def get_charge_and_multiplicity(unknw_res_names, verbose=False):
results = {}
for residue_name in unknw_res_names:
print(residue_name)
if residue_name in results: continue
mol = builder.run(chemical_component=residue_name,
no_output=True, silent=True
)
mol.WritePDB('4antechamber_%s.pdb' %residue_name)
mol.Multiplicitise()
print(mol.DisplayBrief())
results[residue_name] = [mol.charge, mol.multiplicity]
return results
def calculate_amber_files(
code,
pH=8,
):
import tempfile
cwd = os.getcwd()
td = tempfile.mkdtemp()
os.chdir(td)
mol = builder.run(
chemical_component=code,
final_geometry=code,
no_output=True,
quiet=True,
pH=pH,
)
mol.OptimiseHydrogens()
mol.WritePDB('4antechamber_%s.pdb' % code)
mol.Multiplicitise()
print mol.DisplayVeryBrief()
try:
os.remove('sqm.pdb')
except OSError:
pass
cmd='antechamber -i 4antechamber_%s.pdb -fi pdb -o tmp.mol2 -fo mol2 \
-nc %d -m %d -s 2 -pf y -c bcc -at gaff' \
%(code, mol.charge, mol.multiplicity)
print cmd
ero = easy_run.fully_buffered(cmd)
f = open('antelog_%s.txt' % code, 'wb')
ero.show_stdout(out=f)
ero.show_stderr(out=f)
f.write('\nSECOND RUN OF %s\N' % code)
cmd='antechamber -i sqm.pdb -fi pdb -o %s.mol2 -fo mol2 \
-nc %s -m %d -s 2 -pf y -c bcc -at gaff' \
%(code, mol.charge, mol.multiplicity)
print cmd
ero = easy_run.fully_buffered(cmd)
ero.show_stdout(out=f)
ero.show_stderr(out=f)
cmd = 'parmchk2 -i %s.mol2 -f mol2 -o %s.frcmod' % (code, code)
ero = easy_run.fully_buffered(cmd)
ero.show_stdout(out=f)
ero.show_stderr(out=f)
f.close()
print '\nMoving files from', os.getcwd()
cmd = "mv %s %s " % ("antelog_%s.txt" % (code),
os.path.join(cwd, "..", "output", "antelog_%s.txt" %
(code)))
print cmd
easy_run.call(cmd)
cmd = "mv %s %s " % ("sqm.out",
os.path.join(cwd, "..", "output", "sqm_%s.out" %
(code)))
print cmd
easy_run.call(cmd)
cmd = "mv %s %s " % ("4antechamber_%s.pdb" %
(code), os.path.join(cwd, "%s.final.pdb" % (code)))
print cmd
easy_run.call(cmd)
for ext in ["frcmod", "mol2"]:
if not os.path.exists("%s.%s" % (code, ext)): return None
cmd = "mv %s %s" % ("%s.%s" % (code, ext),
os.path.join(cwd, "%s.%s" % (code, ext)))
print cmd
easy_run.call(cmd)
os.chdir(cwd)
import shutil
print "Deleting temporary directory : %s" % td
shutil.rmtree(td)
return True
def get_elbow_molecule_cif_filename(code, kwds={}, return_molecule=False):
def _get_qm_package_kwds(kwds, qm_package):
if qm_package is not None:
if qm_package.lower() == "gamess":
kwds["gamess"] = True
elif qm_package.lower() == "gaussian":
kwds["gaussian"] = True
#else:
# assert 0
del kwds["qm_package"]
return kwds
code = code.upper()
filename = "%s" % code
default_kwds = {
"qm_package": None,
"qm_method": None,
"qm_basis": None,
"qm_solvent_model": None,
"opt_nprocs": 1,
"opt": False,
"mogul": False,
"geostd": False,
"qsub": "",
"automatic": False,
"qm_check": False,
"dry_run": False,
"quiet": True,
#"validate" : True,
"pH": "neutral",
#"xml" : True,
"write_redundant_dihedrals_boolean": False, # special case!!!
