def average(atm):
"""Average value of atom with those of assigned neighbors"""
if atm.has_key('deltaAverage'): del(atm['deltaAverage'])
values = NTlist()
for a in [atm] + atm.topology():
if 'delta' in a and not fpconst.isNaN(a['delta']):
#print '>>', a, a.delta
values.append(a.delta)
#end if
#end for
#print '>>', atm, values
if len(values) > 0:
atm.deltaAverage, sd, n = values.average()
def colorPhiPsiMacro( projects, minValue=2.0, maxValue=4.0 ):
fp = open( projects.path('phipsi.mcr' ), 'w')
fprintf(fp, 'Console off\n')
fprintf(fp, 'ColorPar Property Min,blue, %7.3f\n', minValue)
fprintf(fp, 'ColorPar Property Max,red, %7.3f\n', maxValue)
for p in projects.entries[1:]:
fprintf(fp, 'ColorRes object %d, Gray\n', p.id+1)
fprintf(fp, 'PropRes object %d, -999\n', p.id+1)
for res in p.molecule.allResidues():
if res.has_key('phipsiRmsds'):
if not isNaN(res.phipsiRmsds[0][p.id].value):
fprintf( fp, 'PropRes object %d residue %d, %7.3f\n', p.id+1, res.resNum, res.phipsiRmsds[0][p.id].value)
#end if
#end for
fprintf(fp, 'ColorObject %d, property\n', p.id+1)
#end for
fprintf(fp, 'Console off\n')
fp.close()
def mkYasaraByResidueMacro(projects, keys,
minValue = 0.0, maxValue = 1.0, reverseColorScheme = False,
path = None
):
# nTdebug('mkYasaraByResidueMacro: keys: %s, minValue: %s maxValue: %s', keys, minValue, maxValue)
if path==None:
stream = sys.stdout
else:
stream = open( path, 'w')
#end if
fprintf(stream, 'Console off\n')
fprintf(stream, 'ColorRes All, Gray\n')
fprintf(stream, 'PropRes All, -999\n')
if reverseColorScheme:
fprintf(stream, 'ColorPar Property Min,red,%f\n', minValue)
fprintf(stream, 'ColorPar Property Max,blue,%f\n', maxValue)
else:
fprintf(stream, 'ColorPar Property Min,blue,%f\n', minValue)
fprintf(stream, 'ColorPar Property Max,red,%f\n', maxValue)
for p in projects:
for res in p.molecule.allResidues():
value = getDeepByKeysOrAttributes(res, *keys)
# if res.has_key(property) and res[property] != None and not isNaN(res[property]):
if value != None and not isNaN(value):
fprintf(stream, 'PropRes object %d Residue %d, %.4f\n', p.id+1, res.resNum, value)
#end for
fprintf(stream, 'ColorAll Property\n')
fprintf(stream, 'Console on\n')
if path:
stream.close()
def isNoneorNaN(value):
if value == None:
return True
return isNaN(value)
def isNoneorNaN(value):
if value == None:
return True
return isNaN(value)