def depict_smile(genecluster, structuresfolder):
indigo = Indigo()
renderer = IndigoRenderer(indigo)
query = indigo.loadMoleculeFromFile("genecluster" + str(genecluster) +
".smi")
indigo.setOption("render-coloring", True)
renderer.renderToFile(query, "genecluster" + str(genecluster) + ".png")
indigo.setOption("render-image-size", 200, 150)
renderer.renderToFile(query,
"genecluster" + str(genecluster) + "_icon.png")
dircontents = os.listdir(os.getcwd())
geneclusterstring = "genecluster" + str(genecluster) + ".png"
if geneclusterstring in dircontents:
shutil.copy("genecluster" + str(genecluster) + ".png",
structuresfolder)
shutil.copy("genecluster" + str(genecluster) + "_icon.png",
structuresfolder)
shutil.copy("genecluster" + str(genecluster) + ".smi",
structuresfolder)
os.remove("genecluster" + str(genecluster) + ".png")
os.remove("genecluster" + str(genecluster) + "_icon.png")
os.remove("genecluster" + str(genecluster) + ".smi")
smiles_input = path.join('SMILES', 'input')
if path.exists(smiles_input):
os.remove(smiles_input)
return "success"
else:
return "failed"
def resetIndigo():
global indigo, indigoRenderer, indigoInchi
indigo = Indigo()
indigoRenderer = IndigoRenderer(indigo)
indigoInchi = IndigoInchi(indigo)
# Set default options
indigo.setOption('render-bond-length', '30')
indigo.setOption('render-relative-thickness', '1.3')
indigo.setOption('render-coloring', False)
indigo.setOption('render-comment-font-size', 14.0)
indigo.setOption('render-comment-offset', '10')
def resetIndigo():
global indigo, indigoRenderer, indigoInchi
indigo = Indigo()
indigoRenderer = IndigoRenderer(indigo)
indigoInchi = IndigoInchi(indigo)
# Set default options
indigo.setOption('render-bond-length', '30')
indigo.setOption('render-relative-thickness', '1.3')
indigo.setOption('render-coloring', False)
indigo.setOption('render-comment-font-size', 14.0)
indigo.setOption('render-comment-offset', '10')
def wrapper():
indigo = Indigo()
opts = request.json.get('options', {})
for key, value in opts.items():
try:
indigo.setOption(key, value)
except IndigoException as e:
pass
mol_text = request.json.get("struct")
try:
mol = indigo.loadMolecule(mol_text)
except IndigoException as e:
return jsonify({'msg': str(e)})
return func(mol)
def get_molfile_v3000(compound: str) -> str:
"""Computes the molfile v3000 from a compound string.
Args:
compound: A molfile (either v2000 or v3000), MRV file, etc.
Returns:
The molfile v3000.
"""
indigo = Indigo()
indigo.setOption("molfile-saving-mode", "3000")
molecule = indigo.loadMolecule(compound)
return molecule.molfile()
def indigo_atom_map_reaction(rxn_smiles: str,
timeout_period: int,
existing_mapping="discard",
verbose=False):
try:
# Instantiate the Indigo class object and set the timeout period.
indigo_mapper = Indigo()
indigo_mapper.setOption("aam-timeout", timeout_period)
# Return the atom mapping of the reaction SMILES string.
rxn = indigo_mapper.loadReaction(rxn_smiles)
rxn.automap(existing_mapping)
return rxn.smiles()
# If an exception occurs for any reason, print the message if indicated, and return None.
except Exception as exception:
if verbose:
print(
"Exception occured during atom mapping of the reaction SMILES. Detailed message: {}"
.format(exception))
return None
def smiles(smiles_string):
# Render SMILES to PNG
indigo = Indigo()
renderer = IndigoRenderer(indigo)
mol = indigo.loadMolecule(smiles_string)
mol.layout() # if not called, will be done automatically by the renderer
indigo.setOption("render-output-format", "png")
indigo.setOption("render-image-size", 250, 250)
indigo.setOption("render-background-color", 1.0, 1.0, 1.0)
indigo.setOption("render-coloring", True)
indigo.setOption("aromaticity-model", "generic")
mol.dearomatize()
buf = renderer.renderToBuffer(mol)
buf = io.BytesIO(buf)
return send_file(
buf,
mimetype='image/png',
as_attachment=False,
)
def wrapper():
indigo = Indigo()
opts = request.json.get('options', {})
for key, value in opts.items():
indigo.setOption(key, value)
return func()
# Indigo code acquired from http://www.ggasoftware.com/
from indigo import Indigo
from indigo_renderer import IndigoRenderer
import uuid
import rsvg
import gtk
BORDER_WIDTH = 0
# for more rendering options visit:
# http://www.ggasoftware.com/opensource/indigo/api/options#rendering
_indigo = Indigo()
_renderer = IndigoRenderer(_indigo)
_indigo.setOption('render-output-format', 'svg')
_indigo.setOption('render-margins', 10, 10)
_indigo.setOption('render-stereo-style', 'none')
_indigo.setOption('render-implicit-hydrogens-visible', False)
_indigo.setOption('render-coloring', True)
_indigo.setOption('render-bond-length', 20.0)
_indigo.setOption('render-label-mode', 'hetero')
def smiles2svg(smiles, comment=''):
_indigo.setOption('render-comment', comment)
m = _indigo.loadMolecule(smiles)
m.aromatize()
m.layout()
s = _renderer.renderToBuffer(m).tostring()
id = str(uuid.uuid4())
i = 0
while True:
# Indigo code acquired from http://www.ggasoftware.com/
from indigo import Indigo
from indigo_renderer import IndigoRenderer
import uuid
import rsvg
import gtk
BORDER_WIDTH = 0
# for more rendering options visit:
# http://www.ggasoftware.com/opensource/indigo/api/options#rendering
_indigo = Indigo()
_renderer = IndigoRenderer(_indigo)
_indigo.setOption('render-output-format', 'svg')
_indigo.setOption('render-margins', 10, 10)
_indigo.setOption('render-stereo-style', 'none')
_indigo.setOption('render-implicit-hydrogens-visible', False)
_indigo.setOption('render-coloring', True)
_indigo.setOption('render-bond-length', 20.0)
_indigo.setOption('render-label-mode', 'hetero')
def smiles2svg(smiles, comment=''):
_indigo.setOption('render-comment', comment)
m = _indigo.loadMolecule(smiles)
m.aromatize()
m.layout()
s = _renderer.renderToBuffer(m).tostring()
id = str(uuid.uuid4())
i = 0
def indigo_structure(self):
indigo = Indigo()
indigo.setOption("molfile-saving-mode", "3000")
return indigo.loadStructure(structureStr=self.molfile_v3000)
0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -20, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -10, 0
]
print("Add packed fingerprints to Indigo:")
fp_size_bytes = 64 # or 512 bits, or 8 qwords
from indigo import Indigo
from bingo import Bingo
indigo = Indigo()
bingo = Bingo.createDatabaseFile(indigo, path.join('tempdb'), 'molecule',
'')
indigo.setOption("fp-sim-qwords", fp_size_bytes / 8)
indigo.setOption("fp-ext-enabled", True)
indigo.setOption("fp-ord-qwords", 0) # optional
indigo.setOption("fp-tau-qwords", 0) # optional
indigo.setOption("fp-any-qwords", 0) # optional
molecules = []
for id in range(len(df_descriptors)):
smiles = df_descriptors.ix[id, 'Structure']
descriptors = list(df_descriptors.ix[id])[2:]
normalized = [(f - min_bounds[i]) / (max_bounds[i] - min_bounds[i])
for i, f in enumerate(descriptors)]
fp = pack_normalized_descriptors_to_fingerprint(
normalized, density=0.3, byte_size=fp_size_bytes)
'C1CC(=O)NC2=C1C=CC(=C2)OCCCCN3CCN(CC3)C4=C(C(=CC=C4)Cl)Cl',
'CNC1(CCCCC1=O)C2=CC=CC=C2Cl',
'CN1C2CCC1C(C(C2)OC(=O)C3=CC=CC=C3)C(=O)OC',
'CCCC1=NN(C2=C1NC(=NC2=O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)C)OCC)C'
]
for i, sml in enumerate(smiles):
print("#%2d: %s" % (i, sml))
df_descriptors = []
indigo = Indigo()
# indigo.setOption("similarity-type", "sim")
# indigo.setOption("similarity-type", "chem")
# indigo.setOption("similarity-type", "ECFP2")
indigo.setOption("similarity-type", "ECFP4")
# indigo.setOption("similarity-type", "ECFP6")
# indigo.setOption("similarity-type", "ECFP8")
fingerprints = []
for sml in smiles:
mol = indigo.loadMolecule(sml)
fp = mol.fingerprint("sim")
fingerprints += [fp]
print("*** Fingerprints ***")
for i, fp in enumerate(fingerprints):
str = fp.toString()
density = fp_density(str)
print("#%2d: Density: %f ; FP: %s" % (i, density, str))
