Exemplos de _parseFlag em Python

Exemplo n.º 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)

Exemplo n.º 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)

Exemplo n.º 3

Arquivo: views.py Projeto: 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)

Exemplo n.º 4

Arquivo: views.py Projeto: 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)

Exemplo n.º 5

Arquivo: views.py Projeto: 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)

Exemplo n.º 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)

Exemplo n.º 7

Arquivo: views.py Projeto: 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)

Exemplo n.º 8

Arquivo: views.py Projeto: 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)

Exemplo n.º 9

Arquivo: views.py Projeto: 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)

Exemplo n.º 10

Arquivo: views.py Projeto: 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))

Exemplo n.º 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))

Exemplo n.º 12

Arquivo: views.py Projeto: 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))

Exemplo n.º 13

Arquivo: views.py Projeto: 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)

Exemplo n.º 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)

Exemplo n.º 15

Arquivo: views.py Projeto: 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)

Exemplo n.º 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))

Exemplo n.º 17

Arquivo: views.py Projeto: 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)

Exemplo n.º 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)

Exemplo n.º 19

Arquivo: views.py Projeto: 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)

Exemplo n.º 20

Arquivo: views.py Projeto: 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)

Exemplo n.º 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)

Exemplo n.º 22

Arquivo: views.py Projeto: 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)

Exemplo n.º 23

Arquivo: views.py Projeto: 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)

Exemplo n.º 24

Arquivo: views.py Projeto: 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)

Exemplo n.º 25

Arquivo: views.py Projeto: 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)

Exemplo n.º 26

Arquivo: views.py Projeto: 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)

Exemplo n.º 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.'

Exemplo n.º 28

Arquivo: views.py Projeto: 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

Exemplo n.º 29

Arquivo: views.py Projeto: 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

Exemplo n.º 30

Arquivo: views.py Projeto: 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

Exemplo n.º 31

Arquivo: views.py Projeto: 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

Exemplo n.º 32

Arquivo: views.py Projeto: 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)

Exemplo n.º 33

Arquivo: views.py Projeto: 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)

Exemplo n.º 34

Arquivo: views.py Projeto: 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)

Exemplo n.º 35

Arquivo: views.py Projeto: 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

Exemplo n.º 36

Arquivo: views.py Projeto: 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)

Exemplo n.º 37

Arquivo: views.py Projeto: 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)

Exemplo n.º 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)

Exemplo n.º 39

Arquivo: views.py Projeto: 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

Exemplo n.º 40

Arquivo: views.py Projeto: 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

Exemplo n.º 41

Arquivo: views.py Projeto: 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

Exemplo n.º 42

Arquivo: views.py Projeto: 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)

Exemplo n.º 43

Arquivo: views.py Projeto: 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)

Exemplo n.º 44

Arquivo: views.py Projeto: 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)

Exemplo n.º 45

Arquivo: views.py Projeto: 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)

Exemplo n.º 46

Arquivo: views.py Projeto: jwildenhain/chembl_beaker

def removeHsView(data, params):

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

Exemplo n.º 47

def removeHsView(data, params):

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

Exemplo n.º 48

Arquivo: views.py Projeto: 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)

Exemplo n.º 49

Arquivo: views.py Projeto: 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)

Exemplo n.º 50

Arquivo: views.py Projeto: bkbonde/chembl_beaker

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