def render_r3d(self, name, img_format="png"):
job = Job(self, utils.syspath("render"))
# render writes normal output to stderr (and nothing to stdout)
job.out.file_extension = "out"
job.err.file_extension = "log"
job.args += ["-"+img_format, "%s.%s" % (name, img_format)]
job.stdin_file = name+".r3d"
job.parser = " %s.%s" % (name, img_format)
return job
def find_path():
if os.name == 'nt':
default_path = "C:/WinCoot/runwincoot.bat"
if os.path.exists(default_path):
return default_path
else:
utils.put_error("WinCoot not found.")
else:
return utils.syspath("coot")
def render_r3d(self, name, img_format):
assert img_format is not None
job = Job(self, utils.syspath("render"))
# render writes normal output to stderr (and nothing to stdout)
job.out.file_extension = "out"
job.err.file_extension = "log"
job.args += ["-" + img_format, "%s.%s" % (name, img_format)]
job.stdin_file = name + ".r3d"
job.parser = " %s.%s" % (name, img_format)
return job
def render_r3d(self, name, img_format):
assert img_format is not None
job = Job(self, utils.syspath('render'))
# render writes normal output to stderr (and nothing to stdout)
job.out.file_extension = 'out'
job.err.file_extension = 'log'
job.args += ['-'+img_format, '%s.%s' % (name, img_format)]
job.stdin_file = name + '.r3d'
job.parser = ' %s.%s' % (name, img_format)
return job
def shelxc(self, scain, cell, symmetry):
job = Job(self, utils.syspath('shelxc'))
name = os.path.splitext(scain)[0]
job.args += [name]
job.std_input = '\n'.join([
'SAD %s' % scain,
'CELL %s %s %s %s %s %s' % cell,
'SPAG %s' % symmetry,
])
return job
def find_path():
if os.name == 'nt':
for path in [
"C:/WinCoot/wincoot.bat", # since WinCoot 0.8.8
"C:/WinCoot/runwincoot.bat", # WinCoot prior to 0.8.8
utils.cbin("coot.bat")
]: # CCP4 script added in 2018
if os.path.exists(path):
return path
utils.comment("\nNote: WinCoot not found.\n")
else:
return utils.syspath("coot")
def _check_picture_tools():
ok = True
coot_path, coot_ver = coots.find_path_and_version()
if coot_path:
if coot_ver is None:
put_error("coot not working(?), no pictures")
ok = False
else:
if "with python" not in coot_ver:
put_error("coot with Python support is needed")
ok = False
if "\n0.6." in coot_ver:
put_error("coot 0.7+ is needed (0.6 would crash)")
ok = False
else:
put_error("No coot, no pictures")
ok = False
if not utils.syspath("render"):
put_error("No Raster3d, no pictures")
ok = False
return ok
def _generate_scripts_and_pictures(wf, opt, data, pha=None):
blobs = data['blobs'] if data else []
coot_path = coots.find_path()
if not blobs:
comment('\nUnmodelled blobs not found.')
elif opt.img_format:
if coot_path:
coot_ver = coots.find_version(coot_path)
if coot_ver is None:
put_error('coot not working(?), no pictures')
opt.img_format = None
elif 'with python' not in coot_ver:
put_error('coot with Python support is needed')
opt.img_format = None
else:
put_error('No coot, no pictures')
opt.img_format = None
if not utils.syspath('render'):
put_error('No Raster3d, no pictures')
opt.img_format = None
if opt.img_format:
if len(blobs) == 1:
comment('\nRendering density blob at (%.1f, %.1f, %.1f)' %
blobs[0])
else:
comment('\nRendering 2 largest blobs: at (%.1f, %.1f, %.1f) '
'and at (%.1f, %.1f, %.1f)' % (blobs[0] + blobs[1]))
com = data and data.get('center')
if pha:
normal_map = False
refl = pha
prefix = 'anom-'
else:
normal_map = True
refl = opt.hklout
prefix = ''
# run-coot.py centers on the biggest blob. It uses relative paths -
# it can be run only from the output directory, but is not affected
# by moving that directory to different location.
# There are blobN-coot.py scripts generated below with absolute paths.
# write coot script (apart from pictures) that centers on the biggest blob
script_path = os.path.join(wf.output_dir, prefix + 'run-coot.py')
script = coots.basic_script(pdb=opt.xyzout,
refl=refl,
normal_map=normal_map,
center=(blobs and blobs[0]),
toward=com,
white_bg=opt.white_bg)
_write_script(script_path, script, executable=True)
# blob images, for now for not more than two blobs
d = os.path.abspath(wf.output_dir)
for n, b in enumerate(blobs[:2]):
py_path = os.path.join(wf.output_dir,
'%sblob%d-coot.py' % (prefix, n + 1))
content = coots.basic_script(pdb=os.path.join(d, opt.xyzout),
refl=os.path.join(d, refl),
normal_map=normal_map,
center=blobs[n],
toward=com,
white_bg=opt.white_bg)
_write_script(py_path, content)
# coot.sh - one-line script for convenience
if blobs:
coot_sh_text = '{coot} --no-guano {out}/%sblob1-coot.py\n' % prefix
else:
coot_sh_text = '{coot} --no-guano {out}/final.mtz {out}/final.pdb\n'
coot_sh_path = os.path.join(wf.output_dir, prefix + 'coot.sh')
_write_script(coot_sh_path,
coot_sh_text.format(coot=coot_path or 'coot',
out=wf.output_dir),
executable=True)
if opt.img_format and blobs:
script = ''
basenames = []
# as a workaround for buggy coot the maps are reloaded for each blob
for n, b in enumerate(blobs[:2]):
script += coots.basic_script(pdb=opt.xyzout,
refl=refl,
normal_map=normal_map,
center=b,
toward=com,
white_bg=opt.white_bg)
rs, names = coots.r3d_script(center=b,
toward=com,
blobname='%sblob%s' % (prefix, n + 1))
script += rs
basenames += names
coot_job = wf.coot_py(script)
try:
coot_job.run()
except workflow.JobError:
# check for a possible cause to hint the user
# (possible workaround: change $HOME to non-existing directory)
if utils.silently_run(coot_job.args, cwd=wf.output_dir)[0] != 0:
put_error('coot fails with options: --no-graphics --python',
comment='It happens when scripts in .coot or '
'.coot-preferences are not compatible\n'
'with the --no-graphics mode.')
raise
for n, basename in enumerate(basenames):
try:
job = wf.render_r3d(basename, img_format=opt.img_format)
if n % 3 == 0:
job.run()
else: # minimal output
job.run(show_progress=False, new_line=False)
wf.delete_files([basename + '.r3d'])
except workflow.JobError as e:
# Raster3D may fail saying "increase MAXDET and recompile".
# This is not critical, so Dimple doesn't stop.
put_error('Rendering failed, no picture', comment=' ' + e.note)
return coot_sh_path
def find_blobs(self, hklin, xyzin, sigma=1.0):
# for now search in PATH (which normally includes CBIN)
job = Job(self, utils.syspath("find-blobs"))
job.args += ["-c", "-s%g" % sigma, hklin, xyzin]
job.parser = "_find_blobs_parser"
return job
def find_blobs(self, hklin, xyzin, sigma=1.0):
# for now search in PATH (which normally includes CBIN)
job = Job(self, utils.syspath("find-blobs"))
job.args += ["-c", "-s%g" % sigma, hklin, xyzin]
job.parser = "_find_blobs_parser"
return job
def anode(self, name):
job = Job(self, utils.syspath('anode'))
job.args += [name]
job.parser = '_anode_parser'
return job
def mtz2sca(self, mtzin, scaout):
job = Job(self, utils.syspath('mtz2sca'))
job.args += [mtzin, scaout]
return job
def find_blobs(self, hklin, xyzin, sigma=1.0):
# for now search in PATH (which normally includes CBIN)
job = Job(self, utils.syspath('find-blobs'))
job.args += ['-c', '-s%g' % sigma, hklin, xyzin]
job.parser = '_find_blobs_parser'
return job
def _generate_scripts_and_pictures(wf, opt, data):
blobs = data["blobs"] if data else []
coot_path = coots.find_path()
if not blobs:
comment("\nUnmodelled blobs not found.")
