def OnInit(self):
from frowns import MDL
from StringIO import StringIO
reader = MDL.sdin(StringIO(test))
mol, error, text = reader.next()
wxInitAllImageHandlers()
frame = wxFrame(None, -1, "", size=(350, 200))
drawer = self.drawer = MoleculeDrawer(frame, drawAromatic=0)
drawer.setMolecule(mol)
frame.Show(TRUE)
return TRUE
def OnInit(self):
from frowns import MDL
reader = MDL.sdin(open("data\chiral3.sdf"))
mol, error, text = reader.next()
wxInitAllImageHandlers()
frame = wxFrame(None, -1, "", size=(350,200))
drawer = self.drawer = MoleculeDrawer(frame, drawAromatic=1)
drawer.setMolecule(mol)
frame.Show(TRUE)
return TRUE
def map(self, workingPath, verbose=False):
if verbose:
sys.stderr.write("Brique.map: Will load %s ... wp %s\n" %
(self.cansmiles(), workingPath))
file = self.load(workingPath, verbose=verbose)
if verbose:
sys.stderr.write("Brique.map: %s Loaded ...\n" % workingPath)
if not file:
if verbose:
sys.stderr.write("Brique.map: ring not found ...\n")
# Here we should use AMMOS to generate ring conformation
raise CycleUnknown, "cycle " + self.cansmiles(
) + " is not present in the ring library"
# sys.stderr.write("Brique.map: will read %s ...\n" % file)
f = open(file)
reader = MDL.sdin(f)
# m = reader.next()[0]
m, err, txt = reader.next()
# sys.stderr.write("Brique.map: MDL reader got %s\n" % err)
f.close()
# sys.stderr.write("Brique.map: read as SDF ...\n")
Disambiguate.FreedDisambiguate(m)
atomsSDF = m.atoms[:]
atomsSDF.sort(key=lambda x: x.symorder)
# sys.stderr.write("Brique.map: ordered by symorder ...\n")
try:
Disambiguate.FreedDisambiguate(self.molecule)
atomsBrick = self.molecule.atoms[:]
atomsBrick.sort(key=lambda x: x.symorder)
# sys.stderr.write("Brique.map: Loaded %d atoms ...\n" % len(atomsSDF))
for i in range(len(atomsBrick)):
for oatB in atomsBrick[i].oatoms:
if oatB.symorder not in [
oatS.symorder for oatS in atomsSDF[i].oatoms
]:
for j in range(i):
atomsBrick[j].x = None
atomsBrick[j].y = None
atomsBrick[j].z = None
self.map2(workingPath)
return
atomsBrick[i].x = atomsSDF[i].x
atomsBrick[i].y = atomsSDF[i].y
atomsBrick[i].z = atomsSDF[i].z
except:
# sys.stderr.write("Brique.map: Something went wrong. Attempting map2\n")
self.map2(workingPath)
return
def map(self, workingPath, verbose = False):
if verbose:
sys.stderr.write("Brique.map: Will load %s ... wp %s\n" % (self.cansmiles(), workingPath))
file = self.load(workingPath, verbose = verbose)
if verbose:
sys.stderr.write("Brique.map: %s Loaded ...\n" % workingPath)
if not file :
if verbose:
sys.stderr.write("Brique.map: ring not found ...\n")
# Here we should use AMMOS to generate ring conformation
raise CycleUnknown, "cycle " + self.cansmiles() + " is not present in the ring library"
# sys.stderr.write("Brique.map: will read %s ...\n" % file)
f = open(file)
reader = MDL.sdin(f)
# m = reader.next()[0]
m, err, txt = reader.next()
# sys.stderr.write("Brique.map: MDL reader got %s\n" % err)
f.close()
# sys.stderr.write("Brique.map: read as SDF ...\n")
Disambiguate.FreedDisambiguate(m)
