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Fix issue #299 #300

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Jun 17, 2024
Merged

Fix issue #299 #300

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5aacbcf
Fix docstring for parameterisation function return types.
lohedges Jun 12, 2024
fbe4249
Don't wrap the fileformat string. [closes #299]
lohedges Jun 12, 2024
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2 changes: 1 addition & 1 deletion python/BioSimSpace/IO/_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -764,7 +764,7 @@ def saveMolecules(
continue

# Add the file format to the property map.
_property_map["fileformat"] = _SireBase.wrap(format)
_property_map["fileformat"] = format

# Warn the user if any molecules are parameterised with a force field
# that uses geometric combining rules. While we can write this to file
Expand Down
42 changes: 28 additions & 14 deletions python/BioSimSpace/Parameters/_parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,8 +111,10 @@ def parameterise(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if not isinstance(forcefield, str):
Expand Down Expand Up @@ -208,8 +210,10 @@ def _parameterise_amber_protein(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if not isinstance(forcefield, str):
Expand Down Expand Up @@ -314,8 +318,10 @@ def gaff(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if _amber_home is None:
Expand Down Expand Up @@ -407,8 +413,10 @@ def gaff2(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if _amber_home is None:
Expand Down Expand Up @@ -506,8 +514,10 @@ def _parameterise_openff(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

from sire.legacy.Base import findExe as _findExe
Expand Down Expand Up @@ -1068,8 +1078,10 @@ def _function(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""
return _parameterise_amber_protein(
name,
Expand Down Expand Up @@ -1133,8 +1145,10 @@ def _function(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""
return _parameterise_openff(
name,
Expand Down
2 changes: 1 addition & 1 deletion python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -764,7 +764,7 @@ def saveMolecules(
continue

# Add the file format to the property map.
_property_map["fileformat"] = _SireBase.wrap(format)
_property_map["fileformat"] = format

# Warn the user if any molecules are parameterised with a force field
# that uses geometric combining rules. While we can write this to file
Expand Down
42 changes: 28 additions & 14 deletions python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,8 +111,10 @@ def parameterise(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if not isinstance(forcefield, str):
Expand Down Expand Up @@ -208,8 +210,10 @@ def _parameterise_amber_protein(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if not isinstance(forcefield, str):
Expand Down Expand Up @@ -314,8 +318,10 @@ def gaff(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if _amber_home is None:
Expand Down Expand Up @@ -407,8 +413,10 @@ def gaff2(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

if _amber_home is None:
Expand Down Expand Up @@ -506,8 +514,10 @@ def _parameterise_openff(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""

from sire.legacy.Base import findExe as _findExe
Expand Down Expand Up @@ -1068,8 +1078,10 @@ def _function(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""
return _parameterise_amber_protein(
name,
Expand Down Expand Up @@ -1133,8 +1145,10 @@ def _function(
Returns
-------

molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The parameterised molecule.
process : :class:`Process <BioSimSpace.Parameters._process.Process>`
A process to parameterise the molecule in the background. Call the
.getMolecule() method on the returned process to block until the
parameterisation is complete and get the parameterised molecule.
"""
return _parameterise_openff(
name,
Expand Down