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Fix issue #270 #271

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merged 3 commits into from
Apr 12, 2024
Merged

Fix issue #270 #271

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692849e
Use list rather than set so search strings are reproducible.
lohedges Apr 9, 2024
81d8233
Join protein and nucleic acid residue strings correctly.
lohedges Apr 9, 2024
f44b35e
Use try/except when matching by coordinates.
lohedges Apr 9, 2024
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12 changes: 10 additions & 2 deletions python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -792,7 +792,11 @@ def makeCompatibleWith(
if len(matches) < num_atoms0:
# Atom names or order might have changed. Try to match by coordinates.
matcher = _SireMol.AtomCoordMatcher()
matches = matcher.match(mol0, mol1)

try:
matches = matcher.match(mol0, mol1)
except:
matches = []

# We need to rename the atoms.
is_renamed = True
Expand Down Expand Up @@ -1003,7 +1007,11 @@ def makeCompatibleWith(
matcher = _SireMol.AtomCoordMatcher()

# Get the matches for this molecule and append to the list.
match = matcher.match(mol0, mol)
try:
match = matcher.match(mol0, mol)
except:
match = []

matches.append(match)
num_matches += len(match)

Expand Down
2 changes: 2 additions & 0 deletions python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1888,6 +1888,7 @@ def getRestraintAtoms(
string = (
"(not water) and (resname "
+ ",".join(_prot_res)
+ ","
+ ",".join(_nucl_res)
+ ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)"
)
Expand Down Expand Up @@ -1943,6 +1944,7 @@ def getRestraintAtoms(
string = (
"(not water) and (resname "
+ ",".join(_prot_res)
+ ","
+ ",".join(_nucl_res)
+ ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)"
)
Expand Down
12 changes: 6 additions & 6 deletions python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@
Utilities.
"""

# A set of protein residues. Taken from MDAnalysis.
_prot_res = {
# A list of protein residues. Taken from MDAnalysis.
_prot_res = [
# CHARMM top_all27_prot_lipid.rtf
"ALA",
"ARG",
Expand Down Expand Up @@ -135,10 +135,10 @@
"CMET",
"CME",
"ASF",
}
]

# A set of nucleic acid residues. Taken from MDAnalysis.
_nucl_res = {
# A list of nucleic acid residues. Taken from MDAnalysis.
_nucl_res = [
"ADE",
"URA",
"CYT",
Expand Down Expand Up @@ -173,7 +173,7 @@
"RU3",
"RG3",
"RC3",
}
]

# A list of ion elements.
_ions = [
Expand Down
12 changes: 10 additions & 2 deletions python/BioSimSpace/_SireWrappers/_molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -748,7 +748,11 @@ def makeCompatibleWith(
if len(matches) < num_atoms0:
# Atom names or order might have changed. Try to match by coordinates.
matcher = _SireMol.AtomCoordMatcher()
matches = matcher.match(mol0, mol1)

try:
matches = matcher.match(mol0, mol1)
except:
matches = []

# We need to rename the atoms.
is_renamed = True
Expand Down Expand Up @@ -959,7 +963,11 @@ def makeCompatibleWith(
matcher = _SireMol.AtomCoordMatcher()

# Get the matches for this molecule and append to the list.
match = matcher.match(mol0, mol)
try:
match = matcher.match(mol0, mol)
except:
match = []

matches.append(match)
num_matches += len(match)

Expand Down
2 changes: 2 additions & 0 deletions python/BioSimSpace/_SireWrappers/_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1809,6 +1809,7 @@ def getRestraintAtoms(
string = (
"(not water) and (resname "
+ ",".join(_prot_res)
+ ","
+ ",".join(_nucl_res)
+ ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)"
)
Expand Down Expand Up @@ -1864,6 +1865,7 @@ def getRestraintAtoms(
string = (
"(not water) and (resname "
+ ",".join(_prot_res)
+ ","
+ ",".join(_nucl_res)
+ ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)"
)
Expand Down
12 changes: 6 additions & 6 deletions python/BioSimSpace/_SireWrappers/_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@
Utilities.
"""

# A set of protein residues. Taken from MDAnalysis.
_prot_res = {
# A list of protein residues. Taken from MDAnalysis.
_prot_res = [
# CHARMM top_all27_prot_lipid.rtf
"ALA",
"ARG",
Expand Down Expand Up @@ -135,10 +135,10 @@
"CMET",
"CME",
"ASF",
}
]

# A set of nucleic acid residues. Taken from MDAnalysis.
_nucl_res = {
# A list of nucleic acid residues. Taken from MDAnalysis.
_nucl_res = [
"ADE",
"URA",
"CYT",
Expand Down Expand Up @@ -173,7 +173,7 @@
"RU3",
"RG3",
"RC3",
}
]

# A list of ion elements.
_ions = [
Expand Down