def readSmiles(file):
"""
lit un fichier SMILES et renvoi les infos (liste des molecules, listes des noms, listes des id)
"""
f = open(file)
lines = f.readlines(
) # lit le contenu du fichier, chaque ligne est une chaine de caractere
f.close()
smilesError = "error.smi"
sdfError = "error.sdf"
mol = []
for line in lines: # pour chacune des lignes du fichier
data = line.split(
) # decoupe la ligne en plusieurs chaines de caracteres pr pouvoir acceder a chacune des informations conenues ds la ligne
if len(data) > 1:
try:
mol.append(iMolecule(smiles=data[0], id=data[1]))
except:
ferror = open(smilesError, "w")
ferror.write(data[0] + "\t" + data[1] + "\n")
ferror.close()
os.system("babel -ismi " + smilesError + " -osdf " + sdfError)
mol.extend(readSDF(sdfError))
else:
try:
mol.append(iMolecule(smiles=data[0]))
except:
ferror = open(smilesError, "w")
ferror.write(data[0] + "\n")
ferror.close()
os.system("babel -ismi " + smilesError + " -osdf " + sdfError)
mol.extend(readSDF(sdfError))
return mol
def readSmiles(file):
"""
lit un fichier SMILES et renvoi les infos (liste des molecules, listes des noms, listes des id)
"""
f=open(file)
lines = f.readlines() # lit le contenu du fichier, chaque ligne est une chaine de caractere
f.close()
smilesError = "error.smi"
sdfError = "error.sdf"
mol=[]
for line in lines : # pour chacune des lignes du fichier
data = line.split() # decoupe la ligne en plusieurs chaines de caracteres pr pouvoir acceder a chacune des informations conenues ds la ligne
if len(data)>1 :
try :
mol.append(iMolecule(smiles=data[0],id=data[1]))
except :
ferror=open(smilesError,"w")
ferror.write(data[0]+"\t"+data[1]+"\n")
ferror.close()
os.system("babel -ismi "+smilesError+" -osdf "+sdfError)
mol.extend(readSDF(sdfError))
else :
try :
mol.append(iMolecule(smiles=data[0]))
except :
ferror=open(smilesError,"w")
ferror.write(data[0]+"\n")
ferror.close()
os.system("babel -ismi "+smilesError+" -osdf "+sdfError)
mol.extend(readSDF(sdfError))
return mol
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
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
from iMolecule import *
mOri = iMolecule("c1(C(=NO)Cc2ccccc2)c([n]([c]3[c]1cccc3)C)C")
mOri.graph2molecule()
fileSdf = open("testEnergyThiago1_3D_multiconf_bruno.sdf")
reader = MDL.sdin(fileSdf)
for i in range(21):
m = reader.next()[0]
for at in m.atoms:
at.mmffAtomType = getMMFFAtomType(at)
tmp = str(len(m.atoms)) + "\n500\n100\n"
for atom in m.atoms:
vdwParams = VDW_PARAM[str(atom.mmffAtomType)]
tmp += str(atom.x)+" "+str(atom.y)+" "+str(atom.z)+" "+str(getMMFFPartialAtomicCharge(atom))+" "+ \
