Cheminformatics

11/2/2021

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Cheminformatics (also known as chemoinformatics, chemioinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems in the field of chemistry. --Wikipedia

Open Source Cheminformatics

  • rdkit http://www.rdkit.org

    • BSD License
    • Relatively new, very nicely architected C++ backend
    • Actively developed
    • Native Python interface

  • OpenBabel http://openbabel.org

    • GNU License
    • Older (forked from OpenEye in 2001), a bit crufty and complicated
    • Lots of functionality (e.g., support for more than 100 file formats)
    • Python interface is through SWIG (auto-generated) bindings to C/C++
    • Includes standalone programs: babel, obabel, etc.

  • Pybel

    • A native, user-friendly python interface to OpenBabel
    • Limited functionality (but can always fallback to OpenBabel)
    • Simplest to use
    • Note: Pybel is installed as part of openbabel. There is a completely unrelated python package called PyBEL that is not what you want

File Formats

2D

SMILES

3D

pdb, sdf, mol2

Simplified Molecular Input Line Entry System (SMILES)

Atoms

Specified by their atomic symbols inside brackets

  • [Au], [Fe], [Zn], etc

No brackets needed for organic subset: B, C, N, O, P, S, F, Cl, Br, and I

Aromatic atoms are lower case: c1ccccc1

Bonds

  • Single -
  • Double =
  • Triple #
  • Aromatic :

Single and aromatic can be omitted. E.g ethane (C2H6) is CC.

SMILES, cont.

Branches

Parentheses denote branches and can be nested.

Example: SC(N)CO

Cycles

Break a bond in the cycle and use a digit to label the break.

As long as rings are separate, digits can be reused. Aromatic rings use lower-case e.g. c1ccccc1 is benzene

SMILES, cont.

Disconnections

A period . separates nonbonded molecules.

[Na+].[Cl-]

Isomeric Smiles

Slashes (/ \) denote configuration around double bonds.

At (@) denotes configuration around chiral centers.

Drawing

All but the simplest smiles can be challenging to interpret (especially if chirality is included). Fortunately, you can use pybel (or molecular viewers like MarvinView) to convert them to their 2D representation.

Example: CC(NC1=CC=C(O)C=C1)=O

CH 3 NH OH O

SMARTS

Regular expressions for molecules.

All SMILES are SMARTS (exact matches). Additionally, SMARTS support

  • wild cards
    • C~*~C any atom can be between two carbons using any (~) bond
    • a1aaaaa1 any aromatic 6 atom ring
  • property testing
    • [R] atom in a ring
    • [#6] atomic number is 6 (matches aromatic or aliphatic)
    • [D3] atom with three explicit bonds (degree)
  • logical operators (not - !, and - & ;, or - ,)
    • [!C&R] not aliphatic carbon and in ring
    • [F,Cl,Br,I] one of the first four halogens
  • matching an atomic environment ('recursive' SMARTS)
    • [$(*O);$(*C)] this matches one atom that is bound to both C and O

Pybel Input/Output

pybel.readstring

Takes a format and string with molecular data in it and returns a single molecule.

4

For simple output, use the molecule's write method, which takes the format

 OpenBabel10312213312D

  4  3  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
M  END
$$$$

pybel.readfile

pybel.readfile

Takes a format and file name and returns an iterator over all the molecules in the file.

14
O O OH N N OH 
N#Cc1c(O)c2C(=O)c3ccccc3C(=O)c2c(c1C#N)O	NSC27034
N#Cc1cc2SCCSCCCSCCSc2cc1C#N	NSC680721
N#Cc1cc2CN(CCN(CCN(CCN(Cc2cc1C#N)S(=O)(=O)c1ccc(cc1)C)S(=O)(=O)c1ccc(cc1)C)S(=O)(=O)c1ccc(cc1)C)S(=O)(=O)c1ccc(cc1)C	NSC673657
N#Cc1cc2/C(=N\c3cccc(n3)N)/N=C(c2cc1C#N)Nc1cccc(n1)N	NSC666078
N#Cc1c(OC)ccc(c1C#N)O.COc1ccc(c(c1C#N)C#N)OC	NSC618324
N#Cc1c(C#N)c(O)c2c(c1O)c(N)ccc2	NSC320651
N#Cc1cc(ccc1C#N)NC(=O)CCCC(=O)Nc1ccc(c(c1)C#N)C#N	NSC309816
N#Cc1c(C#N)c(O)c(c(c1O)Cl)Cl	NSC172566
N#Cc1c(C#N)c(O)c2c(c1O)cccc2	NSC128281
N#Cc1cc(ccc1C#N)[N+](=O)[O-]	NSC123374
N#Cc1cc(ccc1C#N)Oc1ccc(c(c1)C#N)C#N	NSC94808
N#Cc1c2c(cc(c1C#N)[N+](=O)[O-])n(c1c2cccc1)C	NSC92934
N#Cc1c(O)ccc(c1C#N)O	NSC43554
N#Cc1ccccc1C#N	NSC17562

