def calcReferenceRms(self, reference, keepH=False, debug=False):
ref = getCoords(getLines(reference), include_hydrogens = keepH)
if not len(ref['coord']) == len(self.results[0]['coord']):
print "[atoms mismatch] Warning! The reference stricture doesn't match the docked ligand!"
print "Reference [ %d ] | Docked ligand [ %d ]" % ( len(ref['coord']), len(self.results[0]['coord']) )
return
rmsdcalc = RMSDCalculator(ref['coord'])
rmsd = [ rmsdcalc.computeRMSD(self.results[0]['coord']) ]
if len(self.results) > 1:
rmsd.append(rmsdcalc.computeRMSD(self.results[1]['coord']))
if debug:
dist_pool = []
for px in self.poses:
p = px['coord']
d = []
for i in range(len(p)):
x = quickdist(p[i], ref['coord'][i], sq=True)
d.append(x)
d.sort()
dist_pool.append(d)
#print "================="
#print d
return rmsd, dist_pool,self.poses
else:
return rmsd
def setReceptor(self, receptor, recname=None):
# pre-process receptor if filename
if isinstance(receptor, str):
if recname == None:
r = os.path.basename(receptor)
recname = os.path.splitext(r)[0]
try:
receptor = getCoords(getLines(receptor))
except:
print "Problem in reading the receptor: %s", receptor
return False
self.receptor = receptor
self.recname = recname
# initialize the bh_tree for the
# interactions calculated later
try:
freeBHtree(self.receptor_bht)
except:
pass
self.rec_bht = bhtreelib.BHtree( self.receptor['coord'], None, 10)
self.rec_bht_indices = zeros( (len(self.receptor['coord']),) ).astype('i')
self.rec_bht_distances = zeros( (len(self.receptor['coord']),) ).astype('f')
pattern = opts['-s']
if DEBUG: print "Pattern : |%s|" % pattern
if '-f' in opts:
files = [ opts['-f'] ]
elif '-d' in opts:
if '-R' in opts:
recursive = True
files = pathToList( path = opts['-d'], recursive = recursive, pattern = pattern )
if not files:
print "WARNING: no VS results in the dir:", opts['-d']
exit(1)
elif '-F' in opts:
try:
files = getLines(opts['-F'], doStrip = True)
print "%d files from list file %s" % (len(files), opts['-F'])
except:
print "ERROR opening the input list: " , opts['-F']
exit(1)
else:
print "ERROR: Either file (-f), directory (-d) or list file (-F) input options must be specified"
usage()
exit(1)
if '-R' in opts and ('-f' in opts or '-F' in opts):
print "WARNING: recursive option ('-R') ignored in file/list mode."
# interaction filters are initialized
int_filter = { 'vdw' : [],
'hba': [],
else:
pworst = float(value)
if '-s' in opts:
pattern = opts['-s']
if DEBUG: print "filename pattern search>", pattern
if '-f' in opts:
files = [ opts['-f'] ]
elif '-d' in opts:
files = pathToList( path = opts['-d'], recursive = recursive, pattern = pattern )
if not files:
print "No VS results in the dir:", opts['-d']
exit(1)
elif '-F' in opts:
try:
files = getLines(opts['-L'])
except:
print "ERROR opening the input list: " % opts['-L']
exit(1)
else:
print "ERROR: Either file (-f), directory (-d) or list file (-F) input options must be specified"
usage()
exit(1)
# interaction filters are initialized
int_filter = { 'vdw' : [],
'hba': [],
'hbd': [],
'hb': [],
'pi' : [],
'ppi' : [],
def getPoses(self, include_hydrogens=False):
"""
- parser of docked poses from a Vina output
- populate self.atomTypes[]
- populate poses dictionary: { "text", "coord", "energy", 'source'}
( for every pose the 'source' specify dlg containing it and the position)
"""
accepted_kw = [ "ATOM", "HETATM", "ROOT", "ENDROOT", "BRANCH", "ENDBRANCH", "TORSDOF", "REMARK" ]
atype_list_complete = False
inside = False
c = 0
lines = getLines(self.input_files)
if "REMARK VINA RESULT" in lines[1]:
if DEBUG: print "[found Vina result pdbqt]"
for l in lines:
if l.strip():
if "MODEL" in l: # initialize pose
text_pose = []
coord = []
flex_res = []
c += 1
in_res = False
elif "ENDMDL" in l:
coord = array( coord, 'f')
if flex_res:
flex_res = getCoords(flex_res) # transform coordinates and process them
# as we do with receptor atoms
# flex res atoms are added to the pose here
self.poses.append( { "text" : text_pose, "coord" : coord, "energy" : e ,\
'source' : (os.path.basename(self.input_files)+":"+str(c)), "flex_res" : flex_res } )
atype_list_complete = True
elif "BEGIN_RES" in l:
in_res = True
self.flexres = True # flex_res trigger
flex_res.append(l)
text_pose.append(l)
elif "END_RES" in l:
in_res = False
flex_res.append(l)
text_pose.append(l)
elif l.startswith("ATOM") or l.startswith("HETATM"):
text_pose.append(l)
if not in_res:
atype = l.rsplit()[-1]
if (not atype == "HD") or include_hydrogens : # HD should be excluded from array/RMSD calculation
try:
coord.append([float(l[30:38]),float(l[38:46]),float(l[46:54])])
if not atype_list_complete: # FUTURE: to be used for the David's reclustering method
self.atomTypes.append( atype )
except:
print ">WARNING! error in parsing coords in file :",self.input_files
self.problematic.append(self.input_files)
break
else:
flex_res.append(l)
elif "REMARK VINA RESULT:" in l:
values = l.split(":")[1]
values = values.split()
e = float(values[0])
lbrms = float(values[1])
ubrms = float(values[2])
self.histogram.append([e, lbrms, ubrms])
elif l.split(None, 1)[0] in accepted_kw:
text_pose.append(l)
self.totRuns = len(self.poses)
else:
print ">WARNING! not a Vina output PDBQT file :",self.input_files
def getPoses(self, include_hydrogens=False, ignoreWaters = False):
"""
- parser of docked poses from the dlg
- populate self.atomTypes[]
- define self.ligName (str)
- populate poses dictionary: { "text", "coord", "energy", 'source'}
( for every pose the 'source' specify dlg containing it and the position)
"""
#accepted_kw = [ "ATOM", "HETATM", "ROOT", "ENDROOT", "BRANCH", "ENDBRANCH", "TORSDOF", "REMARK" ]
accepted_kw = [ "ATOM", "HETATM", "TORSDOF" ]
atype_list_complete = False
#water_found = False
for d in self.input_files: # we expect dlgs
inside = False
c = 0
for l in getLines(d)[50:]:
if l[0:7] == "DOCKED:":
inside = True # used to stop parsing as soon as another keyword (i.e. "DPF> ") is found
l = l[8:]
if "MODEL" in l: # initialize pose
text_pose = []
coord = []
flex_res = []
water = []
c += 1
in_res = False
elif "ENDMDL" in l:
coord = array( coord, 'f')
if len(coord) == 0:
if DEBUG: print "[ Warning! no coordinates found in this dlg: %s ]" % (d)
break
if flex_res:
flex_res = getCoords(flex_res) # transform coordinates and process them
# as we do with receptor atoms
# flex res atoms are added to the pose here
self.poses.append( { "text" : text_pose,
"coord" : coord,
"energy" : e ,
'source' : (os.path.basename(d)+":"+str(c)),
"flex_res" : flex_res,
"water_bridge" : water,
} )
atype_list_complete = True
elif "BEGIN_RES" in l:
in_res = True
self.flexres = True # flex_res trigger
flex_res.append(l)
text_pose.append(l)
elif "END_RES" in l:
in_res = False
flex_res.append(l)
text_pose.append(l)
elif l.startswith("ATOM") or l.startswith("HETATM"): # if the line is atom but *not* flexres
text_pose.append(l)
if not in_res:
atype = l.rsplit()[-1]
if (atype == 'HD' and include_hydrogens) or not ( atype in self.ignore_at):
try:
# NOTE the flex res are not considered in the clustering
coord.append([float(l[30:38]),float(l[38:46]),float(l[46:54])])
if not atype_list_complete: # FUTURE: to be used for the David's reclustering method
self.atomTypes.append( atype )
except:
print ">WARNING! error in parsing coords in file :",d
self.problematic.append(d)
# the entire dlg is ignored if something bad happens
# rude, but efficient on the large scale...
break
elif atype in self.water_types and not ignoreWaters:
water.append(l)
self.isHydrated = True
else:
flex_res.append(l)
elif "USER Estimated Free Energy of Binding =" in l:
e = l.split("=")[1]
e = float(e.split("k")[0])
if e == 0.:
if DEBUG: print "[ Warning! FEB is zero... and it shouldn't ]"
elif l.split(None, 1)[0] in accepted_kw:
text_pose.append(l)
elif l.startswith("DPF> move") and not self.ligName:
self.ligName = l.split("DPF> move ")[1].split(".pdbqt")[0]
if l.startswith("DPF >") and inside: # stop reading dlg file (average lines skipped: ~30%)
break
self.totRuns = len(self.poses) # TODO check this indentation?
# Debugging printing of poses
if self.DEBUG:
for p in self.poses:
for f in p:
print f
print p[f]
print "==================================="
