def write_jobscript(name,
keyword_file,
amoptd,
directory=None,
job_time=86400,
extra_options={}):
"""
Create the script to run MrBump for this PDB.
"""
if not directory:
directory = os.getcwd()
# Next the script to run mrbump
script = Script(directory=directory,
prefix="",
stem=name,
suffix=ample_util.SCRIPT_EXT)
if not sys.platform.startswith("win"):
script.append('[[ ! -d $CCP4_SCR ]] && mkdir $CCP4_SCR\n\n')
# Get the mrbump command-line
jobcmd = mrbump_cmd.mrbump_cmd(name, amoptd['mtz'], amoptd['mr_sequence'],
keyword_file)
script.append(jobcmd)
# Write script
script.write()
logger.debug("Wrote MRBUMP script: %s", script.path)
return script
def generate_script(self, dat_model):
logger.debug(
"Generating script to perform AMORE rotation " + "function on %s",
dat_model.pdb_code)
pdb_model = self.template_model.format(dat_model.pdb_code)
table1 = self.template_table1.format(dat_model.pdb_code)
hklpck1 = self.template_hklpck1.format(dat_model.pdb_code)
clmn0 = self.template_clmn0.format(dat_model.pdb_code)
clmn1 = self.template_clmn1.format(dat_model.pdb_code)
mapout = self.template_mapout.format(dat_model.pdb_code)
conv_py = "\"from simbad.db import convert_dat_to_pdb; convert_dat_to_pdb('{}', '{}')\""
conv_py = conv_py.format(dat_model.dat_path, pdb_model)
tab_cmd = [
self.amore_exe, "xyzin1", pdb_model, "xyzout1", pdb_model,
"table1", table1
]
tab_stdin = self.tabfun_stdin_template.format(x=dat_model.x,
y=dat_model.y,
z=dat_model.z,
a=90,
b=90,
c=120)
rot_cmd = [
self.amore_exe, 'table1', table1, 'HKLPCK1', hklpck1, 'hklpck0',
self.hklpck0, 'clmn1', clmn1, 'clmn0', clmn0, 'MAPOUT', mapout
]
rot_stdin = self.rotfun_stdin_template.format(shres=self.shres,
intrad=dat_model.intrad,
pklim=self.pklim,
npic=self.npic,
step=self.rotastep)
rot_log = self.template_rot_log.format(dat_model.pdb_code)
tmp_dir = self.template_tmp_dir.format(dat_model.pdb_code)
cmd = [
[EXPORT, "CCP4_SCR=" + tmp_dir],
["mkdir", "-p", "$CCP4_SCR\n"],
[CMD_PREFIX, "$CCP4/bin/ccp4-python", "-c", conv_py, os.linesep],
tab_cmd + ["<< eof >", os.devnull],
[tab_stdin],
["eof"],
[os.linesep],
rot_cmd + ["<< eof >", rot_log],
[rot_stdin],
["eof"],
[os.linesep],
["grep", "-m 1", "SOLUTIONRCD", rot_log, os.linesep],
["rm", "-rf", "$CCP4_SCR\n"],
[EXPORT, "CCP4_SCR=" + self.ccp4_scr],
]
amore_script = Script(directory=self.script_log_dir,
prefix="amore_",
stem=dat_model.pdb_code)
for c in cmd:
amore_script.append(' '.join(map(str, c)))
amore_log = amore_script.path.rsplit(".", 1)[0] + '.log'
amore_files = (amore_log, dat_model.dat_path)
amore_script.write()
return amore_script, amore_files
def generate_script(self, dat_model):
logger.debug(
"Generating script to perform PHASER rotation " + "function on %s",
dat_model.pdb_code)
pdb_model = self.template_model.format(dat_model.pdb_code)
template_rot_log = os.path.join("$CCP4_SCR", "{0}_rot.log")
conv_py = "\"from simbad.db import convert_dat_to_pdb; convert_dat_to_pdb('{}', '{}')\""
conv_py = conv_py.format(dat_model.dat_path, pdb_model)
rot_log = template_rot_log.format(dat_model.pdb_code)
tmp_dir = self.template_tmp_dir.format(dat_model.pdb_code)
phaser_cmd = [
"simbad.rotsearch.phaser_rotation_search",
"-eid",
self.eid,
"-hklin",
self.mtz,
"-f",
self.mtz_labels.f,
"-sigf",
self.mtz_labels.sigf,
"-i",
self.mtz_labels.i,
"-sigi",
self.mtz_labels.sigi,
"-pdbin",
pdb_model,
"-logfile",
rot_log,
"-solvent",
dat_model.solvent,
"-nmol",
dat_model.nmol,
"-work_dir",
tmp_dir,
]
phaser_cmd = " ".join(str(e) for e in phaser_cmd)
cmd = [
[EXPORT, "CCP4_SCR=" + tmp_dir],
["mkdir", "-p", "$CCP4_SCR\n"],
[CMD_PREFIX, "$CCP4/bin/ccp4-python", "-c", conv_py, os.linesep],
[
CMD_PREFIX, "$CCP4/bin/ccp4-python", "-m", phaser_cmd,
os.linesep
],
["rm", "-rf", "$CCP4_SCR\n"],
[EXPORT, "CCP4_SCR=" + self.ccp4_scr],
]
phaser_script = Script(directory=self.script_log_dir,
prefix="phaser_",
stem=dat_model.pdb_code)
for c in cmd:
phaser_script.append(' '.join(map(str, c)))
phaser_log = phaser_script.path.rsplit(".", 1)[0] + '.log'
phaser_files = (phaser_log, dat_model.dat_path)
phaser_script.write()
return phaser_script, phaser_files