other fingerprints

[taeoowl]

Hi, Thanks for the great packages!

I have simple question. Maybe my lack of ability.

When running from_smiles(), it only calculate Pubchem FP?
I can't find any function for other FP in Readme.md.

Thank you in advance for any help you might be able to provide.

[tjkessler]

Hi @taeoowl,

Unfortunately I do not believe the command line interface for PaDEL-Descriptor returns any fingerprints besides PubChem fingerprints - further, its documentation for calculating fingerprints using the command line is somewhat ambiguous, not stating which fingerprints are calculated from the command line: http://www.yapcwsoft.com/dd/padeldescriptor/

Here are the fingerprints that PaDELPy returns when fingerprints are calculated from a SMILES string:

from padelpy import from_smiles

fp = from_smiles('CCCCC', descriptors=False, fingerprints=True)
print(list(fp.keys()))

['PubchemFP0', 'PubchemFP1', 'PubchemFP2', 'PubchemFP3', 'PubchemFP4', 'PubchemFP5', 'PubchemFP6', 'PubchemFP7', 'PubchemFP8', 'PubchemFP9', 'PubchemFP10', 'PubchemFP11', 'PubchemFP12', 'PubchemFP13', 'PubchemFP14', 'PubchemFP15', 'PubchemFP16', 'PubchemFP17', 'PubchemFP18', 'PubchemFP19', 'PubchemFP20', 'PubchemFP21', 'PubchemFP22', 'PubchemFP23', 'PubchemFP24', 'PubchemFP25', 'PubchemFP26', 'PubchemFP27', 'PubchemFP28', 'PubchemFP29', 'PubchemFP30', 'PubchemFP31', 'PubchemFP32', 'PubchemFP33', 'PubchemFP34', 'PubchemFP35', 'PubchemFP36', 'PubchemFP37', 'PubchemFP38', 'PubchemFP39', 'PubchemFP40', 'PubchemFP41', 'PubchemFP42', 'PubchemFP43', 'PubchemFP44', 'PubchemFP45', 'PubchemFP46', 'PubchemFP47', 'PubchemFP48', 'PubchemFP49', 'PubchemFP50', 'PubchemFP51', 'PubchemFP52', 'PubchemFP53', 'PubchemFP54', 'PubchemFP55', 'PubchemFP56', 'PubchemFP57', 'PubchemFP58', 'PubchemFP59', 'PubchemFP60', 'PubchemFP61', 'PubchemFP62', 'PubchemFP63', 'PubchemFP64', 'PubchemFP65', 'PubchemFP66', 'PubchemFP67', 'PubchemFP68', 'PubchemFP69', 'PubchemFP70', 'PubchemFP71', 'PubchemFP72', 'PubchemFP73', 'PubchemFP74', 'PubchemFP75', 'PubchemFP76', 'PubchemFP77', 'PubchemFP78', 'PubchemFP79', 'PubchemFP80', 'PubchemFP81', 'PubchemFP82', 'PubchemFP83', 'PubchemFP84', 'PubchemFP85', 'PubchemFP86', 'PubchemFP87', 'PubchemFP88', 'PubchemFP89', 'PubchemFP90', 'PubchemFP91', 'PubchemFP92', 'PubchemFP93', 'PubchemFP94', 'PubchemFP95', 'PubchemFP96', 'PubchemFP97', 'PubchemFP98', 'PubchemFP99', 'PubchemFP100', 'PubchemFP101', 'PubchemFP102', 'PubchemFP103', 'PubchemFP104', 'PubchemFP105', 'PubchemFP106', 'PubchemFP107', 'PubchemFP108', 'PubchemFP109', 'PubchemFP110', 'PubchemFP111', 'PubchemFP112', 