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nomad-lab
pymolfile
Commits
2c31d23f
Commit
2c31d23f
authored
Apr 23, 2018
by
Berk Onat
Browse files
Options
Browse Files
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Plain Diff
Adding functions for structure and trajectory writing through molfile.save
parent
cf9a67ca
Changes
5
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Showing
5 changed files
with
742 additions
and
52 deletions
+742
-52
pymolfile/molfile/libpymolfile.i
pymolfile/molfile/libpymolfile.i
+109
-2
pymolfile/molfile/pymolfile.cxx
pymolfile/molfile/pymolfile.cxx
+516
-2
pymolfile/molfile/pymolfile.h
pymolfile/molfile/pymolfile.h
+4
-0
pymolfile/pymolfile.py
pymolfile/pymolfile.py
+112
-47
setup.py
setup.py
+1
-1
No files found.
pymolfile/molfile/libpymolfile.i
View file @
2c31d23f
...
...
@@ -20,7 +20,7 @@
%
{
/* Python SWIG interface to libpymolfile
Copyright (c) 201
7
Berk Onat <b.onat@warwick.ac.uk>
Copyright (c) 201
8
Berk Onat <b.onat@warwick.ac.uk>
Published with UIUC LICENSE
*/
#
define
SWIG_FILE_WITH_INIT
...
...
@@ -79,7 +79,7 @@ extern PyObject * molfile_plugin_info(PyObject* molcapsule, int plugin_no);
%
inline
%
{
PyObject
*
my_open_file_read
(
PyObject
*
molcapsule
,
char
*
fname
,
char
*
ftype
,
int
natoms
)
{
if
(
PyType_Ready
(
&
MolObjectType)
<
0
)
return
NULL
;
Py_RETURN_NONE
;
PyTypeObject
*
type
=
&
MolObjectType;
MolObject
*
plugin_c
;
molfile_plugin_t
*
plugin
=
(
molfile_plugin_t
*
)
PyMolfileCapsule_AsVoidPtr
(
molcapsule
)
;
...
...
@@ -97,6 +97,82 @@ PyObject * my_open_file_read(PyObject* molcapsule, char* fname, char* ftype, int
}
%
}
%
feature
(
"autodoc"
,
"0"
)
my_open_file_write
;
%
rename
(
open_file_write
)
my_open_file_write
;
%
exception
my_open_file_write
{
$
action
if
(
PyErr_Occurred
())
SWIG_fail
;
}
%
inline
%
{
PyObject
*
my_open_file_write
(
PyObject
*
molcapsule
,
char
*
fname
,
char
*
ftype
,
int
natoms
)
{
if
(
PyType_Ready
(
&
MolObjectType)
<
0
)
Py_RETURN_NONE
;
if
(
natoms
<
1
)
Py_RETURN_NONE
;
PyTypeObject
*
type
=
&
MolObjectType;
MolObject
*
plugin_c
;
molfile_plugin_t
*
plugin
=
(
molfile_plugin_t
*
)
PyMolfileCapsule_AsVoidPtr
(
molcapsule
)
;
plugin_c
=
(
MolObject
*
)
type-
>
tp_alloc
(
type
,
0
)
;
plugin_c-
>
plugin
=
molcapsule
;
void
*
file_handle
=
plugin-
>
open_file_write
(
fname
,
ftype
,
natoms
)
;
plugin_c-
>
file_handle
=
PyMolfileCapsule_FromVoidPtr
(
file_handle
,
del_molfile_file_handle
)
;
if
(
!