#"initial_geometry" : code,
#"smiles" : get_smiles(code),
#"file" : sdf_filename,
#"no_output" : True,
#"output": "ANP_neutral",
"overwrite": True,
}
kwds["chemical_component"] = code
for dk in default_kwds:
if dk not in kwds:
kwds[dk] = default_kwds[dk]
count = 0
for kwd in [
"opt",
#"qm_method",
"mogul",
"automatic",
]:
if kwds[kwd]:
count += 1
assert count <= 1
if 0:
for key in sorted(kwds):
print " %-20s : %s" % (key, kwds[key])
kwds = _get_qm_package_kwds(kwds, kwds["qm_package"])
if "smiles" in kwds and not kwds["smiles"]: return None
if not kwds["overwrite"] and os.path.exists("%s.cif" % filename):
print "CIF found", os.path.abspath("%s.cif" % filename)
if return_molecule: assert 0
return filename
if not kwds["overwrite"] and os.path.exists("%s.pickle" % filename):
print "pickle found", os.path.abspath("%s.pickle" % filename)
if return_molecule: assert 0
f = file(os.path.abspath("%s.pickle" % filename), "rb")
mol = pickle.load(f)
del f
mol.WriteCIF(filename)
return filename
else:
display_kwds(kwds)
if qm_job_not_run(kwds):
print '\n\n\tNo previous job\n\n'
# WHY WAS THIS INDENTED
# if kwds["qm_method"]:
# if qm_job_not_run(kwds):
# print '\n\n\tNo previous job\n\n'
# mol = builder.run(**kwds)
# elif qm_job_run_and_failed(kwds):
# print last_qm_lines(kwds, 100)
# print '\n\n\tPrevious job is failed\n\n'
# mol = builder.run(**kwds)
# elif not qm_job_run_and_finished(kwds):
# print '\n\n\tJob is still running\n\n'
# mol = None
# elif qm_job_run_and_finished(kwds):
# print '\n\n\tJob is finished running\n\n'
# assert 0
# else:
# print 'else'
# mol = None
# else:
mol = builder.run(**kwds)
elif qm_job_run_and_finished(kwds):
print '\n\n\tJob is still running\n\n'
mol = None
elif qm_job_run_and_failed(kwds):
print last_qm_lines(kwds, 100)
print '\n\n\tPrevious job is failed\n\n'
mol = builder.run(**kwds)
else:
print 'else'
mol = None
if mol:
if not os.path.exists(os.path.dirname(filename)):
try:
os.mkdir(os.path.dirname(filename))
except:
pass
mol.WriteCIF(filename)
if return_molecule:
return mol
else:
return filename
def calculate_amber_files(code,
pH=8,
use_temp_file=True,
):
import tempfile
cwd = os.getcwd()
if use_temp_file:
td = tempfile.mkdtemp()
os.chdir(td)
mol = builder.run(chemical_component=code,
final_geometry=code,
no_output=True,
quiet=True,
pH=pH,
)
# a very dull problem
if hasattr(mol, "restraint_class"): del mol.restraint_class
mol.OptimiseHydrogens()
mol.WritePDB('4antechamber_%s.pdb' % code,
pymol_pdb_bond_order=False)
mol.WriteTriposMol2('4antechamber_%s.mol2' % code)
mol.Multiplicitise()
try: os.remove('sqm.pdb')
except OSError: pass
cmd='antechamber -i 4antechamber_%s.mol2 -fi mol2 -o %s.mol2 -fo mol2 \
-nc %d -s 2 -pf y -c bcc -at gaff2 \
-ek "qm_theory=\'AM1\', scfconv=1.d-10, ndiis_attempts=700,maxcyc=0"' \
%(code, code, mol.charge)
print cmd
ero=easy_run.fully_buffered(cmd)
f=open('antelog_%s.txt' % code,'wb')
ero.show_stdout(out=f)
ero.show_stderr(out=f)
cmd='parmchk2 -i %s.mol2 -f mol2 -o %s.frcmod -s 2' %(code,code)
print cmd
ero=easy_run.fully_buffered(cmd)
ero.show_stdout(out=f)
ero.show_stderr(out=f)
f.close()
print '\nMoving files from',os.getcwd()
cmd = "mv %s %s " % ("antelog_%s.txt" % (code),
os.path.join(cwd,"..","output", "antelog_%s.txt" % (code))
)
print cmd
easy_run.call(cmd)
cmd = "mv %s %s " % ("sqm.out",
os.path.join(cwd,"..","output", "sqm_%s.out" % (code))
)
print cmd
