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Fix issues #240 and #246 #247

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merged 3 commits into from
Feb 23, 2024
Merged

Fix issues #240 and #246 #247

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c8eba8d
Fix funnel range used in correction calculation. [closes #246]
lohedges Feb 22, 2024
c2aaf0b
Change file extensions for interchange files to Sire defaults.
lohedges Feb 22, 2024
50b5bb6
Recover missing molecule0 and molecule1 properties. [closes #248]
lohedges Feb 22, 2024
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2 changes: 1 addition & 1 deletion python/BioSimSpace/Metadynamics/CollectiveVariable/_funnel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -592,7 +592,7 @@ def getCorrection(
volume = _Volume(_math.pi * result, "nanometers cubed")

# Estimate the average area of the restraint (in Angstrom squared).
area = (volume / proj_max).angstroms2()
area = (volume / (proj_max - proj_min)).angstroms2()

# Compute the correction. (1/1660 A-3 is the standard concentration.)
correction = _Energy(_math.log((area / 1660).value()), "kt")
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8 changes: 4 additions & 4 deletions python/BioSimSpace/Parameters/_Protocol/_openforcefield.py
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Original file line number Diff line number Diff line change
Expand Up @@ -329,8 +329,8 @@ def run(self, molecule, work_dir=None, queue=None):

# Export AMBER format files.
try:
interchange.to_prmtop(prefix + "interchange.prmtop")
interchange.to_inpcrd(prefix + "interchange.inpcrd")
interchange.to_prmtop(prefix + "interchange.prm7")
interchange.to_inpcrd(prefix + "interchange.rst7")
except Exception as e:
msg = "Unable to write Interchange object to AMBER format!"
if _isVerbose():
Expand All @@ -342,13 +342,13 @@ def run(self, molecule, work_dir=None, queue=None):
# Load the parameterised molecule. (This could be a system of molecules.)
try:
par_mol = _IO.readMolecules(
[prefix + "interchange.prmtop", prefix + "interchange.inpcrd"]
[prefix + "interchange.prm7", prefix + "interchange.rst7"]
)
# Extract single molecules.
if par_mol.nMolecules() == 1:
par_mol = par_mol.getMolecules()[0]
except Exception as e:
msg = "Failed to read molecule from: 'interchange.prmtop', 'interchange.inpcrd'"
msg = "Failed to read molecule from: 'interchange.prm7', 'interchange.rst7'"
if _isVerbose():
msg += ": " + getattr(e, "message", repr(e))
raise IOError(msg) from e
Expand Down
2 changes: 1 addition & 1 deletion python/BioSimSpace/Sandpit/Exscientia/Metadynamics/CollectiveVariable/_funnel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -592,7 +592,7 @@ def getCorrection(
volume = _Volume(_math.pi * result, "nanometers cubed")

# Estimate the average area of the restraint (in Angstrom squared).
area = (volume / proj_max).angstroms2()
area = (volume / (proj_max - proj_min)).angstroms2()

# Compute the correction. (1/1660 A-3 is the standard concentration.)
correction = _Energy(_math.log((area / 1660).value()), "kt")
Expand Down
8 changes: 4 additions & 4 deletions python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -329,8 +329,8 @@ def run(self, molecule, work_dir=None, queue=None):

# Export AMBER format files.
try:
interchange.to_prmtop(prefix + "interchange.prmtop")
interchange.to_inpcrd(prefix + "interchange.inpcrd")
interchange.to_prmtop(prefix + "interchange.prm7")
interchange.to_inpcrd(prefix + "interchange.rst7")
except Exception as e:
msg = "Unable to write Interchange object to AMBER format!"
if _isVerbose():
Expand All @@ -342,13 +342,13 @@ def run(self, molecule, work_dir=None, queue=None):
# Load the parameterised molecule. (This could be a system of molecules.)
try:
par_mol = _IO.readMolecules(
[prefix + "interchange.prmtop", prefix + "interchange.inpcrd"]
[prefix + "interchange.prm7", prefix + "interchange.rst7"]
)
# Extract single molecules.
if par_mol.nMolecules() == 1:
par_mol = par_mol.getMolecules()[0]
except Exception as e:
msg = "Failed to read molecule from: 'interchange.prmtop', 'interchange.inpcrd'"
msg = "Failed to read molecule from: 'interchange.prm7', 'interchange.rst7'"
if _isVerbose():
msg += ": " + getattr(e, "message", repr(e))
raise IOError(msg) from e
Expand Down
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