'PubchemFP113', 'PubchemFP114', 'PubchemFP115', 'PubchemFP116', 'PubchemFP117', 'PubchemFP118', 'PubchemFP119', 'PubchemFP120', 'PubchemFP121', 'PubchemFP122', 'PubchemFP123', 'PubchemFP124', 'PubchemFP125', 'PubchemFP126', 'PubchemFP127', 'PubchemFP128', 'PubchemFP129', 'PubchemFP130', 'PubchemFP131', 'PubchemFP132', 'PubchemFP133', 'PubchemFP134', 'PubchemFP135', 'PubchemFP136', 'PubchemFP137', 'PubchemFP138', 'PubchemFP139', 'PubchemFP140', 'PubchemFP141', 'PubchemFP142', 'PubchemFP143', 'PubchemFP144', 'PubchemFP145', 'PubchemFP146', 'PubchemFP147', 'PubchemFP148', 'PubchemFP149', 'PubchemFP150', 'PubchemFP151', 'PubchemFP152', 'PubchemFP153', 'PubchemFP154', 'PubchemFP155', 'PubchemFP156', 'PubchemFP157', 'PubchemFP158', 'PubchemFP159', 'PubchemFP160', 'PubchemFP161', 'PubchemFP162', 'PubchemFP163', 'PubchemFP164', 'PubchemFP165', 'PubchemFP166', 'PubchemFP167', 'PubchemFP168', 'PubchemFP169', 'PubchemFP170', 'PubchemFP171', 'PubchemFP172', 'PubchemFP173', 'PubchemFP174', 'PubchemFP175', 'PubchemFP176', 'PubchemFP177', 'PubchemFP178', 'PubchemFP179', 'PubchemFP180', 'PubchemFP181', 'PubchemFP182', 'PubchemFP183', 'PubchemFP184', 'PubchemFP185', 'PubchemFP186', 'PubchemFP187', 'PubchemFP188', 'PubchemFP189', 'PubchemFP190', 'PubchemFP191', 'PubchemFP192', 'PubchemFP193', 'PubchemFP194', 'PubchemFP195', 'PubchemFP196', 'PubchemFP197', 'PubchemFP198', 'PubchemFP199', 'PubchemFP200', 'PubchemFP201', 'PubchemFP202', 'PubchemFP203', 'PubchemFP204', 'PubchemFP205', 'PubchemFP206', 'PubchemFP207', 'PubchemFP208', 'PubchemFP209', 'PubchemFP210', 'PubchemFP211', 'PubchemFP212', 'PubchemFP213', 'PubchemFP214', 'PubchemFP215', 'PubchemFP216', 'PubchemFP217', 'PubchemFP218', 'PubchemFP219', 'PubchemFP220', 'PubchemFP221', 'PubchemFP222', 'PubchemFP223', 'PubchemFP224', 'PubchemFP225', 'PubchemFP226', 'PubchemFP227', 'PubchemFP228', 'PubchemFP229', 'PubchemFP230', 'PubchemFP231', 'PubchemFP232', 'PubchemFP233', 'PubchemFP234', 'PubchemFP235', 'PubchemFP236', 'PubchemFP237', 'PubchemFP238', 'PubchemFP239', 'PubchemFP240', 'PubchemFP241', 'PubchemFP242', 'PubchemFP243', 'PubchemFP244', 'PubchemFP245', 'PubchemFP246', 'PubchemFP247', 'PubchemFP248', 'PubchemFP249', 'PubchemFP250', 'PubchemFP251', 'PubchemFP252', 'PubchemFP253', 'PubchemFP254', 'PubchemFP255', 'PubchemFP256', 'PubchemFP257', 'PubchemFP258', 'PubchemFP259', 'PubchemFP260', 'PubchemFP261', 'PubchemFP262', 'PubchemFP263', 'PubchemFP264', 'PubchemFP265', 'PubchemFP266', 'PubchemFP267', 'PubchemFP268', 'PubchemFP269', 'PubchemFP270', 'PubchemFP271', 'PubchemFP272', 'PubchemFP273', 'PubchemFP274', 