def testFunctionAddStructNewModel(self):
pdbID1 = '1P30' # A
pdbID2 = '1CJD' # A, B,C
outFile = "/tmp/model.cif"
aSH1 = emconv.AtomicStructHandler()
aSH2 = emconv.AtomicStructHandler()
#
fileName1 = aSH1.readFromPDBDatabase(pdbID1, type='mmCif', dir='/tmp')
fileName2 = aSH2.readFromPDBDatabase(pdbID2, type='mmCif', dir='/tmp')
aSH1.read(fileName1)
aSH2.read(fileName2)
atomsNum1 = len([atom.id for atom in aSH1.getStructure().get_atoms()])
atomsNum2 = len([atom.id for atom in aSH2.getStructure().get_atoms()])
#
aSH1.addStruct(fileName2, outPDBfileName=outFile, useModel=True)
#
# aSH1.addStruct(fileName2, outPDBfileName=outFile, useModel=False)
chains = [chain.id for chain in aSH1.getStructure().get_chains()]
# compare unordered lists of chains
goal = ['A', 'A', 'B', 'C']
self.assertTrue(
Counter(chains) == Counter(goal), "{} != {}".format(chains, goal))
atomsNumT = len([atom.id for atom in aSH1.getStructure().get_atoms()])
self.assertEqual(atomsNum1 + atomsNum2, atomsNumT)
os.unlink(fileName1)
os.unlink(fileName2)
os.unlink(outFile)
def testFunctionAddStructNoNewModelAddTwice(self):
""" add two atomic structures with overlaping chain ids, last atomic
structure is added two times"""
pdbID1 = '1P30' # A,
pdbID2 = '1CJD' # A, B, C
outFile = "/tmp/nomodel.cif" # A, A002, B, C, A003, B002, C002
aSH1 = emconv.AtomicStructHandler()
aSH2 = emconv.AtomicStructHandler()
#
fileName1 = aSH1.readFromPDBDatabase(pdbID1, type='mmCif', dir='/tmp')
fileName2 = aSH2.readFromPDBDatabase(pdbID2, type='mmCif', dir='/tmp')
aSH1.read(fileName1)
aSH2.read(fileName2)
atomsNum1 = len([atom.id for atom in aSH1.getStructure().get_atoms()])
atomsNum2 = len([atom.id for atom in aSH2.getStructure().get_atoms()])
#
aSH1.addStruct(fileName2, outPDBfileName=outFile, useModel=False)
aSH1.addStruct(fileName2, outPDBfileName=outFile, useModel=False)
chains = [chain.id for chain in aSH1.getStructure().get_chains()]
# compare unordered lists of chains
goal = ['A', 'A002', 'B', 'C', 'A003', 'B002', 'C002']
self.assertTrue(
Counter(chains) == Counter(goal), "{} != {}".format(chains, goal))
atomsNumT = len([atom.id for atom in aSH1.getStructure().get_atoms()])
self.assertEqual(atomsNum1 + atomsNum2 + atomsNum2, atomsNumT)
os.unlink(fileName1)
os.unlink(fileName2)
os.unlink(outFile)
def testPDBToCIF(self):
aSH1 = emconv.AtomicStructHandler(self.PDBFileName)
CIFFileName2 = self.CIFFileName.replace(".cif", "_2.cif")
aSH1.write(CIFFileName2)
aSH2 = emconv.AtomicStructHandler(CIFFileName2)
structure1 = aSH1.getStructure()
structure2 = aSH2.getStructure()
for atom1, atom2 in zip(structure1.get_atoms(),
structure2.get_atoms()):
self.assertEqual(atom1.get_name(), atom2.get_name())
os.unlink(CIFFileName2)
def testWritePDB(self):
aSH = emconv.AtomicStructHandler(self.PDBFileName)
PDBFileName2 = self.PDBFileName.replace(".pdb", "_2.pdb")
aSH._write(PDBFileName2)
aSH2 = emconv.AtomicStructHandler(PDBFileName2)
structure1 = aSH.getStructure()
structure2 = aSH2.getStructure()
for atom1, atom2 in zip(structure1.get_atoms(),
structure2.get_atoms()):
self.assertEqual(atom1.get_name(), atom2.get_name())
os.unlink(PDBFileName2)
def testCenterOfMass(self):
aSH = emconv.AtomicStructHandler()
structure = aSH.read(self.CIFFileName)
x, y, z = aSH.centerOfMass(structure)
self.assertAlmostEqual(x, 8.1593891597, 2)
self.assertAlmostEqual(y, 21.1833304818, 2)
self.assertAlmostEqual(z, 20.0177924407, 2)
def getModelsChainsStep(cls, protocol):
""" Returns (1) list with the information
{"model": %d, "chain": "%s", "residues": %d} (modelsLength)
(2) list with residues, postion and chain (modelsFirstResidue)"""
structureHandler = emconv.AtomicStructHandler()
fileName = ""
if hasattr(protocol, 'pdbId'):
if protocol.pdbId.get() is not None:
pdbID = protocol.pdbId.get()
url = "https://www.rcsb.org/structure/"
URL = url + ("%s" % pdbID)
try:
response = requests.get(URL)
except:
raise Exception("Cannot connect to PDB server")
if (response.status_code >= 400) and (response.status_code <
500):
raise Exception("%s is a wrong PDB ID" % pdbID)
fileName = structureHandler.readFromPDBDatabase(
os.path.basename(pdbID), dir="/tmp/")
else:
fileName = protocol.pdbFile.get()
else:
if protocol.pdbFileToBeRefined.get() is not None:
fileName = os.path.abspath(
protocol.pdbFileToBeRefined.get().getFileName())
structureHandler.read(fileName)
structureHandler.getStructure()
# listOfChains, listOfResidues = structureHandler.getModelsChains()
return structureHandler.getModelsChains()
def testReadFromPDBDatabase(self):
PDBID = '6CUD'
aSH = emconv.AtomicStructHandler()
# EMD-7620
fileName = aSH.readFromPDBDatabase(PDBID, type='pdb', dir='/tmp')
self.assertTrue(os.path.exists(fileName))
os.unlink(fileName)
def pdbDownloadStep(self):
"""Download all pdb files in file_list and unzip them.
"""
aSH = emconv.AtomicStructHandler()
print("retrieving atomic structure with ID = %s" % self.pdbId.get())
atomStructPath = aSH.readFromPDBDatabase(self.pdbId.get(),
type='mmCif',
dir=self._getExtraPath())
self.createOutputStep(atomStructPath)
def testRenameToChains(self):
aSH = emconv.AtomicStructHandler(self.PDBFileName)
structure = aSH.getStructure()
model = structure[0]
chain = model['B']
chain.id = 'CC'
aSH.renameChains(structure)
for chain in structure.get_chains():
self.assertEqual(chain.id, 'C')
def testIntToChain(self):
aSH = emconv.AtomicStructHandler(self.PDBFileName)
solString = [
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M',
'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z',
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'a', 'b', 'c',
'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o', 'p',
'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', "AA"
]
for i in range(63):
self.assertEqual(solString[i], aSH._intToChain(i))
def pdbDownloadStep(self):
"""Download all pdb files in file_list and unzip them.
"""
aSH = emconv.AtomicStructHandler()
ASPaths = []
for pdbId in self.pdbIds.get().split(','):
print("retrieving atomic structure with ID = %s" % pdbId)
ASPaths.append(
aSH.readFromPDBDatabase(pdbId.strip(),
type='mmCif',
dir=self._getExtraPath()))
self.createOutputStep(ASPaths)
def testFunctionSelectChain(self):
pdbID1 = '1P30' # A,B,C
outFile = "/tmp/model.cif"
aSH1 = emconv.AtomicStructHandler()
aSH2 = emconv.AtomicStructHandler()
#
fileName1 = aSH1.readFromPDBDatabase(pdbID1, type='mmCif', dir='/tmp')
aSH1.read(fileName1)
atomsNum1 = len([atom.id for atom in aSH1.getStructure().get_atoms()])
#
chainID = 'A'
outFileName = "/tmp/output.mmcif"
aSH1.extractChain(chainID=chainID,
modelID='0',
end=20,
filename=outFileName)
chains = [chain.id for chain in aSH1.getStructure().get_chains()]
# compare unordered lists of chains
goal = chainID
self.assertTrue(
Counter(chains) == Counter(goal), "{} != {}".format(chains, goal))
aSH2.read(outFileName)
atomsNumT = len([atom.id for atom in aSH2.getStructure().get_atoms()])
self.assertEqual(122, atomsNumT)
def testTransformTranslation(self):
aSHSource = emconv.AtomicStructHandler(self.PDBFileName)
structure = aSHSource.getStructure()
structure_copy = deepcopy(aSHSource.getStructure())
shift = [100., 50., 25.]
# rotation_matrix = euler_matrix(deg2rad(45.), 0., 0., 'szyz')
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(shift)
M = emconv.concatenate_matrices(rotation_matrix, translation)
aSHSource.transform(M)
for atom1, atom2 in zip(structure.get_atoms(),
structure_copy.get_atoms()):
coord1 = atom1.get_coord()
coord2 = [sum(x) for x in zip(atom2.get_coord(), shift)]
for i in range(3):
self.assertAlmostEqual(coord1[i], coord2[i], 2)
def testTransformRotation(self):
aSHSource = emconv.AtomicStructHandler(self.PDBFileName)
structure = aSHSource.getStructure()
structure_copy = deepcopy(structure)
rot = np.deg2rad(10)
theta = np.deg2rad(20.)
psi = np.deg2rad(30.)
rotation_matrix = emconv.euler_matrix(rot, theta, psi, 'szyz')
translation = emconv.translation_matrix([0., 0., 0.])
M = emconv.concatenate_matrices(rotation_matrix, translation)
aSHSource.transform(M)
m = M[:3, :3]
for atom1, atom2 in zip(structure.get_atoms(),
structure_copy.get_atoms()):
coord1 = atom1.get_coord()
coord2 = m.dot(atom2.get_coord())
for i in range(3):
self.assertAlmostEqual(coord1[i], coord2[i], 2)
def testReadCIF(self):
aSH = emconv.AtomicStructHandler(self.CIFFileName)
structure = aSH.getStructure()
solList = ['N', 'CA', 'C', 'O', 'CB']
counter = 0
for atom in structure.get_atoms():
self.assertEqual(solList[counter], atom.get_name())
counter += 1
solDict = {}
solDict['_exptl.method'] = 'x-ray diffraction'
solDict['_struct_keywords.pdbx_keywords'] = 'extracellular matrix'
solDict['_struct.title'] = 'x-ray crystallographic determination ' \
'of a collagen-like peptide with the ' \
'repeating sequence (pro-pro-gly)'
_dict = aSH.readLowLevel(self.CIFFileName)
for k, v in solDict.items():
self.assertEqual(_dict[k][0].strip().lower(), v.lower())
def testReadPDB(self):
aSH = emconv.AtomicStructHandler(self.PDBFileName)
structure = aSH.getStructure()
solDict = {}
solDict['structure_method'] = 'x-ray diffraction'
solDict['head'] = 'extracellular matrix'
solDict['name'] = 'x-ray crystallographic determination ' \
'of a collagen-like peptide with the ' \
'repeating sequence (pro-pro-gly)'
solDict['author'] = 'R.Z.Kramer,L.Vitagliano,J.Bella,R.Berisio,' \
'L.Mazzarella,B.Brodsky,A.Zagari,H.M.Berman'
solDict['deposition_date'] = '1998-01-22'
for k, v in solDict.items():
self.assertEqual(structure.header[k].strip(), v)
solList = ['N', 'CA', 'C', 'O', 'CB']
counter = 0
for atom in structure.get_atoms():
self.assertEqual(solList[counter], atom.get_name())
counter += 1
def testTransformTranslationCoherence(self):
"""
Question: If I transform the PDB and the 3D map with matrix T
do they move in the same direction?
I do not know how to make an automatic test to check this
The following code perform all operations but check that
the PDB and 3D map match. This should be check using
your eye.
change False to True (in the following if) to
perform all or some of the checks
"""
# retrieve "Structure of the human TRPC3
# both 3Dmap and PDB
doTest = False
if not doTest:
print(
"This test is to be tested manually since it opens chimera afterwards"
)
print("For testing this, edit this file and set doTest = True")
return
PDBID = '6CUD'
EMDBID = '7620'
doAll = False
if False or doAll: # set to False if you aready have the 3dmap file
url = 'ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-%s/map/emd_%s.map.gz' % \
(EMDBID, EMDBID)
urlretrieve(url, 'emd_%s.map.gz' % EMDBID)
os.system("gunzip emd_%s.map.gz" % EMDBID) # file is gzipped
if False or doAll: # set to False if you aready have the PDB file
aSH = emconv.AtomicStructHandler()
pdbFileName = aSH.readFromPDBDatabase(PDBID,
type='pdb',
dir=os.getcwd())
else:
pdbFileName = 'pdb%s.ent' % PDBID.lower()
# get 3D map sampling
from pwem.convert.headers import Ccp4Header
header = Ccp4Header("emd_%s.map" % EMDBID, readHeader=True)
sampling, y, z = header.getSampling()
def __runXmippProgram(program, args):
""" Internal function to launch a Xmipp program. """
from pwem import Domain
xmipp3 = Domain.importFromPlugin('xmipp3', doRaise=True)
xmipp3.runXmippProgram(program, args)
def __getXmippEulerAngles(matrix):
""" Internal fuction to convert scipion to xmipp angles"""
from pwem import Domain
geometryFromMatrix = Domain.importFromPlugin('xmipp3.convert',
'geometryFromMatrix',
doRaise=True)
return geometryFromMatrix(matrix, False)
def __applyTransform(suffix, pdbFileName, shift, angles, sampling):
""" auxiliary function, transform PDB and 3dmap files"""
# create a Scipion transformation matrix
from numpy import deg2rad
rotation_matrix = emconv.euler_matrix(deg2rad(angles[0]),
deg2rad(angles[1]),
deg2rad(angles[2]), 'szyz')
translation = emconv.translation_matrix(shift)
M = emconv.concatenate_matrices(rotation_matrix, translation)
# apply it to the pdb file
# if rotation move to center
aSH = emconv.AtomicStructHandler(pdbFileName)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
ih = ImageHandler()
x, y, z, n = ih.getDimensions("emd_%s.map" % EMDBID)
x /= 2.
y /= 2.
z /= 2.
localShift = [-x, -y, -z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.concatenate_matrices(rotation_matrix,
translation)
aSH.transform(localM, sampling=sampling)
aSH.transform(M, sampling=sampling)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
localShift = [x, y, z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.concatenate_matrices(rotation_matrix,
translation)
aSH.transform(localM, sampling=sampling)
aSH.write("%s_%s_transformed.ent" % (suffix, PDBID.lower()))
# get equivalent xmipp transformation
shift, angles = __getXmippEulerAngles(M)
# shift 3map and set sampling
__runXmippProgram(
"xmipp_transform_geometry", '-i emd_%s.map '
'-o %s_emd_%s_transform.map '
'--interp linear '
'--shift %f %f %f '
'--rotate_volume euler %f %f %f ' %
(EMDBID, suffix, EMDBID, shift[0], shift[1], shift[2],
angles[0], angles[1], angles[2]))
header = Ccp4Header("%s_emd_%s_transform.map" % (suffix, EMDBID),
readHeader=True)
header.setSampling(sampling)
# put the sampling back, xmipp_transform_geometry erased it
header.writeHeader()
# view the results with chimera
from pwem.viewers import Chimera
args = "%s %s %s %s" % (
pdbFileName, "emd_%s.map" % EMDBID, "%s_%s_transformed.ent" %
(suffix, PDBID.lower()), "%s_emd_%s_transform.map" %
(suffix, EMDBID))
Chimera.runProgram(args)
# shift atomic structure
doAll = True
if False or doAll:
shift = [20., 0., 0.]
angles = [0., 0., 0.]
__applyTransform("Xshift", pdbFileName, shift, angles, sampling)
# repeat test this time rotation one angle
# problem, xmipp rotates with respect the volume center
# pdb with respect the origin of coordinates (much better convention)
# in order to compare both I need to
# move pdb to origin, rotate it, put it back in the possition
if False or doAll:
shift = [0., 0., 0.]
angles = [30., 0., 0.]
__applyTransform("Rot2D", pdbFileName, shift, angles, sampling)
# repeat test this time rotation in 3 angles
# problem, xmipp rotates with respect the volume center
# pdb with respect the origin of coordinates (much better convention)
if False or doAll:
shift = [0., 0., 0.]
angles = [10., 20., 30.]
__applyTransform("Rot3D", pdbFileName, shift, angles, sampling)
# repeat test this time rotation in 3 angles and shift
# problem, xmipp rotates with respect the volume center
# pdb with respect the origin of coordinates (much better convention)
if False or doAll:
shift = [5., 10., 15.]
angles = [10., 20., 30.]
__applyTransform("Rot3DShift", pdbFileName, shift, angles,
sampling)
def __applyTransform(suffix, pdbFileName, shift, angles, sampling):
""" auxiliary function, transform PDB and 3dmap files"""
# create a Scipion transformation matrix
from numpy import deg2rad
rotation_matrix = emconv.euler_matrix(deg2rad(angles[0]),
deg2rad(angles[1]),
deg2rad(angles[2]), 'szyz')
translation = emconv.translation_matrix(shift)
M = emconv.concatenate_matrices(rotation_matrix, translation)
# apply it to the pdb file
# if rotation move to center
aSH = emconv.AtomicStructHandler(pdbFileName)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
ih = ImageHandler()
x, y, z, n = ih.getDimensions("emd_%s.map" % EMDBID)
x /= 2.
y /= 2.
z /= 2.
localShift = [-x, -y, -z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.concatenate_matrices(rotation_matrix,
translation)
aSH.transform(localM, sampling=sampling)
aSH.transform(M, sampling=sampling)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
localShift = [x, y, z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.concatenate_matrices(rotation_matrix,
translation)
aSH.transform(localM, sampling=sampling)
aSH.write("%s_%s_transformed.ent" % (suffix, PDBID.lower()))
# get equivalent xmipp transformation
shift, angles = __getXmippEulerAngles(M)
# shift 3map and set sampling
__runXmippProgram(
"xmipp_transform_geometry", '-i emd_%s.map '
'-o %s_emd_%s_transform.map '
'--interp linear '
'--shift %f %f %f '
'--rotate_volume euler %f %f %f ' %
(EMDBID, suffix, EMDBID, shift[0], shift[1], shift[2],
angles[0], angles[1], angles[2]))
header = Ccp4Header("%s_emd_%s_transform.map" % (suffix, EMDBID),
readHeader=True)
header.setSampling(sampling)
# put the sampling back, xmipp_transform_geometry erased it
header.writeHeader()
# view the results with chimera
from pwem.viewers import Chimera
args = "%s %s %s %s" % (
pdbFileName, "emd_%s.map" % EMDBID, "%s_%s_transformed.ent" %
(suffix, PDBID.lower()), "%s_emd_%s_transform.map" %
(suffix, EMDBID))
Chimera.runProgram(args)
