deepmolecules tutorial¶

In [2]:

Copied!

from deepmolecules import download_data, kcat, km

# Download additional data
download_data()
from deepmolecules import download_data, kcat, km

# Download additional data
download_data()

2024-12-23 10:51:38,424 INFO     Data already exists at /home/marvin/.cache/deepmolecules/data

In [3]:

Copied!





km.predict(
    substrates=[
        "C00012",
        "InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)"
        "28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)"
        "42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9"
        "(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,"
        "5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p-1/t10-,"
        "11-,13-,14-,15-,16-,20-,21-/m1/s1",
    ],
    enzymes=[
        "MSIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAW"
        "HGDWPLPVKLPLVGGHEGAGVVVGMGENVKWKIGDYAGIKWLNGSCMACEY"
        "CELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILC"
        "AGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGE"
        "GKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEAS"
        "TRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALD"
        "FFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK",
        "MSIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAW"
        "HGDWPLPVKLPLVGGHEGAGVVVGMGENVKWKIGDYAGIKWLNGSCMACEY"
        "CELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILC"
        "AGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGE"
        "GKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEAS"
        "TRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALD"
        "FFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTST",
    ],
).head()

# Webserver prediction as reference: 0.35 mM
km.predict(
    substrates=[
        "C00012",
        "InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)"
        "28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)"
        "42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9"
        "(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,"
        "5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p-1/t10-,"
        "11-,13-,14-,15-,16-,20-,21-/m1/s1",
    ],
    enzymes=[
        "MSIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAW"
        "HGDWPLPVKLPLVGGHEGAGVVVGMGENVKWKIGDYAGIKWLNGSCMACEY"
        "CELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILC"
        "AGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGE"
        "GKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEAS"
        "TRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALD"
        "FFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK",
        "MSIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAW"
        "HGDWPLPVKLPLVGGHEGAGVVVGMGENVKWKIGDYAGIKWLNGSCMACEY"
        "CELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILC"
        "AGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGE"
        "GKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEAS"
        "TRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALD"
        "FFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTST",
    ],
).head()

# Webserver prediction as reference: 0.35 mM

Out[3]:

	substrate	enzyme	GNN rep	enzyme rep	complete	KM [mM]
0	C00012	MSIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHT...	[2.1599, 40.12873, 3.2620366, 2.1908092, 0.0, ...	[-0.07678479, 0.3095483, -0.072399296, -0.0750...	True	0.349176
1	InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17...	MSIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHT...	[20.846977, 173.14688, 12.362773, 110.97217, 0...	[-0.076705605, 0.30694333, -0.06873098, -0.074...	True	0.197812

In [4]:

Copied!





kcat.predict(
    substrates=[
        "InChI=1S/C7H5NO4/c9-8(10)5-1-2-6-7(3-5)"
        "12-4-11-6/h1-3H,4H2;InChI=1S/H2O2/c1-2/h1-2H",
    ],
    products=[
        "InChI=1S/C6H5NO4/c8-5-2-1-4(7(10)11)3-6(5)9/"
        "h1-3,8-9H;InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3);InChI=1S/H2O/h1H2",
    ],
    enzymes=[
        "MKYFPLFPTLVFAARVVAFPAYASLAGLSQQELDAIIPTLEAREP"
        "GLPPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGY"
        "LPRNGVATPVQIINAVQEGLNFDNQAAVFATYAAHLVDGNLITDL"
        "LSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNN"
        "HDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPN"
        "FSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSR"
        "MPDDFFRAPSPRSGTGVEVVIQAHPMQPGRNVGKINSYTVDPTSS"
        "DFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFFFQGVAA"
        "GCTQVFPYGRD",
    ],
).head()

# Webserver prediction as reference: 2.12 [1/sec]
kcat.predict(
    substrates=[
        "InChI=1S/C7H5NO4/c9-8(10)5-1-2-6-7(3-5)"
        "12-4-11-6/h1-3H,4H2;InChI=1S/H2O2/c1-2/h1-2H",
    ],
    products=[
        "InChI=1S/C6H5NO4/c8-5-2-1-4(7(10)11)3-6(5)9/"
        "h1-3,8-9H;InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3);InChI=1S/H2O/h1H2",
    ],
    enzymes=[
        "MKYFPLFPTLVFAARVVAFPAYASLAGLSQQELDAIIPTLEAREP"
        "GLPPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGY"
        "LPRNGVATPVQIINAVQEGLNFDNQAAVFATYAAHLVDGNLITDL"
        "LSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNN"
        "HDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPN"
        "FSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSR"
        "MPDDFFRAPSPRSGTGVEVVIQAHPMQPGRNVGKINSYTVDPTSS"
        "DFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFFFQGVAA"
        "GCTQVFPYGRD",
    ],
).head()

# Webserver prediction as reference: 2.12 [1/sec]

[10:51:51] DEPRECATION WARNING: please use AtomPairGenerator
[10:51:51] DEPRECATION WARNING: please use AtomPairGenerator
[10:51:51] DEPRECATION WARNING: please use AtomPairGenerator
[10:51:51] DEPRECATION WARNING: please use AtomPairGenerator
[10:51:51] DEPRECATION WARNING: please use AtomPairGenerator

Out[4]:

	substrates	products	enzyme	difference_fp	enzyme rep	complete	kcat [s^(-1)]
0	InChI=1S/C7H5NO4/c9-8(10)5-1-2-6-7(3-5)12-4-11...	InChI=1S/C6H5NO4/c8-5-2-1-4(7(10)11)3-6(5)9/h1...	MKYFPLFPTLVFAARVVAFPAYASLAGLSQQELDAIIPTLEAREPG...	[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...	[0.8315532, 0.08632779, -0.4214351, 0.4193583,...	True	216.114853

In [ ]: