In [1]:

    

%matplotlib notebook
import sys
import pandas as pd

#sys.path.insert(0,'/global/project/projectdirs/metatlas/anaconda/lib/python2.7/site-packages' )
import qgrid

from metatlas import metatlas_objects as metob

df = pd.read_csv('20151130_Atlas_POS_HILIC_LS_Validated.csv',sep = ',')

df.columns = [x.lower() for x in df.columns]
qgrid.show_grid(df, precision=5)

# TODO: Make one Atlas.  
# TODO: Add column labels for each mzref, rtref, and fragmentation_ref
# TODO: Make template for this
# TODO: Make error checker to ensure Adduct is conforming to specification
# TODO: make error checker to ensure modification is conforming to specification


    

In [13]:

    

for c in metob.retrieve('Atlas',name='%_LS_%', username='*'):
    print c.name
# 2-acetamido-2-deoxy-beta-D-glucopyranosyl-(1->4)-2-amino-2-deoxy-D-glucopyranose Cite this Record


    

    




20151130_LS_Negative_Hilic_QExactive_Archetypes
20151130_LS_Positive_Hilic_QExactive_Archetypes_ISTDs
20151130_LS_Negative_Hilic_QExactive_Archetypes_ISTDs
20151130_LS_Positive_Hilic_QExactive_Archetypes
20151130_LS_Positive_Hilic_QExactive_Archetypes

In [3]:

    

# compounds that have the wrong compound name will be listed
# Keep running this until no more compounds are listed
for x in df.index:
    if not metob.retrieve('Compounds',name=df.name[x]):
        print df.name[x], "is not in database"


    

    




agmatine is not in database
L-glucose is not in database

In [11]:

    

df.to_csv('saveit.tab', sep='\t')


    

In [12]:

    

myCompounds = []
rt_min = []
rt_max = []
rt_peak = []
mz = []
mz_tolerance = []
for x in df.index:
    c = metob.retrieve('Compounds',name=df.name[x])[0] #currently, all copies of the molecule are returned.  The 0 is the most recent one. 
    #TODO: Consider possible change to make thinkgs like compound should be immutable and not behave this way
    myCompounds.append(c)
    rt_min.append(df.rt_min[x])
    rt_max.append(df.rt_max[x])
    rt_peak.append(df.rt_peak[x])
    mz.append(df.mz[x])
#     mz.append(c.MonoIsotopic_molecular_weight - 1.007276)

    mz_tolerance.append(df.mz_threshold[x])
    dmz = 1e6 * (c.mono_isotopic_molecular_weight + 1.007276 - df.mz[x] ) / ( df.mz[x])
#     if abs(dmz) > 100:
#         dmz = 1e6 * (c.MonoIsotopic_molecular_weight + 59.013851 - df.mz[x] ) / df.mz[x]
#         print c.MonoIsotopic_molecular_weight - df.mz[x]
        
    print '%5.2f'%abs(dmz), "\t", c.name,c.formula,c.mono_isotopic_molecular_weight,c.description, df.rt_min[x], df.rt_max[x], df.mz[x]#, c.InChI  
    #TODO: See above todo's.  this block needs to be rebuilt


    

    




56.05 	L-alanine C3H7NO2 89.0476760864  10.52 11.52 90.06
 2.87 	ectoine C6H10N2O2 142.074234009  9.41 10.41 143.0811
 0.36 	DL-methionine sulfoxide C5H11NO3S 165.045964212 http://pubchem.ncbi.nlm.nih.gov/compound/DL-Methionine_sulfoxide 11.48 12.48 166.0533
 0.80 	L-carnitine C7H15NO3 161.105194092  8.97 9.97 162.1126
 0.28 	5-oxo-L-proline C5H7NO3 129.04258728  9.5 10.5 130.0499
 0.32 	|L-histidine| C6H9N3O2 155.069473267  13.18 14.18 156.0767






    




---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-12-f82b4f5546c9> in <module>()
      6 mz_tolerance = []
      7 for x in df.index:
----> 8     c = metob.retrieve('Compounds',name=df.name[x])[0] #currently, all copies of the molecule are returned.  The 0 is the most recent one.
      9     #TODO: Consider possible change to make thinkgs like compound should be immutable and not behave this way
     10     myCompounds.append(c)

