def _get_fromApp(self, ifile):
app = main.MMPBSA_App(MPI)
info = infofile.InfoFile(app)
info.read_info(ifile)
app.normal_system = app.mutant_system = None
app.parse_output_files()
self.app_namespace = self._get_namespace(app)
self._oringin = {'normal': app.calc_types.normal, 'mutant': app.calc_types.mutant,
'decomp_normal': app.calc_types.decomp_normal, 'decomp_mutant': app.calc_types.decomp_mutant,
'mutant-normal': app.calc_types.mut_norm,
# 'decomp_mutant-normal': app.calc_types.decomp_mut_norm
}
self.data = copy(self._oringin)
self._get_frames()
self._get_data(None)
def load_gmxmmpbsa_info(fname):
"""
Loads up an gmx_MMPBSA info file and returns a mmpbsa_data instance with all
of the data available in numpy arrays if numpy is available. The returned
object is a mmpbsa_data instance.
change the structure to get more easy way to graph per residue
mmpbsa_data attributes:
-----------------------
o Derived from "dict"
o Each solvent model is a dictionary key for a numpy array (if numpy is
available) or array.array (if numpy is unavailable) for each of the
species (complex, receptor, ligand) present in the calculation.
o The alanine scanning mutant data is under another dict denoted by the
'mutant' key.
Data Layout:
------------
Model | Dictionary Key | Data Keys Available
-------------------------------------------------------------------
Generalized Born | 'gb' | EGB, ESURF, *
Poisson-Boltzmann | 'pb' | EPB, EDISPER, ECAVITY, *
3D-RISM (GF) | 'rism gf' |
3D-RISM (Standard)| 'rism std' |
Normal Mode | 'nmode' |
Quasi-harmonic | 'qh' |
* == TOTAL, VDW, EEL, 1-4 EEL, 1-4 VDW, BOND, ANGLE, DIHED
The keys above are entries for the main dict as well as the sub-dict whose
key is 'mutant' in the main dict. Each entry in the main (and mutant sub-)
dict is, itself, a dict with 1 or 3 keys; 'complex', 'receptor', 'ligand';
where 'receptor' and 'ligand' are missing for stability calculations.
If numpy is available, all data will be numpy.ndarray instances. Otherwise,
all data will be array.array instances.
All of the objects referenced by the listed 'Dictionary Key's are dicts in
which the listed 'Data Keys Available' are keys to the data arrays themselves
Examples:
---------
# Load numpy for our analyses (optional)
import numpy as np
# Load the _MMPBSA_info file:
mydata = load_mmpbsa_info('_MMPBSA_info')
# Access the complex GB data structure and calculate the autocorr. fcn.
autocorr = np.correlate(mydata['gb']['complex']['TOTAL'],
mydata['gb']['complex']['TOTAL'])
# Calculate the standard deviation of the alanine mutant receptor in PB
print mydata.mutant['pb']['receptor']['TOTAL'].std()
"""
if not isinstance(fname, Path):
fname = Path(fname)
if not fname.exists():
raise NoFileExists("cannot find %s!" % fname)
os.chdir(fname.parent)
app = main.MMPBSA_App(MPI)
info = infofile.InfoFile(app)
info.read_info(fname)
app.normal_system = app.mutant_system = None
app.parse_output_files()
return_data = mmpbsa_data(app)
# Since Decomp data is parsed in a memory-efficient manner (by not storing
# all of the data in arrays, but rather by printing each data point as it's
# parsed), we need to handle the decomp data separately here
# Open Complex fixed structure to assign per-(residue/wise) residue name
try:
complex_str = parmed.read_PDB(app.FILES.complex_fixed)
except:
complex_str = parmed.read_PDB(app.FILES.prefix + 'COM.pdb')
# Get receptor and ligand masks
mut_index = None
rec = {}
mut_rec = {}
rmstr = app.INPUT['receptor_mask'].strip(':')
rml = rmstr.split(',')
for x in rml:
if len(x.split('-')) > 1:
start, end = x.split('-')
for i in range(int(start), int(end) + 1):
residue = complex_str.residues[i - 1]
icode = f'{residue.insertion_code}'
if icode:
icode = ':' + icode
rec[i] = (f"{residue.chain}:{residue.name}:{residue.number}" +
icode)
mut_rec[i] = (
