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Unverified Commit 65a1f936 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2079 from peastman/altloc 

Handle PDB files with altlocs correctly
parents 553a96bf d11c2f67
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Showing with 66 additions and 2 deletions
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ 65a1f936
...@@ -111,7 +111,7 @@ class PDBFile(object): ...@@ -111,7 +111,7 @@ class PDBFile(object):
atomReplacements = PDBFile._atomNameReplacements[resName] atomReplacements = PDBFile._atomNameReplacements[resName]
else: else:
atomReplacements = {} atomReplacements = {}
for atom in residue.atoms: for atom in residue.iter_atoms():
atomName = atom.get_name() atomName = atom.get_name()
if atomName in atomReplacements: if atomName in atomReplacements:
atomName = atomReplacements[atomName] atomName = atomReplacements[atomName]
...@@ -153,7 +153,7 @@ class PDBFile(object): ...@@ -153,7 +153,7 @@ class PDBFile(object):
coords = [] coords = []
for chain in model.iter_chains(): for chain in model.iter_chains():
for residue in chain.iter_residues(): for residue in chain.iter_residues():
for atom in residue.atoms: for atom in residue.iter_atoms():
pos = atom.get_position().value_in_unit(nanometers) pos = atom.get_position().value_in_unit(nanometers)
coords.append(Vec3(pos[0], pos[1], pos[2])) coords.append(Vec3(pos[0], pos[1], pos[2]))
self._positions.append(coords*nanometers) self._positions.append(coords*nanometers)
......
wrappers/python/tests/TestPdbFile.py
View file @ 65a1f936
...@@ -84,6 +84,13 @@ class TestPdbFile(unittest.TestCase): ...@@ -84,6 +84,13 @@ class TestPdbFile(unittest.TestCase):
if atom.index > 2: if atom.index > 2:
self.assertEqual(None, atom.element) self.assertEqual(None, atom.element)
def test_AltLocs(self):
"""Test reading a file that includes AltLocs"""
pdb = PDBFile('systems/altlocs.pdb')
self.assertEqual(1, pdb.topology.getNumResidues())
self.assertEqual(19, pdb.topology.getNumAtoms())
self.assertEqual(19, len(pdb.positions))
self.assertEqual('ILE', list(pdb.topology.residues())[0].name)
def assertVecAlmostEqual(self, p1, p2, tol=1e-7): def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
unit = p1.unit unit = p1.unit
......
wrappers/python/tests/systems/altlocs.pdb 0 → 100644
View file @ 65a1f936
ATOM 415 N AILE A 25 4.377 15.265 1.447 0.20 2.82 N
ATOM 416 N BILE A 25 4.377 15.265 1.447 0.20 2.82 N
ATOM 417 CA AILE A 25 3.033 14.786 1.800 0.20 2.71 C
ATOM 418 CA BILE A 25 3.033 14.786 1.800 0.20 2.71 C
ATOM 419 C AILE A 25 3.077 13.514 2.641 0.20 2.38 C
ATOM 420 C BILE A 25 3.077 13.514 2.641 0.20 2.38 C
ATOM 421 O AILE A 25 2.310 13.367 3.581 0.20 2.92 O
ATOM 422 O BILE A 25 2.310 13.367 3.581 0.20 2.92 O