elif opt.img_format:
if coot_path:
coot_ver = coots.find_version(coot_path)
if coot_ver is None:
put_error("coot not working(?), no pictures")
opt.img_format = None
elif "with python" not in coot_ver:
put_error("coot with Python support is needed")
opt.img_format = None
else:
put_error("No coot, no pictures")
opt.img_format = None
if not utils.syspath("render"):
put_error("No Raster3d, no pictures")
opt.img_format = None
if opt.img_format:
if len(blobs) == 1:
comment("\nRendering density blob at (%.1f, %.1f, %.1f)" %
blobs[0])
else:
comment("\nRendering 2 largest blobs: at (%.1f, %.1f, %.1f) "
"and at (%.1f, %.1f, %.1f)" % (blobs[0]+blobs[1]))
com = data and data["center"]
# run-coot.py centers on the biggest blob. It uses relative paths -
# it can be run only from the output directory, but is not affected
# by moving that directory to different location.
# There are blobN-coot.py scripts generated below with absolute paths.
# write coot script (apart from pictures) that centers on the biggest blob
script_path = os.path.join(wf.output_dir, "run-coot.py")
script = coots.basic_script(pdb=opt.xyzout, mtz=opt.hklout,
center=(blobs and blobs[0]), toward=com,
white_bg=opt.white_bg)
_write_script(script_path, script, executable=True)
# blob images, for now for not more than two blobs
d = os.path.abspath(wf.output_dir)
for n, b in enumerate(blobs[:2]):
py_path = os.path.join(wf.output_dir, "blob%d-coot.py" % (n+1))
content = coots.basic_script(pdb=os.path.join(d, opt.xyzout),
mtz=os.path.join(d, opt.hklout),
center=blobs[n], toward=com,
white_bg=opt.white_bg)
_write_script(py_path, content)
# coot.sh - one-line script for convenience
if blobs:
coot_sh_text = '{coot} --no-guano {out}/blob1-coot.py\n'
else:
coot_sh_text = '{coot} --no-guano {out}/final.mtz {out}/final.pdb\n'
coot_sh_path = os.path.join(wf.output_dir, "coot.sh")
_write_script(coot_sh_path, coot_sh_text.format(coot=coot_path or 'coot',
out=wf.output_dir),
executable=True)
if opt.img_format and blobs:
script = ''
basenames = []
# as a workaround for buggy coot the maps are reloaded for each blob
for n, b in enumerate(blobs[:2]):
script += coots.basic_script(pdb=opt.xyzout, mtz=opt.hklout,
center=b, toward=com,
white_bg=opt.white_bg)
rs, names = coots.r3d_script(center=b, toward=com,
blobname="blob%s" % (n+1))
script += rs
basenames += names
coot_job = wf.coot_py(script)
try:
coot_job.run()
except workflow.JobError:
# check for a possible cause to hint the user
# (possible workaround: change $HOME to non-existing directory)
if utils.silently_run(coot_job.args, cwd=wf.output_dir)[0] != 0:
put_error("coot fails with options: --no-graphics --python",
comment="It happens when scripts in .coot or "
".coot-preferences are not compatible\n"
"with the --no-graphics mode.")
raise
for n, basename in enumerate(basenames):
job = wf.render_r3d(basename, img_format=opt.img_format)
if n % 3 == 0:
job.run()
else: # minimal output
job.run(show_progress=False, new_line=False)
wf.delete_files([name+".r3d" for name in basenames])
return coot_sh_path