f"{residue.chain}:{residue.name}:{residue.number}" + icode)
if app.INPUT['mutant_res'] == (
f"{residue.chain}:{residue.number}" + icode):
mut_rec[i] = (
f"{residue.chain}:{app.INPUT['mutant']}:{residue.number}"
+ icode)
else:
i = int(x)
residue = complex_str.residues[i - 1]
icode = f'{residue.insertion_code}'
if icode:
icode = ':' + icode
rec[i] = (f"{residue.chain}:{residue.name}:{residue.number}" +
icode)
mut_rec[i] = (f"{residue.chain}:{residue.name}:{residue.number}" +
icode)
if app.INPUT['mutant_res'] == (
f"{residue.chain}:{residue.number}" + icode):
mut_rec[i] = (
f"{residue.chain}:{app.INPUT['mutant']}:{residue.number}" +
icode)
lig = {}
mut_lig = {}
lmstr = app.INPUT['ligand_mask'].strip(':')
lml = lmstr.split(',')
for x in lml:
if len(x.split('-')) > 1:
start, end = x.split('-')
for i in range(int(start), int(end) + 1):
residue = complex_str.residues[i - 1]
icode = f'{residue.insertion_code}'
if icode:
icode = ':' + icode
lig[i] = (f"{residue.chain}:{residue.name}:{residue.number}" +
icode)
mut_lig[i] = (
f"{residue.chain}:{residue.name}:{residue.number}" + icode)
if app.INPUT['mutant_res'] == (
f"{residue.chain}:{residue.number}" + icode):
mut_lig[i] = (
f"{residue.chain}:{app.INPUT['mutant']}:{residue.number}"
+ icode)
else:
i = int(x)
residue = complex_str.residues[i - 1]
icode = f'{residue.insertion_code}'
if icode:
icode = ':' + icode
lig[i] = (f"{residue.chain}:{residue.name}:{residue.number}" +
icode)
mut_lig[i] = (f"{residue.chain}:{residue.name}:{residue.number}" +
icode)
if app.INPUT['mutant_res'] == (
f"{residue.chain}:{residue.number}" + icode):
mut_lig[i] = (
f"{residue.chain}:{app.INPUT['mutant']}:{residue.number}" +
icode)
com = rec.copy()
com.update(lig)
com_res_info = []
for key, value in sorted(com.items()):
com_res_info.append(value)
rec_res_info = []
for key, value in rec.items():
rec_res_info.append(value)
lig_res_info = []
for key, value in lig.items():
lig_res_info.append(value)
mut_com_res_info = []
mut_com = mut_rec.copy()
mut_com.update(mut_lig)
for key, value in sorted(mut_com.items()):
mut_com_res_info.append(value)
mut_rec_res_info = []
for key, value in mut_rec.items():
mut_rec_res_info.append(value)
mut_lig_res_info = []
for key, value in mut_lig.items():
mut_lig_res_info.append(value)
if not app.INPUT['alarun']:
return_data.mutant = {}
if app.INPUT['decomprun']:
# Simplify the decomp class instance creation
if app.INPUT['idecomp'] in (1, 2):
DecompClass = lambda x, part: APIDecompOut(x, part, app)
else:
DecompClass = lambda x, part: APIPairDecompOut(x, part, app)
if not app.INPUT['mutant_only']:
# Do normal GB
if app.INPUT['gbrun']:
return_data['decomp'] = {'gb': {}}
return_data['decomp']['gb']['complex'] = DecompClass(
app.FILES.prefix + 'complex_gb.mdout',
com_res_info).array_data
if not app.stability:
return_data['decomp']['gb']['receptor'] = DecompClass(
app.FILES.prefix + 'receptor_gb.mdout',
rec_res_info).array_data
return_data['decomp']['gb']['ligand'] = DecompClass(
app.FILES.prefix + 'ligand_gb.mdout',
lig_res_info).array_data
return_data['decomp']['gb']['delta'] = get_delta_decomp(
app, 'gb', return_data['decomp'])
# Do normal PB
if app.INPUT['pbrun']:
return_data['decomp'] = {'pb': {}}
return_data['decomp']['pb']['complex'] = DecompClass(
app.FILES.prefix + 'complex_pb.mdout',
com_res_info).array_data
if not app.stability:
return_data['decomp']['pb']['receptor'] = DecompClass(
app.FILES.prefix + 'receptor_pb.mdout',
rec_res_info).array_data
return_data['decomp']['pb']['ligand'] = DecompClass(
app.FILES.prefix + 'ligand_pb.mdout',
lig_res_info).array_data
return_data['decomp']['pb']['delta'] = get_delta_decomp(
app, 'pb', return_data['decomp'])
if app.INPUT['alarun']:
# Do mutant GB
if app.INPUT['gbrun']:
return_data.mutant['decomp'] = {'gb': {}}
return_data.mutant['decomp']['gb']['complex'] = DecompClass(