ATOM 423 CB AILE A 25 2.186 14.577 0.518 0.20 2.90 C
ATOM 424 CB BILE A 25 2.186 14.577 0.518 0.20 2.90 C
ATOM 425 CG1AILE A 25 1.658 15.855 -0.086 0.20 2.48 C
ATOM 426 CG1BILE A 25 1.658 15.855 -0.086 0.20 2.48 C
ATOM 427 CG2AILE A 25 0.962 13.694 0.784 0.20 4.13 C
ATOM 428 CG2BILE A 25 0.962 13.694 0.784 0.20 4.13 C
ATOM 429 CD1AILE A 25 0.623 16.572 0.761 0.20 4.11 C
ATOM 430 CD1BILE A 25 1.222 15.717 -1.500 0.20 5.09 C
ATOM 431 H AILE A 25 4.728 15.070 0.644 0.20 1.70 H
ATOM 432 H BILE A 25 4.728 15.070 0.644 0.20 1.70 H
ATOM 433 HA AILE A 25 2.573 15.480 2.312 0.20 2.56 H
ATOM 434 HA BILE A 25 2.573 15.480 2.312 0.20 2.56 H
ATOM 435 HB AILE A 25 2.769 14.106 -0.118 0.20 3.37 H
ATOM 436 HB BILE A 25 2.769 14.106 -0.118 0.20 3.37 H
ATOM 437 HG12AILE A 25 2.432 16.460 -0.225 0.20 2.73 H
ATOM 438 HG12BILE A 25 1.075 16.325 0.437 0.20 3.30 H
ATOM 439 HG13AILE A 25 1.243 15.658 -0.968 0.20 2.96 H
ATOM 440 HG13BILE A 25 2.432 16.460 -0.225 0.20 2.73 H
ATOM 441 HG21AILE A 25 0.423 14.095 1.506 0.20 3.33 H
ATOM 442 HG21BILE A 25 0.423 14.095 1.506 0.20 3.33 H
ATOM 443 HG22AILE A 25 0.451 13.622 -0.059 0.20 3.57 H
ATOM 444 HG22BILE A 25 0.451 13.622 -0.059 0.20 3.57 H
ATOM 445 HG23AILE A 25 1.278 12.796 1.059 0.20 3.60 H
ATOM 446 HG23BILE A 25 1.278 12.796 1.059 0.20 3.60 H
ATOM 447 HD11AILE A 25 0.989 16.789 1.668 0.20 3.14 H
ATOM 448 HD11BILE A 25 0.515 15.030 -1.466 0.20 4.69 H
ATOM 449 HD12AILE A 25 0.344 17.402 0.282 0.20 3.79 H
ATOM 450 HD12BILE A 25 0.829 16.587 -1.836 0.20 4.59 H
ATOM 451 HD13AILE A 25 -0.170 15.974 0.843 0.20 2.83 H
ATOM 452 HD13BILE A 25 1.946 15.436 -2.128 0.20 4.44 H
ATOM 453 N CLEU A 25 4.377 15.265 1.447 0.60 2.82 N
ATOM 454 CA CLEU A 25 3.033 14.786 1.800 0.60 2.71 C
ATOM 455 C CLEU A 25 3.077 13.514 2.641 0.60 2.38 C
ATOM 456 O CLEU A 25 2.310 13.367 3.581 0.60 2.92 O
ATOM 457 CB CLEU A 25 2.186 14.577 0.518 0.60 2.90 C
ATOM 458 CG CLEU A 25 1.814 15.965 -0.117 0.60 4.43 C
ATOM 459 CD1CLEU A 25 1.222 15.717 -1.500 0.60 5.09 C
ATOM 460 CD2CLEU A 25 0.623 16.572 0.761 0.60 4.11 C
ATOM 461 H CLEU A 25 4.728 15.070 0.644 0.60 1.70 H
ATOM 462 HA CLEU A 25 2.573 15.480 2.312 0.60 2.56 H
ATOM 463 HB2CLEU A 25 2.832 14.186 -0.175 0.60 3.74 H
ATOM 464 HB3CLEU A 25 1.312 14.093 0.720 0.60 3.27 H
ATOM 465 HG CLEU A 25 2.617 16.584 -0.248 0.60 2.73 H
ATOM 466 HD11CLEU A 25 0.515 15.030 -1.466 0.60 4.69 H
ATOM 467 HD12CLEU A 25 0.829 16.587 -1.836 0.60 4.59 H
ATOM 468 HD13CLEU A 25 1.946 15.436 -2.128 0.60 4.44 H
ATOM 469 HD21CLEU A 25 -0.170 15.974 0.843 0.60 2.83 H
ATOM 470 HD22CLEU A 25 0.989 16.789 1.668 0.60 3.14 H
ATOM 471 HD23CLEU A 25 0.344 17.402 0.282 0.60 3.79 H
\ No newline at end of file
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