'PubchemFP275', 'PubchemFP276', 'PubchemFP277', 'PubchemFP278', 'PubchemFP279', 'PubchemFP280', 'PubchemFP281', 'PubchemFP282', 'PubchemFP283', 'PubchemFP284', 'PubchemFP285', 'PubchemFP286', 'PubchemFP287', 'PubchemFP288', 'PubchemFP289', 'PubchemFP290', 'PubchemFP291', 'PubchemFP292', 'PubchemFP293', 'PubchemFP294', 'PubchemFP295', 'PubchemFP296', 'PubchemFP297', 'PubchemFP298', 'PubchemFP299', 'PubchemFP300', 'PubchemFP301', 'PubchemFP302', 'PubchemFP303', 'PubchemFP304', 'PubchemFP305', 'PubchemFP306', 'PubchemFP307', 'PubchemFP308', 'PubchemFP309', 'PubchemFP310', 'PubchemFP311', 'PubchemFP312', 'PubchemFP313', 'PubchemFP314', 'PubchemFP315', 'PubchemFP316', 'PubchemFP317', 'PubchemFP318', 'PubchemFP319', 'PubchemFP320', 'PubchemFP321', 'PubchemFP322', 'PubchemFP323', 'PubchemFP324', 'PubchemFP325', 'PubchemFP326', 'PubchemFP327', 'PubchemFP328', 'PubchemFP329', 'PubchemFP330', 'PubchemFP331', 'PubchemFP332', 'PubchemFP333', 'PubchemFP334', 'PubchemFP335', 'PubchemFP336', 'PubchemFP337', 'PubchemFP338', 'PubchemFP339', 'PubchemFP340', 'PubchemFP341', 'PubchemFP342', 'PubchemFP343', 'PubchemFP344', 'PubchemFP345', 'PubchemFP346', 'PubchemFP347', 'PubchemFP348', 'PubchemFP349', 'PubchemFP350', 'PubchemFP351', 'PubchemFP352', 'PubchemFP353', 'PubchemFP354', 'PubchemFP355', 'PubchemFP356', 'PubchemFP357', 'PubchemFP358', 'PubchemFP359', 'PubchemFP360', 'PubchemFP361', 'PubchemFP362', 'PubchemFP363', 'PubchemFP364', 'PubchemFP365', 'PubchemFP366', 'PubchemFP367', 'PubchemFP368', 'PubchemFP369', 'PubchemFP370', 'PubchemFP371', 'PubchemFP372', 'PubchemFP373', 'PubchemFP374', 'PubchemFP375', 'PubchemFP376', 'PubchemFP377', 'PubchemFP378', 'PubchemFP379', 'PubchemFP380', 'PubchemFP381', 'PubchemFP382', 'PubchemFP383', 'PubchemFP384', 'PubchemFP385', 'PubchemFP386', 'PubchemFP387', 'PubchemFP388', 'PubchemFP389', 'PubchemFP390', 'PubchemFP391', 'PubchemFP392', 'PubchemFP393', 'PubchemFP394', 'PubchemFP395', 'PubchemFP396', 'PubchemFP397', 'PubchemFP398', 'PubchemFP399', 'PubchemFP400', 'PubchemFP401', 'PubchemFP402', 'PubchemFP403', 'PubchemFP404', 'PubchemFP405', 'PubchemFP406', 'PubchemFP407', 'PubchemFP408', 'PubchemFP409', 'PubchemFP410', 'PubchemFP411', 'PubchemFP412', 'PubchemFP413', 'PubchemFP414', 'PubchemFP415', 'PubchemFP416', 'PubchemFP417', 'PubchemFP418', 'PubchemFP419', 'PubchemFP420', 'PubchemFP421', 'PubchemFP422', 'PubchemFP423', 'PubchemFP424', 'PubchemFP425', 'PubchemFP426', 'PubchemFP427', 'PubchemFP428', 'PubchemFP429', 'PubchemFP430', 'PubchemFP431', 'PubchemFP432', 'PubchemFP433', 'PubchemFP434', 'PubchemFP435', 'PubchemFP436', 