pybel.Outputfile

To output many molecules to the same file, use pybel.Outputfile

Molecules

The molecule object provides a number of methods and access to the molecules atoms and bonds.

6 6 6 6 6 6 6 7 6 7

Atom properties include atomicmass, atomicnum, coords, formalcharge, hyb, isotope, partialcharge and degree

Atoms can also be accessed in mol.atoms

SMARTS Matching

SMARTS matching is done by initializing a pybel.Smarts object with a SMARTS expression. This can then be applied to any molecule to identify the matching atoms.

N N 
[(1, 6, 5, 4, 3, 2)]

The returned matches are atom indices that can be accessed through mol.atoms

5
8
NH 2 OH N N OH
OH N N OH

Molecular Properties

128.13076

{'abonds': 6.0, 'atoms': 10.0, 'bonds': 10.0, 'cansmi': nan, 'cansmiNS': nan, 'dbonds': 0.0, 'formula': nan, 'HBA1': 2.0, 'HBA2': 2.0, 'HBD': 0.0, 'InChI': nan, 'InChIKey': nan, 'L5': nan, 'logP': 1.42996, 'MR': 35.872, 'MW': 128.13076, 'nF': 0.0, 'rotors': 0.0, 's': nan, 'sbonds': 2.0, 'smarts': nan, 'tbonds': 2.0, 'title': nan, 'TPSA': 47.58}

1.42996

Lipinski's Rule of Five

In 1997 Christopher Lipinski analyzed existing drugs and came up with a set of molecular property rules for classifying a small molecule as drug-like.

  • No more than 5 hydrogen bond donors
  • No more than 10 hydrogen bond acceptors
  • Molecular weight less than 500 daltons
  • Partition coefficient logP less than 5
  • There is no fifth rule
True
True
False
True
True
True
True
True
True
True
True
True
True
True

Fingerprints

A molecular fingerprint reduces the chemical features of a molecule into a bit vector. The features of the fingerprint correspond to a bit in the vector. This bit is set if the compound has that feature.

The most common type of fingerprint is a Daylight style fingerprint where all the paths (up to a given length) are enumerated and hashed to their bit positions.

Fingerprints, cont.

Bit vectors can easily be compared, most commonly with the Tanimoto coefficient: $$\frac{A \cap B}{A \cup B}$$

This provides a quantitative measure of chemical similarity.

Similarity search is a surprisingly effective mechanism of virtual screening (given enough data).

openbabel.pybel.Fingerprint
[75, 82, 224, 279, 296, 299, 348, 440, 442, 474, 503, 598, 656, 671, 711, 716, 728, 870, 906, 913, 937]

Chemical Similarity

Tanimoto coefficient

$\Large \frac{A \cap B}{A \cup B}$ 1.0 means identical

e.g. Tanimoto coefficient of the bitstrings 1001 and 0011 is 0.5

To calculate the Tanimoto similarity between two fingerprints, use the | operator

0.28
0.3
0.19626168224299065
0.12138728323699421
0.5
0.4666666666666667
0.29577464788732394
0.42857142857142855
0.6176470588235294
0.4117647058823529
0.4772727272727273
0.22826086956521738
0.6363636363636364
1.0

2D -> 3D

(0.7656749137001738, -0.08415478296300143, -0.15465954760011352)
(1.2410627944678445, 0.05282849408781525, 0.10746537534097979)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

sdf Molecules

10
(-0.5939, -56.8911, 14.3139)