app.FILES.prefix + 'mutant_complex_gb.mdout',
mut_com_res_info).array_data
if not app.stability:
return_data.mutant['decomp']['gb'][
'receptor'] = DecompClass(
app.FILES.prefix + 'mutant_receptor_gb.mdout',
mut_rec_res_info).array_data
return_data.mutant['decomp']['gb']['ligand'] = DecompClass(
app.FILES.prefix + 'mutant_ligand_gb.mdout',
mut_lig_res_info).array_data
return_data.mutant['decomp']['gb'][
'delta'] = get_delta_decomp(
app, 'gb', return_data.mutant['decomp'])
# Do mutant PB
if app.INPUT['pbrun']:
return_data.mutant['decomp'] = {'pb': {}}
return_data.mutant['decomp']['pb']['complex'] = DecompClass(
app.FILES.prefix + 'mutant_complex_pb.mdout',
mut_com_res_info).array_data
if not app.stability:
return_data.mutant['decomp']['pb'][
'receptor'] = DecompClass(
app.FILES.prefix + 'mutant_receptor_pb.mdout',
mut_rec_res_info).array_data
return_data.mutant['decomp']['pb']['ligand'] = DecompClass(
app.FILES.prefix + 'mutant_ligand_pb.mdout',
mut_lig_res_info).array_data
return_data.mutant['decomp']['pb'][
'delta'] = get_delta_decomp(
app, 'pb', return_data.mutant['decomp'])
else:
return_data.mutant = None
app_namespace = SimpleNamespace(FILES=app.FILES,
INPUT=app.INPUT,
numframes=app.numframes,
numframes_nmode=app.numframes_nmode)
return return_data, app_namespace
def gmxmmpbsa():
stream_handler = logging.StreamHandler()
stream_handler.setLevel(logging.INFO)
formatter = logging.Formatter("[%(levelname)-7s] %(message)s")
stream_handler.setFormatter(formatter)
logging.basicConfig(
level=logging.DEBUG,
format="[%(levelname)-7s] %(message)s",
handlers=[logging.FileHandler("gmx_MMPBSA.log", 'w'), stream_handler])
# Just for compatibility as mpi4py works as serial when run without mpirun
# (since v1.4.2)
if len(sys.argv) > 1 and sys.argv[1] in ['MPI', 'mpi']:
from mpi4py import MPI
else:
# If we're not running "gmx_MMPBSA MPI", bring MPI into the top-level namespace
# (which will overwrite the MPI from mpi4py, which we *want* to do in serial)
from GMXMMPBSA.fake_mpi import MPI
# Set up error/signal handlers
main.setup_run()
# Instantiate the main MMPBSA_App
app = main.MMPBSA_App(MPI)
# Read the command-line arguments
try:
app.get_cl_args(sys.argv[1:])
except CommandlineError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.exit(1)
if app.FILES.createinput is not None:
args_list = create_input_args(app.FILES.createinput)
app.input_file.print_contents('mmpbsa.in', args_list)
logging.info(
f'Input file creation successful. Path: {Path("mmpbsa.in").absolute()}'
)
sys.exit(0)
# Perform our MMPBSA --clean now
if app.FILES.clean:
logging.info('Cleaning temporary files and quitting.\n')
app.remove(-1)
sys.exit(0)
# See if we wanted to print out our input file options
if app.FILES.infilehelp:
app.input_file.print_contents(sys.stdout)
sys.exit(0)
# If we're not rewriting output do whole shebang, otherwise load info and parms
# Throw up a barrier before and after running the actual calcs
if not app.FILES.rewrite_output:
try:
app.read_input_file()
except InputError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.stderr.write(' Enter `%s --help` for help\n' %
(split(sys.argv[0])[1]))
sys.exit(1)
app.process_input()
app.check_for_bad_input()
app.make_prmtops()
app.loadcheck_prmtops()
app.file_setup()
app.run_mmpbsa()
# If we are rewriting output, load the info and check prmtops
else:
info = InfoFile(app)
info.read_info()
app.loadcheck_prmtops()
# Now we parse the output, print, and finish
app.parse_output_files()
app.write_final_outputs()
app.finalize()
def gmxmmpbsa():
# Adapted to run with MPI ?
if len(sys.argv) > 1 and sys.argv[1] in ['MPI', 'mpi']:
args = sys.argv
args.pop(1) # remove mpi arg before passed it to app
try:
from mpi4py import MPI
except ImportError:
raise MMPBSA_Error(
'Could not import mpi4py package! Use serial version '
'or install mpi4py.')