'PubchemFP437', 'PubchemFP438', 'PubchemFP439', 'PubchemFP440', 'PubchemFP441', 'PubchemFP442', 'PubchemFP443', 'PubchemFP444', 'PubchemFP445', 'PubchemFP446', 'PubchemFP447', 'PubchemFP448', 'PubchemFP449', 'PubchemFP450', 'PubchemFP451', 'PubchemFP452', 'PubchemFP453', 'PubchemFP454', 'PubchemFP455', 'PubchemFP456', 'PubchemFP457', 'PubchemFP458', 'PubchemFP459', 'PubchemFP460', 'PubchemFP461', 'PubchemFP462', 'PubchemFP463', 'PubchemFP464', 'PubchemFP465', 'PubchemFP466', 'PubchemFP467', 'PubchemFP468', 'PubchemFP469', 'PubchemFP470', 'PubchemFP471', 'PubchemFP472', 'PubchemFP473', 'PubchemFP474', 'PubchemFP475', 'PubchemFP476', 'PubchemFP477', 'PubchemFP478', 'PubchemFP479', 'PubchemFP480', 'PubchemFP481', 'PubchemFP482', 'PubchemFP483', 'PubchemFP484', 'PubchemFP485', 'PubchemFP486', 'PubchemFP487', 'PubchemFP488', 'PubchemFP489', 'PubchemFP490', 'PubchemFP491', 'PubchemFP492', 'PubchemFP493', 'PubchemFP494', 'PubchemFP495', 'PubchemFP496', 'PubchemFP497', 'PubchemFP498', 'PubchemFP499', 'PubchemFP500', 'PubchemFP501', 'PubchemFP502', 'PubchemFP503', 'PubchemFP504', 'PubchemFP505', 'PubchemFP506', 'PubchemFP507', 'PubchemFP508', 'PubchemFP509', 'PubchemFP510', 'PubchemFP511', 'PubchemFP512', 'PubchemFP513', 'PubchemFP514', 'PubchemFP515', 'PubchemFP516', 'PubchemFP517', 'PubchemFP518', 'PubchemFP519', 'PubchemFP520', 'PubchemFP521', 'PubchemFP522', 'PubchemFP523', 'PubchemFP524', 'PubchemFP525', 'PubchemFP526', 'PubchemFP527', 'PubchemFP528', 'PubchemFP529', 'PubchemFP530', 'PubchemFP531', 'PubchemFP532', 'PubchemFP533', 'PubchemFP534', 'PubchemFP535', 'PubchemFP536', 'PubchemFP537', 'PubchemFP538', 'PubchemFP539', 'PubchemFP540', 'PubchemFP541', 'PubchemFP542', 'PubchemFP543', 'PubchemFP544', 'PubchemFP545', 'PubchemFP546', 'PubchemFP547', 'PubchemFP548', 'PubchemFP549', 'PubchemFP550', 'PubchemFP551', 'PubchemFP552', 'PubchemFP553', 'PubchemFP554', 'PubchemFP555', 'PubchemFP556', 'PubchemFP557', 'PubchemFP558', 'PubchemFP559', 'PubchemFP560', 'PubchemFP561', 'PubchemFP562', 'PubchemFP563', 'PubchemFP564', 'PubchemFP565', 'PubchemFP566', 'PubchemFP567', 'PubchemFP568', 'PubchemFP569', 'PubchemFP570', 'PubchemFP571', 'PubchemFP572', 'PubchemFP573', 'PubchemFP574', 'PubchemFP575', 'PubchemFP576', 'PubchemFP577', 'PubchemFP578', 'PubchemFP579', 'PubchemFP580', 'PubchemFP581', 'PubchemFP582', 'PubchemFP583', 'PubchemFP584', 'PubchemFP585', 'PubchemFP586', 'PubchemFP587', 'PubchemFP588', 'PubchemFP589', 'PubchemFP590', 'PubchemFP591', 'PubchemFP592', 'PubchemFP593', 'PubchemFP594', 'PubchemFP595', 'PubchemFP596', 'PubchemFP597', 'PubchemFP598', 'PubchemFP599', 