ZINC78996542


 39 44  0  0  0  0  0  0  0  0999 V2000
   -0.5939  -56.8911   14.3139 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3154  -57.8883   15.8741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3628  -55.5394   14.9296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0440  -55.7357   15.4805 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3058  -57.7869   14.5684 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2724  -57.1748   15.3144 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1864  -57.3893   16.5881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5650  -58.0576   12.9536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4112  -58.0403   11.5707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4635  -57.8375   13.7859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1560  -57.8031   11.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1883  -57.5962   13.2480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0573  -57.5833   11.8565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9942  -57.3574   14.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7971  -57.1312   13.5121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6648  -57.1197   12.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8049  -57.3464   11.2822 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5742  -56.9136   11.4820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7364  -57.3419   10.3001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7198  -58.5030   16.2901 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5010  -56.2171   16.2506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7946  -58.5045   17.6831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5759  -56.2186   17.6435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0729  -57.3592   15.5739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2227  -57.3625   18.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3046  -57.3655   19.8487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3111  -54.6466   15.3638 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2563  -53.8710   14.6948 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8121  -54.3645   13.5073 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6178  -52.1004   11.5954 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4057  -52.3452   11.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0836  -54.8943   14.7675 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9949  -53.3368   13.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7496  -53.5881   12.8303 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9229  -52.5915   12.8100 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4640  -53.0881   11.6153 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6585  -59.9707   15.9992 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1564  -60.0645   16.2196 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3350  -59.3635   15.5577 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  1  0  0  0
 10 12  1  0  0  0
 20 24  1  0  0  0
 21 23  1  0  0  0
 27 32  1  0  0  0
 22 25  1  0  0  0
 28 33  1  0  0  0
 11 13  1  0  0  0
 29 34  1  0  0  0
 24 14  1  0  0  0
 12 14  1  0  0  0
 33 34  1  0  0  0
 13 17  1  0  0  0
 15  1  1  0  0  0
 15 16  1  0  0  0
 16 17  1  0  0  0
  2  6  1  0  0  0
  3  1  1  0  0  0
  3  4  1  0  0  0
  4 32  1  0  0  0
  4  6  1  0  0  0
 26 25  1  0  0  0
 37 39  1  0  0  0
 38 39  1  0  0  0
 39  2  1  0  0  0
  6  5  1  0  0  0
  8 10  2  0  0  0
  9 11  2  0  0  0
 20 22  2  0  0  0
 21 24  2  0  0  0
 27 28  2  0  0  0
 23 25  2  0  0  0
 29 32  2  0  0  0
 30 31  2  0  0  0
 30 35  2  0  0  0
 31 36  2  0  0  0
 12 13  2  0  0  0
 33 35  2  0  0  0
 34 36  2  0  0  0
 14 15  2  0  0  0
  1  5  2  0  0  0
 16 18  2  0  0  0
  2  7  2  0  0  0
 17 19  1  0  0  0
M  END
> <minimizedAffinity>
-7.83433

> <minimizedRMSD>
1.45522

> <molecular weight>
475.372

$$$$
ZINC78996542


 39 44  0  0  0  0  0  0  0  0999 V2000
   -0.5722  -56.8468   14.3132 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3170  -57.8869   15.8829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3244  -55.4995   14.9316 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0775  -55.7161   15.4874 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3140  -57.7556   14.5698 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2862  -57.1582   15.3202 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1923  -57.4012   16.6007 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5452  -57.9747   12.9290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3911  -57.9310   11.5468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4434  -57.7729   13.7658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1352  -57.6858   10.9997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1676  -57.5240   13.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0362  -57.4846   11.8422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9733  -57.3042   14.0987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7756  -57.0691   13.5066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6429  -57.0290   12.0089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7832  -57.2393   11.2727 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5516  -56.8149   11.4815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7144  -57.2159   10.2909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7038  -58.4927   16.2574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4766  -56.2038   16.2618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7789  -58.5209   17.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5521  -56.2319   17.6545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0525  -57.3342   15.5634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2031  -57.3905   18.3484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2855  -57.4221   19.8372 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3565  -54.6510   15.3845 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3151  -53.8880   14.7200 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8755  -54.3614   13.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7196  -52.1345   11.6161 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5100  -52.3693   11.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1314  -54.8885   14.7794 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0693  -53.3564   13.4560 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8264  -53.5977   12.8421 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0099  -52.6234   12.8352 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559  -53.0999   11.6229 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6348  -59.9861   16.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1325  -60.0490   16.2302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3170  -59.3619   15.5646 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  1  0  0  0
 10 12  1  0  0  0
 20 24  1  0  0  0
 21 23  1  0  0  0
 27 32  1  0  0  0
 22 25  1  0  0  0
 28 33  1  0  0  0
 11 13  1  0  0  0
 29 34  1  0  0  0
 24 14  1  0  0  0
 12 14  1  0  0  0
 33 34  1  0  0  0
 13 17  1  0  0  0
 15  1  1  0  0  0
 15 16  1  0  0  0
 16 17  1  0  0  0
  2  6  1  0  0  0
  3  1  1  0  0  0
  3  4  1  0  0  0
  4 32  1  0  0  0
  4  6  1  0  0  0
 26 25  1  0  0  0
 37 39  1  0  0  0
 38 39  1  0  0  0
 39  2  1  0  0  0
  6  5  1  0  0  0
  8 10  2  0  0  0
  9 11  2  0  0  0
 20 22  2  0  0  0
 21 24  2  0  0  0
 27 28  2  0  0  0
 23 25  2  0  0  0
 29 32  2  0  0  0
 30 31  2  0  0  0
 30 35  2  0  0  0
 31 36  2  0  0  0
 12 13  2  0  0  0
 33 35  2  0  0  0
 34 36  2  0  0  0
 14 15  2  0  0  0
  1  5  2  0  0  0
 16 18  2  0  0  0
  2  7  2  0  0  0
 17 19  1  0  0  0
M  END
> <minimizedAffinity>
-7.7915

> <minimizedRMSD>
1.18555

> <molecular weight>
475.372

$$$$
ZINC78996534


 39 44  0  0  0  0  0  0  0  0999 V2000
   -0.6060  -58.4259   14.4308 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2622  -57.0761   15.7885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3848  -59.6010   15.3414 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0076  -59.2726   15.8653 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2852  -57.4884   14.4946 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2358  -57.9070   15.3815 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1167  -57.3919   16.6176 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5490  -57.6468   12.7169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3640  -57.9721   11.3766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4660  -57.6655   13.6007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0959  -58.3170   10.9188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1782  -58.0108   13.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
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sdf files can have arbitrary data embedded in them:

M  END
> <minimizedAffinity>
-7.83433

> <minimizedRMSD>
1.45522

> <molecular weight>
475.372

$$$$
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M  END
> <minimizedAffinity>
-7.60183

> <minimizedRMSD>
2.26383

> <molecular weight>
475.372

$$$$
ZINC78996542


 39 44  0  0  0  0  0  0  0  0999 V2000
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{'MOL Chiral Flag': '0', 'minimizedAffinity': '-7.83433', 'minimizedRMSD': '1.45522', 'molecular weight': '475.372', 'OpenBabel Symmetry Classes': '27 24 14 23 12 26 2 6 7 16 15 31 35 32 29 34 30 4 5 13 13 11 11 28 21 1 10 17 20 9 8 25 36 33 18 19 3 3 22'}
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M  END
> <minimizedAffinity>
-7.58798

> <minimizedRMSD>
1.876

> <molecular weight>
475.372

$$$$
ZINC35448294


 33 38  0  0  0  0  0  0  0  0999 V2000
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M  END
> <minimizedAffinity>
-7.52352

> <minimizedRMSD>
6.72818

> <molecular weight>
407.767

$$$$
ZINC72314638


 34 38  0  0  0  0  0  0  0  0999 V2000
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M  END
> <minimizedAffinity>
-7.51168

> <minimizedRMSD>
1.81673

> <molecular weight>
411.326

$$$$
ZINC72314638


 34 38  0  0  0  0  0  0  0  0999 V2000
   -6.9192  -60.0250   14.8266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9223  -60.5532   13.5393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7590  -59.4409   15.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7655  -60.4980   12.7677 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5813  -59.3753   14.5807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6073  -59.9120   13.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3283  -58.7583   15.1036 C   0  0  0  0  0  0  0  0  0  0  0  0

Beyond Pybel

Recall that Pybel is a python-native wrapper around the OpenBabel SWIG bindings. The underlying OpenBabel objects are always accessible if you need to use the additional functionality provided by OpenBabel (this may be necessary if you modifying or creating molecule objects).

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<openbabel.openbabel.vector3; proxy of <Swig Object of type 'OpenBabel::vector3 *' at 0x00000206118F8660> >
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  2  4  2  0  0  0
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M  END
> <minimizedAffinity>
-7.51156

> <minimizedRMSD>
2.07052

> <molecular weight>
411.326

$$$$
ZINC39912421


 35 39  0  0  0  0  0  0  0  0999 V2000
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M  END
> <minimizedAffinity>
-7.49363

> <minimizedRMSD>
1.94002

> <molecular weight>
442.764

$$$$
ZINC39912421


 35 39  0  0  0  0  0  0  0  0999 V2000
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 19 20  1  0  0  0
M  END
> <minimizedAffinity>
-7.49359

> <minimizedRMSD>
2.12367

> <molecular weight>
442.764

$$$$
ZINC39912344


 35 39  0  0  0  0  0  0  0  0999 V2000
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   -7.1891  -63.1276   13.2804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4861  -60.8499   14.7295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5641  -64.3456   12.5058 C   0  0  0  0  0  0  0  0  0  0  0  0
 21 25  1  0  0  0
 22 24  1  0  0  0
 29 33  1  0  0  0
 30 32  1  0  0  0
 31 34  1  0  0  0
 23 26  1  0  0  0
 11 13  1  0  0  0
 12 14  1  0  0  0
 13  2  1  0  0  0
  1  2  1  0  0  0
 15 16  1  0  0  0
 16 19  1  0  0  0
 26 27  1  0  0  0
  3  4  1  0  0  0
  3  7  1  0  0  0
  4  8  1  0  0  0
  5 25  1  0  0  0
  5  1  1  0  0  0
  5  8  1  0  0  0
 35 33  1  0  0  0
 17 14  1  0  0  0
 18 15  1  0  0  0
 28 34  1  0  0  0
 28  8  1  0  0  0
  7  6  1  0  0  0
 21 23  2  0  0  0
 22 25  2  0  0  0
 29 31  2  0  0  0
 30 33  2  0  0  0
 32 34  2  0  0  0
 24 26  2  0  0  0
 11 14  2  0  0  0
 12 15  2  0  0  0
 13 16  2  0  0  0
  1  3  2  0  0  0
  2  6  2  0  0  0
  4  9  2  0  0  0
  7 10  1  0  0  0
 19 20  1  0  0  0
M  END
> <minimizedAffinity>
-7.4906

