def write_3d_pdf(self, filename, verbose=False, quiet=False, **kwargs):
"""
Write interactive 3D pictures of the molecules to a pdf file, one per page.
@param filename: File to write
@param kwargs: Keywords to pass to JMolRenderer.write_3d_pdf
"""
latex_out = path_join(self.tempdir, "output.tex")
#----------------------------------------#
pbar = ProgressBar(len(self.molecules))
if not quiet:
pbar.update(0)
with open(latex_out, "w+") as f:
f.write(pdf_3d_header)
for mol in self.molecules:
renderer = JmolRenderer(mol)
if mol.description is not None:
f.write(
pdf_description_template.replace(
"@@@LABEL@@@", mol.description))
renderer.write_3d_pdf(filename=None,
verbose=verbose,
latex_file_handler=f,
**kwargs)
if mol is not self.molecules[-1]:
f.write(r"\clearpage")
if not quiet:
pbar += 1
f.write(pdf_3d_footer)
#----------------------------------------#
pdflatex_cmd_list = [pdflatex_path] + pdflatex_args + ["output"]
with working_directory(self.tempdir):
# Run 3 times to get references right
JmolRenderer._safe_run(pdflatex_cmd_list,
"pdflatex",
require_empty_stderr=True,
require_zero_exit=False)
if verbose: print(" ...run 1 complete")
JmolRenderer._safe_run(pdflatex_cmd_list,
"output",
require_empty_stderr=True,
require_zero_exit=False)
if verbose: print(" ...run 2 complete")
JmolRenderer._safe_run(pdflatex_cmd_list,
"output",
require_empty_stderr=True,
require_zero_exit=False)
if verbose: print(" ...run 3 complete")
#----------------------------------------#
move(path_join(self.tempdir, "output.pdf"), filename)
def write_3d_pdf(self, filename,
verbose=False,
quiet=False,
**kwargs
):
"""
Write interactive 3D pictures of the molecules to a pdf file, one per page.
@param filename: File to write
@param kwargs: Keywords to pass to JMolRenderer.write_3d_pdf
"""
latex_out = path_join(self.tempdir, "output.tex")
#----------------------------------------#
pbar = ProgressBar(len(self.molecules))
if not quiet:
pbar.update(0)
with open(latex_out, "w+") as f:
f.write(pdf_3d_header)
for mol in self.molecules:
renderer = JmolRenderer(mol)
if mol.description is not None:
f.write(pdf_description_template.replace("@@@LABEL@@@", mol.description))
renderer.write_3d_pdf(
filename=None, verbose=verbose,
latex_file_handler=f,
**kwargs
)
if mol is not self.molecules[-1]:
f.write(r"\clearpage")
if not quiet:
pbar += 1
f.write(pdf_3d_footer)
#----------------------------------------#
pdflatex_cmd_list = [pdflatex_path] + pdflatex_args + ["output"]
with working_directory(self.tempdir):
# Run 3 times to get references right
JmolRenderer._safe_run(pdflatex_cmd_list, "pdflatex",
require_empty_stderr=True, require_zero_exit=False)
if verbose: print(" ...run 1 complete")
JmolRenderer._safe_run(pdflatex_cmd_list, "output",
require_empty_stderr=True, require_zero_exit=False)
if verbose: print(" ...run 2 complete")
JmolRenderer._safe_run(pdflatex_cmd_list, "output",
require_empty_stderr=True, require_zero_exit=False)
if verbose: print(" ...run 3 complete")
#----------------------------------------#
move(path_join(self.tempdir, "output.pdf"), filename)
def write_3d_pdf(self,
filename,
verbose=False,
extra_latex_before="",
extra_latex_after="",
latex_file_handler=None,
toolbar=False,
quiet=False,
**kwargs):
self._ensure_tmp_xyz()
#----------------------------------------#
if not _have_meshlab:
raise RuntimeError(
"You need to have meshlab.app installed (currently it must be installed in /Applications/ to work...) to do make 3D pdfs. Get it from Sourceforge"
)
#----------------------------------------#
new_kw = JmolRenderer.default_keywords.copy()
# 3d keywords are higher priority
new_kw.update(JmolRenderer.default_3d_keywords)
# user preferences always have veto power
new_kw.update(kwargs)
extra_lines = self._get_kwarg_script_lines(**new_kw)
#----------------------------------------#
if verbose: print("Generating idtf file with Jmol...")
