyCapsule_GetPointer(obj, "plugin_handle");
if (ret == NULL) {
PyErr_Clear();
}
@@ -70,7 +70,7 @@ static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(PyObject *))
{
- PyObject *ret = PyCapsule_New(ptr, NULL, destr);
+ PyObject *ret = PyCapsule_New(ptr, "plugin_handle", destr);
if (ret == NULL) {
PyErr_Clear();
}
diff --git a/pymolfile/molfile/vmd_molfile_plugins/Make-arch b/pymolfile/molfile/vmd_molfile_plugins/Make-arch
index a79c02dd93f796515fc8a0a319c8346401ab2da0..c97290cebd0c343b6f5b2d7cf46456c0b37bff42 100755
--- a/pymolfile/molfile/vmd_molfile_plugins/Make-arch
+++ b/pymolfile/molfile/vmd_molfile_plugins/Make-arch
@@ -29,6 +29,8 @@ make-arch-help:
@echo " MACOSX"
@echo " MACOSXX86"
@echo " MACOSXX86_64"
+ @echo " MACOSXX86_64GCC"
+ @echo " MACOSXX86_64GCCTNG"
@echo " NETBSD"
@echo " OPENPOWER"
@echo " SOLARIS2"
@@ -499,6 +501,27 @@ MACOSXX86_64:
"TCLSHLD = c++ -dynamiclib"
MACOSXX86_64GCC:
+ $(MAKE) dynlibs staticlibs bins \
+ "ARCH = MACOSXX86_64GCC" \
+ "COPTO = -m64 -fPIC -o " \
+ "LOPTO = -m64 -fPIC -o " \
+ "CC = gcc-7" \
+ "CXX = g++-7" \
+ "DEF = -D" \
+ "CCFLAGS = -m64 -Os -Wall -fPIC -dynamic" \
+ "CXXFLAGS = -m64 -Os -Wall -fPIC -dynamic" \
+ "TCLLDFLAGS = -ltcl8.5" \
+ "NETCDFLDFLAGS = -lnetcdf" \
+ "NETCDFLIB = -L/usr/local/Cellar/netcdf/4.4.1.1_6/lib " \
+ "NETCDFINC = -I/usr/local/Cellar/netcdf/4.4.1.1_6/include " \
+ "AR = ar" \
+ "NM = nm -p" \
+ "RANLIB = ranlib" \
+ "LIBTOOL = libtool -dynamic" \
+ "SHLD = g++-7 -shared" \
+ "TCLSHLD = g++-7 -dynamiclib"
+
+MACOSXX86_64GCCTNG:
$(MAKE) dynlibs staticlibs bins \
"ARCH = MACOSXX86_64GCC" \
"COPTO = -m64 -fPIC -o " \
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin-s.o
deleted file mode 100644
index 02dcbe695b7e0d5252e37da16906c1f931355049..0000000000000000000000000000000000000000
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin-s.o and /dev/null differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin.o
deleted file mode 100644
index 32eab9e2adb7b19e7ee1fbbd099a0c8c636f2b3d..0000000000000000000000000000000000000000
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin.o and /dev/null differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin.so
deleted file mode 100755
index 30d75a56dde6c660f76000ab2215e61a76cec856..0000000000000000000000000000000000000000
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/hoomdplugin.so and /dev/null differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.a b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.a
index 0e53d339f0336cf2c58997d13b20181adfc279ab..f4e208badc74bca6caed07bf4ebf6ba5f906e2ca 100644
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.a and b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.a differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.h b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.h
index 8c25b6dac3da210c2d5f0bf89ce255cd828be693..3eec061a70c95d39acb51cd4027d769ddf04f4be 100644
--- a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.h
+++ b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/libmolfile_plugin.h
@@ -204,12 +204,6 @@ extern int molfile_maeffplugin_fini(void);
extern int molfile_netcdfplugin_init(void);
extern int molfile_netcdfplugin_register(void *, vmdplugin_register_cb);
extern int molfile_netcdfplugin_fini(void);
-extern int molfile_hoomdplugin_init(void);
-extern int molfile_hoomdplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_hoomdplugin_fini(void);
-extern int molfile_tngplugin_init(void);
-extern int molfile_tngplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_tngplugin_fini(void);
#define MOLFILE_INIT_ALL \
molfile_abinitplugin_init(); \
@@ -278,8 +272,6 @@ extern int molfile_tngplugin_fini(void);
molfile_dtrplugin_init(); \
molfile_maeffplugin_init(); \
molfile_netcdfplugin_init(); \
- molfile_hoomdplugin_init(); \
- molfile_tngplugin_init(); \
#define MOLFILE_REGISTER_ALL(v, cb) \
molfile_abinitplugin_register(v, cb); \
@@ -348,8 +340,6 @@ extern int molfile_tngplugin_fini(void);
molfile_dtrplugin_register(v, cb); \
molfile_maeffplugin_register(v, cb); \
molfile_netcdfplugin_register(v, cb); \
- molfile_hoomdplugin_register(v, cb); \
- molfile_tngplugin_register(v, cb); \
#define MOLFILE_FINI_ALL \
molfile_abinitplugin_fini(); \
@@ -418,8 +408,6 @@ extern int molfile_tngplugin_fini(void);
molfile_dtrplugin_fini(); \
molfile_maeffplugin_fini(); \
molfile_netcdfplugin_fini(); \
- molfile_hoomdplugin_fini(); \
- molfile_tngplugin_fini(); \
#ifdef __cplusplus
}
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin-s.o
deleted file mode 100644
index 726261002f304e578717594280d2f8a5c5746995..0000000000000000000000000000000000000000
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin-s.o and /dev/null differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin.o
deleted file mode 100644
index d9db5f9d3e7fd3d5e0c357d4ca1b63d6c73b78ae..0000000000000000000000000000000000000000
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin.o and /dev/null differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin.so
deleted file mode 100755
index 5e35447d790c7ccc92a3a7d31cc7d45e4e63f764..0000000000000000000000000000000000000000
Binary files a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64GCC/molfile/tngplugin.so and /dev/null differ
diff --git a/pymolfile/plugin_list.py b/pymolfile/plugin_list.py
new file mode 100644
index 0000000000000000000000000000000000000000..6665034e5e077518aaa9b7c8add1474c3b393047
--- /dev/null
+++ b/pymolfile/plugin_list.py
@@ -0,0 +1,63 @@
+import warnings
+import sys
+
+from .molfile import libpymolfile
+try:
+ from .molfile import libpymolfile
+except ImportError:
+ warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
+
+MAX_NUM_PLUGINS = 200
+C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
+
+def byte_str_decode(data, dectype=None):
+ try:
+ return data.decode(dectype)
+ except AttributeError:
+ return data
+
+def plugins():
+ """ Information on the available molfile plugins
+
+ Example tuple: ('psf', 'psf', 1, 1, 1, 0, 1, 1, 1, 0,
+ 'CHARMM,NAMD,XPLOR PSF', 'mol file reader',
+ 'Justin Gullingsrud, John Stone', 1, 9, 17, 1)
+
+ The fields in the tuple represent info in ordered as follows:
+ 1: format extension
+ 2: format name
+ 3: read_structure is avaliable if 1
+ 4: read_bonds is avaliable if 1
+ 5: read_angles is avaliable if 1
+ 6: read_next_timestep is avaliable if 1
+ 7: write_structure is avaliable if 1
+ 8: write_bonds is avaliable if 1
+ 9: write_angles is avaliable if 1
+ 10: write_timestep is avaliable if 1
+ 11: long name of the plugin
+ 12: type of plugin
+ 13: authors of the plugin
+ 14: major version of the plugin
+ 15: minor version of the plugin
+ 16: ABI version of the plugin
+ 17: 1 if is reentrant (returns is_reentrant)
+
+ Returns: A list of tuples that includes the information and
+ capabilities of each molfile plugin. The information is
+ extracted from molfile_plugin_t.