plugin_c-
>
file_handle
)
{
Py_RETURN_NONE
;
}
else
{
plugin_c-
>
natoms
=
natoms
;
return
(
PyObject
*
)
plugin_c
;
}
}
%
}
/*
%feature("autodoc", "0") my_set_file_write_stdout;
%rename (set_file_write_stdout) my_set_file_write_stdout;
%exception my_set_file_write_stdout {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * my_set_file_write_stdout(PyObject* molpack) {
MolObject* plugin_handle = (MolObject*) molpack;
PyObject* filecapsule = plugin_handle->file_handle;
void *file_handle = (void*) PyMolfileCapsule_AsVoidPtr(filecapsule);
if(file_handle->fd){
fclose(file_handle->fd);
file_handle->fd = stdout;
}
else if(file_handle->fp){
fclose(file_handle->fp);
file_handle->fp = stdout;
}
else if(file_handle->file){
fclose(file_handle->file);
file_handle->file = stdout;
}
else if(file_handle->mf){
fclose(file_handle->mf);
file_handle->mf = stdout;
}
else if(file_handle->writer){
if(file_handle->writer->fd){
fclose(file_handle->writer->fd);
file_handle->writer->fd = stdout;
}
}
else (file_handle){
fclose(file_handle);
file_handle = stdout;
}
plugin_handle->file_handle = PyMolfileCapsule_FromVoidPtr(file_handle, del_molfile_file_handle);
if (!plugin_c->file_handle) {
Py_RETURN_NONE;
} else {
return (PyObject *)plugin_handle;
}
}
%}
*/
%
feature
(
"autodoc"
,
"0"
)
my_close_file_read
;
%
rename
(
close_file_read
)
my_close_file_read
;
%
exception
my_close_file_read
{
...
...
@@ -115,18 +191,49 @@ PyObject * my_close_file_read(PyObject* molpack) {
}
%
}
%
feature
(
"autodoc"
,
"0"
)
my_close_file_write
;
%
rename
(
close_file_write
)
my_close_file_write
;
%
exception
my_close_file_write
{
$
action
if
(
PyErr_Occurred
())
SWIG_fail
;
}
%
inline
%
{
PyObject
*
my_close_file_write
(
PyObject
*
molpack
)
{
MolObject
*
plugin_handle
=
(
MolObject
*
)
molpack
;
PyObject
*
plugincapsule
=
plugin_handle-
>
plugin
;
PyObject
*
filecapsule
=
plugin_handle-
>
file_handle
;
molfile_plugin_t
*
plugin
=
(
molfile_plugin_t
*
)
PyMolfileCapsule_AsVoidPtr
(
plugincapsule
)
;
void
*
file_handle
=
(
void
*
)
PyMolfileCapsule_AsVoidPtr
(
filecapsule
)
;
plugin-
>
close_file_write
(
file_handle
)
;
Py_RETURN_TRUE
;
}
%
}
%
feature
(
"autodoc"
,
"0"
)
read_fill_structure
;
extern
PyObject
*
read_fill_structure
(
PyObject
*
molpack
,
PyObject
*
prototype
)
;
%
feature
(
"autodoc"
,
"0"
)
write_fill_structure
;
extern
PyObject
*
write_fill_structure
(
PyObject
*
molpack
,
PyObject
*
molarray
)
;
%
feature
(
"autodoc"
,
"0"
)
read_fill_bonds
;
extern
PyObject
*
read_fill_bonds
(
PyObject
*
molpack
)
;
%
feature
(
"autodoc"
,
"0"
)
write_fill_bonds
;
extern
PyObject
*
write_fill_bonds
(
PyObject
*
molpack
,
PyObject
*
moldict
)
;
%
feature
(
"autodoc"
,
"0"
)
read_fill_angles
;
extern
PyObject
*
read_fill_angles
(
PyObject
*
molpack
)
;
%
feature
(
"autodoc"
,
"0"
)
write_fill_angles
;
extern
PyObject
*
write_fill_angles
(
PyObject
*
molpack
,
PyObject
*
moldict
)
;
%
feature
(
"autodoc"
,
"0"
)
read_fill_next_timestep
;
extern
PyObject
*
read_fill_next_timestep
(
PyObject
*
molpack
)
;
%
feature
(
"autodoc"
,
"0"
)
write_fill_timestep
;
extern
PyObject
*
write_fill_timestep
(
PyObject
*
molpack
,
PyObject
*
moldict
)
;
%
feature
(
"autodoc"
,
"0"
)
are_plugins_same
;
PyObject
*
are_plugins_same
(
PyObject
*
molpack_a
,
PyObject
*
molpack_b
)
;
...
...
pymolfile/molfile/pymolfile.cxx
View file @
2c31d23f
This diff is collapsed.
Click to expand it.
pymolfile/molfile/pymolfile.h
View file @
2c31d23f
...
...
@@ -263,9 +263,13 @@ static PyTypeObject MolObjectType = {
PyObject
*
molfile_plugin_info
(
PyObject
*
molcapsule
,
int
plugin_no
);
PyObject
*
read_fill_structure
(
PyObject
*
molpack
,
PyObject
*
prototype
);
PyObject
*
write_fill_structure
(
PyObject
*
molpack
,
PyObject
*
molarray
);
PyObject
*
read_fill_bonds
(
PyObject
*
molpack
);
PyObject
*
write_fill_bonds
(
PyObject
*
molpack
,
PyObject
*
moldict
);
PyObject
*
read_fill_angles
(
PyObject
*
molpack
);
PyObject
*
write_fill_angles
(
PyObject
*
molpack
,
PyObject
*
moldict
);
PyObject
*
read_fill_next_timestep
(
PyObject
*
molpack
);
PyObject
*
write_fill_timestep
(
PyObject
*
molpack
,
PyObject
*
moldict
);
PyObject
*
are_plugins_same
(
PyObject
*
molpack_a
,
PyObject
*
molpack_b
);
PyObject
*
are_filehandles_same
(
PyObject
*
molpack_a
,
PyObject
*
molpack_b
);
PyObject
*
get_plugin
(
PyObject
*
molcapsule
,
int
plug_no
);
...
...
pymolfile/pymolfile.py
View file @
2c31d23f
...
...
@@ -7,6 +7,9 @@ import re
import
sys
import
numpy
as
np
from
contextlib
import
contextmanager
import
platform
import
ctypes
import
tempfile
import
warnings
if
sys
.
version_info
>
(
3
,):
...
...
@@ -19,6 +22,18 @@ except ImportError:
from
.plugin_list
import
plugins
,
byte_str_decode
,
MOLFILE_PLUGINS
,
C_MOLFILE_PLUGINS
if
platform
.
system
()
==
"Windows"
:
libc
=
ctypes
.
cdll
.
msvcrt
else
:
libc
=
ctypes
.
CDLL
(
None
)
if
platform
.
system
()
==
"Windows"
:
c_stdout
=
ctypes
.
c_void_p
.
in_dll
(
libc
,
'stdout'
)
elif
"Darwin"
in
platform
.
system
():
c_stdout
=
ctypes
.
c_void_p
.
in_dll
(
libc
,
'__stdoutp'
)
else
:
c_stdout
=
ctypes
.
c_void_p
.
in_dll
(
libc
,
'stdout'
)
def
list_plugins
():
global
MOLFILE_PLUGINS
return
MOLFILE_PLUGINS
[:]
...
...
@@ -49,6 +64,8 @@ def stdout_redirected(to=os.devnull):
####assert libc.fileno(ctypes.c_void_p.in_dll(libc, "stdout")) == fd == 1
def
_redirect_stdout
(
to
):
# Flush the C-level buffer stdout
libc
.
fflush
(
c_stdout
)
sys
.
stdout
.
close
()
# + implicit flush()
os
.
dup2
(
to
.
fileno
(),
fd
)
# fd writes to 'to' file
sys
.
stdout
=
os
.
fdopen
(
fd
,
'w'
)
# Python writes to fd
...
...
@@ -63,6 +80,42 @@ def stdout_redirected(to=os.devnull):
# buffering and flags such as
# CLOEXEC may be different
# The function stdout_redirect_stream is taken from
#https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python/
@
contextmanager
def
stdout_redirect_stream
(
stream
):
# The original fd stdout points to. Usually 1 on POSIX systems.
original_stdout_fd
=
sys
.
stdout
.
fileno
()
def
_redirect_stdout
(
to_fd
):
"""Redirect stdout to the given file descriptor."""
# Flush the C-level buffer stdout
libc
.
fflush
(
c_stdout
)
# Flush and close sys.stdout - also closes the file descriptor (fd)
sys
.
stdout
.
close
()
# Make original_stdout_fd point to the same file as to_fd
os
.
dup2
(
to_fd
,
original_stdout_fd
)
# Create a new sys.stdout that points to the redirected fd
sys
.
stdout
=
io
.
TextIOWrapper
(
os
.
fdopen
(
original_stdout_fd
,
'wb'
))
# Save a copy of the original stdout fd in saved_stdout_fd
saved_stdout_fd
=
os
.
dup
(
original_stdout_fd
)
try
:
# Create a temporary file and redirect stdout to it
tfile
=
tempfile
.
TemporaryFile
(
mode
=
'w+b'
)
_redirect_stdout
(
tfile
.
fileno
())
# Yield to caller, then redirect stdout back to the saved fd
yield
_redirect_stdout
(
saved_stdout_fd
)
# Copy contents of temporary file to the given stream
tfile
.
flush
()
tfile
.
seek
(
0
,
io
.
SEEK_SET
)
stream
.
write
(
tfile
.
read
())
finally
:
tfile
.
close
()
os
.
close
(
saved_stdout_fd
)
def
get_dir_base_extension
(
file_name
):
""" Splits directory, file base and file extensions
...
...
@@ -346,6 +399,64 @@ class Trajectory(object):
finally
:
del
iter_obj
def
molfile_prototype
(
file_format
=
None
):
""" Generates a prototype numpy array that has the same struct
definition as in molfile_atom_t arrays.
Returns: numpy.array
"""
if
file_format
is
None
:
file_format
=
''
#if 0 && vmdplugin_ABIVERSION > 17
# /* The new PDB file formats allows for much larger structures, */
# /* which can therefore require longer chain ID strings. The */
# /* new PDBx/mmCIF file formats do not have length limits on */
# /* fields, so PDB chains could be arbitrarily long strings */
# /* in such files. At present, we know we need at least 3-char */
# /* chains for existing PDBx/mmCIF files. */
# char chain[4]; /**< required chain name, or "" */
#else
# char chain[2]; /**< required chain name, or "" */
#endif
#
# Change 'chain', S2 to S4
#
#if('pdb' in file_format or
# 'psf' in file_format):
chain_size
=
'S4'
#else:
# chain_size = 'S2'
if
(
'dtr'
in
file_format
.
lower
()
or
'stk'
in
file_format
.
lower
()
or
'atr'
in
file_format
.
lower
()):
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'
)
]
)
return
prototype
def
read_topology
(
file_name
,
file_format
,
plugin
,
silent
):
""" Reads structure, bonds, angles, dihedrals, impropers and
additional informations through molfile_plugin if the
...
...
@@ -373,53 +484,7 @@ def read_topology(file_name, file_format, plugin, silent):
plugin
is
not
None
):
natoms
=
0
topo
=
Topology
(
plugin
,
file_name
,
file_format
,
natoms
,
silent
)
#if 0 && vmdplugin_ABIVERSION > 17
# /* The new PDB file formats allows for much larger structures, */
# /* which can therefore require longer chain ID strings. The */
# /* new PDBx/mmCIF file formats do not have length limits on */
# /* fields, so PDB chains could be arbitrarily long strings */
# /* in such files. At present, we know we need at least 3-char */
# /* chains for existing PDBx/mmCIF files. */
# char chain[4]; /**< required chain name, or "" */
#else
# char chain[2]; /**< required chain name, or "" */
#endif
#
# Change 'chain', S2 to S4
#
#if('pdb' in file_format or
# 'psf' in file_format):
chain_size
=
'S4'
#else:
# chain_size = 'S2'
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'
)
]
)
prototype
=
molfile_prototype
(
file_format
)
if
topo
.
read_structure
(
prototype
)
is
not
None
:
topo
.
structure
=
decode_array
(
topo
.
_structure
)
...
...
setup.py
View file @
2c31d23f
...
...
@@ -98,7 +98,7 @@ def check_tcl_version():
val
=
None
return
val
VERSION
=
"0.0.
4
"
VERSION
=
"0.0.
5
"
CLASSIFIERS
=
[
"Development Status :: 1 - Alpha"
,
"Intended Audience :: Science/Research"
,
...
...
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