class QueueConfig(OrderedObject):
def __init__(self, **kwargs):
OrderedObject.__init__(self, **kwargs)
self.name = String('default')
self.maxCores = Integer()
self.allowMPI = Boolean()
self.allowThreads = Boolean()
self.maxHours = Integer()
def getName(self):
return self.name.get()
def getMaxCores(self):
return self.maxCores.get()
def getAllowMPI(self):
return self.allowMPI.get()
def getAllowThreads(self):
return self.allowThreads.get()
def getMaxHours(self):
return self.maxHours.get()
def setName(self, name):
self.name.set(name)
def setMaxCores(self, maxCores):
self.maxCores.set(maxCores)
def setAllowMPI(self, allowMPI):
self.allowMPI.set(allowMPI)
def setAllowThreads(self, allowThreads):
self.allowThreads.set(allowThreads)
def setMaxHours(self, maxHours):
self.maxHours.set(maxHours)
projName = sys.argv[1]
manager = Manager()
project = manager.loadProject(projName)
if project is None:
usage("Project '%s' does not exist in: \n %s" % (projName, projectsDir))
setReadOnly = False
setLifeTime = False
for arg in sys.argv:
if arg.startswith('readOnly='):
setReadOnly = True
value = arg.split('readOnly=')[1]
b = Boolean(value=value)
readOnlyValue = b.get()
elif arg.startswith('lifeTime='):
setLifeTime = True
value = arg.split('lifeTime=')[1]
lifeTimeValue = None if value == 'None' else int(value)
if setReadOnly:
project.setReadOnly(readOnlyValue)
if setLifeTime:
project.settings.setLifeTime(lifeTimeValue)
if setReadOnly or setLifeTime:
# Truly write settings
project.settings.write()
class ChimeraProtContacts(EMProtocol):
"""Identifies interatomic clashes and contacts based on van der Waals radii
"""
_label = 'contacts'
_program = ""
commandDropView = """DROP view IF EXISTS {viewName}"""
TetrahedralOrientation = ['222', 'z3']
@classmethod
def getClassPackageName(cls):
return "chimerax"
def __init__(self, **args):
EMProtocol.__init__(self, **args)
self.SYMMETRY = Boolean(True)
def _defineParams(self, form):
form.addSection(label='Input')
# pdbFileToBeRefined name is needed by the wizard. Do not change it
form.addParam('pdbFileToBeRefined',
PointerParam,
pointerClass="AtomStruct",
label='Atomic Structure:',
allowsNull=True,
important=True,
help="Input atomic structure.")
form.addParam(
'chainStructure',
StringParam,
default="",
label='Chain Labeling',
help="Dictionary that maps chains to labels.\n"
"Example: {'A':'h1', 'B':'h1', 'E':'h2'}\n"
"Contacts are calculated between two chains with distinct "
"labels. Two chains with the same label are considered as "
"a group. Contacts will be computed between any chain included "
"in this group and any other group/chain. However, no contacts "
"among members of the group will be calculated.")
form.addParam(
'applySymmetry',
BooleanParam,
label="Apply symmetry:",
default=True,
help=
"'Symmetry = Yes' indicates that symmetry will be applied, and then"
" contacts will be computed between any two chains of the "
"atomic structure (the unit cell) "
"and between a chain of the unit cell and another chain of a "
"neigbour unit cell. Output results will show only non "
"redundant contatcs, i.e., contacts than you can infer by"
" symmetry will not be shown.\n'Symmetry = No' indicates that "
"symmetry will not be applied, and then "
"contacts will only be calculated between chains within the "
"atomic structure. Output results will show all contacts between"
" any couple of interacting chains.\n")
form.addParam(
'symmetryGroup',
EnumParam,
choices=CHIMERA_LIST,
default=CHIMERA_I222,
label="Symmetry",
condition='applySymmetry',
help=
"https://scipion-em.github.io/docs/release-2.0.0/docs/developer/symmetries.html?highlight=symmetry"
"Symmetry for a description of the symmetry groups "
"format in CHIMERA.\n"
"If no symmetry is present, use _c1_."
'More information: \n'
'https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html'
)
form.addParam('symmetryOrder',
IntParam,
default=1,
condition='applySymmetry and symmetryGroup<=%d' %
SYM_DIHEDRAL_X,
label='Symmetry Order',
help='Select the order of cyclic or dihedral symmetry.')
group = form.addGroup('Fit params for clashes and contacts')
group.addParam(
'cutoff',
FloatParam,
label="cutoff (Angstroms): ",
default=-0.4,
expertLevel=LEVEL_ADVANCED,
help="Large positive cutoff identifies the more severe clashes, "
"whereas negative cutoff indicates favorable contacts:\n"
"default contact rule: -0.4 (from 0.0 to -1.0)\n"
"default clash rule: 0.6 (from 0.4 to 1.0)\n"
'More information: \n'
'https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/findclash.html'
)
group.addParam(
'allowance',
FloatParam,
label="allowance (Angstroms): ",
default=0.0,
expertLevel=LEVEL_ADVANCED,
help="default contact rule: 0.0\n"
"default clash rule: 0.4\n"
'More information: \n'
'https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/findclash.html'
)
form.addLine('')
# --------------------------- INSERT steps functions --------------------
def _insertAllSteps(self):
self.sym = CHIMERA_SYM_NAME[self.symmetryGroup.get()]
self.symOrder = self.symmetryOrder.get()
if not self.applySymmetry:
self.sym = "Cn"
self.symOrder = 1
self.SYMMETRY = Boolean(False)
elif (self.sym == "Cn" or self.sym == "Dn") and self.symOrder == 1:
self.SYMMETRY = Boolean(False)
# connect to database, delete table and recreate it
# execute chimera findclash
self._insertFunctionStep('chimeraClashesStep')
self._insertFunctionStep('postProcessStep')
self._store()
def postProcessStep(self):
c, conn = connectDB(self.getDataBaseName(), None)
self.removeDuplicates(c)
def chimeraClashesStep(self):
labelDictAux = json.loads(self.chainStructure.get(),
object_pairs_hook=collections.OrderedDict)
labelDict = collections.OrderedDict(
sorted(labelDictAux.items(), key=itemgetter(1)))
# labelDict = collections.OrderedDict(sorted(list(labelDictAux.items()), key=itemgetter(1)))
pdbFileName = os.path.abspath(
self.pdbFileToBeRefined.get().getFileName())
# first element of dictionary
firstValue = labelDict[list(labelDict)[0]]
outFiles = []
f = open(self.getChimeraScriptFileName1(), "w")
f.write("from chimerax.core.commands import run\n")
f.write("run(session, 'open {}')\n".format(pdbFileName))
if self.sym == "Cn" and self.symOrder != 1:
f.write("run(session,'sym #1 C%d copies t')\n" % self.symOrder)
elif self.sym == "Dn" and self.symOrder != 1:
f.write("run(session,'sym #1 d%d copies t')\n" % self.symOrder)
elif self.sym == "T222" or self.sym == "TZ3":
f.write("run(session,'sym #1 t,%s copies t')\n" % self.sym[1:])
elif self.sym == "O":
f.write("run(session,'sym #1 O copies t')\n")
elif self.sym == "I222" or self.sym == "I222r" or self.sym == "In25" or \
self.sym == "In25r" or self.sym == "I2n3" or self.sym == "I2n3r" or \
self.sym == "I2n5" or self.sym == "I2n5r":
f.write("run(session,'sym #1 i,%s copies t')\n" % self.sym[1:])
self.SYMMETRY = self.SYMMETRY.get()
if self.SYMMETRY:
f.write("run(session,'delete #2 & #1 #>3')\n")
f.write("run(session,'save {symmetrizedModelName} #2')\n".format(
symmetrizedModelName=self.getSymmetrizedModelName()))
f.write("run(session, 'close #1')\n")
f.write("run(session, 'rename #2 id #1')\n")
self.endChimeraScript(firstValue, labelDict, outFiles, f)
f.write("run(session, 'exit')\n")
f.close()
args = " --nogui --script " + self.getChimeraScriptFileName1()
self._log.info('Launching: ' + Plugin.getProgram() + ' ' + args)
Chimera.runProgram(Plugin.getProgram(), args)
if self.SYMMETRY and not os.path.exists(
self.getSymmetrizedModelName()):
# When self.SYMMETRY = TRUE and no one neighbor unit cell has not been
# generated at less than 3 Angstroms, probably because the symmetry
# center is not equal to the origin of coordinates, at least we have the
# contacts that are within the unit cell.
print(
red("Error: No neighbor unit cells are available. "
"Is the symmetry center equal to the origin of "
"coordinates?"))
self.SYMMETRY = False
f = open(self.getChimeraScriptFileName2(), "w")
f.write("from chimerax.core.commands import run\n")
f.write("session, run('open {}')\n".format(pdbFileName))
self.endChimeraScript(firstValue, labelDict, outFiles, f)
f.write("run(session, 'exit')\n")
f.close()
args = " --nogui --script " + self.getChimeraScriptFileName2()
self._log.info('Launching: ' + Plugin.getProgram() + ' ' + args)
Chimera.runProgram(Plugin.getProgram(), args)
# parse all files created by chimera
c, conn = self.prepareDataBase()
self.parseFiles(outFiles, c)
conn.commit()
conn.close()
# return outFiles
def prepareDataBase(self, drop=True):
if drop:
return connectDB(self.getDataBaseName(), self.getTableName())
else:
return connectDB(self.getDataBaseName())
def parseFiles(self, outFiles, c):
labelDictAux = json.loads(self.chainStructure.get(),
object_pairs_hook=collections.OrderedDict)
labelDict = collections.OrderedDict(
sorted(labelDictAux.items(), key=itemgetter(1)))
# labelDict = collections.OrderedDict(sorted(list(labelDictAux.items()), key=itemgetter(1)))
d = {}
d1 = {}
d2 = {}
anyResult = False
for inFile in outFiles:
print("processing file", inFile)
if not os.path.exists(inFile):
continue
else:
anyResult = True
counter = 0
# parse contact files. Note that C1 symmetry file is different from the rest
for line in open(inFile):
if counter < 8:
# print ("skip line", line
counter += 1
else:
# if not self.SYMMETRY:
if not self.SYMMETRY or line.split()[0].startswith("/"):
# Second option (line.split()[0].startswith("/") stands for
# cases in which the result of applying symmetry is identical
# to the starting structure (see test testContactsSymC2_b
# where after deleting the #2 submodel far more than 3 A from
# the input model, the resulting model is the same as the initial one.
info = line.split(
) # ['/A002', 'HEM', '1', 'ND', '/A', 'HIS', '87', 'NE2', '0.620', '2.660']
d1['modelId'] = "'" + "#1" + "'"
d1['aaName'] = "'" + info[1][0] + info[1][1:].lower(
) + "'" # 'Hem'
d1['aaNumber'] = info[2] # '1'
d1['chainId'] = "'" + info[0].split(
"/")[1] + "'" # 'A002'
d1['atomId'] = "'" + info[3] + "'" # 'ND'
d1['protId'] = "'" + labelDict[info[0].split("/")
[1]] + "'"
d2['modelId'] = "'" + "#1" + "'"
d2['aaName'] = "'" + info[5][0] + info[5][1:].lower(
) + "'" # 'His'
d2['aaNumber'] = info[6] # '87'
d2['chainId'] = "'" + info[4].split(
"/")[1] + "'" # 'A'
d2['protId'] = "'" + labelDict[info[4].split("/")
[1]] + "'"
d2['atomId'] = "'" + info[7] + "'" # 'NE2'
d['overlap'] = info[8] # '0.620'
d['distance'] = info[9] # '2.660'
else:
info = line.split()
# 5ni1_unit_cell_HEM.cif #1.2/A002 HEM 1 ND 5ni1_unit_cell_HEM.cif #1.2/A HIS 87 NE2 0.620 2.660
d1['modelId'] = "'" + info[1].split(
"/")[0] + "'" # '#1.2'
d1['aaName'] = "'" + info[2][0] + info[2][1:].lower(
) + "'" # 'Hem'
d1['aaNumber'] = info[3] # '1'
d1['chainId'] = "'" + info[1].split(
"/")[1] + "'" # 'A002'
d1['atomId'] = "'" + info[4] + "'" # 'ND'
d1['protId'] = "'" + labelDict[info[1].split("/")
[1]] + "'" # 'HEM_A'
d2['modelId'] = "'" + info[6].split(
"/")[0] + "'" # '#1.2'
d2['aaName'] = "'" + info[7][0] + info[7][1:].lower(
) + "'" # 'His'
d2['aaNumber'] = info[8] # '87'
d2['chainId'] = "'" + info[6].split("/")[1] + "'" # N
d2['protId'] = "'" + labelDict[info[6].split("/")
[1]] + "'" # 'chainA'
d2['atomId'] = "'" + info[9] + "'" # 'NE2'
d['overlap'] = info[10] # '0.620'
d['distance'] = info[11] # '2.660'
if d1['modelId'] == d2['modelId']:
if d1['protId'] <= d2['protId']:
for k in d1.keys():
# for k in list(d1.keys()):
d[k + '_1'] = d1[k]
d[k + '_2'] = d2[k]
else:
for k in d1.keys():
# for k in list(d1.keys()):
d[k + '_1'] = d2[k]
d[k + '_2'] = d1[k]
else:
if d1['modelId'] <= d2['modelId']:
for k in d1.keys():
# for k in list(d1.keys()):
d[k + '_1'] = d1[k]
d[k + '_2'] = d2[k]
else:
for k in d1.keys():
# for k in list(d1.keys()):
d[k + '_1'] = d2[k]
d[k + '_2'] = d1[k]
command = "INSERT INTO contacts "
keys = "("
values = " ("
for key, value in d.items():
keys += key + ", "
values += str(value) + ", "
keys = keys[:-2] + ")"
values = values[:-2] + ")"
command += keys + " VALUES " + values
# print(command)
c.execute(command)
return anyResult
# --------- util functions -----
def getDataBaseName(self):
return self._getExtraPath("overlaps.sqlite")
def getSymmetrizedModelName(self):
return os.path.abspath(self._getExtraPath("symModel.cif"))
# return self._getExtraPath("symModel.pdb")
def getTableName(self):
return "contacts"
def getView2Name(self):
return "view_ND_2"
def getView1Name(self):
return "view_ND_1"
def getChimeraScriptFileName1(self):
return os.path.abspath(self._getTmpPath("chimera1.cxc"))
def getChimeraScriptFileName2(self):
return os.path.abspath(self._getTmpPath("chimera2.cxc"))
def endChimeraScript(self, firstValue, labelDict, outFiles, f):
protId = firstValue
chains = ""
comma = ''
for k, v in labelDict.items():
if protId == v:
# chains += "{}/{}".format(comma, k)
chains += "{}{}".format(comma, k)
comma = ','
outFileBase = v
else:
outFile = os.path.abspath(
self._getExtraPath("{}.over".format(outFileBase)))
# outFile = self._getExtraPath("{}.over".format(outFileBase))
outFiles.append(outFile)
f.write(
"run(session,'echo {}')\nrun(session, 'contacts #1{} "
"intersubmodel true "
"intramol False "
"restrict any "
"saveFile {} overlapCutoff {} hbondAllowance {} namingStyle simple')\n"
.format(chains, chains, outFile, self.cutoff,
self.allowance))
protId = v
# chains = "/{}".format(k)
chains = "{}".format(k)
outFileBase = v
chains = "/" + chains.split("/")[-1]
outFile = os.path.abspath(
self._getExtraPath("{}.over".format(outFileBase)))
# outFile = self._getExtraPath("{}.over".format(outFileBase))
outFiles.append(outFile)
f.write(
"run(session,'echo {}')\nrun(session, 'contacts #1{} "
"intersubmodel true "
"intramol False "
"restrict any "
"savefile {} overlap {} hbond {} namingStyle simple')\n".format(
chains, chains, outFile, self.cutoff, self.allowance))
# f.write("run('save %s')\n" % os.path.abspath(self._getExtraPath(sessionFile)))
def removeDuplicates(self, c):
# Remove duplicate contacts
# that is, given chains A,B
# we have contact A-B and B-A
commandEliminateDuplicates = """CREATE VIEW {} AS
SELECT DISTINCT modelId_1,
protId_1,
chainId_1,
aaName_1,
aaNumber_1,
atomId_1,
modelId_2,
protId_2,
chainId_2,
aaName_2,
aaNumber_2,
atomId_2,
overlap,
distance
FROM {}
"""
commandEliminateDuplicates2 = """
CREATE VIEW {} AS
SELECT *
FROM {}
EXCEPT -- Each bound appears two times, delete one of them
SELECT ca.*
FROM {} ca, {} cb
WHERE
ca.protId_1 = cb.protId_2
AND cb.protId_1 = ca.protId_2
AND cb.chainId_1 = ca.chainId_2
AND ca.aaNumber_1 = cb.aaNumber_2
AND cb.aaNumber_1 = ca.aaNumber_2
AND ca.atomId_1 = cb.atomId_2
AND cb.atomId_1 = ca.atomId_2
AND ca.modelId_2 > cb.modelId_2
EXCEPT -- Interprotein bounds in the same model are not allowed
SELECT ca.*
FROM {} ca
WHERE ca.modelId_1 = ca.modelId_2
AND ca.protId_1 = ca.protId_2
"""
if self.SYMMETRY:
sqlCommand = """
SELECT count(*) FROM {} ca
WHERE ca.modelId_1 = '#1.1'
""".format(self.getTableName())
c.execute(sqlCommand)
row = c.fetchone()
if int(row[0]) == 0:
self.SYMMETRY = False
else:
commandEliminateDuplicates2 += """
EXCEPT -- One of the atoms must belong to the input unit cell
SELECT ca.*
FROM {} ca
WHERE ca.modelId_1 != '#1.1' AND
ca.modelId_2 != '#1.1'
""".format(self.getView1Name())
# # Remove duplicate contacts
# that is, given chains A,B
# we have contact A.a-B.b and B.b-A.a
c.execute(self.commandDropView.format(viewName="view_ND_1"))
# TODO: remove second contacts
c.execute(
commandEliminateDuplicates.format("view_ND_1", "contacts",
"contacts", "contacts"))
# remove duplicate contacts due to symmetry
# h1-h1p, h1-h2p
c.execute(self.commandDropView.format(viewName="view_ND_2"))
c.execute(
commandEliminateDuplicates2.format("view_ND_2", "view_ND_1",
"view_ND_1", "view_ND_1",
"view_ND_1"))
def _validate(self):
errors = []
if self.symmetryOrder.get() <= 0:
errors.append("Error: Symmetry Order should be a positive integer")
return errors