+ """
+ global C_MOLFILE_PLUGINS
+ numlist = libpymolfile.molfile_init()
+ if sys.version_info > (3,):
+ basestring = str
+ plugins_list = [
+ [byte_str_decode(item,
+ dectype="unicode_escape") for item in libpymolfile.molfile_plugin_info(
+ C_MOLFILE_PLUGINS, i)
+ ] for i in range(numlist)
+ ]
+ libpymolfile.molfile_finish()
+ return plugins_list
+
+MOLFILE_PLUGINS = plugins()
+
diff --git a/pymolfile/plugin_list.pyc b/pymolfile/plugin_list.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..e2ae09006f8595e1ab959ded1fa70b1e9e6da63d
Binary files /dev/null and b/pymolfile/plugin_list.pyc differ
diff --git a/pymolfile/pymolfile.py b/pymolfile/pymolfile.py
index b96887b61467d291b7a59818c779864098ea0ce0..6a1ce670e90f2ce25a25cace31a6d33719e76b1b 100644
--- a/pymolfile/pymolfile.py
+++ b/pymolfile/pymolfile.py
@@ -16,41 +16,18 @@ try:
except ImportError:
warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
+from .plugin_list import plugins, byte_str_decode, MOLFILE_PLUGINS, C_MOLFILE_PLUGINS
-def plugins():
- """ Information on the available molfile plugins
-
- Example tuple: ('psf', 'psf', 1, 1, 1, 0, 1, 1, 1, 0,
- 'CHARMM,NAMD,XPLOR PSF', 'mol file reader',
- 'Justin Gullingsrud, John Stone', 1, 9, 17, 1)
-
- The fields in the tuple represent info in ordered as follows:
- 1: format extension
- 2: format name
- 3: read_structure is avaliable if 1
- 4: read_bonds is avaliable if 1
- 5: read_angles is avaliable if 1
- 6: read_next_timestep is avaliable if 1
- 7: write_structure is avaliable if 1
- 8: write_bonds is avaliable if 1
- 9: write_angles is avaliable if 1
- 10: write_timestep is avaliable if 1
- 11: long name of the plugin
- 12: type of plugin
- 13: authors of the plugin
- 14: major version of the plugin
- 15: minor version of the plugin
- 16: ABI version of the plugin
- 17: 1 if is reentrant (returns is_reentrant)
-
- Returns: A list of tuples that includes the information and
- capabilities of each molfile plugin. The information is
- extracted from molfile_plugin_t.
- """
- numlist = libpymolfile.molfile_init()
- plugins_list = [libpymolfile.molfile_plugin_info(C_MOLFILE_PLUGINS, i) for i in range(numlist)]
- libpymolfile.molfile_finish()
- return plugins_list
+def list_plugins():
+ global MOLFILE_PLUGINS
+ return MOLFILE_PLUGINS
+
+def decode_array(inarray):
+ return [
+ [byte_str_decode(element,
+ dectype="unicode_escape") for element in item
+ ] for item in inarray
+ ]
def get_dir_base_extension(file_name):
""" Splits directory, file base and file extensions
@@ -86,6 +63,9 @@ def get_plugin_with_ext(file_ext):
Returns: Plugin no in the list and the list item (the plugin info tuple)
"""
+ global MOLFILE_PLUGINS
+ global C_MOLFILE_PLUGINS
+
if not MOLFILE_PLUGINS:
MOLFILE_PLUGINS = plugins()
@@ -93,14 +73,17 @@ def get_plugin_with_ext(file_ext):
plugin_no = -1
for plugin_info in MOLFILE_PLUGINS:
plugin_no += 1
- if file_ext == plugin_info[1]:
- return (plugin_no, plugin_info)
+ plugin_ext_info = str(plugin_info[0]).replace('*|',
+ '').replace('*', '').replace('|', ',').replace(' ', '')
+ for ext_item in str(plugin_ext_info).split(','):
+ if str(file_ext) == str(ext_item):
+ return (plugin_no, plugin_info)
return None
def plugins_same(plugin_one, plugin_two):
- if((plugin_one[1] == plugin_two[1]) and
- (plugin_one[2][2] == plugin_two[2][2])):
+ if((plugin_one[0] == plugin_two[0]) and
+ (plugin_one[1][1] == plugin_two[1][1])):
return True
else:
return False
@@ -111,6 +94,9 @@ def get_plugin_with_name(plugin_name):
Returns: Plugin no in the list and the list item (the plugin info tuple)
"""
+ global MOLFILE_PLUGINS
+ global C_MOLFILE_PLUGINS
+
if not MOLFILE_PLUGINS:
MOLFILE_PLUGINS = plugins()
@@ -118,58 +104,113 @@ def get_plugin_with_name(plugin_name):
plugin_no = -1
for plugin_info in MOLFILE_PLUGINS:
plugin_no += 1
- if plugin_name == plugin_info[2]:
+ if(str(plugin_name) in str(plugin_info[1]) or
+ str(plugin_name) in str(plugin_info[10])):
return (plugin_no, plugin_info)
return None
-class Topology( object ):
+class Topology(object):
- def __init__(self):
+ def __init__(self, fplugin, fname, ftype, natoms):
self.natoms = None
self.structure = None
self.bonds = None
self.angles = None
+ self._structure = None
+ self._bonds = None
+ self._angles = None
+ self.pluginhandle = None
+ try:
+ self.pluginhandle = libpymolfile.open_file_read(fplugin,
+ fname, ftype, natoms)
+ self.natoms = self.pluginhandle.natoms
+ except (IOError, OSError, AttributeError):
+ pass
+
+ def read_structure(self, prototype):
+ try:
+ self._structure = libpymolfile.read_fill_structure(self.pluginhandle, prototype)
+ return self._structure
+ except (AttributeError, SystemError):
+ return None
+
+ def read_bonds(self):
+ try:
+ self._bonds = libpymolfile.read_fill_bonds(self.pluginhandle)
+ return self._bonds
+ except (AttributeError, SystemError):
+ return None
+
+ def read_angles(self):
+ try:
+ self._angles = libpymolfile.read_fill_angles(self.pluginhandle)
+ return self._angles
+ except (AttributeError, SystemError):
+ return None
def __del__( self ):
- pass
+ if self.pluginhandle is not None:
+ libpymolfile.close_file_read(self.pluginhandle)
-class Trajectory( object ):
+class Trajectory(object):
def __init__(self, file_name, file_format, plugin, natoms):
+ global MOLFILE_PLUGINS
+ global C_MOLFILE_PLUGINS
self.natoms = None
self.atoms = None
self.plugin = None
+ self.handle = None
self.fname = None
self.ftype = None
self.fname = file_name
self.ftype = file_format
self.plugin = plugin
- self.natoms = natoms
+ self.natoms = 0
- def iread(self, chunk=None):
- numlist = libpymolfile.molfile_init()
- tplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
- self.plugin[1])
- pluginhandle = libpymolfile.open_file_read(tplugin,
- file_name, file_format, natoms)
+ if natoms is not None:
+ self.natoms = natoms
- step=0
- while True:
+ numlist = libpymolfile.molfile_init()
+ self.fplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
+ self.plugin[0])
+ self.pluginhandle = None
+ if self.natoms > 0:
try:
- x = libpymolfile.read_fill_next_timestep(
- pluginhandle)
+ self.pluginhandle = libpymolfile.open_file_read(self.fplugin,
+ self.fname, self.ftype, self.natoms)
+ except (IOError, OSError, AttributeError):
+ pass
+
+ def read_next(self):
+ return libpymolfile.read_fill_next_timestep(self.pluginhandle)
+
+ def iter_on_traj(self):
+ try:
+ empty = False
+ self.step = 0
+ while not empty:
+ print(f)
+ x = self.read_next()
if x is None:
- break
- step=step+1
- if x is not None:
- self.atoms = x
+ empty = True
+ else:
+ self.step += 1
yield x
- except (AttributeError,OSError):
- pass
+ except (IOError, AttributeError, OSError):
+ return
- libpymolfile.close_file_read(pluginhandle)
- libpymolfile.molfile_finish()
+ def iread(self):
+ iter_obj = iter(self.iter_on_traj())
+ try:
+ while True:
+ self.atoms = next(iter_obj)
+ return self.atoms
+ except StopIteration:
+ pass
+ finally:
+ del iter_obj
# def read_frame(self, index_no):
# numlist = libpymolfile.molfile_init()
@@ -187,40 +228,9 @@ class Trajectory( object ):
# file_name, file_format, natoms)
# libpymolfile.molfile_finish()
- def __del__( self ):
- pass
-
-class Molfile(object):
-
- def __init__(self, file_name, **kwargs):
- self.plugin_list = MOLFILE_PLUGINS
- self.c_plugin_list = C_MOLFILE_PLUGINS
- self.trajectory = None
- self.topology = None
- self.fplugin = None
- self.tplugin = None
- self.smolplugin = None
- self.cmolplugin = None
- self.kwords = {
- "file_format" : None,
- "file_plugin" : None,
- "topology" : None,
- "topology_format" : None,
- "topology_plugin" : None,
- "natoms" : None
- }
-
- if not C_MOLFILE_PLUGINS:
- C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
- if not MOLFILE_PLUGINS:
- MOLFILE_PLUGINS = plugins()
- if(MOLFILE_PLUGINS and self.plugin_list is None):
- self.plugin_list = MOLFILE_PLUGINS
- if(C_MOLFILE_PLUGINS and self.c_plugin_list is None):
- self.c_plugin_list = C_MOLFILE_PLUGINS
-
- def __del__( self ):
- pass
+ def __del__(self):
+ if self.pluginhandle is not None:
+ libpymolfile.close_file_read(self.pluginhandle)
def read_topology(self, file_name, file_format, plugin):
""" Reads structure, bonds, angles, dihedrals, impropers and
@@ -241,13 +251,15 @@ def read_topology(self, file_name, file_format, plugin):
function returns None
"""
topo = None
+ structure = None
+ bonds = None
+ angles = None
if(file_name is not None and
file_format is not None and
plugin is not None):
natoms=0
- pluginhandle = libpymolfile.open_file_read(plugin,
- file_name, file_format, natoms)
- natoms = pluginhandle.natoms
+ topo = Topology(plugin, file_name, file_format, natoms)
+ topo.natoms = natoms
#if 0 && vmdplugin_ABIVERSION > 17
# /* The new PDB file formats allows for much larger structures, */
# /* which can therefore require longer chain ID strings. The */
@@ -266,46 +278,50 @@ def read_topology(self, file_name, file_format, plugin):
chain_size = 'S2'
else:
chain_size = 'S4'
- prototype = numpy.array([
- ('C1','C','ACE',0,'','','','',1.0,1.0,1.0,1.0,1.0,6),
- ('C2','C','ACE',0,'','','','',1.0,1.0,1.0,1.0,1.0,6)
- ],
- dtype=[
- ('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
- ('resid', 'i4'), ('segid', 'S8'), ('chain', chain_size),
- ('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f4'),
- ('bfactor', 'f4'), ('mass', 'f4'), ('charge', 'f4'),
- ('radius', 'f4'), ('atomicnumber', 'i4')
- ]
- )
- structure = libpymolfile.read_fill_structure(pluginhandle, prototype)
- try:
- bonds = libpymolfile.read_fill_bonds(pluginhandle)
- except (AttributeError, SystemError):
- pass
-
- try:
- angles = libpymolfile.read_fill_angles(pluginhandle)
- except (AttributeError, SystemError):
- pass
-
- if structure:
- topo = Topology()
- topo.natoms = natoms
- topo.structure = structure
- if bonds:
- topo.bonds = bonds
- if angles:
- topo.angles = angles
-
- libpymolfile.close_file_read(pluginhandle)
-
- if topo:
+ if('dtr' in file_format or
+ 'stk' in file_format or
+ 'atr' in file_format):
+ prototype = np.array([
+ ('','','',0,'','','','',1.0,1.0,1.0,1.0,1.0,6,0),
+ ('','','',0,'','','','',1.0,1.0,1.0,1.0,1.0,6,0)
+ ],
+ dtype=[
+ ('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
+ ('resid', 'i4'), ('segid', 'S8'), ('chain', chain_size),
+ ('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f4'),
+ ('bfactor', 'f4'), ('mass', 'f4'), ('charge', 'f4'),
+ ('radius', 'f4'), ('atomicnumber', 'i4'), ('ctnumber', 'i4')
+ ]
+ )
+ else:
+ prototype = np.array([
+ ('','','',0,'','','','',1.0,1.0,1.0,1.0,1.0,6),
+ ('','','',0,'','','','',1.0,1.0,1.0,1.0,1.0,6)
+ ],
+ dtype=[
+ ('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
+ ('resid', 'i4'), ('segid', 'S8'), ('chain', chain_size),
+ ('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f4'),
+ ('bfactor', 'f4'), ('mass', 'f4'), ('charge', 'f4'),
+ ('radius', 'f4'), ('atomicnumber', 'i4')
+ ]
+ )
+
+ if topo.read_structure(prototype) is not None:
+ topo.structure = decode_array(topo._structure)
+ if topo.read_bonds() is not None:
+ topo.bonds = topo._bonds
+ if topo.read_angles() is not None:
+ topo.angles = topo._angles
+
+ if(topo.structure is not None or
+ topo.bonds is not None or
+ topo.angles is not None):
return topo
else:
return None
-class OpenMolfile(Molfile):
+class OpenMolfile(object):
""" The main class/function to read topology and
trajectory files
@@ -315,13 +331,40 @@ class OpenMolfile(Molfile):
without topology information. (the number of atoms must be known)
If both files are supplied, it returns trajectory class with
topology information.
