"""
Interfaces for molecular viewers
================================
The viewers defined here are meant to be used for quick interactive structure
and trajectory display. All viewer functions are actually callable instances of
:class:`ViewFactory`, and thus have the same call signature:
.. automethod:: ViewFactory.__call__
VMD
---
Use :func:`view_vmd_xyz` or :func:`view_vmd_axsf`. To execute a tcl script
after the struct has loaded (in the shell: ``vmd -e script.tcl foo.xyz``), use::
>>> tr = crys.Trajectory(...)
>>> view_vmd_axsf(tr, options='-e script.tcl')
Note that the viewer (in this case VMD) is simply called like ``vmd
structfile``, which can take very long for big MD data b/c the VMD default
is to use smth like ``mol new ... waitfor 1``, which is slow. In that case you
want to call VMD directly::
$ vmd
vmd > mol new /tmp/foo.axsf type xsf waitfor all
vmd > set molid 0
vmd > source ~/work/vmd/ca_salt.tcl
The trick here is ``... waitfor all``. See the VMD manual for the ``mol``
command. Or you place these lines in a script and use::
$ vmd script_to_execute.tcl
"""
from tempfile import mkstemp
import os
from pwtools import io, common
[docs]
class ViewFactory:
"""Factory for creating interface functions to external molecular
viewers."""
[docs]
def __init__(self, cmd=None, assert_cmd=None, suffix='.axsf',
writer=io.write_axsf):
"""
Parameters
----------
cmd : str
Shell command to call the viewer. Used as ``<cmd>
<structfile>``. Example: 'jmol', 'xcrysden --axsf'.
assert_cmd : callable
Function which accepts a single arg. Called as ``assert_cmd(obj)``
where `obj` = Structure or Trajectory instance usually). Will be
called early. Use to make additional tests on `obj`.
suffix : str
File end for written structure file.
writer : callable
Called as ``writer(obj, structfile)``. Write struct file to read by
viewer.
Examples
--------
>>> viewer = ViewFactory(...)
>>> viewer(struct)
>>> # To start more than one viewer, use bg=True to send the spawned
>>> # process to the background. Will leave temp files on disk.
>>> viewer(struct1, bg=True)
>>> viewer(struct2, bg=True)
"""
self.cmd = cmd
self.assert_cmd = assert_cmd
self.suffix = suffix
self.writer = writer
[docs]
def __call__(self, obj, logfile=None, structfile=None, disp=False,
keepfiles=False, tmpdir='/tmp', wait=True, bg=False,
options=''):
"""
Call viewer.
The executed shell command is::
<cmd> <options> <structfile> > <logfile>
Parameters
----------
obj : Structure or Trajectory
logfile : str, optional
Filename of a logfile for the viewer's text output.
structfile : str, optional
Filename of a file to write the structure to.
disp : bool
Display text output (i.e. `logfile`'s content).
keepfiles : bool
Keep `structfile` and `logfile` on disk.
tmpdir : str, optional
Directory where temp files are written to.
wait : bool, optional
`wait` passed to common.system(), wait (or not) for command to exit
bg : bool
Background mode. If True then this is an alias for `wait=False` +
`keepfiles=True`. The latter is needed b/c with just `wait=False`,
temp files will be deleted right after the shell call and the
viewer program may complain.
"""
if bg:
wait = False
keepfiles = True
if self.assert_cmd is not None:
self.assert_cmd(obj)
self._set_dummy_symbols(obj)
if structfile is None:
fd1,structfile = mkstemp(dir=tmpdir,
prefix='pwtools_view_struct_',
suffix=self.suffix)
if logfile is None:
fd2,logfile = mkstemp(dir=tmpdir,
prefix='pwtools_view_log_')
self.writer(structfile, obj)
if disp:
cmd_str = "%s %s %s 2>&1 | tee %s" %(self.cmd, options, structfile, logfile)
else:
cmd_str = "%s %s %s > %s 2>&1" %(self.cmd, options, structfile, logfile)
common.system(cmd_str, wait=wait)
if not keepfiles:
os.unlink(structfile)
os.unlink(logfile)
def _set_dummy_symbols(self, obj):
if obj.symbols is None:
print("object has no symbols, setting all to 'H'")
obj.symbols = ['H']*obj.natoms
[docs]
def assert_struct(obj):
assert obj.is_struct, ("input is not Structure instance")
view_xcrysden = \
ViewFactory(cmd='xcrysden --axsf',
suffix='.axsf',
writer=io.write_axsf)
view_vmd_axsf = \
ViewFactory(cmd='vmd',
suffix='.axsf',
writer=io.write_axsf)
view_vmd_xyz = \
ViewFactory(cmd='vmd',
suffix='.xyz',
writer=io.write_xyz)
view_jmol = \
ViewFactory(cmd='jmol',
suffix='.cif',
writer=io.write_cif,
assert_cmd=assert_struct)
avogadro_cmd = r"""
__f(){
if which avogadro2 > /dev/null; then
avogadro2 $@
else
avogadro $@
fi
};
__f """
view_avogadro = \
ViewFactory(cmd=avogadro_cmd,
suffix='.cif',
writer=io.write_cif,
assert_cmd=assert_struct)
