def getParentView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', False))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
return _get_parent(data, **kwargs)
def chemblDescriptorsView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', True))
return json.dumps(_getChemblDescriptors(data, **kwargs))
def checkView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', False))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
return _check(data, **kwargs)
def excludeView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
return _exclude(data, **kwargs)
def getAlertsView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
return _get_alerts(data, **kwargs)
def smarts2ctabView(data, params):
kwargs = dict()
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))
kwargs['delimiter'] = params.get('delimiter', ' ')
kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
return _smarts2ctab(data, **kwargs)
def standardizeView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', False))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
return _standardize(data, **kwargs)
def ctab2smilesView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', True))
kwargs['delimiter'] = params.get('delimiter', ' ')
kwargs['nameHeader'] = params.get('nameHeader', 'Name')
kwargs['includeHeader'] = _parseFlag(params.get('includeHeader', True))
return _ctab2smiles(data, **kwargs)
def inchi2svgView(data, params):
kwargs = dict()
kwargs['size'] = int(params.get('size', 300))
kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))
response.content_type = 'image/svg+xml'
return _inchi2svg(data, **kwargs)
def image2ctabView(img, params):
kwargs = dict()
kwargs['jaggy'] = _parseFlag(params.get('jaggy', False))
kwargs['adaptive'] = _parseFlag(params.get('adaptive', False))
kwargs['unpaper'] = int(params.get('unpaper', 0))
known_location = '/usr/local/bin/osra'
if not os.path.exists(known_location):
known_location = '/usr/bin/osra'
return _image2ctab(img, config.get('osra_binaries_location',
known_location), **kwargs)
def ctab2svgView(data, params):
kwargs = dict()
kwargs['size'] = int(params.get('size', 300))
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
kwargs['kekulize'] = _parseFlag(params.get('kekulize', False))
kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', False))
response.content_type = 'image/svg+xml'
return _ctab2svg(data, **kwargs)
def smiles2ctabView(data, params):
kwargs = dict()
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))
kwargs['delimiter'] = params.get('delimiter', ' ')
kwargs['smilesColumn'] = int(params.get('smilesColumn', 0))
kwargs['nameColumn'] = int(params.get('nameColumn', 1))
kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
if params.get('titleLine') is None and not data.startswith(b'SMILES Name'):
kwargs['titleLine'] = False
else:
kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))
return _smiles2ctab(data, **kwargs)
def sdf2SimilarityMapSvgView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
kwargs['width'] = int(params.get('width', 500))
kwargs['height'] = int(params.get('height', 500))
kwargs['radius'] = int(params.get('radius', 2))
kwargs['fingerprint'] = params.get('fingerprint', 'morgan')
kwargs['format'] = 'svg'
response.content_type = 'image/svg+xml'
ret = _sdf2SimilarityMapSVG(data, **kwargs)
return ret
def canonicalizeSmilesView(data, params):
kwargs = dict()
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', False))
kwargs['in_delimiter'] = params.get('in_delimiter', ' ')
kwargs['out_delimiter'] = params.get('out_delimiter', ' ')
kwargs['smilesColumn'] = int(params.get('smilesColumn', 0))
kwargs['nameColumn'] = int(params.get('nameColumn', 1))
kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
kwargs['nameHeader'] = params.get('nameHeader', 'Name')
kwargs['includeHeader'] = _parseFlag(params.get('includeHeader', True))
if params.get('titleLine') is None and not data.startswith(b'SMILES Name'):
kwargs['titleLine'] = False
else:
kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))
return _canonicalize_smiles(data, **kwargs)
def smiles2svgView(data, params):
kwargs = dict()
kwargs['size'] = int(params.get('size', 300))
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))
kwargs['delimiter'] = params.get('delimiter', ' ')
kwargs['smilesColumn'] = int(params.get('smilesColumn', 0))
kwargs['nameColumn'] = int(params.get('nameColumn', 1))
kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
if params.get('titleLine') is None and not data.startswith(b'SMILES Name'):
kwargs['titleLine'] = False
else:
kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))
response.content_type = 'image/svg+xml'
return _smiles2svg(data, **kwargs)
def smiles2SimilarityMapSvgView(data, params):
kwargs = dict()
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', False))
kwargs['delimiter'] = params.get('delimiter', ' ')
kwargs['smilesColumn'] = int(params.get('smilesColumn', 0))
kwargs['nameColumn'] = int(params.get('nameColumn', 1))
kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
kwargs['width'] = int(params.get('width', 500))
kwargs['height'] = int(params.get('height', 500))
kwargs['radius'] = int(params.get('radius', 2))
kwargs['fingerprint'] = params.get('fingerprint', 'morgan')
kwargs['format'] = 'svg'
if params.get('titleLine') is None and not data.startswith(b'SMILES Name'):
kwargs['titleLine'] = False
else:
kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))
response.content_type = 'image/svg+xml'
ret = _smiles2SimilarityMapSVG(data, **kwargs)
return ret
def mcsView(data, params):
kwargs = dict()
kwargs['asSmiles'] = _parseFlag(params.get('asSmiles', '0'))
kwargs['atomCompare'] = params.get('atomCompare', 'elements')
kwargs['bondCompare'] = params.get('bondCompare', 'bondtypes')
kwargs['ringMatchesRingOnly'] = _parseFlag(
params.get('ringMatchesRingOnly', False))
kwargs['completeRingsOnly'] = _parseFlag(
params.get('completeRingsOnly', False))
kwargs['threshold'] = params.get('threshold', None)
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
kwargs['canonical'] = _parseFlag(params.get('canonical', True))
kwargs['kekuleSmiles'] = _parseFlag(params.get('kekuleSmiles', False))
return _mcs(data, **kwargs)
def highlightCtabFragmentSvgView(data, params):
kwargs = dict()
smarts = params.get('smarts', '')
kwargs['size'] = int(params.get('size', 300))
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', False))
kwargs['kekulize'] = _parseFlag(params.get('kekulize', False))
kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', False))
kwargs['force'] = _parseFlag(params.get('force', False))
response.content_type = 'image/svg+xml'
return _highlightCtabFragmentSVG(data, smarts, **kwargs)
def ctab2smartsView(data, params):
kwargs = dict()
kwargs['loadMol'] = _parseFlag(params.get('loadMol', True))
kwargs['useRDKitChemistry'] = _parseFlag(
params.get('useRDKitChemistry', True))
return _ctab2smarts(data, **kwargs)
