def write_mols_to_sdf(unique_list, sdf_filename, min_rmsd, out_filename):
"""Creates new sdf file and writes unique molecules into it"""
if out_filename:
out_mol = pybel.Outputfile('sdf', out_filename)
else:
out_mol = pybel.Outputfile('sdf', sdf_filename)
for pymol in unique_list:
out_mol.write(pymol)
out_filename = out_mol.filename
out_mol.close()
return out_filename
def generate_report(results,
outfile='dw_scores.sdf',
vendors_list=None,
zinc=True):
if vendors_list:
sd = pybel.Outputfile('sdf', "ltd_" + outfile, overwrite=True)
else:
sd = pybel.Outputfile('sdf', outfile, overwrite=True)
if zinc:
for j, (smiles, xid, label, vendors, zincid) in enumerate(results):
mol = pybel.readstring('smi', str(smiles))
mol.data['ZINCID'] = zincid
mol.data['Smiles'] = smiles
mol.data['Rank'] = j + 1
mol.data['x*'] = xid
mol.data['Label'] = label
mol.data['log P'] = mol.calcdesc(descnames=['logP'])['logP']
if vendors_list:
v = [re.compile(vend) for vend in vendors_list]
approved = []
for patt in v:
for co in list(
set([
b for c in [x.keys() for x in vendors]
for b in c
])):
if re.search(patt, co):
approved.append(co)
mol.data['vendors'] = '\n'.join(list(set(approved)))
if len(mol.data['vendors']) > 0:
sd.write(mol)
else:
mol.data['vendors'] = '\n'.join(
list(
set([
b for c in [x.keys() for x in vendors] for b in c
])))
sd.write(mol)
sd.close()
else:
for j, (smiles, xid, label) in enumerate(results):
mol = pybel.readstring('smi', str(smiles))
mol.data['x*'] = xid
mol.data['Label'] = label
sd.write(mol)
sd.close()
def rotateGroupSingleMol(self, xyzName, modList):
myMol = pybel.readfile('xyz', xyzName).next()
statusTotal = True
coords = [iatom.coords for iatom in myMol.atoms]
[angle, groupA, groupB] = modList
if len(groupA) < 1:
print "Nothing to rotate along direction "
return statusTotal
#Get the center of set B
vcenter = np.array([0.0, 0.0, 0.0])
for i in groupB:
vcenter += np.array(coords[i])
vcenter /= len(groupB)
#Get the axis of the plan defined by set B
v1 = np.array(coords[groupB[0]]) - np.array(coords[groupB[1]])
v2 = np.array(coords[groupB[2]]) - np.array(coords[groupB[1]])
axis = np.cross(v1, v2)
vnorm = np.linalg.norm(axis)
axis /= vnorm
#Now do the rotation
for i in groupA:
oldcoord = np.array(coords[i])
newcoord = self.rotateAroundAxis(oldcoord, vcenter, axis, angle)
newcoordV3 = pybel.ob.vector3(newcoord[0], newcoord[1],
newcoord[2])
atomToMove = myMol.OBMol.GetAtom(i + 1)
atomToMove.SetVector(newcoordV3)
# delete the original xyz file
subprocess.call(['rm', '-r', xyzName])
# if succeeded, overwrite and get new xyz
if statusTotal == True:
output = pybel.Outputfile("xyz", xyzName)
output.write(myMol)
output.close()
return statusTotal
def moveGroupSingleMol(self, xyzName, modList):
myMol = pybel.readfile('xyz', xyzName).next()
statusTotal = True
coords = [iatom.coords for iatom in myMol.atoms]
for mod in modList:
[dist, d1, d2, groupAtoms] = mod
if len(groupAtoms) < 1:
print "Nothing to move along direction ", d1, "-->", d2
[dist, d1, d2, groupAtoms] = mod
v1 = np.array(coords[d1])
v2 = np.array(coords[d2])
v = v2 - v1
vnorm = np.linalg.norm(v)
v /= vnorm
for i in groupAtoms:
newcoord = np.array(coords[i]) + dist * v
newcoordV3 = pybel.ob.vector3(newcoord[0], newcoord[1],
newcoord[2])
atomToMove = myMol.OBMol.GetAtom(i + 1)
atomToMove.SetVector(newcoordV3)
# delete the original xyz file
subprocess.call(['rm', '-r', xyzName])
# if succeeded, overwrite and get new xyz
if statusTotal == True:
output = pybel.Outputfile("xyz", xyzName)
output.write(myMol)
output.close()
return statusTotal
def modifyBondsSingleMol(self, xyzName, bondList):
myMol = pybel.readfile('xyz', xyzName).next()
statusTotal = True
for bond in bondList:
[bondLength, i0, i1] = bond
bondToChange = myMol.OBMol.GetBond(i0 + 1, i1 + 1)
if bondToChange == None:
print "WARNING! The specified bond ", i0, "-", i1, " does not exist"