jscript = """
load "{molfile}"
{extra_lines}
write "{tempdir}/output.idtf"
""".format(molfile=self._geom_path,
tempdir=self.tempdir,
extra_lines=extra_lines)
self._run_jmol_script(jscript)
idtf_path = path_join(self.tempdir, "output.idtf")
if not exists(idtf_path):
raise RuntimeError("Jmol command failed to produce "
"file '{}'. Script was:\n{}".format(
idtf_path, indent(jscript)))
#----------------------------------------#
# now convert to u3d format
# TODO make this portable
if verbose: print("Converting idtf file to u3d file...")
idtf_cmd = _idtf_to_u3d_template.format(
input=path_join(self.tempdir, "output.idtf"),
output=path_join(self.tempdir, "output.u3d"))
JmolRenderer._safe_run(shlex.split(idtf_cmd),
descr="IDTF to u3d conversion")
#shlex.os.system(idtf_cmd)
#----------------------------------------#
# Now embed in a latex document and run PDFLatex
if verbose:
print("Constructing latex document...".format(
pdflatex_path, self.tempdir))
with open(path_join(self.tempdir, "output.idtf.tex")) as f:
jmol_latex_data = f.read()
stuff3d = jmol_latex_data.split("toolbar=false,")[1].split(
"inline=true,")[0].strip()
if latex_file_handler is None:
f = open(path_join(self.tempdir, "output.tex"), "w+")
run_pdflatex = True
else:
f = latex_file_handler
run_pdflatex = False
if run_pdflatex:
f.write(pdf_3d_header)
pdf3d_section = pdf_3d_entry_template\
.replace("@@@LABEL@@@", "molecule")\
.replace("@@@3DSTUFF@@@", stuff3d)\
.replace("@@@FNAME@@@", path_join(self.tempdir, "output.u3d"))
if toolbar:
pdf3d_section = pdf3d_section.replace("toolbar=false",
"toolbar=true")
f.write(extra_latex_before)
f.write(pdf3d_section)
f.write(extra_latex_after)
if run_pdflatex:
f.write(pdf_3d_footer)
#- - - - - - - - - - - - - - - - - - - - #
if run_pdflatex:
if verbose:
print("Running '{} {} output' in directory {}...".format(
pdflatex_path, " ".join(pdflatex_args), self.tempdir))
pdflatex_cmd_list = [pdflatex_path] + pdflatex_args + ["output"]
with working_directory(self.tempdir):
# Run 3 times to get references right
JmolRenderer._safe_run(pdflatex_cmd_list,
"pdflatex",
require_empty_stderr=True,
require_zero_exit=False)
if verbose: print(" ...run 1 complete")
JmolRenderer._safe_run(pdflatex_cmd_list,
"output",
require_empty_stderr=True,
require_zero_exit=False)
if verbose: print(" ...run 2 complete")
JmolRenderer._safe_run(pdflatex_cmd_list,
"output",
require_empty_stderr=True,
require_zero_exit=False)
if verbose: print(" ...run 3 complete")
#----------------------------------------#
# Finally, copy back the temporary output to the requested file path
# but only if we wrote the file
move(path_join(self.tempdir, "output.pdf"), filename)
def write_3d_pdf(self, filename,
verbose=False,
extra_latex_before="",
extra_latex_after="",
latex_file_handler=None,
toolbar=False,
quiet=False,
**kwargs
):
self._ensure_tmp_xyz()
#----------------------------------------#
if not _have_meshlab:
raise RuntimeError("You need to have meshlab.app installed (currently it must be installed in /Applications/ to work...) to do make 3D pdfs. Get it from Sourceforge")
#----------------------------------------#
new_kw = JmolRenderer.default_keywords.copy()
# 3d keywords are higher priority
new_kw.update(JmolRenderer.default_3d_keywords)
# user preferences always have veto power
new_kw.update(kwargs)
extra_lines = self._get_kwarg_script_lines(**new_kw)
#----------------------------------------#
if verbose: print("Generating idtf file with Jmol...")
jscript = """
load "{molfile}"
{extra_lines}
write "{tempdir}/output.idtf"
""".format(
molfile=self._geom_path,
tempdir=self.tempdir,
extra_lines=extra_lines
)
self._run_jmol_script(jscript)
idtf_path = path_join(self.tempdir, "output.idtf")
if not exists(idtf_path):
raise RuntimeError("Jmol command failed to produce "
"file '{}'. Script was:\n{}".format(
idtf_path,
indent(jscript)
))
#----------------------------------------#
# now convert to u3d format
# TODO make this portable
if verbose: print("Converting idtf file to u3d file...")
idtf_cmd = _idtf_to_u3d_template.format(
input=path_join(self.tempdir, "output.idtf"),
output=path_join(self.tempdir, "output.u3d")
)
JmolRenderer._safe_run(shlex.split(idtf_cmd), descr="IDTF to u3d conversion")
#shlex.os.system(idtf_cmd)
#----------------------------------------#
# Now embed in a latex document and run PDFLatex
if verbose: print("Constructing latex document...".format(pdflatex_path, self.tempdir))
with open(path_join(self.tempdir, "output.idtf.tex")) as f:
jmol_latex_data = f.read()
stuff3d = jmol_latex_data.split("toolbar=false,")[1].split("inline=true,")[0].strip()
if latex_file_handler is None:
f = open(path_join(self.tempdir, "output.tex"), "w+")
run_pdflatex = True
else:
f = latex_file_handler
run_pdflatex = False
if run_pdflatex:
f.write(pdf_3d_header)
pdf3d_section = pdf_3d_entry_template\
.replace("@@@LABEL@@@", "molecule")\
.replace("@@@3DSTUFF@@@", stuff3d)\
.replace("@@@FNAME@@@", path_join(self.tempdir, "output.u3d"))
if toolbar:
pdf3d_section = pdf3d_section.replace("toolbar=false", "toolbar=true")
f.write(extra_latex_before)
f.write(pdf3d_section)
f.write(extra_latex_after)
if run_pdflatex:
f.write(pdf_3d_footer)
#- - - - - - - - - - - - - - - - - - - - #
if run_pdflatex:
if verbose: print("Running '{} {} output' in directory {}...".format(pdflatex_path, " ".join(pdflatex_args), self.tempdir))
pdflatex_cmd_list = [pdflatex_path] + pdflatex_args + ["output"]
with working_directory(self.tempdir):
# Run 3 times to get references right
JmolRenderer._safe_run(pdflatex_cmd_list, "pdflatex",
require_empty_stderr=True, require_zero_exit=False)
if verbose: print(" ...run 1 complete")
JmolRenderer._safe_run(pdflatex_cmd_list, "output",
require_empty_stderr=True, require_zero_exit=False)
if verbose: print(" ...run 2 complete")
JmolRenderer._safe_run(pdflatex_cmd_list, "output",
require_empty_stderr=True, require_zero_exit=False)
if verbose: print(" ...run 3 complete")
#----------------------------------------#
# Finally, copy back the temporary output to the requested file path
# but only if we wrote the file
move(path_join(self.tempdir, "output.pdf"), filename)
def __input_check(self):
with working_directory(self.directory):
if not self.input_generator.generated:
self.input_generator.generate(self.runner.input_file)
