def _validate(self):
errors = checkInputHasFasta(self)
from pyworkflow.utils.which import which
if which("curl") == "":
errors.append("Cannot find curl in the path. Install with apt-get install curl, yum install wget or equivalent in your system")
if which("wget") == "":
errors.append("Cannot find curl in the path. Install with apt-get install wget, yum install wget or equivalent in your system")
return errors
def _validate(self):
errors = []
if self.email.get() == "":
errors.append("The email cannot be empty")
from pyworkflow.utils.which import which
if which("curl") == "":
errors.append(
"Cannot find curl in the path. Install with apt-get install curl, yum install curl or equivalent in your system"
)
if which("wget") == "":
errors.append(
"Cannot find curl in the path. Install with apt-get install wget, yum install wget or equivalent in your system"
)
return errors
def _validate(self):
errors = []
nmaBin = Plugin.getVar(NMA_HOME)
nma_programs = [
'nma_check_modes', 'nma_diag_arpack', 'nma_diagrtb',
'nma_elnemo_pdbmat'
]
# Check Xmipp was compiled with NMA flag to True and
# some of the nma programs are under the Xmipp/bin/ folder
for prog in nma_programs:
if not exists(join(nmaBin, prog)):
errors.append(
"Some NMA programs are missing in the NMA folder.")
#errors.append("Check that Scipion was installed with NMA: 'scipion installb nma'")
errors.append("Check that Scipion was installed with NMA")
break
from pyworkflow.utils.which import which
if (which("csh") == "") and (which("bash") == ""):
errors.append(
"Please install csh (can be a link to tcsh) or bash (e.g., on Ubuntu 'sudo apt-get install csh' or 'sudo apt-get install bash')"
)
return errors
def _validate(self):
errors = []
nmaBin = os.environ["NMA_HOME"]
nma_programs = ["nma_check_modes", "nma_diag_arpack", "nma_diagrtb", "nma_elnemo_pdbmat"]
# Check Xmipp was compiled with NMA flag to True and
# some of the nma programs are under the Xmipp/bin/ folder
for prog in nma_programs:
if not exists(join(nmaBin, prog)):
errors.append("Some NMA programs are missing in the NMA folder.")
errors.append("Check that Scipion was installed with NMA: 'scipion install nma'")
break
from pyworkflow.utils.which import which
if which("csh") == "":
errors.append("Cannot find csh in the PATH")
return errors
def _validate(self):
errors = []
nmaBin = Plugin.getVar(NMA_HOME)
nma_programs = [
'nma_check_modes', 'nma_diag_arpack', 'nma_diagrtb',
'nma_elnemo_pdbmat'
]
# Check Xmipp was compiled with NMA flag to True and
# some of the nma programs are under the Xmipp/bin/ folder
for prog in nma_programs:
if not exists(join(nmaBin, prog)):
errors.append(
"Some NMA programs are missing in the NMA folder.")
errors.append(
"Check that Scipion was installed with NMA: 'scipion install nma'"
)
break
from pyworkflow.utils.which import which
if which("csh") == "":
errors.append("Cannot find csh in the PATH")
return errors
def qualifyModesStep(self,
numberOfModes,
collectivityThreshold,
structureEM,
suffix=''):
self._enterWorkingDir()
fnVec = glob("modes/vec.*")
if len(fnVec) < numberOfModes:
msg = "There are only %d modes instead of %d. "
msg += "Check the number of modes you asked to compute and/or consider increasing cut-off distance."
msg += "The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times"
msg += "the number of RTB blocks and for pseudoatomic normal mode analysis 3 times the number of pseudoatoms. "
msg += "However, the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of"
msg += "modes is below the minimum between these two numbers, consider increasing cut-off distance."
self._printWarnings(redStr(msg % (len(fnVec), numberOfModes)))
print(
redStr('Warning: There are only %d modes instead of %d.' %
(len(fnVec), numberOfModes)))
print(
redStr(
"Check the number of modes you asked to compute and/or consider increasing cut-off distance."
))
print(
redStr(
"The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times"
))
print(
redStr(
"the number of RTB blocks and for pseudoatomic normal mode analysis 3 times the number of pseudoatoms."
))
print(
redStr(
"However, the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of"
))
print(
redStr(
"modes is below the minimum between these two numbers, consider increasing cut-off distance."
))
fnDiag = "diagrtb.eigenfacs"
if structureEM:
if which("csh") != "":
self.runJob("nma_reformatForElNemo.csh",
"%d" % len(fnVec),
env=getNMAEnviron())
else:
if which("bash") != "":
self.runJob("nma_reformatForElNemo.sh",
"%d" % len(fnVec),
env=getNMAEnviron())
fnDiag = "diag_arpack.eigenfacs"
self.runJob("echo",
"%s | nma_check_modes" % fnDiag,
env=getNMAEnviron())
cleanPath(fnDiag)
fh = open("Chkmod.res")
mdOut = xmippLib.MetaData()
collectivityList = []
for n in range(len(fnVec)):
line = fh.readline()
collectivity = float(line.split()[1])
collectivityList.append(collectivity)
objId = mdOut.addObject()
modefile = self._getPath("modes", "vec.%d" % (n + 1))
mdOut.setValue(xmippLib.MDL_NMA_MODEFILE, modefile, objId)
mdOut.setValue(xmippLib.MDL_ORDER, long(n + 1), objId)
if n >= 6:
mdOut.setValue(xmippLib.MDL_ENABLED, 1, objId)
else:
mdOut.setValue(xmippLib.MDL_ENABLED, -1, objId)
mdOut.setValue(xmippLib.MDL_NMA_COLLECTIVITY, collectivity, objId)
if collectivity < collectivityThreshold:
mdOut.setValue(xmippLib.MDL_ENABLED, -1, objId)
fh.close()
idxSorted = [
i[0] for i in sorted(
enumerate(collectivityList), key=lambda x: x[1], reverse=True)
]
score = []
for j in range(len(fnVec)):
score.append(0)
modeNum = []
l = 0
for k in range(len(fnVec)):
modeNum.append(k)
l += 1
# score = [0]*numberOfModes
for i in range(len(fnVec)):
score[idxSorted[i]] = idxSorted[i] + modeNum[i] + 2
i = 0
for objId in mdOut:
score_i = float(score[i]) / (2.0 * l)
mdOut.setValue(xmippLib.MDL_NMA_SCORE, score_i, objId)
i += 1
mdOut.write("modes%s.xmd" % suffix)
cleanPath("Chkmod.res")
self._leaveWorkingDir()