def rmsd_launcher(input, ref_file):
"""
Calculate RMSD
"""
runner = [os.path.join(os.environ['SCHRODINGER'], 'run'), 'rmsd.py']
counter = 0
for file in input:
counter += 1
print('%s %s' % (counter, file))
cmd = ["-use_neutral_scaffold", "-c", "rmsd_%s_vs_%s.csv" % (file, os.path.basename(ref_file)), "-m",
"-norenumber",
"-m",
"-verbose",
# '-asl', "(chain.name H) AND NOT atom.ele H",
os.path.join(INPUT_DIR, '%s_0-out.mae' % file),
'%s.mae' % ref_file,
'-HOST', "localhost:8"]
# job = jc.launch_job(runner + cmd)
try:
job = jc.launch_job(runner + cmd)
job.wait()
print(job.getDuration())
print('Finish - %s' % job.Status)
except:
print('Something is wrong')
def run(self):
"""
Downloads, calculates, and prepares the pdb, cif, cns, smap,
and cmd files to view a pdb structure and electron density maps.
"""
cmd_file_name = "%s.cmd" % self.jobname
if not (self.downloadPDBFile() and self.downloadSFFile()):
logger.info("Failed to download the required files.")
return
inp_file = self.writePrimeXCreateMapInputFile()
logger.info("Running PrimeX map generation job...")
px_job = jobcontrol.launch_job(["primex", inp_file])
px_job.wait()
if not px_job.succeeded():
logger.info("PrimeX map generation failed.")
return
this_jobbe = jobcontrol.get_backend()
launch_dir = os.getcwd()
if this_jobbe:
# SMAP needs a path for the files, which will the launch
# dir when jobcontrol has copied them back.
launch_dir = this_jobbe.getJob().Dir
# This job only outputs maps.
for map_file in px_job.OutputFiles:
this_jobbe.addOutputFile(map_file)
mae_file_name = "%s.mae" % self.jobname
mae_file_path = os.path.join(launch_dir, mae_file_name)
smap_file_name = "%s.smap" % self.jobname
smap_fh = open(smap_file_name, 'w')
smap = """# smap version 1.0
%s
primex_%s-out-1.cns:1
primex_%s-out-0.cns:1
#end
""" % (mae_file_name, self.jobname, self.jobname)
smap_fh.write(smap)
smap_fh.close()
cmd_fh = open(cmd_file_name, 'w')
# smap mechanism seem to need abs paths to trigger extradata.
cmd_fh.write('entryimport extradata=true "%s"\n' % mae_file_path)
cmd_fh.write('showpanel managesurfaces\n')
cmd_fh.write('fit\n')
cmd_fh.close()
if this_jobbe:
this_jobbe.setStructureOutputFile(mae_file_name)
this_jobbe.addOutputFile(mae_file_name)
this_jobbe.addOutputFile(cmd_file_name)
this_jobbe.addOutputFile(smap_file_name)
logger.info("Run this command file within Maestro: %s" % cmd_file_name)
return
def mini(structures, frozen_atoms=None, fix_torsions=None):
"""
Takes many structures, minimizes them and returns the minimized structures.
It's faster to do multiple structures at once.
Arguments
---------
structure : list of Schrödinger structure
Returns
-------
list of Schrödinger structure
"""
import schrodinger.application.macromodel.utils as mmodutils
import schrodinger.job.jobcontrol as jobcontrol
from setup_com_from_mae import MyComUtil
print(' - ATTEMPTING MINI')
sch_writer = sch_struct.StructureWriter('TEMP.mae')
sch_writer.extend(structures)
sch_writer.close()
# Setup the minimization.
com_setup = MyComUtil()
com_setup.my_mini(
mae_file='TEMP.mae',
com_file='TEMP.com',
out_file='TEMP_OUT.mae',
frozen_atoms=frozen_atoms,
fix_torsions=fix_torsions)
command = ['bmin', '-WAIT', 'TEMP']
# Run the minimization.
job = jobcontrol.launch_job(command)
job.wait()
# Read the minimized structures.
sch_reader = sch_struct.StructureReader('TEMP_OUT.mae')
new_structures = []
for structure in sch_reader:
new_structures.append(structure)
sch_reader.close()
if len(new_structures) > 0:
print(' - MINI SUCCEEDED')
structures = [new_structures[0]]
else:
print(' - MINI FAILED. CONTINUING W/O MINI')
if DEBUG:
raw_input('Press any button to continue.')
# Remove temporary files.
os.remove('TEMP.mae')
os.remove('TEMP.com')
os.remove('TEMP_OUT.mae')
os.remove('TEMP.log')
return structures
def run_mmgbsa(structures, ligand_asl, njobs=1):
"""
Run a prime mmgbsa calculations on a series of trajectory frames
:param structures:
:param ligand_asl:
:param njobs:
:return:
"""
logger.info('Launching {} subjobs'.format(njobs))
# Run MMGBSA calculation
inp = []
jobs = []
for i, chunk in enumerate(np.array_split(np.arange(len(structures)),
njobs)):
jobname = 'mmgbsa_input{}'.format(i)
infile = 'mmgbsa_input{}.mae'.format(i)
for j in chunk:
st = structures[j]
st.append(infile)
inp.append(jobname)
args = [
MMGBSA_CMD,
infile,
]
mmgbsa_options = copy.copy(MMGBSA_OPTIONS)
mmgbsa_options['-jobname'] = jobname
mmgbsa_options['-ligand'] = ligand_asl
for kv in mmgbsa_options.items():
args.extend(kv)
logger.info('Running Prime MMGBSA:')
logger.info('$SCHRODINGER/' + ' '.join(args))
job = jobcontrol.launch_job(args)
jobs.append(job)
outfiles = []
for job in jobs:
job.wait()
if job.succeeded():
outfiles.append(job.getOutputFiles())
else:
raise RuntimeError(
'ProteinPreparationWizard failed with {}'.format(
job.ExitStatus))
return outfiles
def mini(structures, frozen_atoms=None, fix_torsions=None):
"""
Takes many structures, minimizes them and returns the minimized structures.
It's faster to do multiple structures at once.
Arguments
---------
structure : list of Schrödinger structure
Returns
-------
list of Schrödinger structure
"""
import schrodinger.application.macromodel.utils as mmodutils
import schrodinger.job.jobcontrol as jobcontrol
from setup_com_from_mae import MyComUtil
print(' - ATTEMPTING MINI')
sch_writer = sch_struct.StructureWriter('TEMP.mae')
sch_writer.extend(structures)
sch_writer.close()
# Setup the minimization.
com_setup = MyComUtil()
com_setup.my_mini(
mae_file='TEMP.mae',
com_file='TEMP.com',
out_file='TEMP_OUT.mae',
frozen_atoms=frozen_atoms,
fix_torsions=fix_torsions)
command = ['bmin', '-WAIT', 'TEMP']
# Run the minimization.
job = jobcontrol.launch_job(command)
job.wait()
# Read the minimized structures.
sch_reader = sch_struct.StructureReader('TEMP_OUT.mae')
new_structures = []
for structure in sch_reader:
new_structures.append(structure)
sch_reader.close()
if len(new_structures) > 0:
print(' - MINI SUCCEEDED')
structures = [new_structures[0]]
else:
print(' - MINI FAILED. CONTINUING W/O MINI')
if DEBUG:
raw_input('Press any button to continue.')
# Remove temporary files.
os.remove('TEMP.mae')
os.remove('TEMP.com')
os.remove('TEMP_OUT.mae')
os.remove('TEMP.log')
return structures
def mcmm(structures, frozen_atoms=None):
"""
Takes many structures, and does a short MCMM search on them.
Arguments
---------
structure : list of Schrödinger structure
Returns
-------
list of Schrödinger structure
"""
import schrodinger.application.macromodel.utils as mmodutils
import schrodinger.job.jobcontrol as jobcontrol
from setup_com_from_mae import MyComUtil
print(' - ATTEMPTING MCMM')
sch_writer = sch_struct.StructureWriter('TEMP.mae')
sch_writer.extend(structures)
sch_writer.close()
com_setup = MyComUtil()
com_setup.my_mcmm(
mae_file='TEMP.mae',
com_file='TEMP.com',
out_file='TEMP_OUT.mae',
nsteps=50,
frozen_atoms=frozen_atoms)
command = ['bmin', '-WAIT', 'TEMP']
job = jobcontrol.launch_job(command)
job.wait()
sch_reader = sch_struct.StructureReader('TEMP_OUT.mae')
new_structures = []
for structure in sch_reader:
new_structures.append(structure)
sch_reader.close()
if len(new_structures) > 0:
print(' - MCMM SUCCEEDED')
structures = [new_structures[0]]
else:
print(' - MCMM FAILED. CONTINUING W/O MCMM')
if DEBUG:
raw_input('Press any button to continue.')
# Remove temporary files.
os.remove('TEMP.mae')
os.remove('TEMP.com')
os.remove('TEMP_OUT.mae')
os.remove('TEMP.log')
return structures
def mcmm(structures, frozen_atoms=None):
"""
Takes many structures, and does a short MCMM search on them.
Arguments
---------
structure : list of Schrödinger structure
Returns
-------
list of Schrödinger structure
"""
import schrodinger.application.macromodel.utils as mmodutils
import schrodinger.job.jobcontrol as jobcontrol
from setup_com_from_mae import MyComUtil
print(' - ATTEMPTING MCMM')
sch_writer = sch_struct.StructureWriter('TEMP.mae')
sch_writer.extend(structures)
sch_writer.close()
com_setup = MyComUtil()
com_setup.my_mcmm(
mae_file='TEMP.mae',
com_file='TEMP.com',
out_file='TEMP_OUT.mae',
nsteps=50,
frozen_atoms=frozen_atoms)
command = ['bmin', '-WAIT', 'TEMP']
job = jobcontrol.launch_job(command)
job.wait()
sch_reader = sch_struct.StructureReader('TEMP_OUT.mae')
new_structures = []
for structure in sch_reader:
new_structures.append(structure)
sch_reader.close()
if len(new_structures) > 0:
print(' - MCMM SUCCEEDED')
structures = [new_structures[0]]
else:
print(' - MCMM FAILED. CONTINUING W/O MCMM')
if DEBUG:
raw_input('Press any button to continue.')
# Remove temporary files.
os.remove('TEMP.mae')
os.remove('TEMP.com')
os.remove('TEMP_OUT.mae')
os.remove('TEMP.log')
return structures
def launch(cmd):
'''
使用jobcontrol启动一项job并等待结束
Parameters
----------
cmd： 等待执行的命令字符串
'''
cmd_list = cmd.split(' ') # launch_job以列表形式提交参数
job = jc.launch_job(cmd_list)
print('JobId: %s' % job.JobId, end='\n')
print('Job Name: %s' % job.Name, end='\n')
print('Job Status: %s' % job.Status, end='\n')
print('Job Running...')
job.wait() # 阻塞进程 等待Job结束
print('\nJob %s Complete.\n' % job.Name)
def rmsd_individual(mae_file, ref_file):
"""
Calculate RMSD
"""
runner = [os.path.join(os.environ['SCHRODINGER'], 'run'), 'rmsd.py']
cmd = ["-use_neutral_scaffold", "-c", "rmsd_%s_vs_%s.csv" % (mae_file, os.path.basename(ref_file)),
"-norenumber",
"-m",
"-verbose",
# '-asl', "(chain.name H) AND NOT atom.ele H",
mae_file,
ref_file,
'-HOST', "localhost:8"]
try:
job = jc.launch_job(runner + cmd)
job.wait()
print(job.getDuration())
print('Finish - %s' % job.Status)
except:
print('Something is wrong')
def homology_multirun(start, end):
"""
Homology building from separate fasta files in input from start to end file
"""
fasta_path = os.getcwd()
current = os.getcwd()
runner = [os.path.join(os.environ['SCHRODINGER'], 'run'), 'homology.py']
counter = 0
inp = [os.path.splitext(f)[0] for f in os.listdir(fasta_path) if os.path.splitext(f)[1] == '.fasta']
out = [f[:-10] for f in os.listdir(fasta_path) if f[-10:] == '_0-out.mae']
input = [f for f in inp if f not in out]
# print "run job for %s files" % len(range(start, end))
for file in input[start:end]:
counter += 1
os.mkdir('%s' % file)
os.chdir('%s' % file)
# print('Building %s (%s of %s)' % (file, counter, len(input[start:end])))
cmd = ['-i', os.path.join(fasta_path, '%s.fasta' % file), # input fasta
'-n', '1', # Number of templates to use
'-r', # Re-align sequences before building the model
'-J', '%s' % file,
# '-b', 'sort_key=gaps',
'-p', 'BUILD_DELETIONS=false',
'BUILD_TRANSITIONS=false',
'KNOWLEDGE_BASED=false'
]
try:
job = jc.launch_job(runner + cmd)
except:
pass
os.chdir(current)
src = os.path.join(current, '%s' % file, '%s_0-out.mae' % file)
dst = current
try:
shutil.copy(src, dst)
except:
pass
def rmsd_launch(ref_file, start):
"""
Calculate RMSD
ref_file = "path/to/file" no ext!