easy_run.call(cmd)
# copy the geometry used to create the inputs
cmd = "mv %s %s " % ("4antechamber_%s.pdb" % (code),
os.path.join(cwd, "%s.final.pdb" % (code))
)
print cmd
easy_run.call(cmd)
for ext in ["frcmod", "mol2"]:
if not os.path.exists("%s.%s" % (code, ext)): return None
cmd = "mv %s %s" % ("%s.%s" % (code, ext),
os.path.join(cwd, "%s.%s" % (code,ext))
)
print cmd
easy_run.call(cmd)
os.chdir(cwd)
import shutil
if use_temp_file:
print "Deleting temporary directory : %s" % td
shutil.rmtree(td)
return True
def get_elbow_molecule_cif_filename(code, kwds={}, return_molecule=False):
def _get_qm_package_kwds(kwds, qm_package):
if qm_package is not None:
if qm_package.lower()=="gamess":
kwds["gamess"]=True
elif qm_package.lower()=="gaussian":
kwds["gaussian"]=True
#else:
# assert 0
del kwds["qm_package"]
return kwds
if code in skip_codes:
print 'code %s in skip list' % code
return None
code=code.upper()
filename = "%s" % code
default_kwds = {
"qm_package" : None,
"qm_method" : None,
"qm_basis" : None,
"qm_solvent_model" : None,
"opt_nprocs" : 1,
"opt" : False,
"mogul" : False,
"geostd" : False,
"qsub" : "",
"automatic" : False,
"qm_check" : False,
"dry_run" : False,
"quiet" : True,
#"validate" : True,
"pH" : "neutral",
#"xml" : True,
"write_redundant_dihedrals_boolean" : False, # special case!!!
#"initial_geometry" : code,
#"smiles" : get_smiles(code),
#"file" : sdf_filename,
#"no_output" : True,
#"output": "ANP_neutral",
"overwrite" : True,
}
kwds["chemical_component"] = code
for dk in default_kwds:
if dk not in kwds:
kwds[dk]=default_kwds[dk]
count = 0
for kwd in [
"opt",
#"qm_method",
"mogul",
"automatic",
]:
if kwds[kwd]:
count+=1
assert count<=1
if 0:
for key in sorted(kwds):
print " %-20s : %s" % (key, kwds[key])
kwds = _get_qm_package_kwds(kwds, kwds["qm_package"])
if "smiles" in kwds and not kwds["smiles"]: return None
if not kwds["overwrite"] and os.path.exists("%s.cif" % filename):
print "CIF found",os.path.abspath("%s.cif" % filename)
if return_molecule: assert 0
return filename
if not kwds["overwrite"] and os.path.exists("%s.pickle" % filename):
print "pickle found",os.path.abspath("%s.pickle" % filename)
if return_molecule: assert 0
f=file(os.path.abspath("%s.pickle" % filename), "rb")
mol = pickle.load(f)
del f
mol.WriteCIF(filename)
return filename
else:
display_kwds(kwds)
if qm_job_not_run(kwds):
print '\n\n\tNo previous job\n\n'
# WHY WAS THIS INDENTED
# if kwds["qm_method"]:
# if qm_job_not_run(kwds):
# print '\n\n\tNo previous job\n\n'
# mol = builder.run(**kwds)
# elif qm_job_run_and_failed(kwds):
# print last_qm_lines(kwds, 100)
# print '\n\n\tPrevious job is failed\n\n'
# mol = builder.run(**kwds)
# elif not qm_job_run_and_finished(kwds):
# print '\n\n\tJob is still running\n\n'
# mol = None
# elif qm_job_run_and_finished(kwds):
# print '\n\n\tJob is finished running\n\n'
# assert 0
# else:
# print 'else'
# mol = None
# else:
mol = builder.run(**kwds)
elif not qm_job_run_and_finished(kwds):
print '\n\n\tJob is still running\n\n'
mol = None
elif qm_job_run_and_failed(kwds):
print last_qm_lines(kwds, 100)
print '\n\n\tPrevious job is failed\n\n'
mol = builder.run(**kwds)
else:
print 'else'
mol = None
if mol:
if not os.path.exists(os.path.dirname(filename)):
try: os.mkdir(os.path.dirname(filename))
except: pass
mol.WriteCIF(filename)
if return_molecule:
return mol
else:
return filename