'PubchemFP600', 'PubchemFP601', 'PubchemFP602', 'PubchemFP603', 'PubchemFP604', 'PubchemFP605', 'PubchemFP606', 'PubchemFP607', 'PubchemFP608', 'PubchemFP609', 'PubchemFP610', 'PubchemFP611', 'PubchemFP612', 'PubchemFP613', 'PubchemFP614', 'PubchemFP615', 'PubchemFP616', 'PubchemFP617', 'PubchemFP618', 'PubchemFP619', 'PubchemFP620', 'PubchemFP621', 'PubchemFP622', 'PubchemFP623', 'PubchemFP624', 'PubchemFP625', 'PubchemFP626', 'PubchemFP627', 'PubchemFP628', 'PubchemFP629', 'PubchemFP630', 'PubchemFP631', 'PubchemFP632', 'PubchemFP633', 'PubchemFP634', 'PubchemFP635', 'PubchemFP636', 'PubchemFP637', 'PubchemFP638', 'PubchemFP639', 'PubchemFP640', 'PubchemFP641', 'PubchemFP642', 'PubchemFP643', 'PubchemFP644', 'PubchemFP645', 'PubchemFP646', 'PubchemFP647', 'PubchemFP648', 'PubchemFP649', 'PubchemFP650', 'PubchemFP651', 'PubchemFP652', 'PubchemFP653', 'PubchemFP654', 'PubchemFP655', 'PubchemFP656', 'PubchemFP657', 'PubchemFP658', 'PubchemFP659', 'PubchemFP660', 'PubchemFP661', 'PubchemFP662', 'PubchemFP663', 'PubchemFP664', 'PubchemFP665', 'PubchemFP666', 'PubchemFP667', 'PubchemFP668', 'PubchemFP669', 'PubchemFP670', 'PubchemFP671', 'PubchemFP672', 'PubchemFP673', 'PubchemFP674', 'PubchemFP675', 'PubchemFP676', 'PubchemFP677', 'PubchemFP678', 'PubchemFP679', 'PubchemFP680', 'PubchemFP681', 'PubchemFP682', 'PubchemFP683', 'PubchemFP684', 'PubchemFP685', 'PubchemFP686', 'PubchemFP687', 'PubchemFP688', 'PubchemFP689', 'PubchemFP690', 'PubchemFP691', 'PubchemFP692', 'PubchemFP693', 'PubchemFP694', 'PubchemFP695', 'PubchemFP696', 'PubchemFP697', 'PubchemFP698', 'PubchemFP699', 'PubchemFP700', 'PubchemFP701', 'PubchemFP702', 'PubchemFP703', 'PubchemFP704', 'PubchemFP705', 'PubchemFP706', 'PubchemFP707', 'PubchemFP708', 'PubchemFP709', 'PubchemFP710', 'PubchemFP711', 'PubchemFP712', 'PubchemFP713', 'PubchemFP714', 'PubchemFP715', 'PubchemFP716', 'PubchemFP717', 'PubchemFP718', 'PubchemFP719', 'PubchemFP720', 'PubchemFP721', 'PubchemFP722', 'PubchemFP723', 'PubchemFP724', 'PubchemFP725', 'PubchemFP726', 'PubchemFP727', 'PubchemFP728', 'PubchemFP729', 'PubchemFP730', 'PubchemFP731', 'PubchemFP732', 'PubchemFP733', 'PubchemFP734', 'PubchemFP735', 'PubchemFP736', 'PubchemFP737', 'PubchemFP738', 'PubchemFP739', 'PubchemFP740', 'PubchemFP741', 'PubchemFP742', 'PubchemFP743', 'PubchemFP744', 'PubchemFP745', 'PubchemFP746', 'PubchemFP747', 'PubchemFP748', 'PubchemFP749', 'PubchemFP750', 'PubchemFP751', 'PubchemFP752', 'PubchemFP753', 'PubchemFP754', 'PubchemFP755', 'PubchemFP756', 'PubchemFP757', 'PubchemFP758', 'PubchemFP759', 'PubchemFP760', 'PubchemFP761', 