else:
# If we're not running "gmx_MMPBSA MPI", bring MPI into the top-level namespace
# (which will overwrite the MPI from mpi4py, which we *want* to do in serial)
from GMXMMPBSA.fake_mpi import MPI
args = sys.argv
# Set up error/signal handlers
main.setup_run()
# Instantiate the main MMPBSA_App
app = main.MMPBSA_App(MPI)
# Read the command-line arguments
try:
app.get_cl_args(args[1:])
except CommandlineError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.exit(1)
# Perform our MMPBSA --clean now
if app.FILES.clean:
sys.stdout.write('Cleaning temporary files and quitting.\n')
app.remove(0)
sys.exit(0)
# See if we wanted to print out our input file options
if app.FILES.infilehelp:
app.input_file.print_contents(sys.stdout)
sys.exit(0)
# If we're not rewriting output do whole shebang, otherwise load info and parms
# Throw up a barrier before and after running the actual calcs
if not app.FILES.rewrite_output:
try:
app.read_input_file()
except InputError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.stderr.write(' Enter `%s --help` for help\n' %
(split(sys.argv[0])[1]))
sys.exit(1)
app.process_input()
app.check_for_bad_input()
app.loadcheck_prmtops()
app.file_setup()
app.run_mmpbsa()
# If we are rewriting output, load the info and check prmtops
else:
info = InfoFile(app)
info.read_info()
app.loadcheck_prmtops()
# Now we parse the output, print, and finish
app.parse_output_files()
app.write_final_outputs()
app.finalize()
def load_gmxmmpbsa_info(fname):
"""
Loads up an gmx_MMPBSA info file and returns a mmpbsa_data instance with all
of the data available in numpy arrays if numpy is available. The returned
object is a mmpbsa_data instance.
change the structure to get more easy way to graph per residue
mmpbsa_data attributes:
-----------------------
o Derived from "dict"
o Each solvent model is a dictionary key for a numpy array (if numpy is
available) or array.array (if numpy is unavailable) for each of the
species (complex, receptor, ligand) present in the calculation.
o The alanine scanning mutant data is under another dict denoted by the
'mutant' key.
Data Layout:
------------
Solvent Model | Dictionary Key | Data Keys Available
-------------------------------------------------------------------
Generalized Born | 'gb' | EGB, ESURF, *
Poisson-Boltzmann | 'pb' | EPB, EDISPER, ECAVITY, *
3D-RISM (GF) | 'rism gf' |
3D-RISM (Standard)| 'rism std' |
Normal Mode | 'nmode' |
Quasi-harmonic | 'qh' |
* == TOTAL, VDW, EEL, 1-4 EEL, 1-4 VDW, BOND, ANGLE, DIHED
The keys above are entries for the main dict as well as the sub-dict whose
key is 'mutant' in the main dict. Each entry in the main (and mutant sub-)
dict is, itself, a dict with 1 or 3 keys; 'complex', 'receptor', 'ligand';
where 'receptor' and 'ligand' are missing for stability calculations.
If numpy is available, all data will be numpy.ndarray instances. Otherwise,
all data will be array.array instances.
All of the objects referenced by the listed 'Dictionary Key's are dicts in
which the listed 'Data Keys Available' are keys to the data arrays themselves
Examples:
---------
# Load numpy for our analyses (optional)
import numpy as np
# Load the _MMPBSA_info file:
mydata = load_mmpbsa_info('_MMPBSA_info')
# Access the complex GB data structure and calculate the autocorr. fcn.
autocorr = np.correlate(mydata['gb']['complex']['TOTAL'],
mydata['gb']['complex']['TOTAL'])
# Calculate the standard deviation of the alanine mutant receptor in PB
print mydata.mutant['pb']['receptor']['TOTAL'].std()
"""
if not HAS_NUMPY:
warnings.warn(
'numpy was not found. Data will be packed in normal Python '
'arrays. Install numpy for more efficient array handling.',
NotImplemented)
if not os.path.exists(fname):
raise NoFileExists("cannot find %s!" % fname)
app = main.MMPBSA_App(MPI)
info = infofile.InfoFile(app)
info.read_info(fname)
app.normal_system = app.mutant_system = None
app.parse_output_files()
return_data = mmpbsa_data(app)
# Since Decomp data is parsed in a memory-efficient manner (by not storing
# all of the data in arrays, but rather by printing each data point as it's
# parsed), we need to handle the decomp data separately here
if not app.INPUT['alarun']:
return_data.mutant = None
lig_res = None
if app.INPUT['decomprun']:
# Simplify the decomp class instance creation
if app.INPUT['idecomp'] in (1, 2):
DecompClass = lambda x, y, z=None: APIDecompOutGMX(
x,
y,
app.mpi_size,
app.INPUT['dec_verbose'],
app.numframes,
lig_num=z)
else:
DecompClass = lambda x, y, z=None: APIPairDecompOutGMX(
x,
y,
app.mpi_size,
app.INPUT['dec_verbose'],
app.numframes,
lig_num=z)
if not app.INPUT['mutant_only']:
# Do normal GB
if app.INPUT['gbrun']:
return_data['decomp'] = {'gb': {}}
return_data['decomp']['gb']['complex'] = DecompClass(
app.FILES.prefix + 'complex_gb.mdout',
app.INPUT['surften']).array_data
com_res = []
for k in return_data['decomp']['gb']['complex']['TDC']:
if k not in com_res:
com_res.append(k)
if not app.stability:
return_data['decomp']['gb']['receptor'] = DecompClass(
app.FILES.prefix + 'receptor_gb.mdout',
app.INPUT['surften']).array_data
rec_res = []
for k in return_data['decomp']['gb']['receptor']['TDC']:
if k not in rec_res:
rec_res.append(k)
lig_res = com_res[len(rec_res):]
return_data['decomp']['gb']['ligand'] = DecompClass(
app.FILES.prefix + 'ligand_gb.mdout',
app.INPUT['surften'], lig_res).array_data
return_data['decomp']['gb']['delta'] = get_delta_decomp(
app, 'gb', return_data['decomp'])
# Do normal PB
if app.INPUT['pbrun']:
return_data['decomp'] = {'pb': {}}
return_data['decomp']['pb']['complex'] = DecompClass(
app.FILES.prefix + 'complex_pb.mdout',
app.INPUT['surften']).array_data
if not app.stability:
return_data['decomp']['pb']['receptor'] = DecompClass(
app.FILES.prefix + 'receptor_pb.mdout',
app.INPUT['surften']).array_data
return_data['decomp']['pb']['ligand'] = DecompClass(
app.FILES.prefix + 'ligand_pb.mdout',
app.INPUT['surften'], lig_res).array_data
return_data['decomp']['pb']['delta'] = get_delta_decomp(
app, 'pb', return_data['decomp'])
if app.INPUT['alarun']:
# Do mutant GB
if app.INPUT['gbrun']:
return_data.mutant['decomp'] = {'gb': {}}
return_data.mutant['decomp']['gb']['complex'] = DecompClass(
app.FILES.prefix + 'mutant_complex_gb.mdout',
app.INPUT['surften']).array_data
if not app.stability:
return_data.mutant['decomp']['gb'][
'receptor'] = DecompClass(
app.FILES.prefix + 'mutant_receptor_gb.mdout',
app.INPUT['surften']).array_data
return_data.mutant['decomp']['gb']['ligand'] = DecompClass(
app.FILES.prefix + 'mutant_ligand_gb.mdout',
app.INPUT['surften'], lig_res).array_data
return_data.mutant['decomp']['gb'][
'delta'] = get_delta_decomp(
app, 'gb', return_data.mutant['decomp'])
# Do mutant PB
if app.INPUT['pbrun']:
return_data.mutant['decomp'] = {'pb': {}}
return_data.mutant['decomp']['pb']['complex'] = DecompClass(
app.FILES.prefix + 'mutant_complex_pb.mdout',
app.INPUT['surften']).array_data
if not app.stability:
return_data.mutant['decomp']['pb'][
'receptor'] = DecompClass(
app.FILES.prefix + 'mutant_receptor_pb.mdout',
app.INPUT['surften']).array_data
return_data.mutant['decomp']['pb']['ligand'] = DecompClass(
app.FILES.prefix + 'mutant_ligand_pb.mdout',
app.INPUT['surften'], lig_res).array_data
return_data.mutant['decomp']['pb'][
'delta'] = get_delta_decomp(
app, 'pb', return_data.mutant['decomp'])
else:
return_data.mutant = None
return return_data, app