Clean, add text and fig

app.py

@@ -27,7 +27,6 @@ def setup():
         urllib.request.urlretrieve(url, target_path)
 
     # Run simple example as a test and to download weights
-    # Download example spectra file
     example_url = 'https://raw.githubusercontent.com/pluskal-lab/DreaMS/cc806fa6fea281c1e57dd81fc512f71de9290017/data/examples/example_5_spectra.mgf'
     example_path = Path('./data/example_5_spectra.mgf')
     example_path.parent.mkdir(parents=True, exist_ok=True)
@@ -95,25 +94,28 @@ def predict(lib_pth, in_pth):
     #     display(Chem.MolFromSmiles(row['library_SMILES']))
 
     # Sort hits by DreaMS similarity
-    # df_top1 = df[df['topk'] == 1].sort_values('DreaMS_similarity', ascending=False)
-    # df = df.set_index('feature_id').loc[df_top1['feature_id'].values].reset_index()
-    # df
+    df_top1 = df[df['topk'] == 1].sort_values('DreaMS_similarity', ascending=False)
+    df = df.set_index('feature_id').loc[df_top1['feature_id'].values].reset_index()
 
     return df, str(df_path)
 
 
 setup()
-app = gr.Blocks(theme=gr.themes.Default(primary_hue="green", secondary_hue="pink"))
+app = gr.Blocks(theme=gr.themes.Default(primary_hue="yellow", secondary_hue="pink"))
 with app:
 
     # Input GUI
+    # gr.Markdown(value="""# DreaMS""")
+    gr.Image("https://raw.githubusercontent.com/pluskal-lab/DreaMS/cc806fa6fea281c1e57dd81fc512f71de9290017/assets/dreams_background.png", label="DreaMS")
     gr.Markdown(value="""
-        # DreaMS
+        DreaMS (Deep Representations Empowering the Annotation of Mass Spectra) is a transformer-based
+         neural network designed to interpret tandem mass spectrometry (MS/MS) data. Pre-trained in a
+         self-supervised way on millions of unannotated spectra from our new GeMS (GNPS Experimental
+         Mass Spectra) dataset, DreaMS acquires rich molecular representations by predicting masked
+         spectral peaks and chromatographic retention orders. When fine-tuned for tasks such as spectral
+         similarity, chemical properties prediction, and fluorine detection, DreaMS achieves state-of-the-art
+         performance across various mass spectrometry interpretation tasks (<a href="https://www.nature.com/articles/s41587-025-02663-3">Bushuiev et al., Nature Biotechnology, 2025</a>).
     """)
-    # gr.Image("assets/readme-dimer-close-up.png")
-    # gr.Markdown(value="""
-    #     TODO Some description
-    # """)
     with gr.Row(equal_height=True):
         in_pth = gr.File(
             file_count="single",
@@ -132,9 +134,6 @@ with app:
         datatype=["number", "number", "number", "str", "str", "number", "number", "number", "number"],
         col_count=(9, "fixed"),
     )
-    # dropdown = gr.Dropdown(interactive=True, visible=False)
-    # dropdown_choices_to_plot_args = gr.State([])
-    # plot = gr.HTML()
 
     # Main logic
     inputs = [in_pth]
@@ -142,8 +141,5 @@ with app:
     predict = partial(predict, lib_pth)
     predict_button.click(predict, inputs=inputs, outputs=outputs)
 
-    # Update plot on dropdown change
-    # dropdown.change(update_plot, inputs=[dropdown, dropdown_choices_to_plot_args], outputs=[plot])
-
 
 app.launch(allowed_paths=['./assets'])

