def loadPDBmacro( projects ):
fp = open( projects.path('loadPDB.mcr' ), 'w')
fprintf(fp, 'Console off\n')
for p in projects.entries:
#fprintf(fp, 'loadPDB %s\n', os.path.abspath(projects.path(p.name+'.pdb')))
fprintf(fp, 'loadPDB %s,Center=No\n', projects.path(p.name+'.pdb'))
#end for
fprintf(fp, 'Style Ribbon\n')
fprintf(fp, 'macro %s\n', projects.path('colorPDB.mcr'))
fprintf(fp, 'Console on\n')
fp.close()
def printRmsds( title, rmsds, stream=sys.stdout ):
n = len(rmsds)
printTitle(title, 20*(n+1), stream)
fprintf( stream, '%-20s%s\n','', rmsds.zap('group').format(' %-16s '))
for row in rmsds:
fprintf( stream, '%-20s%s\n', row.group, row.format('%-18s '))
fprintf( stream, '%s\n', '_'*20*(n+1))
def obj2XML(obj, stream=None, path=None):
"""Convert an object to XML
output to stream or path
gwv 13 Jun08: return object or None on error
"""
if obj is None:
io.error("obj2XML: no object\n")
return None
if stream is None and path is None:
io.error("obj2XML: no output defined\n")
return None
closeFile = 0
if not stream:
stream = open(path, 'w')
closeFile = 1
fprintf(stream, '<?xml version="1.0" encoding="ISO-8859-1"?>\n')
nTtoXML(obj, depth=0, stream=stream, indent=' ')
if closeFile:
stream.close()
return obj
def rogMacro( projects ):
stream = open( projects.path('ROG.mcr' ), 'w')
fprintf(stream, 'Console off\n')
fprintf(stream, 'ColorRes All, Gray\n')
yasaraColorDict = dict(green = 240, orange = 150, red = 120)
for p in projects:
selectedResidues = p.molecule.setResiduesFromRanges(projects.ranges)
for res in p.molecule.allResidues():
if res in selectedResidues:
pass
else:
fprintf(stream, 'ColorRes object %d residue %d, %s\n', p.id+1, res.resNum, yasaraColorDict[res.rogScore.colorLabel])
#end for
fprintf(stream, 'Console on\n')
def colorPDBmacro( projects ):
fp = open( projects.path('colorPDB.mcr' ), 'w')
fprintf(fp, 'Console off\n')
for p in projects.entries:
#fprintf(fp, 'loadPDB %s\n', os.path.abspath(projects.path(p.name+'.pdb')))
selectedResidues = p.molecule.setResiduesFromRanges(projects.ranges)
#print '>>', selectedResidues
if p.has_key('color'):
fprintf(fp, 'ColorObject %d, %d\n', p.id+1, p.color)
for res in p.molecule.allResidues():
#print res,
if res in selectedResidues:
pass
else:
fprintf(fp, 'ColorRes object %d residue %d, grey\n', p.id+1, res.resNum)
#end if
#end for
#end if
#end for
fprintf(fp, 'Console on\n')
fp.close()
def nTtoXML(obj, depth=0, stream=sys.stdout, indent='\t', lineEnd='\n'):
"""Generate XML:
check for method toXML
or
standard types int, float, tuple, list, dict
"""
if (obj == None):
nTindent(depth, stream, indent)
fprintf(stream, "<None/>")
fprintf(stream, lineEnd)
elif hasattr(obj, 'toXML'):
obj.toXML(depth, stream, indent, lineEnd)
elif (type(obj) == int):
nTindent(depth, stream, indent)
fprintf(stream, "<int>%s</int>", repr(obj))
fprintf(stream, lineEnd)
elif (type(obj) == bool):
nTindent(depth, stream, indent)
fprintf(stream, "<bool>%s</bool>", repr(obj))
fprintf(stream, lineEnd)
elif (type(obj) == float):
nTindent(depth, stream, indent)
fprintf(stream, "<float>%s</float>", repr(obj))
fprintf(stream, lineEnd)
elif (type(obj) == str):
nTindent(depth, stream, indent)
# fprintf( stream, "<string>%s</string>", saxutils.escape( obj ) )
fprintf(stream, "<string>%s</string>", unicode(saxutils.escape(obj)))
fprintf(stream, lineEnd)
elif (type(obj) == unicode):
nTindent(depth, stream, indent)
fprintf(stream, "<unicode>%s</unicode>", unicode(saxutils.escape(obj)))
fprintf(stream, lineEnd)
elif (type(obj) == list):
nTindent(depth, stream, indent)
fprintf(stream, "<list>")
fprintf(stream, lineEnd)
for a in obj:
nTtoXML(a, depth+1, stream, indent, lineEnd)
#end for
nTindent(depth, stream, indent)
fprintf(stream, "</list>")
fprintf(stream, lineEnd)
elif (type(obj) == tuple):
nTindent(depth, stream, indent)
fprintf(stream, "<tuple>")
fprintf(stream, lineEnd)
for a in list(obj):
nTtoXML(a, depth+1, stream, indent, lineEnd)
#end for
nTindent(depth, stream, indent)
fprintf(stream, "</tuple>")
fprintf(stream, lineEnd)
elif (type(obj) == dict):
nTindent(depth, stream, indent)
fprintf(stream, "<dict>")
fprintf(stream, lineEnd)
for key, value in obj.iteritems():
nTindent(depth+1, stream, indent)
fprintf(stream, "<key name=%s>", quote(key))
fprintf(stream, lineEnd)
nTtoXML(value, depth+2, stream, indent, lineEnd)
nTindent(depth+1, stream, indent)
fprintf(stream, "</key>")
fprintf(stream, lineEnd)
#end for
nTindent(depth, stream, indent)
fprintf(stream, "</dict>")
fprintf(stream, lineEnd)
else:
pass
io.error('nTtoXML: undefined object "{0}": cannot generate XML\n', obj) # reenable when done testing.
