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)