+ If file has both topology and trajectory info, both info will be
+ available in the class
+ If none of the above is available, the topology and
+ trajectory will be None in the return object
"""
- def __init__(self, file_name, **kwargs):
+ def __init__(self, *args, **kwargs):
+ self.initialize_settings()
+ #super(OpenMolfile, self).__init__(*args, **kwargs)
+ global MOLFILE_PLUGINS
+ global C_MOLFILE_PLUGINS
+ file_name = None
+
+ if args:
+ for arg in args:
+ if isinstance(arg, dict):
+ self.reset_kwords()
+ for k, v in arg.items():
+ if k in self.kwords:
+ self.kwords[k] = v
+ elif isinstance(arg, (list, tuple)):
+ self.kwords["file_name"] = arg[0]
+ elif isinstance(arg, str):
+ self.kwords["file_name"] = arg
+ else:
+ self.kwords["file_name"] = arg
+
if kwargs:
for k, v in kwargs.items():
if k in self.kwords:
self.kwords[k] = v
+
+ if self.kwords["file_name"] is not None:
+ file_name = self.kwords["file_name"]
if file_name:
if self.kwords["file_format"] is None:
@@ -338,34 +381,35 @@ class OpenMolfile(Molfile):
plugin_item = get_plugin_with_ext(self.kwords["file_format"])
if plugin_item:
self.fplugin = plugin_item
- self.kwords["file_plugin"] = plugin_item[2][2]
+ self.kwords["file_plugin"] = plugin_item[1][1]
else:
self.kwords["file_plugin"] = None
-
+
if self.kwords["file_plugin"]:
# Check if file_plugin reads structure info
# for the given file format.
- if self.fplugin[2][3] == 1:
+ if self.fplugin[1][2] == 1:
# Topology may be read with the plugin.
# This will override topology information
# if a 'topology' is supplied in keywords.
if self.kwords["file_format"] is not None:
numlist = libpymolfile.molfile_init()
self.smolplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
- self.fplugin[1])
- self.topology = read_topology(file_name,
+ self.fplugin[0])
+ self.topology = read_topology(self,
+ file_name,
self.kwords["file_format"],
self.smolplugin)
- libpymolfile.molfile_finish()
+ #libpymolfile.molfile_finish()
- if self.fplugin[2][3] == 0:
+ if self.fplugin[1][2] == 0:
# Topology can not be read with plugin from
# the file. If 'topology' is not set but 'natoms'
# is set, only the trajectory will be available.
if self.kwords["topology"] is not None:
- if isinstance(self.kwords["topology"], Molfile):
+ if isinstance(self.kwords["topology"], OpenMolfile):
self.topology = self.kwords["topology"].topology
- elif isinstance(elf.kwords["topology"], Topology):
+ elif isinstance(self.kwords["topology"], Topology):
self.topology = self.kwords["topology"]
else:
if self.kwords["topology_format"] is None:
@@ -383,30 +427,30 @@ class OpenMolfile(Molfile):
topo_plugin_item = get_plugin_with_ext(self.kwords["topology_format"])
if topo_plugin_item:
self.tplugin = topo_plugin_item
- self.kwords["topology_plugin"] = topo_plugin_item[2][2]
+ self.kwords["topology_plugin"] = topo_plugin_item[1][1]
else:
self.kwords["topology_plugin"] = None
if self.kwords["topology_plugin"]:
# Check if topology_plugin reads structure info
# for the given file format.
- if self.tplugin[2][3] == 1:
+ if self.tplugin[1][2] == 1:
# Topology may be read with the plugin.
# This will override the topology information.
if self.kwords["topology_format"] is not None:
numlist = libpymolfile.molfile_init()
self.smolplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
- self.fplugin[1])
+ self.fplugin[0])
self.topology = read_topology(file_name,
self.kwords["topology_format"],
self.smolplugin)
- libpymolfile.molfile_finish()
+ #libpymolfile.molfile_finish()
else:
- print("Pymolfile can not determine the {0} file format " +
- "of the file {1}" % (self.kwords["topology_format"],
- topo_file_base + "." + topo_file_ext))
+ print("Pymolfile can not find a plugin to open the '" +
+ self.kwords["topology_format"] + "' file format of the file " +
+ str(topo_file_base) + "." + str(topo_file_ext))
- if(self.fplugin[2][6] == 1):
+ if(self.fplugin[1][5] == 1):
num_atoms = 0
if self.topology:
num_atoms = self.topology.natoms
@@ -416,11 +460,55 @@ class OpenMolfile(Molfile):
if num_atoms>0:
self.trajectory = Trajectory(file_name,
self.kwords["file_format"],
- self.kwords["file_plugin"],
+ self.fplugin,
num_atoms)
else:
- print("Pymolfile can not determine the {0} file format " +
- "of the file {1}" % (self.kwords["file_format"],
- file_base + "." + file_ext))
+ print("Pymolfile can not find a plugin to open the '" + self.kwords["file_format"] +
+ "' file format of the file " + str(file_base) + "." + str(file_ext))
+
+ def initialize_settings(self):
+ global MOLFILE_PLUGINS
+ global C_MOLFILE_PLUGINS
+ self.plugin_list = MOLFILE_PLUGINS
+ self.c_plugin_list = C_MOLFILE_PLUGINS
+ self.trajectory = None
+ self.topology = None
+ self.fplugin = None
+ self.tplugin = None
+ self.smolplugin = None
+ self.cmolplugin = None
+ self.kwords = {
+ "file_name" : None,
+ "file_format" : None,
+ "file_plugin" : None,
+ "topology" : None,
+ "topology_format" : None,
+ "topology_plugin" : None,
+ "natoms" : None
+ }
+
+ if not C_MOLFILE_PLUGINS:
+ C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
+ if not MOLFILE_PLUGINS:
+ MOLFILE_PLUGINS = plugins()
+ if(MOLFILE_PLUGINS and self.plugin_list is None):
+ self.plugin_list = MOLFILE_PLUGINS
+ if(C_MOLFILE_PLUGINS and self.c_plugin_list is None):
+ self.c_plugin_list = C_MOLFILE_PLUGINS
+ def reset_kwords(self):
+ self.kwords.update({
+ "file_name" : None,
+ "file_format" : None,
+ "file_plugin" : None,
+ "topology" : None,
+ "topology_format" : None,
+ "topology_plugin" : None,
+ "natoms" : None
+ })
+
+ def __del__(self):
+ del self.topology
+ del self.trajectory
+ libpymolfile.molfile_finish()
diff --git a/pymolfile/pymolfile.pyc b/pymolfile/pymolfile.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..ad428713b68f97c74134807f79a3bc1f2769ca3b
Binary files /dev/null and b/pymolfile/pymolfile.pyc differ
diff --git a/pymolfile/test.py b/pymolfile/test.py
deleted file mode 100644
index 35fb3d9cfb303bc5ded90f2ca018938d5d82bc26..0000000000000000000000000000000000000000
--- a/pymolfile/test.py
+++ /dev/null
@@ -1,20 +0,0 @@
-import numpy
-import pymolfile as pym
-
-sfname="../test/DPDP.pdb"
-cfname="../test/DPDP.nc"
-
-#sfname="../test/ala3.pdb"
-#sfname="../test/ala3.psf"
-#cfname="../test/ala3.dcd"
-
-#sfname="../test/md.gro"
-#cfname="../test/md.trr"
-#cfname="../test/md.xtc"
-
-#sfname="../test/md_1u19.gro"
-#cfname="../test/md_1u19.xtc"
-
-molfile = pym.OpenMolfile(sfname)
-print(molfile)
-
diff --git a/pymolfile/test_libpymolfile.py b/pymolfile/test_libpymolfile.py
index 59d978e27129152aa349c63f7f60354467f772c1..a509ef39b8dd2d91171f1cd1c4389330123337e1 100644
--- a/pymolfile/test_libpymolfile.py
+++ b/pymolfile/test_libpymolfile.py
@@ -9,22 +9,22 @@ for i in range(numlist):
testplugin = pym.molfile_plugin_info(mylist, i)
print(i, testplugin)
-splugin = pym.get_plugin(mylist, 99) #pdb
+#splugin = pym.get_plugin(mylist, 99) #pdb
#cplugin = pym.get_plugin(mylist, 83) #trr
#cplugin = pym.get_plugin(mylist, 85) #xtc
-#splugin = pym.get_plugin(mylist, 105) #psf
+splugin = pym.get_plugin(mylist, 105) #psf
#splugin = pym.get_plugin(mylist, 81) #gro
-#cplugin = pym.get_plugin(mylist, 69) #dcd
-cplugin = pym.get_plugin(mylist, 126) #nc
+cplugin = pym.get_plugin(mylist, 69) #dcd
+#cplugin = pym.get_plugin(mylist, 126) #nc
print(splugin)
print(cplugin)
natoms=0
-sfname="../test/DPDP.pdb"
-cfname="../test/DPDP.nc"
+#sfname="../test/DPDP.pdb"
+#cfname="../test/DPDP.nc"
#sfname="../test/ala3.pdb"
-#sfname="../test/ala3.psf"
-#cfname="../test/ala3.dcd"
+sfname="../test/ala3.psf"
+cfname="../test/ala3.dcd"
#sfname="../test/md.gro"
#cfname="../test/md.trr"
@@ -33,13 +33,13 @@ cfname="../test/DPDP.nc"
#sfname="../test/md_1u19.gro"
#cfname="../test/md_1u19.xtc"
-sftype="pdb"
+#sftype="pdb"
#cftype="trr"
#cftype="xtc"
-#sftype="psf"
+sftype="psf"
#sftype="gro"
-#cftype="dcd"
-cftype="nc"
+cftype="dcd"
+#cftype="nc"
print("Structure plugin:")
spluginhandle = pym.open_file_read(splugin, sfname, sftype, natoms)
diff --git a/test.py b/test.py
new file mode 100644
index 0000000000000000000000000000000000000000..18a33d08a980c431750cb27586dba33fd8cc117d
--- /dev/null
+++ b/test.py
@@ -0,0 +1,44 @@
+import numpy
+from pymolfile import pymolfile as pym
+
+#sfname="./test/DPDP.pdb"
+#cfname="./test/DPDP.nc"
+
+#sfname="./test/ala3.pdb"
+sfname="./test/ala3.psf"
+cfname="./test/ala3.dcd"
+
+#sfname="./test/md.gro"
+#cfname="./test/md.trr"
+#cfname="./test/md.xtc"
+
+#sfname="./test/md_1u19.gro"
+#cfname="./test/md_1u19.xtc"
+
+print("Reading topology")
+moltopo = pym.OpenMolfile(sfname)
+if moltopo.topology is not None:
+ if moltopo.topology.structure is not None:
+ print(moltopo.topology.structure)
+ if moltopo.topology.bonds is not None:
+ print(moltopo.topology.bonds)
+ if moltopo.topology.angles is not None:
+ print(moltopo.topology.angles)
+
+if True:
+ print("Reading trajectory")
+ moltraj = pym.OpenMolfile(cfname, topology=moltopo)
+ print(moltraj)
+ print(moltraj.trajectory)
+
+ if moltraj.trajectory is not None:
+ step=0
+ while True:
+ positions = moltraj.trajectory.iread()
+ if positions is not None:
+ print("STEP:",step)
+ print(positions)
+ step += 1
+ else:
+ break
+