start calls the goal ASL
"""
mae_path = os.getcwd()
runner = [os.path.join(os.environ['SCHRODINGER'], 'run'), 'rmsd.py']
asl_dict = {'loop': "(res.num 99-112) AND NOT atom.ele H",
'rmsd': "not (res.num 26-32,52-57,99-124) AND NOT atom.ele H"}
counter = 0
for file in [f[:-10] for f in os.listdir(mae_path) if f[-10:] == '_0-out.mae']:
counter += 1
# print('%s %s' % (counter, file))
cmd = ["-use_neutral_scaffold", "-c", "%s_%s.csv" % (start, file),
"-norenumber",
"-m",
"-verbose",
'-asl', "%s" % asl_dict[start],
'%s.mae' % ref_file,
os.path.join(mae_path, '%s_0-out.mae' % file)
]
# job = jc.launch_job(runner + cmd)
try:
job = jc.launch_job(runner + cmd)
job.wait()
print(job.getDuration())
print('Finish - %s' % job.Status)
except:
pass
def start(self):
"""
Runs the enrichment calculation job and populates the text area
with the results.
"""
pdb_code = str(self.ui.pdb_lineedit.text())
if not pdb_code.strip():
self.info("Please enter a four character pdb code.")
return
script_args = ['run', __file__, pdb_code]
fo_fc = self.ui.fo_minus_fc_checkbox.isChecked()
two_fo_fc = self.ui.two_fo_minus_fc_checkbox.isChecked()
if fo_fc and two_fo_fc:
script_args.extend(['-mapcoeff', 'both'])
elif two_fo_fc and not fo_fc:
script_args.extend(['-mapcoeff', '2FoFc'])
elif fo_fc and not two_fo_fc:
script_args.extend(['-mapcoeff', 'FoFc'])
else:
self.info("At least one map coeffient type must be checked.")
return
if self.ui.omit_ligands_checkbox.isChecked():
script_args.append('-omit_ligands')
if self.ui.composite_radiobutton.isChecked():
script_args.extend(['-composite_omit', '5.0'])
# Add -HOST, -DISP, -PROJ
script_args.extend(self.jobparam.commandLineArgs())
job = jobcontrol.launch_job(script_args)
self.monitorJob(job.job_id)
return
keys.sort()
lines = []
#Different methods availables by ConfGen to generate conformers
methods = ['VERY_FAST', 'FAST', 'INTERMEDIATE', 'COMPREHENSIVE', 'FAST_CF', 'PHASE_FAST', 'PHASE_QUALITY']
for method in methods:
for hetid in hetids:
ligprep = path_to_ligprep + hetid + "_ligprep.mae"
CWD = os.getcwd()
os.chdir(path_to_ligprep)
print hetid
#Command to generate conformers by Confgen. Methods: -VERY_FAST; -FAST; -INTERMEDIATE; -COMPREHENSIVE; -FAST_CF; -PHASE_FAST; -PHASE_QUALITY
confgen = os.path.join(os.environ['SCHRODINGER'], 'confgen') + " '-" + method + ",-MIN_OUT' " + os.path.basename(ligprep)
job = jobcontrol.launch_job(confgen.split())
os.chdir(CWD)
#Output of conformers
conformers = output_CONFGEN + method +'/'
if not os.path.isdir(conformers):
os.makedirs(conformers)
#Select CPU time from .log files.
log = path_to_ligprep + hetid + "_ligprep.log"
job.wait()
filelog = open(log, 'rb')
for line in filelog:
lines.append(line)
time_line = lines[-2]
ctime = time_line.split('u')[0]