'PubchemFP762', 'PubchemFP763', 'PubchemFP764', 'PubchemFP765', 'PubchemFP766', 'PubchemFP767', 'PubchemFP768', 'PubchemFP769', 'PubchemFP770', 'PubchemFP771', 'PubchemFP772', 'PubchemFP773', 'PubchemFP774', 'PubchemFP775', 'PubchemFP776', 'PubchemFP777', 'PubchemFP778', 'PubchemFP779', 'PubchemFP780', 'PubchemFP781', 'PubchemFP782', 'PubchemFP783', 'PubchemFP784', 'PubchemFP785', 'PubchemFP786', 'PubchemFP787', 'PubchemFP788', 'PubchemFP789', 'PubchemFP790', 'PubchemFP791', 'PubchemFP792', 'PubchemFP793', 'PubchemFP794', 'PubchemFP795', 'PubchemFP796', 'PubchemFP797', 'PubchemFP798', 'PubchemFP799', 'PubchemFP800', 'PubchemFP801', 'PubchemFP802', 'PubchemFP803', 'PubchemFP804', 'PubchemFP805', 'PubchemFP806', 'PubchemFP807', 'PubchemFP808', 'PubchemFP809', 'PubchemFP810', 'PubchemFP811', 'PubchemFP812', 'PubchemFP813', 'PubchemFP814', 'PubchemFP815', 'PubchemFP816', 'PubchemFP817', 'PubchemFP818', 'PubchemFP819', 'PubchemFP820', 'PubchemFP821', 'PubchemFP822', 'PubchemFP823', 'PubchemFP824', 'PubchemFP825', 'PubchemFP826', 'PubchemFP827', 'PubchemFP828', 'PubchemFP829', 'PubchemFP830', 'PubchemFP831', 'PubchemFP832', 'PubchemFP833', 'PubchemFP834', 'PubchemFP835', 'PubchemFP836', 'PubchemFP837', 'PubchemFP838', 'PubchemFP839', 'PubchemFP840', 'PubchemFP841', 'PubchemFP842', 'PubchemFP843', 'PubchemFP844', 'PubchemFP845', 'PubchemFP846', 'PubchemFP847', 'PubchemFP848', 'PubchemFP849', 'PubchemFP850', 'PubchemFP851', 'PubchemFP852', 'PubchemFP853', 'PubchemFP854', 'PubchemFP855', 'PubchemFP856', 'PubchemFP857', 'PubchemFP858', 'PubchemFP859', 'PubchemFP860', 'PubchemFP861', 'PubchemFP862', 'PubchemFP863', 'PubchemFP864', 'PubchemFP865', 'PubchemFP866', 'PubchemFP867', 'PubchemFP868', 'PubchemFP869', 'PubchemFP870', 'PubchemFP871', 'PubchemFP872', 'PubchemFP873', 'PubchemFP874', 'PubchemFP875', 'PubchemFP876', 'PubchemFP877', 'PubchemFP878', 'PubchemFP879', 'PubchemFP880']

I'm going to keep this issue open, perhaps someone more experienced with the ins-and-outs of PaDEL-Descriptor could provide some insight.

Best,
Travis

[alexgcsa]

Hello,

You need to have a XML file describing the fingerprints that will be available...This is something that happens when you use by command line.

https://stackoverflow.com/questions/43972179/padel-descriptor-on-command-line

You need to set the options of the fingerprints, descriptors, etc that you want to "true".

The XML file can be set with the option "-descriptortypes".

descriptors.xml.zip

[tjkessler]

Perfect, this looks like the correct solution. Maybe this is worth building into PaDELPy in the future...