def run(nmrCalcRun):
""" Run Program
Input:
nmrCalcRun: NmrCalc.Run
NBNB TBD change dictionary keys for data to use COSMOS names.
"""
COSMOS_LIB = os.path.join(os.path.expandvars('${COSMOS_HOME}'), 'lib')
if COSMOS_LIB not in sys.path:
sys.path.append(COSMOS_LIB)
from PyCOSMOS import runCOSMOS
# check we are not overriding an old run
if not intUtil.runIsWritable(nmrCalcRun):
raise Exception("Cannot read into %s - has already been used" %
nmrCalcRun)
data, options = cosmosIo.getCosmosData(nmrCalcRun)
fp = open('/home/rhf22/CosmosTestData.txt', 'w')
fp.write(json.dumps(data, sort_keys=2, indent=2))
fp = open('/home/rhf22/CosmosTestOpts.txt', 'w')
fp.write(json.dumps(options, sort_keys=2, indent=2))
fp.close()
# determine and create absolute outputdir
outputdir = options.get('OUTPUT_DIR')
if outputdir:
# converts relative to absoulte directories
outputdir = os.path.join(os.getcwd(), outputdir)
else:
outputdir = os.getcwd()
options['OUTPUT_DIR'] = outputdir
if not os.path.exists(outputdir):
os.makedirs(outputdir)
nmrCalcRun.status = 'active'
output = runCOSMOS(data, options)
# put output into NmrCalc instance
cosmosIo.mergeCosmosData(nmrCalcRun, output)
def read(nmrCalcRun, dataDir):
""" Read Output files for Rosetta run
Input:
nmrCalcRun: NmrCalc.Run
dataDir: directory directly containing program output.
"""
# set up
files = {}
data = {}
fileNames = stdFileNames.copy()
#fileNames['properties'] = intIo.propFileName
# check presence of files:
if not os.path.isdir(dataDir):
raise IOError("Data directory %s not found" % dataDir)
for tag in (
'scores',
'rms',
'rawRms',
):
ss = uniIo.joinPath(dataDir, fileNames[tag])
files[tag] = ss
if not os.path.isfile(ss):
raise IOError("%s file %s not found in directory %s" %
(tag, ss, dataDir))
# check NmrCalcRun:
if not intUtil.runIsWritable(nmrCalcRun):
raise Exception("Cannot read into %s - has already been used" %
nmrCalcRun)
# get simple data records
#ss = fileNames.get('input')
#if ss:
# path = uniIo.joinPath(dataDir, ss)
# if os.path.isfile(path):
# data = open(path).read()
# nmrCalcRun.newRunParameter(name='inputUsed', code=stdFileNames['input'],
# ioRole='output', textValue=data,
# )
#details='Input data, as used by Rosetta')
#NBNB TBD remove. Not there. Properties is an input thing.
#ss = fileNames.get('properties')
#if ss:
# path = uniIo.joinPath(dataDir, ss)
# if os.path.isfile(path):
# data = open(ss).read()
# nmrCalcRun.newRunParameter(name='propertiesUsed',
# code=stdFileNames['properties'],
# ioRole='output', textValue=data,
# details='Properties file, as used by Rosetta')
# read data arrays and sort by Rosetta score
scoreFile = open(files['scores'])
rmsFile = open(files['rms'])
rawRmsFile = open(files['rawRms'])
data = []
for ss in scoreFile:
rms = float(rmsFile.next().split()[1])
rawRms = float(rawRmsFile.next().split(None, 1)[0])
tt = ss.split()
# Order is: score, rawscore shiftChi2, rms, rawrms, name
data.append(
(float(tt[3]), float(tt[1]), float(tt[2]), rms, rawRms, tt[0]))
data.sort()
scores, rawScores, shiftChi2, rms, rawRms, names = zip(*data)
# Set scores data in NmrCalc matrices
docTemplate = (
"Rosetta %s for all calculated structures, sorted by corrected score")
ss = 'corrected scores'
nmrCalcRun.newFloatMatrixData(code='scores',
name=ss,
ioRole='output',
shape=(0, ),
data=scores,
details=docTemplate % ss)
ss = 'raw scores'
nmrCalcRun.newFloatMatrixData(code='rawScores',
name=ss,
ioRole='output',
shape=(0, ),
data=rawScores,
details=docTemplate % ss)
ss = 'shift chi2 scores'
nmrCalcRun.newFloatMatrixData(code='shiftChi2',
name=ss,
ioRole='output',
shape=(0, ),
data=shiftChi2,
details=docTemplate % 'Chemical' + ss)
ss = 'RMS to best struct'
nmrCalcRun.newFloatMatrixData(code='rms',
name=ss,
ioRole='output',
shape=(0, ),
data=rms,
details=docTemplate %
'RMS to structure with best corrected score')
ss = 'RMS to best raw struct'
nmrCalcRun.newFloatMatrixData(code='rawRms',
name=ss,
ioRole='output',
shape=(0, ),
data=rawRms,
details=docTemplate %
'RMS to structure with best raw score')
# Get MolSystem
molResidueData = nmrCalcRun.findFirstData(className='MolResidueData',
ioRole='input')
molSystem = molResidueData.molSystem
# read structures in order of lowest corrected score
paths = []
for modelNum, fileName in enumerate(names):
path = uniIo.joinPath(dataDir, fileName + '.pdb')
if os.path.isfile(path):
paths.append(path)
else:
break
ensemble = StructureIo.getStructureFromFiles(molSystem,
paths,
fileType='rough')
ss = "Rosetta calculated structures, sorted by corrected score"
nmrCalcRun.newStructureEnsembleData(name='result',
ioRole='output',
structureEnsemble=ensemble,
details=docTemplate % ss)
# Make Nmr.StructureCalculation
nmrProject = nmrCalcRun.nmrCalcStore.nmrProject
nmrCalcRun.structureGeneration = nmrProject.newStructureGeneration(
generationType='denovo', name='CSRosetta', structureEnsemble=ensemble)