IndexError: list index out of range

In [6]:

    

c


    

    
Out[6]:





{'creation_time': '2015-10-08T11:37:24',
 'description': u'',
 'formula': u'C6H9N3O2',
 'functional_sets': [],
 'head_id': u'cac6a7a3914c454982c247b4bc4d3cd6',
 'inchi': u'InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 155.069473266602,
 'name': u'|L-histidine|',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'cac6a7a3914c454982c247b4bc4d3cd6',
 'url': u'',
 'username': u'jimmy'}

In [ ]:

    




    

In [7]:

    

#     myID.description = 'mz=%5.4f,ppm=%5.4f,RTmin=%5.4f,RTmax=%5.4f,RTpeak=%5.4f'%(mz[i],
#                                                                                  mz_tolerance[i],
#                                                                                  rt_min[i],
#                                                                                  rt_max[i],
#                                                                                  rt_peak[i])
#     print myID.references


all_identifications = []
for i,c in enumerate(myCompounds):
    mzRef = metob.MzReference()

    # take the mz value from the spreadsheet
    mzRef.mz = mz[i]
    
    #TODO: calculate the mz from theoretical adduct and modification if provided.
#     mzRef.mz = c.MonoIso topic_molecular_weight + 1.007276
    mzRef.mz_tolerance = mz_tolerance[i]
    mzRef.mz_tolerance_units = 'ppm'
    mzRef.detected_polarity = 'positive'
#     mzRef.adduct = '[M-H]'
    
    rtRef = metob.RtReference()
    rtRef.rt_units = 'min'
    rtRef.rt_min = rt_min[i]
    rtRef.rt_max = rt_max[i]
    rtRef.rt_peak = rt_peak[i]
    
    myID = metob.CompoundIdentification()
    myID.compound = [c]
    myID.mz_references = [mzRef]
    myID.rt_references = [rtRef]

    all_identifications.append(myID)

myAtlas = metob.Atlas()
#metob.Atlas() has "compound_identifications" and a "name"
# myAtlas.name = '20151130_LS_Negative_Hilic_QExactive_Archetypes'
myAtlas.name = '20151210_SJ_Positive_Hilic_QTOF6550_HMArkin'
myAtlas.compound_identifications = all_identifications
metob.store(myAtlas)


    

In [8]:

    

myAtlas


    

    
Out[8]:





{'compound_identifications': [{'compound': [{'creation_time': '2015-10-08T11:37:24',
 'description': u'',
 'formula': u'C3H7NO2',
 'functional_sets': [],
 'head_id': u'8666a6d45ea14c049923f8e0eb7c005e',
 'inchi': u'InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 89.0476760864258,
 'name': u'L-alanine',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'8666a6d45ea14c049923f8e0eb7c005e',
 'url': u'',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'frag_references': [],
 'head_id': u'72736e2dde8f48688703a8aacc3e1b63',
 'identification_grade': None,
 'last_modified': '2016-01-25T09:37:49',
 'mz_references': [{'adduct': u'',
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'detected_polarity': 'positive',
 'enabled': True,
 'head_id': u'1e70396cd8d7423c91620d9d04df4fc2',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'modification': u'',
 'mz': 90.06,
 'mz_tolerance': 15.0,
 'mz_tolerance_units': 'ppm',
 'name': u'Untitled',
 'observed_formula': u'',
 'prev_uid': u'795b945d73b64ed5b2f0bd459079870a',
 'ref_type': u'',
 'unique_id': u'1e70396cd8d7423c91620d9d04df4fc2',
 'username': u'jimmy'}],
 'name': u'Untitled',
 'prev_uid': u'df50f8f3c1a1465997c62cd04dea2a8e',
 'rt_references': [{'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'enabled': True,
 'head_id': u'fe030ec269494334aaad0ec7905cf2d0',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'name': u'Untitled',
 'prev_uid': u'4c757708e59a458eaa8d30d660022954',
 'ref_type': u'',
 'rt_max': 11.52,
 'rt_min': 10.52,
 'rt_peak': 11.02,
 'rt_units': 'min',
 'unique_id': u'fe030ec269494334aaad0ec7905cf2d0',
 'username': u'jimmy'}],
 'unique_id': u'72736e2dde8f48688703a8aacc3e1b63',
 'username': u'jimmy'},
                              {'compound': [{'creation_time': '2015-10-08T11:36:11',
 'description': u'',
 'formula': u'C6H10N2O2',
 'functional_sets': [],
 'head_id': u'b8f05afffaee46789c2931ef65c7c99d',
 'inchi': u'InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 142.074234008789,
 'name': u'ectoine',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'b8f05afffaee46789c2931ef65c7c99d',
 'url': u'',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'frag_references': [],
 'head_id': u'e59611d82abc43b08c5c5cbec2424721',
 'identification_grade': None,
 'last_modified': '2016-01-25T09:37:49',
 'mz_references': [{'adduct': u'',
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'detected_polarity': 'positive',
 'enabled': True,
 'head_id': u'1231a4e372454c41825b8c89f4fdc0f9',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'modification': u'',
 'mz': 143.0811,
 'mz_tolerance': 15.0,
 'mz_tolerance_units': 'ppm',
 'name': u'Untitled',
 'observed_formula': u'',
 'prev_uid': u'b433ab4424a74446a76bfb3981393899',
 'ref_type': u'',
 'unique_id': u'1231a4e372454c41825b8c89f4fdc0f9',
 'username': u'jimmy'}],
 'name': u'Untitled',
 'prev_uid': u'c6361e303cce4feabc5b62b8b5af0fb7',
 'rt_references': [{'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'enabled': True,
 'head_id': u'2bd76cba6a274b7cab08d7890da264f7',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'name': u'Untitled',
 'prev_uid': u'54148a47adb9454494b84d2306eb81ea',
 'ref_type': u'',
 'rt_max': 10.41,
 'rt_min': 9.41,
 'rt_peak': 9.91,
 'rt_units': 'min',
 'unique_id': u'2bd76cba6a274b7cab08d7890da264f7',
 'username': u'jimmy'}],
 'unique_id': u'e59611d82abc43b08c5c5cbec2424721',
 'username': u'jimmy'},
                              {'compound': [{'creation_time': '2015-11-30T14:38:39',
 'description': u'http://pubchem.ncbi.nlm.nih.gov/compound/DL-Methionine_sulfoxide',
 'formula': u'C5H11NO3S',
 'functional_sets': [],
 'head_id': u'0b2df1e9a37247b5ab1b8c3c5fca78bd',
 'inchi': u'InChI=1S/C5H11NO3S/c1-10(9)3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 165.045964212,
 'name': u'DL-methionine sulfoxide',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'0b2df1e9a37247b5ab1b8c3c5fca78bd',
 'url': u'',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'frag_references': [],
 'head_id': u'c86be8103e57485c94b1ed6c0151e24e',
 'identification_grade': None,
 'last_modified': '2016-01-25T09:37:49',
 'mz_references': [{'adduct': u'',
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'detected_polarity': 'positive',
 'enabled': True,
 'head_id': u'0e4c818217764aae992e4769cf090073',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'modification': u'',
 'mz': 166.0533,
 'mz_tolerance': 15.0,
 'mz_tolerance_units': 'ppm',
 'name': u'Untitled',
 'observed_formula': u'',
 'prev_uid': u'38553ddff4834943866f507c0411b464',
 'ref_type': u'',
 'unique_id': u'0e4c818217764aae992e4769cf090073',
 'username': u'jimmy'}],
 'name': u'Untitled',
 'prev_uid': u'fe24ffcc60d64556865d5cc9d786e66c',
 'rt_references': [{'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'enabled': True,
 'head_id': u'bef19e217d3a47019c0367667a9c6d33',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'name': u'Untitled',
 'prev_uid': u'8573722d4e3a44eea7a4818088ac321b',
 'ref_type': u'',
 'rt_max': 12.48,
 'rt_min': 11.48,
 'rt_peak': 11.98,
 'rt_units': 'min',
 'unique_id': u'bef19e217d3a47019c0367667a9c6d33',
 'username': u'jimmy'}],
 'unique_id': u'c86be8103e57485c94b1ed6c0151e24e',
 'username': u'jimmy'},
                              {'compound': [{'creation_time': '2015-10-08T11:37:11',
 'description': u'',
 'formula': u'C7H15NO3',
 'functional_sets': [],
 'head_id': u'cef4301ee5a84227ba7361fc22b62c20',
 'inchi': u'InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3/t6-/m1/s1',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 161.105194091797,