data/example_5_spectra.mgf

@@ -0,0 +1,350 @@
+BEGIN IONS
+NAME=DMAPT
+DESCRIPTION=MCE bioactive compounds library
+EXACTMASS=293.199094
+FORMULA=C17H27NO3
+INCHI=InChI=1S/C17H27NO3/c1-11-6-5-9-17(2)15(21-17)14-12(8-7-11)13(10-18(3)4)16(19)20-14/h6,12-15H,5,7-10H2,1-4H3/b11-6-/t12-,13+,14-,15+,17+/m0/s1
+INCHIAUX=UJNSFDHVIBGEJZ-CMRIBGNTSA-N
+SMILES=C/C1=C/CC[C@@]2(C)O[C@@H]2[C@H]2OC(=O)[C@H](CN(C)C)[C@@H]2CC1
+FEATURE_ID=-1
+MSLEVEL=2
+RTINSECONDS=69.34
+ADDUCT=[M+H]+
+PEPMASS=294.20637
+CHARGE=1
+SPECTYPE=ALL_ENERGIES
+Collision energy=60.0
+FRAGMENTATION_METHOD=HCD
+ISOLATION_WINDOW=1.2000000476839432
+Acquisition=Crude
+INSTRUMENT_TYPE=Orbitrap
+SOURCE_INSTRUMENT=Orbitrap ID-X
+IMS_TYPE=none
+ION_SOURCE=ESI
+IONMODE=Positive
+PI=Tomas Pluskal
+DATACOLLECTOR=Corinna Brungs
+DATASET_ID=MSVPLACEHOLDERID
+USI=mzspec:MSVPLACEHOLDERID:20220601_100AGC_pluskal_mce_1D1_A13_id.mzML:-1
+SCANS=-1
+PRECURSOR_PURITY=1.0
+QUALITY_CHIMERIC=PASSED
+QUALITY_EXPLAINED_INTENSITY=0.95719075
+QUALITY_EXPLAINED_SIGNALS=0.91803277
+Num peaks=61
+42.033739 2.023
+43.017743 1.244
+43.041538 0.375
+44.049385 0.271
+46.064932 0.633
+55.053921 0.247
+56.049297 0.434
+58.061086 0.921
+58.064829 100
+58.068315 4.309
+58.071661 1.067
+58.074808 0.3
+67.053963 0.832
+69.069565 0.262
+79.053978 1.014
+81.069616 1.317
+82.064804 0.901
+84.080497 0.567
+91.053903 1.516
+93.069577 2.084
+94.064888 0.298
+95.048843 0.28
+95.085147 0.577
+97.088348 0.201
+98.059745 0.372
+105.069597 1.626
+106.064804 0.358
+107.085253 1.159
+108.080338 0.242
+109.064416 0.257
+109.100923 0.465
+110.096075 1.043
+116.070213 0.429
+117.069763 0.601
+119.085279 1.489
+121.100884 0.483
+129.069626 0.285
+131.085311 0.665
+133.10089 0.474
+134.059753 0.937
+135.117294 0.205
+144.093231 0.522
+145.100601 0.202
+147.11673 0.298
+149.13218 2.214
+159.116485 2.567
+161.131911 0.35
+164.107071 0.243
+164.143127 0.255
+175.112091 0.209
+177.127193 1.388
+185.13264 0.432
+192.174698 0.38
+203.14307 0.317
+222.185104 0.206
+231.13818 0.57
+249.148476 2.331
+250.216614 0.841
+251.117976 1.62
+294.128296 0.191
+294.206632 26.983
+END IONS
+
+BEGIN IONS
+NAME=Mirk-IN-1
+DESCRIPTION=MCE bioactive compounds library
+EXACTMASS=497.065759
+FORMULA=C23H17Cl2N5O4
+INCHI=InChI=1S/C23H17Cl2N5O4/c1-34-23-27-11-14-8-16(22(33)29-19(14)30-23)21(32)28-18-9-13(5-6-17(18)25)20(31)26-10-12-3-2-4-15(24)7-12/h2-9,11H,10H2,1H3,(H,26,31)(H,28,32)(H,27,29,30,33)
+INCHIAUX=CQKBSRPVZZLCJE-UHFFFAOYSA-N
+SMILES=COc1ncc2cc(C(=O)Nc3c(Cl)ccc(C(=O)NCc4cc(Cl)ccc4)c3)c(=O)[nH]c2n1
+FEATURE_ID=-1
+MSLEVEL=2
+RTINSECONDS=115.08
+ADDUCT=[M+H]+
+PEPMASS=498.07304
+CHARGE=1
+SPECTYPE=ALL_MSN_TO_PSEUDO_MS2
+Collision energy=60.0
+FRAGMENTATION_METHOD=HCD
+ISOLATION_WINDOW=1.2000000476839432
+Acquisition=Crude
+INSTRUMENT_TYPE=Orbitrap
+SOURCE_INSTRUMENT=Orbitrap ID-X
+IMS_TYPE=none
+ION_SOURCE=ESI
+IONMODE=Positive
+PI=Tomas Pluskal
+DATACOLLECTOR=Corinna Brungs
+DATASET_ID=MSVPLACEHOLDERID
+USI=mzspec:MSVPLACEHOLDERID:20220601_pluskal_mce_1D1_A4_id.mzML:-1
+SCANS=-1
+PRECURSOR_PURITY=1.0
+QUALITY_CHIMERIC=PASSED
+QUALITY_EXPLAINED_INTENSITY=0.93082154
+QUALITY_EXPLAINED_SIGNALS=0.88461536
+Num peaks=52
+42.033703 6.933
+58.028778 11.37
+59.032055 2.116
+60.03299 1.268
+63.022655 2.006
+64.017876 2.374
+65.038353 0.923
+66.033494 2.134
+69.992175 1.938
+78.033541 4.097
+79.028745 1.257
+86.060081 9.959
+87.06353 3.769
+88.064438 1.499
+91.017532 3.789
+93.044386 7.213
+104.049591 5.292
+105.044537 4.776
+105.052979 3.494
+106.028389 1.142
+120.055412 7.778
+121.039436 6.751
+125.014962 2.948
+133.027011 2.074
+133.039425 3.979
+135.018616 0.908
+148.050389 4.721
+154.005085 2.139
+160.050642 3.311
+161.034588 1.467
+176.045663 22.882
+194.056314 24.336
+204.040476 24.707
+221.080734 1.76
+222.05116 100
+222.087845 1.473
+223.089127 1.679
+248.069031 1.01
+249.074326 2.424
+250.078537 2.556
+251.081848 1.513
+277.029205 1.552
+293.066956 1.309
+308.148193 1.723
+309.15033 3.711
+310.153687 1.904
+321.062225 1.269
+357.03932 4.785
+411.191315 1.423
+412.193907 5.738
+413.196318 8.005
+498.073273 1.812
+END IONS
+
+BEGIN IONS
+NAME=1373215-15-6
+DESCRIPTION=MCE bioactive compounds library
+EXACTMASS=484.212198
+FORMULA=C25H29FN4O5
+INCHI=InChI=1S/C25H29FN4O5/c1-27-25(32)35-22-15-34-21-7-6-18(29-8-10-30(11-9-29)19-13-33-14-19)12-20(21)23(22)28-24(31)16-2-4-17(26)5-3-16/h2-7,12,19,22-23H,8-11,13-15H2,1H3,(H,27,32)(H,28,31)/t22-,23-/m0/s1
+INCHIAUX=NDEBZCZEAVMSQF-GOTSBHOMSA-N
+SMILES=CNC(=O)O[C@H]1COc2c(cc(N3CCN(C4COC4)CC3)cc2)[C@@H]1NC(=O)c1ccc(F)cc1
+FEATURE_ID=-1
+MSLEVEL=2
+RTINSECONDS=77.81
+ADDUCT=[M+H]+
+PEPMASS=485.21947
+CHARGE=1
+SPECTYPE=SAME_ENERGY
+Collision energy=30.0
+FRAGMENTATION_METHOD=HCD
+ISOLATION_WINDOW=1.2000000476839432
+Acquisition=Crude
+INSTRUMENT_TYPE=Orbitrap
+SOURCE_INSTRUMENT=Orbitrap ID-X
+IMS_TYPE=none
+ION_SOURCE=ESI
+IONMODE=Positive
+PI=Tomas Pluskal
+DATACOLLECTOR=Corinna Brungs
+DATASET_ID=MSVPLACEHOLDERID
+USI=mzspec:MSVPLACEHOLDERID:20220601_pluskal_mce_1D1_A8_id.mzML:-1
+SCANS=-1
+PRECURSOR_PURITY=1.0
+QUALITY_CHIMERIC=PASSED
+QUALITY_EXPLAINED_INTENSITY=1.0
+QUALITY_EXPLAINED_SIGNALS=1.0
+Num peaks=15
+70.064962 2.862
+84.080627 1.511
+109.076332 1.385
+114.091324 2.886
+123.023911 14.149
+161.059692 2.52
+202.086288 1.435
+230.105148 3.367
+241.133691 26.664
+261.159847 3.062
+271.144251 41.501
+289.154956 100
+346.175893 26.1
+351.136749 1.2
+410.186693 8.75
+END IONS
+
+BEGIN IONS
+NAME=IPSU
+DESCRIPTION=MCE bioactive compounds library
+EXACTMASS=405.216475
+FORMULA=C23H27N5O2
+INCHI=InChI=1S/C23H27N5O2/c1-30-20-7-11-24-22(26-20)27-13-9-23(10-14-27)8-4-12-28(21(23)29)16-17-15-25-19-6-3-2-5-18(17)19/h2-3,5-7,11,15,25H,4,8-10,12-14,16H2,1H3
+INCHIAUX=PCMHOSYCWRRHTG-UHFFFAOYSA-N
+SMILES=COc1nc(N2CCC3(CCCN(Cc4c[nH]c5ccccc45)C3=O)CC2)ncc1
+FEATURE_ID=660
+MSLEVEL=2
+RTINSECONDS=110.45
+ADDUCT=[M+H]+
+PEPMASS=406.22375
+CHARGE=1
+Collision energy=20.0
+FRAGMENTATION_METHOD=HCD
+ISOLATION_WINDOW=1.2000000476839432
+Acquisition=Crude
+INSTRUMENT_TYPE=Orbitrap
+SOURCE_INSTRUMENT=Orbitrap ID-X
+IMS_TYPE=none
+ION_SOURCE=ESI
+IONMODE=Positive
+PI=Tomas Pluskal
+DATACOLLECTOR=Corinna Brungs
+DATASET_ID=MSVPLACEHOLDERID
+USI=mzspec:MSVPLACEHOLDERID:20220601_pluskal_mce_1D1_A1_id.mzML:660
+SCANS=660
+PRECURSOR_PURITY=0.9731724062527856
+QUALITY_CHIMERIC=PASSED
+QUALITY_EXPLAINED_INTENSITY=0.99532574
+QUALITY_EXPLAINED_SIGNALS=0.8888889
+Num peaks=9
+45.134823 1.082
+45.13699 1.064
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+130.064972 13.97
+136.111862 0.874
+277.16571 100
+289.165924 52.842
+307.177856 0.793
+406.223083 43.696
+END IONS
+
+BEGIN IONS
+NAME=Vadimezan
+DESCRIPTION=MCE bioactive compounds library
+EXACTMASS=282.089209
+FORMULA=C17H14O4
+INCHI=InChI=1S/C17H14O4/c1-9-6-7-13-15(20)12-5-3-4-11(8-14(18)19)17(12)21-16(13)10(9)2/h3-7H,8H2,1-2H3,(H,18,19)
+INCHIAUX=XGOYIMQSIKSOBS-UHFFFAOYSA-N
+SMILES=Cc1c(C)c2c(cc1)c(=O)c1cccc(CC(=O)O)c1o2
+FEATURE_ID=474
+MSLEVEL=2
+RTINSECONDS=113.94
+ADDUCT=[M+H]+
+PEPMASS=283.09648
+CHARGE=1
+Collision energy=60.0
+FRAGMENTATION_METHOD=HCD
+ISOLATION_WINDOW=1.2000000476839432
+Acquisition=Crude
+INSTRUMENT_TYPE=Orbitrap
+SOURCE_INSTRUMENT=Orbitrap ID-X
+IMS_TYPE=none
+ION_SOURCE=ESI
+IONMODE=Positive
+PI=Tomas Pluskal
+DATACOLLECTOR=Corinna Brungs
+DATASET_ID=MSVPLACEHOLDERID
+USI=mzspec:MSVPLACEHOLDERID:20220601_pluskal_mce_1D1_A2_id.mzML:474
+SCANS=474
+PRECURSOR_PURITY=0.973405752811273
+QUALITY_CHIMERIC=PASSED
+QUALITY_EXPLAINED_INTENSITY=0.99386805
+QUALITY_EXPLAINED_SIGNALS=0.9444444
+Num peaks=36
+91.053741 1.144
+105.069382 1.254
+141.069168 1.139
+152.061859 1.019
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+155.085022 0.966
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+166.077545 9.805
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+181.06459 6.555
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+194.07254 10.324
+195.080231 21.628
+196.087906 3.722
+208.088181 2.735
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+209.096024 59.124
+209.119858 0.749
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+221.096359 0.981
+222.067566 2.431
+223.0755 19.616
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+236.083176 2.085
+237.090988 100
+238.098816 15.987
+239.106781 0.935
+283.096832 2.447
+END IONS