atomsSDF = m.atoms[:]
atomsSDF.sort(key = lambda x: x.symorder)
# sys.stderr.write("Brique.map: ordered by symorder ...\n")
try:
Disambiguate.FreedDisambiguate(self.molecule)
atomsBrick = self.molecule.atoms[:]
atomsBrick.sort(key = lambda x: x.symorder)
# sys.stderr.write("Brique.map: Loaded %d atoms ...\n" % len(atomsSDF))
for i in range(len(atomsBrick)):
for oatB in atomsBrick[i].oatoms:
if oatB.symorder not in [oatS.symorder for oatS in atomsSDF[i].oatoms]:
for j in range(i):
atomsBrick[j].x = None
atomsBrick[j].y = None
atomsBrick[j].z = None
self.map2(workingPath)
return
atomsBrick[i].x = atomsSDF[i].x
atomsBrick[i].y = atomsSDF[i].y
atomsBrick[i].z = atomsSDF[i].z
except:
# sys.stderr.write("Brique.map: Something went wrong. Attempting map2\n")
self.map2(workingPath)
return
def readSDF(file):
"""
idem ci-dessus pr fichier SDF
"""
f = open(file)
reader = MDL.sdin(f)
mo = []
try:
m = reader.next()[0]
while m:
if m.fields.keys():
for key in m.fields.keys():
if "ID" in key:
mo.append(iMolecule(sd=m, id=m.fields[key]))
break
else:
mo.append(iMolecule(sd=m, id=m.name))
m = reader.next()[0]
except:
f.close()
return mo
def readSDF(file) :
"""
idem ci-dessus pr fichier SDF
"""
f = open(file)
reader = MDL.sdin(f)
mo = []
try :
m = reader.next()[0]
while m :
if m.fields.keys():
for key in m.fields.keys():
if "ID" in key :
mo.append(iMolecule(sd=m,id=m.fields[key]))
break
else :
mo.append(iMolecule(sd=m,id=m.name))
m = reader.next()[0]
except :
f.close()
return mo
from frowns import MDL
from frowns.mdl_parsers import sdfile
file = open("data\\bad_compounds.sdf")
for mol, error, record in MDL.sdin(file):
print type(mol), `error`, len(record)
from frowns import MDL
from frowns.mdl_parsers import sdfile
file = open("data\\bad_compounds.sdf")
for mol, error, record in MDL.sdin(file):
print type(mol), ` error `, len(record)
from frowns import MDL
for mol, text, error in MDL.sdin(open("../../test/data/bad.sdf")):
if not mol:
print "cannot parse sd file"
print error
print text
else:
print mol.cansmiles()
print "data"
for key, value in mol.fields.items():
print "\t%s: %s" % (key, value)
from Tkinter import *
from frowns.Depict.TkMoleculeDrawer import MoleculeDrawer
from frowns import MDL
# read in a molecule
reader = MDL.sdin(open("bad.sdf"))
mol, error, text = reader.next()
# create the moleculedock widget and place it
# into a tk window
tk = top = Tk()
m = MoleculeDrawer(top, mol, 0)
m.pack(fill=BOTH, expand=1)
mainloop()
from frowns import MDL
for mol, text, error in MDL.sdin(open("../../test/data/bad.sdf")):
if not mol:
print "cannot parse sd file"
print error
print text
else:
print mol.cansmiles()
print "data"
for key, value in mol.fields.items():
print "\t%s: %s"%(key, value)
from frowns import MDL
from frowns.Depict.wxMoleculeDrawer import MoleculeDrawer
for mol, error, text in MDL.sdin(open("data\chiral.sdf")):
for bond in mol.bonds:
print bond.stereo
print mol, error
print mol.cansmiles()
from wxPython.wx import *
class testApp(wxApp):
def OnInit(self):
from frowns import MDL
reader = MDL.sdin(open("data\chiral3.sdf"))
mol, error, text = reader.next()
wxInitAllImageHandlers()
frame = wxFrame(None, -1, "", size=(350,200))
drawer = self.drawer = MoleculeDrawer(frame, drawAromatic=1)
drawer.setMolecule(mol)
frame.Show(TRUE)
return TRUE
def load(self, workingPath, verbose = False) :
"""
charger le fichier sdf de la brique
"""
if verbose:
sys.stderr.write("Brique.load: %s\n" % LIBRARY_PATH)
if not LIBRARY_PATH :
sys.stderr.wirte( "variable path de la classe Brique non initialisee\n")
return 0
try:
listFile = os.listdir(LIBRARY_PATH) # liste des fichier contenu ds 'PAHT' -> listFile
except:
sys.stderr.write("Brique.load: Failed to access ring library at %s\n" % LIBRARY_PATH)
# sys.exit(0)
name = self.cansmiles()
if verbose:
sys.stderr.write("Brique.load: Attempting %s ...\n" % str(name))
# print "Brique.load:",name
if workingPath[-1] != "/":
workingPath += "/"
fileSmi = open(workingPath + "brique.smi", "w")
fileSmi.write(name + "\n")
fileSmi.close()
if verbose:
sys.stderr.write("Brique.load: babel sdf conversion ...\n")
os.system(BABEL_PATH + " -ismi " + workingPath + "brique.smi -osdf " + workingPath + "brique.sdf 2> /dev/null")
os.system("echo '$$$$' >> " + workingPath + "brique.sdf")
# sys.stderr.write("Brique.load: Will read %s/brique.sdf\n" % (workingPath))
fileSdf = open(workingPath + "brique.sdf")
reader = MDL.sdin(fileSdf)
name2 = reader.next()[0].cansmiles()
# sys.stderr.write("Brique.load: read sdf as %s\n" % name2)
fileSdf.close()
# print "brique", name, name2
# if name2 in listFile: # si le fichier est ds la liste
# return LIBRARY_PATH+name2 # on renvoie le chemin complet du fichier
# elif name in listFile:
# return LIBRARY_PATH+name
if name in listFile:
return LIBRARY_PATH+name
else:
# 11 fevrier 2010: We attempt to generate using AMMOS, not to use babel conversion for name.
name2 = name
if verbose:
sys.stderr.write("Brique.load: Building %s as %s ...\n" % ( str(name), str(name2)))
try:
# Generer du mol2.
uName = name2.replace("(","\(").replace(")","\)").replace("[","\[").replace("]","\]")
# f =open("%s/%s.smi" % (LIBRARY_PATH, name2), "w")
sys.stderr.write("Creating %s%s.smi\n" % (LIBRARY_PATH, uName))
f = open("%s%s.smi" % (LIBRARY_PATH, name2), "w") # in python do not escape names !!!
f.write("%s\n" % name2)
f.close()
cmd = "%s -h -ismi %s/%s.smi -omol2 %s/%s.mol2" % (BABEL_PATH, LIBRARY_PATH, uName, LIBRARY_PATH, uName)
# cmd = "%s -h -ismi %s/%s.smi -omol2 %s/%s.mol2" % (BABEL_PATH, LIBRARY_PATH, "itest", LIBRARY_PATH, "itest")
sys.stderr.write("%s\n" % cmd)
os.system(cmd)
# Generer le fichier input.param
# path_of_DG-AMMOS= /Users/DG-AMMOS
# bank= input_dataset.mol2
f= open("%s/%s.dgammos" % (LIBRARY_PATH, name2), "w")
# f= open("%s.dgammos" % ("itest"), "w")
f.write("path_of_DG-AMMOS= %s\n" % DGAMMOSHOME)
f.write("bank= %s%s.mol2\n" % (LIBRARY_PATH, name2))
# f.write("bank= %s%s.mol2\n" % (LIBRARY_PATH, "itest"))
f.close()
sys.stderr.write("Generated %s/%s.dgammos\n" % (LIBRARY_PATH, uName))
sys.stderr.write("Generating %s/%s.mol2\n" % (LIBRARY_PATH, uName))
cmd = "%s %s/%s.dgammos" % (AMMOSBUILD, LIBRARY_PATH, uName)
# cmd = "%s %s.dgammos" % (AMMOSBUILD, uName)
sys.stderr.write("DG_AMMOS cmd: %s\n" % (cmd))
os.system(cmd)
# sys.exit(0)
# Convertir en sdf, oter les H
# cmd = "%s -d -imol2 %s/%s_Built.mol2 -osdf %s/%s.sdf 2> %s/%s.log" % (BABEL_PATH, LIBRARY_PATH, name2, LIBRARY_PATH, name2, LIBRARY_PATH, name2)
cmd = "%s -d -imol2 %s/%s_Built.mol2 -osdf %s/%s 2> %s/%s.log" % (BABEL_PATH, LIBRARY_PATH, uName, LIBRARY_PATH, uName, LIBRARY_PATH, uName)
os.system(cmd)
os.system("echo '$$$$' >> %s/%s" % (LIBRARY_PATH, uName))
# sys.exit(0)
# self.load(workingPath)
return LIBRARY_PATH+name2
# SI AMMOS N'A PAS PUS GENERER LE CYCLE: le mol2 sera dans %s/%s_BadMolecules.mol2
# os.system(cmd)
except:
return 0
return 0
def map2(self, workingPath) :
"""
#correspondance entre atomes de la brique et du fichier sdf
"""
file = self.load(workingPath)
if not file :
raise CycleUnknown, self.cansmiles()
f = open(file)
reader = MDL.sdin(f)
m = reader.next()[0]
# mx = reader.next() # ou while reader.next()
# m = mx[0]
f.close()
# output :
i = j = tentativeRate = 0
cyclesChecked = []
cyclesMapped = []
#print "nb cycles", len(self.molecule.cycles)
while tentativeRate < len(self.molecule.cycles): # boucle tant que le nb de tentative rate de mapping n'est pas egale au nb de cycle ds la molecule
#print j,i,len(self.molecule.cycles[j]),len(m.cycles[i])
if len(self.molecule.cycles[j]) == len(m.cycles[i]) : # si les 2 cycles ont le meme nb d'atomes, on peut essayer de les mapper
if mapCycles(self.molecule.cycles[j],m.cycles[i]) :
#print "mapCycles(self.molecule.cycles[j],m.cycles[i])"
cyclesChecked.append(i)
cyclesMapped.append(j)
j += 1
tentativeRate = 0
break
else :
tentativeRate += 1
else :
tentativeRate += 1
i += 1
while len(cyclesMapped) < len(self.molecule.cycles) and tentativeRate < len(self.molecule.cycles)-len(cyclesChecked) :
if i in cyclesChecked :
i += 1
continue
if i == len(m.cycles) :
i = 0
continue
if j in cyclesMapped :
j += 1
continue
if j == len(self.molecule.cycles) :
j = 0
continue
coord = 0
for atom in self.molecule.cycles[j].atoms :
if atom.x != None :
coord = 1
break
if not coord :
j += 1
continue
if len(self.molecule.cycles[j]) == len(m.cycles[i]) :
if mapCycles2(self.molecule.cycles[j],m.cycles[i]) :
cyclesChecked.append(i)
cyclesMapped.append(j)
j += 1
tentativeRate = 0
else :
tentativeRate += 1
else :
tentativeRate += 1
i += 1
return tentativeRate == 0
def map2(self, workingPath):
"""
#correspondance entre atomes de la brique et du fichier sdf
"""
file = self.load(workingPath)
if not file:
raise CycleUnknown, self.cansmiles()
f = open(file)
reader = MDL.sdin(f)
m = reader.next()[0]
# mx = reader.next() # ou while reader.next()
# m = mx[0]
f.close()
# output :
i = j = tentativeRate = 0
cyclesChecked = []
cyclesMapped = []
#print "nb cycles", len(self.molecule.cycles)
while tentativeRate < len(
self.molecule.cycles
): # boucle tant que le nb de tentative rate de mapping n'est pas egale au nb de cycle ds la molecule
#print j,i,len(self.molecule.cycles[j]),len(m.cycles[i])
if len(self.molecule.cycles[j]) == len(
m.cycles[i]
): # si les 2 cycles ont le meme nb d'atomes, on peut essayer de les mapper
if mapCycles(self.molecule.cycles[j], m.cycles[i]):
#print "mapCycles(self.molecule.cycles[j],m.cycles[i])"
cyclesChecked.append(i)
cyclesMapped.append(j)
j += 1
tentativeRate = 0
break
else:
tentativeRate += 1
else:
tentativeRate += 1
i += 1
while len(cyclesMapped) < len(
self.molecule.cycles) and tentativeRate < len(
self.molecule.cycles) - len(cyclesChecked):
if i in cyclesChecked:
i += 1
continue
if i == len(m.cycles):
i = 0
continue
if j in cyclesMapped:
j += 1
continue
if j == len(self.molecule.cycles):
j = 0
continue
coord = 0
for atom in self.molecule.cycles[j].atoms:
if atom.x != None:
coord = 1
break
if not coord:
j += 1
continue
if len(self.molecule.cycles[j]) == len(m.cycles[i]):
if mapCycles2(self.molecule.cycles[j], m.cycles[i]):
cyclesChecked.append(i)
cyclesMapped.append(j)
j += 1
tentativeRate = 0
else:
tentativeRate += 1
else:
tentativeRate += 1
i += 1
return tentativeRate == 0
> <LIBRARY> (ST012965) TimTec > <96PLATE> (ST012965) TIMTEC010 > <96ROW> (ST012965) B > <96COL> (ST012965) 6 > <384PLATE> (ST012965) TIC384003 > <384COL> (ST012965) 12 > <384ROW> (ST012965) C $$$$""" from cStringIO import StringIO data = StringIO(text) from frowns import MDL mol, errors, text = MDL.sdin(data).next() print mol
def load(self, workingPath, verbose=False):
"""
charger le fichier sdf de la brique
"""
if verbose:
sys.stderr.write("Brique.load: %s\n" % LIBRARY_PATH)
if not LIBRARY_PATH:
sys.stderr.wirte(
"variable path de la classe Brique non initialisee\n")
return 0
try:
listFile = os.listdir(
LIBRARY_PATH
) # liste des fichier contenu ds 'PAHT' -> listFile
except:
sys.stderr.write(
"Brique.load: Failed to access ring library at %s\n" %
LIBRARY_PATH)
# sys.exit(0)
name = self.cansmiles()
if verbose:
sys.stderr.write("Brique.load: Attempting %s ...\n" % str(name))
# print "Brique.load:",name
if workingPath[-1] != "/":
workingPath += "/"
fileSmi = open(workingPath + "brique.smi", "w")
fileSmi.write(name + "\n")
fileSmi.close()
if verbose:
sys.stderr.write("Brique.load: babel sdf conversion ...\n")
os.system(BABEL_PATH + " -ismi " + workingPath + "brique.smi -osdf " +
workingPath + "brique.sdf 2> /dev/null")
os.system("echo '$$$$' >> " + workingPath + "brique.sdf")
# sys.stderr.write("Brique.load: Will read %s/brique.sdf\n" % (workingPath))
fileSdf = open(workingPath + "brique.sdf")
reader = MDL.sdin(fileSdf)
name2 = reader.next()[0].cansmiles()
# sys.stderr.write("Brique.load: read sdf as %s\n" % name2)
fileSdf.close()
# print "brique", name, name2
# if name2 in listFile: # si le fichier est ds la liste
# return LIBRARY_PATH+name2 # on renvoie le chemin complet du fichier
# elif name in listFile:
# return LIBRARY_PATH+name
if name in listFile:
return LIBRARY_PATH + name
else:
# 11 fevrier 2010: We attempt to generate using AMMOS, not to use babel conversion for name.
name2 = name
if verbose:
sys.stderr.write("Brique.load: Building %s as %s ...\n" %
(str(name), str(name2)))
try:
# Generer du mol2.
uName = name2.replace("(", "\(").replace(")", "\)").replace(
"[", "\[").replace("]", "\]")
# f =open("%s/%s.smi" % (LIBRARY_PATH, name2), "w")
sys.stderr.write("Creating %s%s.smi\n" % (LIBRARY_PATH, uName))
f = open("%s%s.smi" % (LIBRARY_PATH, name2),
"w") # in python do not escape names !!!
f.write("%s\n" % name2)
f.close()
cmd = "%s -h -ismi %s/%s.smi -omol2 %s/%s.mol2" % (
BABEL_PATH, LIBRARY_PATH, uName, LIBRARY_PATH, uName)
# cmd = "%s -h -ismi %s/%s.smi -omol2 %s/%s.mol2" % (BABEL_PATH, LIBRARY_PATH, "itest", LIBRARY_PATH, "itest")
sys.stderr.write("%s\n" % cmd)
os.system(cmd)
# Generer le fichier input.param
# path_of_DG-AMMOS= /Users/DG-AMMOS
# bank= input_dataset.mol2
f = open("%s/%s.dgammos" % (LIBRARY_PATH, name2), "w")
# f= open("%s.dgammos" % ("itest"), "w")
f.write("path_of_DG-AMMOS= %s\n" % DGAMMOSHOME)
f.write("bank= %s%s.mol2\n" % (LIBRARY_PATH, name2))
# f.write("bank= %s%s.mol2\n" % (LIBRARY_PATH, "itest"))
f.close()
sys.stderr.write("Generated %s/%s.dgammos\n" %
(LIBRARY_PATH, uName))
sys.stderr.write("Generating %s/%s.mol2\n" %
(LIBRARY_PATH, uName))
cmd = "%s %s/%s.dgammos" % (AMMOSBUILD, LIBRARY_PATH, uName)
# cmd = "%s %s.dgammos" % (AMMOSBUILD, uName)
sys.stderr.write("DG_AMMOS cmd: %s\n" % (cmd))
os.system(cmd)
# sys.exit(0)
# Convertir en sdf, oter les H
# cmd = "%s -d -imol2 %s/%s_Built.mol2 -osdf %s/%s.sdf 2> %s/%s.log" % (BABEL_PATH, LIBRARY_PATH, name2, LIBRARY_PATH, name2, LIBRARY_PATH, name2)
cmd = "%s -d -imol2 %s/%s_Built.mol2 -osdf %s/%s 2> %s/%s.log" % (
BABEL_PATH, LIBRARY_PATH, uName, LIBRARY_PATH, uName,
LIBRARY_PATH, uName)
os.system(cmd)
os.system("echo '$$$$' >> %s/%s" % (LIBRARY_PATH, uName))
# sys.exit(0)
# self.load(workingPath)
return LIBRARY_PATH + name2
# SI AMMOS N'A PAS PUS GENERER LE CYCLE: le mol2 sera dans %s/%s_BadMolecules.mol2
# os.system(cmd)
except:
return 0
return 0
-0.3583 0.2083 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.3583 1.0333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3583 -1.4416 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0708 1.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.0666 -0.2083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0666 -1.0333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3583 1.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.0708 -1.4458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
2 5 1 0 0 0 0
2 10 1 0 0 0 0
3 4 1 1 0 0 0
3 7 1 0 0 0 0
4 6 2 0 0 0 0
4 9 1 0 0 0 0
5 8 1 0 0 0 0
7 8 1 0 0 0 0
M END
$$$$
"""
if __name__ == "__main__":
import StringIO
from frowns import MDL
mol, error, text = MDL.sdin(StringIO.StringIO(__test__)).next()
print mol
# app = wxPySimpleApp()
d = Drawer()
print d.makeGif(mol)