 'name': u'L-carnitine',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'cef4301ee5a84227ba7361fc22b62c20',
 'url': u'',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'frag_references': [],
 'head_id': u'fa8d4cf8e0854278989b42ee1d618159',
 'identification_grade': None,
 'last_modified': '2016-01-25T09:37:49',
 'mz_references': [{'adduct': u'',
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'detected_polarity': 'positive',
 'enabled': True,
 'head_id': u'a4910c738e6f4d31aeebb5ba28cd634c',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'modification': u'',
 'mz': 162.1126,
 'mz_tolerance': 15.0,
 'mz_tolerance_units': 'ppm',
 'name': u'Untitled',
 'observed_formula': u'',
 'prev_uid': u'ee762d1c95af4719b2028b58e36e1e86',
 'ref_type': u'',
 'unique_id': u'a4910c738e6f4d31aeebb5ba28cd634c',
 'username': u'jimmy'}],
 'name': u'Untitled',
 'prev_uid': u'265892c153774b41a0a266190c4dad0a',
 'rt_references': [{'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'enabled': True,
 'head_id': u'2c8bfb90720148ebbf0e144ec249034e',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'name': u'Untitled',
 'prev_uid': u'317ff2669e734912bc3edb53c9e0596f',
 'ref_type': u'',
 'rt_max': 9.97,
 'rt_min': 8.97,
 'rt_peak': 9.47,
 'rt_units': 'min',
 'unique_id': u'2c8bfb90720148ebbf0e144ec249034e',
 'username': u'jimmy'}],
 'unique_id': u'fa8d4cf8e0854278989b42ee1d618159',
 'username': u'jimmy'},
                              {'compound': [{'creation_time': '2015-10-08T11:36:20',
 'description': u'',
 'formula': u'C5H7NO3',
 'functional_sets': [],
 'head_id': u'80bad1959ed84c408f7d840ab8abd51d',
 'inchi': u'InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/p-1/t3-/m0/s1',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 129.042587280273,
 'name': u'5-oxo-L-proline',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'80bad1959ed84c408f7d840ab8abd51d',
 'url': u'',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'frag_references': [],
 'head_id': u'ead7a62f270c4fdba158cc4e454f6ccb',
 'identification_grade': None,
 'last_modified': '2016-01-25T09:37:49',
 'mz_references': [{'adduct': u'',
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'detected_polarity': 'positive',
 'enabled': True,
 'head_id': u'59ac69bf3b1e41dfa3c24cad7987a7b4',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'modification': u'',
 'mz': 130.0499,
 'mz_tolerance': 15.0,
 'mz_tolerance_units': 'ppm',
 'name': u'Untitled',
 'observed_formula': u'',
 'prev_uid': u'9cdb0a6af7834e04a4bd0c14f5713c7f',
 'ref_type': u'',
 'unique_id': u'59ac69bf3b1e41dfa3c24cad7987a7b4',
 'username': u'jimmy'}],
 'name': u'Untitled',
 'prev_uid': u'a5e8a58beec14d5b928c685f9d594fa6',
 'rt_references': [{'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'enabled': True,
 'head_id': u'17d84f56f27f4606b77b47a88452b3d3',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'name': u'Untitled',
 'prev_uid': u'a1b4ddd321524f069a85286d621bc418',
 'ref_type': u'',
 'rt_max': 10.5,
 'rt_min': 9.5,
 'rt_peak': 10.0,
 'rt_units': 'min',
 'unique_id': u'17d84f56f27f4606b77b47a88452b3d3',
 'username': u'jimmy'}],
 'unique_id': u'ead7a62f270c4fdba158cc4e454f6ccb',
 'username': u'jimmy'},
                              {'compound': [{'creation_time': '2015-10-08T11:37:24',
 'description': u'',
 'formula': u'C6H9N3O2',
 'functional_sets': [],
 'head_id': u'cac6a7a3914c454982c247b4bc4d3cd6',
 'inchi': u'InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1',
 'inchi_key': None,
 'last_modified': '2016-01-23T22:23:18',
 'mono_isotopic_molecular_weight': 155.069473266602,
 'name': u'|L-histidine|',
 'neutralized_2d_inchi': None,
 'neutralized_2d_inchi_key': None,
 'neutralized_inchi': None,
 'neutralized_inchi_key': None,
 'number_components': None,
 'permanent_charge': None,
 'prev_uid': u'origin',
 'reference_xrefs': [],
 'synonyms': u'',
 'unique_id': u'cac6a7a3914c454982c247b4bc4d3cd6',
 'url': u'',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'frag_references': [],
 'head_id': u'2b8b9717a94a487e9b5af40850ce4f89',
 'identification_grade': None,
 'last_modified': '2016-01-25T09:37:49',
 'mz_references': [{'adduct': u'',
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'detected_polarity': 'positive',
 'enabled': True,
 'head_id': u'c657487ba8fb454c8199764cefa8e635',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'modification': u'',
 'mz': 156.0767,
 'mz_tolerance': 15.0,
 'mz_tolerance_units': 'ppm',
 'name': u'Untitled',
 'observed_formula': u'',
 'prev_uid': u'1a3109492f694131985779f58608c78f',
 'ref_type': u'',
 'unique_id': u'c657487ba8fb454c8199764cefa8e635',
 'username': u'jimmy'}],
 'name': u'Untitled',
 'prev_uid': u'136830c7192a455183e2fe82083c13ad',
 'rt_references': [{'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'enabled': True,
 'head_id': u'b87705ba5e7b41878b9c1c7a831eb691',
 'last_modified': '2016-01-25T09:37:49',
 'lcms_run': None,
 'name': u'Untitled',
 'prev_uid': u'ccbdb5e971f948f299ac89663319ee97',
 'ref_type': u'',
 'rt_max': 14.18,
 'rt_min': 13.18,
 'rt_peak': 13.68,
 'rt_units': 'min',
 'unique_id': u'b87705ba5e7b41878b9c1c7a831eb691',
 'username': u'jimmy'}],
 'unique_id': u'2b8b9717a94a487e9b5af40850ce4f89',
 'username': u'jimmy'}],
 'creation_time': '2016-01-25T09:37:49',
 'description': u'No description',
 'head_id': u'e24c06fb715441b98f939d7d5c2e181b',
 'last_modified': '2016-01-25T09:37:49',
 'name': u'20151210_SJ_Positive_Hilic_QTOF6550_HMArkin',
 'prev_uid': u'42125e9a874e46d087acafd2fc35e8ff',
 'unique_id': u'e24c06fb715441b98f939d7d5c2e181b',
 'username': u'jimmy'}