print "Creating bond ", i0, "-", i1, " and then process the bondlength modification request"
bondOrder = 1
addBondStatus = myMol.OBMol.AddBond(i0 + 1, i1 + 1, bondOrder)
if addBondStatus == False:
print "Failed to add specified bond ", i0, "-", i1
statusTotal = False
break
else:
bondToChange = myMol.OBMol.GetBond(i0 + 1, i1 + 1)
atomToFix = myMol.OBMol.GetAtom(i0 + 1)
bondToChange.SetLength(atomToFix, bondLength)
if self.localopt_ == True:
myMol.localopt(steps=500)
# delete the original xyz file
subprocess.call(['rm', '-r', xyzName])
# if succeeded, overwrite and get new xyz
if statusTotal == True:
output = pybel.Outputfile("xyz", xyzName)
output.write(myMol)
output.close()
return statusTotal
def addHydrogenSingleMol(self, xyzName, HPositionList):
myMol = pybel.readfile('xyz', xyzName).next()
statusTotal = True
for HPosition in HPositionList:
#Calculate new hydrogen position and add hydrogen
Htype = HPosition[0]
if Htype == "sp2":
status = self.addHydrogenSp2(myMol, HPosition)
#Print out Hydrogen addition result
if status == False:
if self.indexed_ == 0:
print 'Failed to add sp2 H atom to molecule: ', xyzName, ', at atom ', i0, '(', i1, i2, '), bondlength:', round(
bondlength, 2)
else:
print 'Failed to add sp2 H atom to molecule: ', xyzName, ', at atom ', i0 + 1, '(', i1 + 1, i2 + 1, '), bondlength:', round(
bondlength, 2)
statusTotal = False
break
else:
#TODO: implement this part
print "sp3 H adding not implemented yet"
statusTotal = False
break
# delete the original xyz file
subprocess.call(['rm', '-r', xyzName])
# if succeeded, overwrite and get new xyz
if statusTotal == True:
output = pybel.Outputfile("xyz", xyzName, overwrite=True)
output.write(myMol)
output.close()
return statusTotal
def main():
parser = argparse.ArgumentParser(
description="Change the title from a molecule file to metadata \
value of a given-id of the same molecule file.",
)
parser.add_argument('--infile', '-i',
required=True, help="path to the input file")
parser.add_argument('--outfile', '-o',
required=True, help="path to the output file")
parser.add_argument('--key', '-k',
required=True, help="the metadata key from the sdf file which should inlcude the new title")
parser.add_argument('--random', '-r',
action="store_true", help="Add random suffix to the title.")
args = parser.parse_args()
output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
for mol in pybel.readfile("sdf", args.infile):
if args.key in mol.data:
mol.title = mol.data[args.key]
if args.random:
suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13))
mol.title += '__%s' % suffix
output.write( mol )
output.close()
def align(self):
print self.step_, 'Align all effective conformers to the lowest-energy conformer'
checkAndRemoveFile(self.mdXyzFileName_)
print 'Wring out effective conformers to file:', self.mdXyzFileName_
mdXyzFile = open(self.mdXyzFileName_, 'a')
for i in range(0, self.numEffectMin_):
name = self.nameEnergyList_[i][0]
subprocess.call(['cat', name], stdout=mdXyzFile)
mdXyzFile.close()
#Get Topology file to be used in mdtraj
topXyzName = self.nameEnergyList_[0][0]
topPdbName = topXyzName.replace('xyz', 'pdb')
checkAndRemoveFile(topPdbName)
mol = pybel.readfile('xyz', topXyzName).next()
output = pybel.Outputfile('pdb', topPdbName, overwrite=True)
output.write(mol)
output.close()
#Load conformers into mdtraj and analyze
t = md.load(self.mdXyzFileName_, top=topPdbName)
self.t_aligned_ = t.superpose(t,
frame=0,
atom_indices=self.alignedAtoms_)
checkAndRemoveFile('all_aligned.xyz')
self.t_aligned_.save_xyz('all_aligned.xyz')
printLine()
self.step_ += 1
def format_conversion(self):
'''
A Tool: convert the small molecules from the origin format to the object format.
meanwhile, it will add hydrogen and give atomic particle charge under charge model:
(eem, eem2015ba, eem2015bm, eem2015bn, eem2015ha, eem2015hm, eem2015hn, eqeq,
fromfile, gasteiger, mmff94, none, qeq, qtpie).
'''
import os, sys
try:
import pybel
except Exception as exc:
sys.stdout.write('\n\033[1;31mThere is a problem:\033[0m\t%s\n' %
exc)
sys.exit(
'\n\033[1;36mPlease use pip/conda to install it or append its path to PYTHONPATH.\033[0m\n'
)
with open(self.temp_illustration, 'a') as tmp_f0:
tmp_f0.write(
'# ligand with charge from pybel(charge model: %s).\n\t%s\n' %
(self.charge_model, 'lig_pybel.mol2'))
with open('lig_pybel.mol2', 'w') as lig_object:
for lig_file in list(self.name.split(',')):
in_format = lig_file.split('.')[-1]
in_put = lig_file.strip()
out_put = pybel.Outputfile('mol2', 'lig_pybel_tmp.mol2')
mol = list(pybel.readfile(in_format, in_put))[0]
mol.addh()
if self.draw_key:
mol.draw(show=False,
filename='%s.png' % lig_file.split('.')[0])
mol.calccharges(model=self.charge_model)
out_put.write(mol)
lig_object.writelines([_ for _ in open('lig_pybel_tmp.mol2')])
os.unlink('lig_pybel_tmp.mol2')
def main(input_ext, inputfile, output_ext, outputfilename, nconfs, rmsd_cutoff,
energy_cutoff):
ff = pybel._forcefields['mmff94']
outputfile = pybel.Outputfile(output_ext, outputfilename, overwrite=True)
for i, mol in enumerate(pybel.readfile(input_ext, inputfile)):
t = time.time()
print "**Molecule %d\n..title = %s" % (i, mol.title)
print "..number of rotatable bonds = %d" % mol.OBMol.NumRotors()
mol.addh()
ff.Setup(mol.OBMol)
ff.DiverseConfGen(rmsd_cutoff, nconfs, energy_cutoff)
ff.GetConformers(mol.OBMol)
confdata = pybel.ob.toConformerData(
mol.OBMol.GetData(pybel.ob.ConformerData))
energies = confdata.GetEnergies()
N = mol.OBMol.NumConformers()
assert N == len(energies)
print "..generated %d conformers"
u = time.time()
data = []
for i in range(N):
mol.OBMol.SetConformer(i)
outputfile.write(mol)
print "..(overall time = %.1fs writing results = %.1fs)" % (
time.time() - t, time.time() - u)
print "\n"
outputfile.close()
def filter_by_name(args):
outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
for mol in pybel.readfile('sdf', args.input):
for name in open(args.list_of_names):
if mol.title.strip() == name.strip():
outfile.write(mol)
outfile.close()
def main():
#Initializes paths using system arguments
readPath = str(
sys.argv[1]) #the user input the path to read sdf files from
storePath = str(sys.argv[2]) #the user inputs path to store the poses into
os.chdir(
readPath) #Navigate to the folder containing the sdf files to read
nameList = []
#Keep track of all file names inside of the read folder
for filename in os.listdir(os.getcwd()):
if not filename.startswith('.'):
nameList.append(filename)
i = 0 #Variable used to increment the filenames inside of the output folder
#Splits the sdf file by each molecule and saves under an incrementing file name
for j in range(len(nameList)):
os.chdir(readPath)
for mol in pybel.readfile(
'sdf', nameList[j]): #reads each sdf file in readPath
os.chdir(storePath)
while os.path.exists(
'pose%s.sdf' %
i): #increments i to find next highest file name
i += 1
out = pybel.Outputfile('sdf',
'pose%s.sdf' % i) #creates new .sdf file
out.write(mol)
out.close()
def main():
parser = argparse.ArgumentParser(
description="Change the title from a molecule file to metadata \
value of a given-id of the same molecule file.", )
parser.add_argument('--infile',
'-i',
required=True,
help="path to the input file")
parser.add_argument('--outfile',
'-o',
required=True,
help="path to the output file")
parser.add_argument(
'--key',
'-k',
required=True,
help=
"the metadata key from the sdf file which should inlcude the new title"
)
args = parser.parse_args()
output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
for mol in pybel.readfile("sdf", args.infile):
if args.key in mol.data:
mol.title = mol.data[args.key]
output.write(mol)
output.close()
def saveMol(prot, outPref, outFmt):
# apply eventual patches due to amber top to openbabel format differences and output docking format file
currDir = os.getcwd()
# adjust H
for atom in prot:
if atom.atomicnum == 1:
atom.OBAtom.SetType('H')
for res in ob.OBResidueIter(prot.OBMol):
resname = res.GetName()
if resname == 'HEM':
#nhem=res.GetNum()
for atm in ob.OBResidueAtomIter(res):
if atm.GetType() == 'FE':
atm.SetType('Fe')
if atm.GetType() == 'Du':
atName = res.GetAtomID(atm).lstrip()
atm.SetType(atName[0])
print "save mol2 for docking"
templfn = os.path.join(currDir, "%s.%s" % (outPref, outFmt))
out = pb.Outputfile(outFmt, templfn, overwrite=True)
out.write(prot)
out.close()
return templfn
def main(workdir):
"""
Main method for generating many kinbot runs to get a large dataset of initial ts structures
"""
dir = os.path.expanduser(workdir)
#read the .dat file
f = open('{}smi.dat'.format(dir))
par = imp.load_source('par', '', f)
#make a sdf file for visualization
output = pybel.Outputfile("sdf", dir + "species.sdf",overwrite=True)
for name in par.smiles:
smi = par.smiles[name]
obmol = pybel.readstring("smi",smi)
output.write(obmol)
output.close()
#list with the jobs that need to be done
jobs = []
#iterate the input files
for name in par.smiles:
#name = input_file.replace('.inp','') #name of the calculation
test_dir = dir + name #location where the calculations will be done
if not os.path.exists(test_dir):
os.mkdir(test_dir)
#copy the input file to the working directory
write_input_file(par,name,par.smiles[name],test_dir + '/input.inp')
job = workdir + name + '/'
jobs.append(job)
run_threads(jobs, 'eric', max_running = 3)
def main():
commandLineParser = argparse.ArgumentParser(description="Docking Results Ranking to Three Dimensions: takes \
a table generated by DRranker.py and builds a file \
with the coordinates of the docked molecules")
commandLineParser.add_argument("rankingFile", help="file generated by DRranker.py")
commandLineParser.add_argument("outputFile", help="output filename")
commandLineParser.add_argument("-r", "--lowest-ranking", dest="lowestRanking", default=1, type=int, help="Last ranking level to be processed. Default: 1")
commandLineParser.add_argument("-f", "--output-format", dest="outputFormat", default="sdf", help="Format of the file to be written. It must be a openbabel supported output format. Deafult: sdf")
options = commandLineParser.parse_args()
(ranking,basenames) = processRanking(options.rankingFile, options.lowestRanking)
for (basename,coordFile) in basenames:
try:
mols = pybel.readfile("sdf", coordFile)
except:
print("Can't open " + coordFile, file=sys.stderr)
exit()
for mol in mols:
if (mol.title,basename) in ranking:
ranking[(mol.title,basename)] = pybel.Molecule(pybel.ob.OBMol(mol.OBMol))
out = pybel.Outputfile(filename=options.outputFile, format=options.outputFormat, overwrite=True)
for (molname,basename) in list(ranking.keys()):
mol = ranking[(molname,basename)]
mol.title += "_" + basename
out.write(mol)
out.close()
def __init__(self,
inputFile,
reference=None,
cutoff=10.0,
residueList=None):
"""Initialization of the protein, defined by a list of residues"""
self.residueList = residueList
self.residues = {}
self.inputFile = inputFile
fileExtension = os.path.splitext(inputFile)[1]
if fileExtension.lower() == '.mol2':
self.residuesFromMOL2File()
elif fileExtension.lower() == '.pdb':
for mol in pybel.readfile("pdb", inputFile):
# print(dir(mol))
outfile = inputFile.replace('.pdb', '_conv.mol2')
output = pybel.Outputfile("mol2", outfile, overwrite=True)
output.write(mol)
output.close()
self.inputFile = outfile
else:
raise ValueError(
'{} files are not supported for the protein.'.format(
fileExtension[1:].upper()))
self.residuesFromMOL2File()
# if not self.residueList:
# self.residueList = self.detectCloseResidues(reference, cutoff)
self.cleanResidues()
def makefiles(filename, folder, length, repunit=1):
monos = getmonomers(filename)
smiles = []
for i, smile in enumerate(monos):
if repunit == 1:
smiles.append(smile * length)
elif repunit == 2:
smiles.extend([
"%s%s" % (smile, x) * (length / repunit) for x in monos[i + 1:]
])
info = open(os.path.join(folder, folder + ".txt"), "w")
sdf = pybel.Outputfile("sdf",
os.path.join(folder, folder + ".sdf"),
overwrite=True)
for i, smile in enumerate(smiles):
print i, str(smile)
print >> info, str(smile)
mol = pybel.readstring("smi", smile)
globalopt(mol)
gaussian = (header + "\n\n" + smile + "\n" + "\n".join(
mol.write("gau").replace("0 3\n", "0 1\n").split("\n")[3:]) +
header_b) % (i, i)
with open(os.path.join(folder, "%d.gjf" % i), "w") as output:
output.write(gaussian)
mol.title = str(i)
sdf.write(mol)
info.close()
sdf.close()
def compute_properties(args):
if args.oformat == 'sdf':
outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
else:
outfile = open(args.output, 'w')
if args.header:
mol = next(pybel.readfile(args.iformat, args.input))
metadata = cheminfolib.get_properties_ext(mol)
outfile.write(
'%s\n' %
'\t'.join([cheminfolib.ColumnNames[key] for key in metadata]))
for mol in pybel.readfile(args.iformat, args.input):
if mol.OBMol.NumHvyAtoms() > 5:
metadata = cheminfolib.get_properties_ext(mol)
if args.oformat == 'sdf':
[
mol.data.update(
{cheminfolib.ColumnNames[key]: metadata[key]})
for key in metadata
]
outfile.write(mol)
else:
outfile.write(
'%s\n' %
('\t'.join([str(metadata[key]) for key in metadata])))
outfile.close()
def aggregate(self):
"""remove hydrogen and add <MOLID>
"""
untarred_dir = self.requires().output().path
zincs = glob(os.path.join(untarred_dir, "ZINC*"))
mols = []
for zinc in zincs:
try:
mols.append(list(pybel.readfile('sdf', zinc)))
except Exception:
print("WARNING: ",
"Fail to load zinc ligand %s" % zinc,
file=sys.stderr)
mols = [mol for sub in mols for mol in sub]
ofn = os.path.join(self.subset_work_dir, self.ligand_code + '_1.sdf')
self.aggregated_ofn = ofn
ofs = pybel.Outputfile('sdf', ofn, overwrite=True)
try:
for mol in mols:
mol.removeh()
mol.data['MOLID'] = mol.title
ofs.write(mol)
except Exception as detail:
print("WARNING:", detail, file=sys.stderr)
finally:
ofs.close()
def main():
#replace with path you will read the sdf files from
readPath = '/Users/brycekroencke/Documents/Fellowship/data/largeSdfFiles'
#replace with path you want to store .sdf poses in
storePath = '/Users/brycekroencke/Documents/Fellowship/data/poses'
os.chdir(
readPath) #Navigate to the folder containing the sdf files to read
nameList = []
#Keep track of all file names inside of the read folder
for filename in os.listdir(os.getcwd()):
nameList.append(filename)
i = 0 #Variable used to increment the filenames inside of the output folder
#Splits the sdf file by each molecule and saves under an incrementing file name
for j in range(len(nameList)):
os.chdir(readPath)
for mol in pybel.readfile(
'sdf', nameList[j]): #reads each sdf file in readPath
os.chdir(storePath)
while os.path.exists(
'pose%s.sdf' %
i): #increments i to find next highest file name
i += 1
out = pybel.Outputfile('sdf',
'pose%s.sdf' % i) #creates new .sdf file
out.write(mol)
out.close()
def convertData(startExt, targetExt, path):
outputfile = f"{os.path.splitext(path)[0]}.{targetExt}"
if os.path.isfile(outputfile): return
w = pybel.readfile(startExt, path)
mol = next(w)
out = pybel.Outputfile(targetExt, outputfile)
out.write(mol)
out.close()
def addh(args):
outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
for mol in pybel.readfile(args.iformat, args.input):
if mol.OBMol.NumHvyAtoms() > 5:
mol.removeh()
mol.OBMol.AddHydrogens(args.polar, True, args.pH)
outfile.write(mol)
outfile.close()
def remove_ions(args):
outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
for mol in pybel.readfile(args.iformat, args.input):
if mol.OBMol.NumHvyAtoms() > 5:
mol.OBMol.StripSalts(0)
# Check if new small fragments have been created and remove them
if mol.OBMol.NumHvyAtoms() > 5:
outfile.write(mol)
outfile.close()
def get_pybel_mol(self):
'''
If the object has a rdkit molecule, use this to get a pybel molecule
'''
temp_sdf = self.name+'_temp.sdf'
output = pybel.Outputfile('sdf', temp_sdf)
output.write(self._rdkit_mol)
self._pybel_mol = readfile('sdf', temp_sdf).next()
os.remove(temp_sdf)
def __init__(self, smiles, file_format='pdb', filename='main'):
self.smiles = smiles
self.format = file_format
self.filename = filename + '.' + file_format
mol = pybel.readstring('smi', self.smiles)
mol.make3D()
mol.localopt(forcefield='mmff94', steps=1500)
output = pybel.Outputfile(self.format, self.filename)
output.write(mol)
output.close()
def convertData(namespace, startExt, targetExt, proteinnumber, path):
paths, complexes = Preprocessing.getAllMolPaths(
path, namespace + '.' + startExt)
w = pybel.readfile(startExt, paths[proteinnumber])
molec = next(w)
out = pybel.Outputfile(
targetExt, path + complexes[proteinnumber] + '/' +
complexes[proteinnumber] + namespace + '.' + targetExt)
out.write(molec)
out.close()
def main():
if len(sys.argv) < 2:
print "No input file provided: Murcko.py filetosprocess.ext"
print "The script will determine which file type to read from by the extension."
print "It is recommended you run your structures through,\nfor example, ChemAxon's Standardizer first."
sys.exit(1)
molnum = 0
Fragments = dict()
for mol in pybel.readfile(sys.argv[1].split('.')[1], sys.argv[1]):
molnum += 1
if not (molnum % 10):
print "Molecules processed:", molnum
#if molnum == 210:
# break
#print mol
mol.OBMol.DeleteHydrogens()
smiles = mol.write("smi").split("\t")[0]
#print smiles
#out.write(mol)
#print "Number of rings:", len(mol.sssr)
canmol = pybel.readstring("smi", smiles)
FusedRingsMatrix = GetFusedRingsMatrix(canmol)
FusedRings = GetFusedRings(FusedRingsMatrix, len(canmol.sssr))
#print FusedRings
RingSystems = GetAtomsInRingSystems(canmol, FusedRings, inclexo=True)
# Delete all non-ring atoms: this is now done in GetCanonicalFragments()
#for ringnum in range(len(mol.sssr)):
# mol = pybel.readstring("smi", smiles)
# ratoms = list(mol.sssr[ringnum]._path)
# #print "Atoms in ring:", sorted(ratoms, reverse=True)
# #Delete complementary atoms
# remove = list(set(range(1,len(mol.atoms)+1)).difference(set(ratoms)))
# for a in sorted(remove, reverse=True):
# mol.OBMol.DeleteAtom(mol.atoms[a-1].OBAtom)
# #print mol
# #out.write(mol)
# Get all rings/ring systems
frags = GetCanonicalFragments(smiles, RingSystems)
for frag in frags:
if frag in Fragments:
Fragments[frag] += 1
else:
Fragments[frag] = 1
# Write results to file
print "Writing results to file."
out = pybel.Outputfile("sdf", "fragments.sdf", overwrite=True)
d = Fragments
for k, v in sorted(d.items(), key=itemgetter(1), reverse=True):
mol = pybel.readstring("smi", k)
mol.data["COUNT"] = v
mol.OBMol.DeleteHydrogens()
out.write(mol)
out.close()
def separate(self, molecule_type, outfile):
output = pybel.Outputfile(molecule_type, outfile, overwrite=True)
split_mol = self.mol.OBMol.Separate()
for mol in split_mol:
mol = pybel.Molecule(mol)
mol.data.update({
"parent name": self.parent_name,
"parent canonical smiles": self.parent_can,
})
output.write(mol)
output.close()
def d3_viewer(self, molecule, viewer='avogadro'):
"""
Opens the geometry of the molecule in a 3d viewer.
Currently only avogadro is supported, but you can test it with other programms as well.
"""
mol = self.one_mol_from_sdf(molecule)
output = pybel.Outputfile('sdf', ".tmp.sdf", overwrite=True)
output.write(mol)
call([viewer, '.tmp.sdf'])
os.remove(".tmp.sdf")