Python _parseFlag Examples

Example #1

def rulesView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    return _rules(data, **kwargs)

Example #2

def standardiseView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    return _standardise(data, **kwargs)

Example #3

File: views.py Project: bkbonde/chembl_beaker

def ctab2smartsView(data, params):
    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
    return _ctab2smarts(data, **kwargs)

Example #4

File: views.py Project: nclopezo/chembl_beaker

def ctab2smartsView(data, params):
    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
    return _ctab2smarts(data, **kwargs)

Example #5

File: views.py Project: chembl/chembl_beaker

def standardiseView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    return _standardise(data, **kwargs)

Example #6

def addHsView(data, params):

    kwargs = dict()
    kwargs['explicitOnly'] = _parseFlag(params.get('explicitOnly', False))
    kwargs['addCoords'] = _parseFlag(params.get('addCoords', False))

    return _addHs(data, **kwargs)

Example #7

File: views.py Project: jwildenhain/chembl_beaker

def addHsView(data, params):

    kwargs = dict()
    kwargs['explicitOnly'] = _parseFlag(params.get('explicitOnly', False))
    kwargs['addCoords'] = _parseFlag(params.get('addCoords', False))

    return _addHs(data, **kwargs)

Example #8

File: views.py Project: bkbonde/chembl_beaker

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)

Example #9

File: views.py Project: chembl/chembl_beaker

def rulesView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    return _rules(data, **kwargs)

Example #10

File: views.py Project: chembl/chembl_beaker

def bondRingsView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    return json.dumps(_bondRings(data, **kwargs))

Example #11

def sssrView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    return json.dumps(_sssr(data, **kwargs))

Example #12

File: views.py Project: jwildenhain/chembl_beaker

def symmSSSRView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    return json.dumps(_symmsssr(data, **kwargs))

Example #13

File: views.py Project: thntran/chembl_beaker

def ctab23DView(data, params):
    kwargs = dict()
    kwargs['multi'] = int(params.get('multi', False))
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['mmff'] = _parseFlag(params.get('mmff', False))

    return _ctab23D(data, **kwargs)

Example #14

def neutraliseView(data, params):

    kwargs = dict()
    kwargs['balance'] = int(params.get('balance', False))
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    return _neutralise(data, **kwargs)

Example #15

File: views.py Project: chembl/chembl_beaker

def neutraliseView(data, params):

    kwargs = dict()
    kwargs['balance'] = int(params.get('balance', False))
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    return _neutralise(data, **kwargs)

Example #16

def atomIsInRingView(data, params):

    kwargs = dict()
    kwargs['index'] = int(params.get('index'))
    kwargs['size'] = int(params.get('size'))
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    return json.dumps(_isAtomInRing(data, **kwargs))

Example #17

File: views.py Project: bkbonde/chembl_beaker

def image2smilesView(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 _image2smiles(img, config.get('osra_binaries_location', known_location), **kwargs)

Example #18

def sdf2fpsView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['type'] = params.get('type', 'morgan')
    kwargs['radius'] = int(params.get('radius', 2))
    kwargs['n_bits'] = int(params.get('n_bits', 2048))

    return _sdf2fps(data, **kwargs)

Example #19

File: views.py Project: chembl/chembl_beaker

def ctab2jsonView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    kwargs['legend'] = params.get('legend','')
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    response.content_type = 'application/json'

    return _ctab2json(data, **kwargs)

Example #20

File: views.py Project: thntran/chembl_beaker

def ctab2jsonView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    kwargs['legend'] = params.get('legend','')
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))

    response.content_type = 'application/json'

    return _ctab2json(data, **kwargs)

Example #21

def inchi2svgView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    kwargs['legend'] = params.get('legend', '')
    kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
    kwargs['wedgeBonds'] = _parseFlag(params.get('wedgeBonds', True))
    kwargs['fitImage'] = _parseFlag(params.get('fitImage', 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)

Example #22

File: views.py Project: jwildenhain/chembl_beaker

def inchi2svgView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    kwargs['legend'] = params.get('legend','')
    kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
    kwargs['wedgeBonds'] = _parseFlag(params.get('wedgeBonds', True))
    kwargs['fitImage'] = _parseFlag(params.get('fitImage', 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)

Example #23

File: views.py Project: bkbonde/chembl_beaker

def highlightSmilesFragmentSvgView(data, params):

    kwargs = dict()
    smarts = params.get('smarts', '')
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    kwargs['size'] = int(params.get('size', 200))
    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['wedgeBonds'] = _parseFlag(params.get('wedgeBonds', True))
    kwargs['fitImage'] = _parseFlag(params.get('fitImage', True))
    kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['force'] = _parseFlag(params.get('force', True))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'image/svg+xml'
    return _highlightSmilesFragmentSVG(data, smarts, **kwargs)