In [9]:

    

atlases = metob.retrieve('Atlas',name='20151130_LS_Positive_Hilic_QExactive_Archetypes')
a = atlases[0]
a.compound_identifications[0].mz_references


    

    
Out[9]:





[{'adduct': u'[M+H]+',
  'creation_time': '2015-11-30T14:43:49',
  'description': u'No description',
  'detected_polarity': 'positive',
  'enabled': True,
  'head_id': u'566d6fa9bb6746d3b31122326b2a19de',
  'last_modified': '2016-01-23T22:23:18',
  'lcms_run': None,
  'modification': u'',
  'mz': 90.0549520864258,
  'mz_tolerance': 15.0,
  'mz_tolerance_units': 'ppm',
  'name': u'Untitled',
  'observed_formula': u'',
  'prev_uid': u'origin',
  'ref_type': u'',
  'unique_id': u'566d6fa9bb6746d3b31122326b2a19de',
  'username': u'jimmy'}]

In [10]:

    

print atlases[0].compound_identifications[0].compound[0].name
print atlases[0].compound_identifications[0].mz_references[0].mz
print atlases[0].compound_identifications[0].rt_references[0].rt_peak
# print atlases[0].compound_identifications[0].references[2].RTpeak
print atlases[0].compound_identifications[0].description.split(',')
print atlases[0].compound_identifications[0].name


    

    




L-alanine
90.0549520864
11.02
[u'No description']
Untitled

In [ ]: