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Extract overlap matrix from pymbar output. [ref #193]
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lohedges committed Apr 27, 2021
1 parent 7a107fc commit 88e106a
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Showing 3 changed files with 90 additions and 34 deletions.
14 changes: 12 additions & 2 deletions python/BioSimSpace/FreeEnergy/_binding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,13 +204,23 @@ def analyse(self):
simulation. The data is a list of tuples, where each tuple
contains the lambda value, the PMF, and the standard error.
pmf_vacuum : [(float, :class:`Energy <BioSimSpace.Types.Energy>`, :class:`Energy <BioSimSpace.Types.Energy>`)]
The potential of mean force (PMF) for the vacuum leg of the
pmf_bound : [(float, :class:`Energy <BioSimSpace.Types.Energy>`, :class:`Energy <BioSimSpace.Types.Energy>`)]
The potential of mean force (PMF) for the bound leg of the
simulation. The data is a list of tuples, where each tuple
contains the lambda value, the PMF, and the standard error.
free_energy : (:class:`Energy <BioSimSpace.Types.Energy>`, :class:`Energy <BioSimSpace.Types.Energy>`)
The binding free energy difference and its associated error.
overlap_free : [ [ float, float, ... ] ]
The overlap matrix. This gives the overlap between each window
of the free leg. This parameter is only computed for the SOMD
engine and will be None when GROMACS is used.
overlap_bound : [ [ float, float, ... ] ]
The overlap matrix. This gives the overlap between each window
of the bound leg. This parameter is only computed for the SOMD
engine and will be None when GROMACS is used.
"""

# This method is just a wrapper to provide simulation specific doc
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100 changes: 68 additions & 32 deletions python/BioSimSpace/FreeEnergy/_free_energy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -309,7 +309,7 @@ def _analyse_gromacs(self):
# Bundle the free energy and its associated error.
free_energy = (free_energy, error)

return (leg0, leg1, free_energy)
return (leg0, leg1, free_energy, None, None)

def _analyse_somd(self):
"""Analyse the SOMD free energy data.
Expand All @@ -329,6 +329,16 @@ def _analyse_somd(self):
free_energy : (:class:`Energy <BioSimSpace.Types.Energy>`, :class:`Energy <BioSimSpace.Types.Energy>`)
The free energy difference and its associated error.
overlap0 : [ [ float, float, ... ] ]
The overlap matrix. This gives the overlap between each window
of the first leg. This parameter is only computed for the SOMD
engine and will be None when GROMACS is used.
overlap1 : [ [ float, float, ... ] ]
The overlap matrix. This gives the overlap between each window
of the second leg. This parameter is only computed for the SOMD
engine and will be None when GROMACS is used.
"""

# Create the commands for the two legs.
Expand All @@ -350,66 +360,92 @@ def _analyse_somd(self):
leg0 = []
leg1 = []

# Initialise lists to hold the overlap matrix for each leg.
overlap0 = []
overlap1 = []

# Extract the data from the output files.

# First leg.
with open("%s/mbar_leg0.txt" % self._work_dir) as file:

# Read all of the lines into a list.
lines = []
# Process the MBAR data.
for line in file:
lines.append(line.rstrip())
# Process the overlap matrix.
if "#Overlap matrix" in line:

# Find the MBAR data.
for x, line in enumerate(lines):
if "PMF from MBAR" in line:
# Increment the line index.
x += 1
# Get the next row.
row = next(file)

# Loop until we hit the next section.
while not row.startswith("#DG"):
# Extract the data for this row.
data = [float(x) for x in row.split()]

# Append to the overlap matrix.
overlap0.append(data)

# Get the next line.
row = next(file)

# Process the PMF.
elif "PMF from MBAR" in line:
# Get the next row.
row = next(file)

# Loop until we hit the next comment.
while lines[x][0] != "#":
# Loop until we hit the next section.
while not row.startswith("#TI"):
# Split the line.
data = lines[x].split()
data = row.split()

# Append the data.
leg0.append((float(data[0]),
float(data[1]) * _Units.Energy.kcal_per_mol,
float(data[2]) * _Units.Energy.kcal_per_mol))

# Increment the line index.
x += 1
# Get the next line.
row = next(file)

break

# Second leg.
if self._is_dual:
with open("%s/mbar_leg1.txt" % self._work_dir) as file:

# Read all of the lines into a list.
lines = []
# Process the MBAR data.
for line in file:
lines.append(line.rstrip())
# Process the overlap matrix.
if "#Overlap matrix" in line:

# Find the MBAR data.
for x, line in enumerate(lines):
if "PMF from MBAR" in line:
# Increment the line index.
x += 1
# Get the next row.
row = next(file)

# Loop until we hit the next comment.
while lines[x][0] != "#":
# Loop until we hit the next section.
while not row.startswith("#DG"):
# Extract the data for this row.
data = [float(x) for x in row.split()]

# Append to the overlap matrix.
overlap1.append(data)

# Get the next line.
row = next(file)

# Process the PMF.
elif "PMF from MBAR" in line:
# Get the next row.
row = next(file)

# Loop until we hit the next section.
while not row.startswith("#TI"):
# Split the line.
data = lines[x].split()
data = row.split()

# Append the data.
leg1.append((float(data[0]),
float(data[1]) * _Units.Energy.kcal_per_mol,
float(data[2]) * _Units.Energy.kcal_per_mol))

# Increment the line index.
x += 1

break
# Get the next line.
row = next(file)

# Work out the difference in free energy.
if self._is_dual:
Expand All @@ -436,7 +472,7 @@ def _analyse_somd(self):
# Bundle the free energy and its associated error.
free_energy = (free_energy, error)

return (leg0, leg1, free_energy)
return (leg0, leg1, free_energy, overlap0, overlap1)

def _initialise_runner(self, system0, system1):
"""Internal helper function to initialise the process runner.
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10 changes: 10 additions & 0 deletions python/BioSimSpace/FreeEnergy/_solvation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,16 @@ def analyse(self):
free_energy : (:class:`Energy <BioSimSpace.Types.Energy>`, :class:`Energy <BioSimSpace.Types.Energy>`)
The solvation free energy difference and its associated error.
overlap_free : [ [ float, float, ... ] ]
The overlap matrix. This gives the overlap between each window
of the free leg. This parameter is only computed for the SOMD
engine and will be None when GROMACS is used.
overlap_vacuum : [ [ float, float, ... ] ]
The overlap matrix. This gives the overlap between each window
of the vacuum leg. This parameter is only computed for the SOMD
engine and will be None when GROMACS is used.
"""

# This method is just a wrapper to provide simulation specific doc
Expand Down

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