def nTindent(depth, stream, indent):
"""
Indent stream to depth; to pretty format XML
"""
for dummy in range(depth):
fprintf(stream, indent)
def exportDef(self, stream=sys.stdout, convention=constants.INTERNAL):
"""export name definitions to stream"""
io.fprintf(stream, "convention = %r\n", convention)
for residue in self:
residue.exportDef(stream=stream, convention=convention)
def write( self, stream=sys.stdout):
"""
Write tab to stream
"""
for r in self.remarks:
fprintf( stream, 'REMARK %s\n', r )
#end for
fprintf( stream, '\n' )
for d,v in self.data.iteritems():
fprintf( stream, 'DATA %s %s\n', d, v ) # Note: only ONE space between DATA and identifier!!!
#end for
fprintf( stream, '\n' )
fprintf( stream, 'VARS ' )
for c in self.columnDefs:
if not c.hide:
fprintf( stream, '%s ', c.name )
#end for
fprintf( stream, '\n' )
fprintf( stream, 'FORMAT ' )
for c in self.columnDefs:
if not c.hide:
fprintf( stream, '%s ', c.fmt )
#end for
fprintf( stream, '\n' )
fprintf( stream, '\n' )
for row in self:
fprintf( stream, '%s\n', row )
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 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 printRestraintScores( projects, stream=sys.stdout ):
n = len(projects)
if n == 0:
return
# print constants.dots20*(n+1)
# print ' Restraints target', projects[0].target
# print constants.dots20*(n+1)
# print
hlen=40
printTitle('Restraint scores target '+projects.name, 110, stream)
for p in projects:
header = sprintf('%s project %-20s %s', '-'*hlen, p.name, '-'*hlen)
fprintf( stream,'%s\n', header)
if len(p.dihedrals)+len(p.distances) == 0:
fprintf( stream,'%s\n%s\n\n', " No restraints",'-'*len(header))
continue
if len( p.distances ) > 0:
fprintf( stream, '%-25s %5s %5s %5s %5s %5s %5s %-7s %4s %4s %4s %4s rmsd\n',
'DistanceRestraintLists', 'count', 'intra', 'seq', 'med', 'long', 'amb', 'ROG','low','>0.1','>0.3','>0.5'
)
for r in p.distances:
fprintf( stream,' %-23s %5d %5d %5d %5d %5d %5d %-7s %4d %4d %4d %4d %5.3f +- %5.3f\n',
r.name,
len(r), len(r.intraResidual), len(r.sequential), len(r.mediumRange), len(r.longRange), len(r.ambiguous),
r.rogScore,
r.violCountLower, r.violCount1, r.violCount3, r.violCount5,
r.rmsdAv, r.rmsdSd
)
fprintf(stream, "\n")
#end if
if len(p.dihedrals) > 0:
fprintf( stream, '%-25s %5s %5s %5s %5s %5s %5s %-7s %4s %4s %4s %4s rmsd\n',
'DihedralRestraintsLists', 'count', '','','','','', 'ROG','','>1','>3','>5',
)
for r in p.dihedrals:
fprintf( stream,' %-23s %5s %5s %5s %5s %5s %5s %-7s %4s %4d %4d %4d %5.3f +- %5.3f\n',
r.name,
len(r), '.', '.', '.', '.', '.',
r.rogScore, '.',
r.violCount1, r.violCount3, r.violCount5,
r.rmsdAv, r.rmsdSd
)
#end if
fprintf( stream,'%s\n\n', '-'*len(header))
def printOverallScores( projects, stream = sys.stdout ):
# Overall scores
n = len(projects)
if n == 0:
return
printTitle('Overall scores target '+projects.name, 20*(n+1), stream)
# line = constants.dots20*(n+1)
# fprintf( stream, '%s\n Overall scores %s\n%s\n\n', line, projects.name, line )
fprintf( stream, '%-20s%s\n\n', 'Parameter', projects.entries.zap('group').format('%-20s'))
# rmsds
fprintf( stream, '%-20s%s\n','rmsdToMean', projects.entries.zap('summaryDict','rmsdToMean_backboneAverage').format(' %-18s') )
fprintf( stream, '%-20s%s\n','pairwiseRmsd', projects.entries.zap('summaryDict','pairwiseRmsd').format('%-16s ') )
fprintf( stream, '%-20s%s\n\n','pairwiseRmsdTo_'+projects.entries[0].group, projects.entries.zap(
'summaryDict','pairwiseRmsdToFirst').format('%-18s ') )
# CING scores
for key in ['CING_red', 'CING_orange', 'CING_green']:
fprintf( stream, '%-20s%s\n',key, projects.entries.zap('summaryDict',key).format('%-18s ') )
fprintf( stream, '\n')
# Procheck scores
for key in ['PC_core','PC_allowed','PC_generous','PC_disallowed','PC_gf']:
fprintf( stream, '%-20s%s\n',key, projects.entries.zap('summaryDict',key).format('%-18s ') )
fprintf( stream, '\n')
# Whatif scores
for checkId in projects[0].molecule.runWhatif.summaryCheckIdList:
key = 'WI_'+projects[0].molecule.runWhatif.cingCheckId(checkId)
fprintf( stream, '%-20s%s\n',key, projects.entries.zap('summaryDict',key).format('%-18s ') )
fprintf( stream, '\n')
def printTitle(title, length, stream=sys.stdout ):
line = '-'*length
fprintf( stream, '%s\n %s\n%s\n', line, title, line )