Example #24

File: views.py Project: chembl/chembl_beaker

def highlightSmilesFragmentSvgView(data, params):

    kwargs = dict()
    smarts = params.get('smarts', '')
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    kwargs['size'] = int(params.get('size', 200))
    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['wedgeBonds'] = _parseFlag(params.get('wedgeBonds', True))
    kwargs['fitImage'] = _parseFlag(params.get('fitImage', True))
    kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['force'] = _parseFlag(params.get('force', True))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'image/svg+xml'
    return _highlightSmilesFragmentSVG(data, smarts, **kwargs)

Example #25

File: views.py Project: bkbonde/chembl_beaker

def smiles2inchiKeyView(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))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    return _smiles2inchiKey(data, **kwargs)

Example #26

File: views.py Project: nclopezo/chembl_beaker

def smiles2inchiKeyView(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))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    return _smiles2inchiKey(data, **kwargs)

Example #27

def alignView(data, template, params):
    force = _parseFlag(params.get('force', False))
    ret = _align(data, template, force)
    if ret:
        return ret
    response.status = 404
    response.body = 'No template found in any of structures given.'

Example #28

File: views.py Project: thntran/chembl_beaker

def sdf2SimilarityMapView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['width'] = int(params.get('width', 100))
    kwargs['height'] = int(params.get('height', 100))
    kwargs['radius'] = int(params.get('radius', 2))
    kwargs['fingerprint'] = params.get('fingerprint', 'morgan')

    response.content_type = 'image/png'
    ret = _sdf2SimilarityMap(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #29

File: views.py Project: jwildenhain/chembl_beaker

def sdf2SimilarityMapView(data, params):

    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['width'] = int(params.get('width', 100))
    kwargs['height'] = int(params.get('height', 100))
    kwargs['radius'] = int(params.get('radius', 2))
    kwargs['fingerprint'] = params.get('fingerprint', 'morgan')

    response.content_type = 'image/png'
    ret = _sdf2SimilarityMap(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #30

File: views.py Project: thntran/chembl_beaker

def ctab2imageView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))

    response.content_type = 'image/png'
    ret = _ctab2image(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #31

File: views.py Project: jwildenhain/chembl_beaker

def ctab2imageView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))

    response.content_type = 'image/png'
    ret = _ctab2image(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #32

File: views.py Project: thntran/chembl_beaker

def smiles2jsonView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    kwargs['legend'] = params.get('legend','')
    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))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'application/json'
    return _smiles2json(data, **kwargs)

Example #33

File: views.py Project: chembl/chembl_beaker

def smiles2jsonView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    kwargs['legend'] = params.get('legend','')
    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))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'application/json'
    return _smiles2json(data, **kwargs)

Example #34

File: views.py Project: jwildenhain/chembl_beaker

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['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    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)

Example #35

File: views.py Project: bkbonde/chembl_beaker

def highlightSmilesFragmentView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    separator = params.get('separator', '|')
    smarts = params.get('smarts', '')
    kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
    kwargs['legend'] = params.get('legend', '').split(separator)
    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['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['force'] = _parseFlag(params.get('force', True))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'image/png'
    ret = _highlightSmilesFragment(data, smarts, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #36

File: views.py Project: bkbonde/chembl_beaker

def highlightCtabFragmentSvgView(data, params):

    kwargs = dict()
    smarts = params.get('smarts', '')
    kwargs['size'] = int(params.get('size', 200))
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
    kwargs['wedgeBonds'] = _parseFlag(params.get('wedgeBonds', True))
    kwargs['fitImage'] = _parseFlag(params.get('fitImage', True))
    kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))
    kwargs['force'] = _parseFlag(params.get('force', True))

    response.content_type = 'image/svg+xml'
    return _highlightCtabFragmentSVG(data, smarts, **kwargs)

Example #37

File: views.py Project: chembl/chembl_beaker

def highlightCtabFragmentSvgView(data, params):

    kwargs = dict()
    smarts = params.get('smarts', '')
    kwargs['size'] = int(params.get('size', 200))
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['kekulize'] = _parseFlag(params.get('kekulize', True))
    kwargs['wedgeBonds'] = _parseFlag(params.get('wedgeBonds', True))
    kwargs['fitImage'] = _parseFlag(params.get('fitImage', True))
    kwargs['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))
    kwargs['computeCoords'] = _parseFlag(params.get('computeCoords', True))
    kwargs['force'] = _parseFlag(params.get('force', True))

    response.content_type = 'image/svg+xml'
    return _highlightCtabFragmentSVG(data, smarts, **kwargs)

Example #38

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['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    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)

Example #39

File: views.py Project: jwildenhain/chembl_beaker

def smiles2imageView(data, params):

    kwargs = dict()
    kwargs['size'] = int(params.get('size', 200))
    separator = params.get('separator', '|')
    kwargs['legend'] = params.get('legend', '').split(separator)
    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['atomMapNumber'] = _parseFlag(params.get('atomMapNumber', False))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'image/png'
    ret = _smiles2image(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #40

File: views.py Project: jwildenhain/chembl_beaker

def smiles2SimilarityMapView(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', 100))
    kwargs['height'] = int(params.get('height', 100))
    kwargs['radius'] = int(params.get('radius', 2))
    kwargs['fingerprint'] = params.get('fingerprint', 'morgan')

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'image/png'
    ret = _smiles2SimilarityMap(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #41

File: views.py Project: thntran/chembl_beaker

def smiles2SimilarityMapView(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', 100))
    kwargs['height'] = int(params.get('height', 100))
    kwargs['radius'] = int(params.get('radius', 2))
    kwargs['fingerprint'] = params.get('fingerprint', 'morgan')

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    response.content_type = 'image/png'
    ret = _smiles2SimilarityMap(data, **kwargs)
    if request.is_ajax:
        ret = base64.b64encode(ret)
    return ret

Example #42

File: views.py Project: bkbonde/chembl_beaker

def ctab2smilesView(data, params):
    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['delimiter'] = params.get('delimiter', ' ')
    kwargs['nameHeader'] = params.get('nameHeader', 'Name')
    kwargs['includeHeader'] = _parseFlag(params.get('includeHeader', True))
    kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
    kwargs['kekuleSmiles'] = _parseFlag(params.get('kekuleSmiles', False))
    return _ctab2smiles(data, **kwargs)

Example #43

File: views.py Project: nclopezo/chembl_beaker

def ctab2smilesView(data, params):
    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    kwargs['delimiter'] = params.get('delimiter', ' ')
    kwargs['nameHeader'] = params.get('nameHeader', 'Name')
    kwargs['includeHeader'] = _parseFlag(params.get('includeHeader', True))
    kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
    kwargs['kekuleSmiles'] = _parseFlag(params.get('kekuleSmiles', False))
    return _ctab2smiles(data, **kwargs)

Example #44

File: views.py Project: bkbonde/chembl_beaker

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))
    kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
    kwargs['kekuleSmiles'] = _parseFlag(params.get('kekuleSmiles', False))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    return _canonicalize_smiles(data, **kwargs)

Example #45

File: views.py Project: nclopezo/chembl_beaker

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))
    kwargs['isomericSmiles'] = _parseFlag(params.get('isomericSmiles', False))
    kwargs['kekuleSmiles'] = _parseFlag(params.get('kekuleSmiles', False))

    if params.get('titleLine') is None and not data.startswith('SMILES Name'):
        kwargs['titleLine'] = False
    else:
        kwargs['titleLine'] = _parseFlag(params.get('titleLine', True))

    return _canonicalize_smiles(data, **kwargs)

Example #46

File: views.py Project: jwildenhain/chembl_beaker

def removeHsView(data, params):

    kwargs = dict()
    kwargs['implicitOnly'] = _parseFlag(params.get('implicitOnly', False))
    return _removeHs(data, **kwargs)

Example #47

def removeHsView(data, params):

    kwargs = dict()
    kwargs['implicitOnly'] = _parseFlag(params.get('implicitOnly', False))
    return _removeHs(data, **kwargs)

Example #48

File: views.py Project: nclopezo/chembl_beaker

def ctab2inchiKeyView(data, params):
    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    return _ctab2inchiKey(data, **kwargs)

Example #49

File: views.py Project: bkbonde/chembl_beaker

def ctab2inchiKeyView(data, params):
    kwargs = dict()
    kwargs['sanitize'] = _parseFlag(params.get('sanitize', True))
    kwargs['removeHs'] = _parseFlag(params.get('removeHs', True))
    kwargs['strictParsing'] = _parseFlag(params.get('strictParsing', True))
    return _ctab2inchiKey(data, **kwargs)

Example #50

File: views.py Project: bkbonde/chembl_beaker

def ctab2xyzView(data, params):
    computeCoords = _parseFlag(params.get('computeCoords', True))
    return _ctab2xyz(data, computeCoords)