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pdbfixer
Commit 33d2d841 by Kyle Beauchamp
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Add hydrogens afterward in examples and tests.

parent 68e6c01f
Showing with 5 additions and 0 deletions
pdbfixer/pdbfixer.py
...@@ -579,6 +579,7 @@ class PDBFixer(object): ...@@ -579,6 +579,7 @@ class PDBFixer(object):
>>> fixer = PDBFixer(pdbid='1VII') >>> fixer = PDBFixer(pdbid='1VII')
>>> fixer.applyMutations(["ALA-16-GLY"]) >>> fixer.applyMutations(["ALA-16-GLY"])
>>> fixer.addMissingHydrogens(7.0)
""" """
......
tests/test_mutate.py
...@@ -6,18 +6,21 @@ import tempfile ...@@ -6,18 +6,21 @@ import tempfile
def test_mutate_1(): def test_mutate_1():
fixer = pdbfixer.PDBFixer(pdbid='1VII') fixer = pdbfixer.PDBFixer(pdbid='1VII')
fixer.applyMutations(["ALA-16-GLY"]) fixer.applyMutations(["ALA-16-GLY"])
fixer.addMissingHydrogens(7.0)
app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile()) app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
def test_mutate_2(): def test_mutate_2():
fixer = pdbfixer.PDBFixer(pdbid='1VII') fixer = pdbfixer.PDBFixer(pdbid='1VII')
fixer.applyMutations(["ALA-16-GLY", "SER-15-ALA"]) fixer.applyMutations(["ALA-16-GLY", "SER-15-ALA"])
fixer.addMissingHydrogens(7.0)
app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile()) app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
@raises(ValueError) @raises(ValueError)
def test_mutate_3_fails(): def test_mutate_3_fails():
fixer = pdbfixer.PDBFixer(pdbid='1VII') fixer = pdbfixer.PDBFixer(pdbid='1VII')
fixer.applyMutations(["ALA-15-GLY", "SER-15-ALA"]) fixer.applyMutations(["ALA-15-GLY", "SER-15-ALA"])
fixer.addMissingHydrogens(7.0)
app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile()) app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
...@@ -25,4 +28,5 @@ def test_mutate_3_fails(): ...@@ -25,4 +28,5 @@ def test_mutate_3_fails():
def test_mutate_4_fails(): def test_mutate_4_fails():
fixer = pdbfixer.PDBFixer(pdbid='1VII') fixer = pdbfixer.PDBFixer(pdbid='1VII')
fixer.applyMutations(["ALA-16-WTF", "SER-15-ALA"]) fixer.applyMutations(["ALA-16-WTF", "SER-15-ALA"])
fixer.addMissingHydrogens(7.0)
app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile()) app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
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