> <minimizedRMSD>
1.79745

> <molecular weight>
419.322

$$$$

['AddAtom',
 'AddBond',
 'AddConformer',
 'AddHydrogens',
 'AddNewHydrogens',
 'AddNonPolarHydrogens',
 'AddPolarHydrogens',
 'AddResidue',
 'Align',
 'AreInSameRing',
 'AssignSpinMultiplicity',
 'AssignTotalChargeToAtoms',
 'AutomaticFormalCharge',
 'AutomaticPartialCharge',
 'BeginAtom',
 'BeginAtoms',
 'BeginBond',
 'BeginBonds',
 'BeginConformer',
 'BeginData',
 'BeginInternalCoord',
 'BeginModify',
 'BeginResidue',
 'BeginResidues',
 'Center',
 'ClassDescription',
 'Clear',
 'CloneData',
 'ConnectTheDots',
 'ContigFragList',
 'ConvertDativeBonds',
 'ConvertZeroBonds',
 'CopyConformer',
 'CopySubstructure',
 'CorrectForPH',
 'DataSize',
 'DecrementMod',
 'DeleteAtom',
 'DeleteBond',
 'DeleteConformer',
 'DeleteData',
 'DeleteHydrogen',
 'DeleteHydrogens',
 'DeleteNonPolarHydrogens',
 'DeletePolarHydrogens',
 'DeleteResidue',
 'DestroyAtom',
 'DestroyBond',
 'DestroyResidue',
 'DoTransformations',
 'Empty',
 'EndAtom',
 'EndAtoms',
 'EndBond',
 'EndBonds',
 'EndData',
 'EndModify',
 'EndResidue',
 'EndResidues',
 'FindAngles',
 'FindChildren',
 'FindLSSR',
 'FindLargestFragment',
 'FindRingAtomsAndBonds',
 'FindSSSR',
 'FindTorsions',
 'GetAllData',
 'GetAngle',
 'GetAtom',
 'GetAtomById',
 'GetBond',
 'GetBondById',
 'GetConformer',
 'GetConformers',
 'GetCoordinates',
 'GetData',
 'GetDimension',
 'GetEnergies',
 'GetEnergy',
 'GetExactMass',
 'GetFirstAtom',
 'GetFlags',
 'GetFormula',
 'GetGIDVector',
 'GetGIVector',
 'GetGTDVector',
 'GetInternalCoord',
 'GetLSSR',
 'GetMod',
 'GetMolWt',
 'GetNextFragment',
 'GetResidue',
 'GetSSSR',
 'GetSpacedFormula',
 'GetTitle',
 'GetTorsion',
 'GetTotalCharge',
 'GetTotalSpinMultiplicity',
 'Has2D',
 'Has3D',
 'HasAromaticPerceived',
 'HasAtomTypesPerceived',
 'HasChainsPerceived',
 'HasChiralityPerceived',
 'HasClosureBondsPerceived',
 'HasData',
 'HasFlag',
 'HasHybridizationPerceived',
 'HasHydrogensAdded',
 'HasLSSRPerceived',
 'HasNonZeroCoords',
 'HasPartialChargesPerceived',
 'HasRingAtomsAndBondsPerceived',
 'HasRingTypesPerceived',
 'HasSSSRPerceived',
 'HasSpinMultiplicityAssigned',
 'IncrementMod',
 'InsertAtom',
 'IsCorrectedForPH',
 'IsPeriodic',
 'IsReaction',
 'MakeDativeBonds',
 'NewAtom',
 'NewBond',
 'NewResidue',
 'NextConformer',
 'NextInternalCoord',
 'NumAtoms',
 'NumBonds',
 'NumConformers',
 'NumHvyAtoms',
 'NumResidues',
 'NumRotors',
 'PerceiveBondOrders',
 'RenumberAtoms',
 'ReserveAtoms',
 'Rotate',
 'Separate',
 'SetAromaticPerceived',
 'SetAtomTypesPerceived',
 'SetAutomaticFormalCharge',
 'SetAutomaticPartialCharge',
 'SetChainsPerceived',
 'SetChiralityPerceived',
 'SetClosureBondsPerceived',
 'SetConformer',
 'SetConformers',
 'SetCoordinates',
 'SetCorrectedForPH',
 'SetData',
 'SetDimension',
 'SetEnergies',
 'SetEnergy',
 'SetFlag',
 'SetFlags',
 'SetFormula',
 'SetHybridizationPerceived',
 'SetHydrogensAdded',
 'SetInternalCoord',
 'SetIsPatternStructure',
 'SetIsReaction',
 'SetLSSRPerceived',
 'SetPartialChargesPerceived',
 'SetPeriodicMol',
 'SetRingAtomsAndBondsPerceived',
 'SetRingTypesPerceived',
 'SetSSSRPerceived',
 'SetSpinMultiplicityAssigned',
 'SetTitle',
 'SetTorsion',
 'SetTotalCharge',
 'SetTotalSpinMultiplicity',
 'StripSalts',
 'ToInertialFrame',
 'Translate',
 'UnsetFlag',
 '__class__',
 '__delattr__',
 '__dict__',
 '__dir__',
 '__doc__',
 '__eq__',
 '__format__',
 '__ge__',
 '__getattribute__',
 '__gt__',
 '__hash__',
 '__iadd__',
 '__init__',
 '__init_subclass__',
 '__le__',
 '__lt__',
 '__module__',
 '__ne__',
 '__new__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__setattr__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 '__swig_destroy__',
 '__weakref__',
 'this',
 'thisown']

Project: Dimensionality Reduced Molecules

Given a SMILES file where the molecules names are property (e.g. binding affinity), map the molecules into 2D space using PCA and visualize the data colored by the property.

  • Read SMILES
  • Save title as property to label with
  • Compute fingerprint
  • Convert fingerprint bits into an array of size 1024 of zeroes and ones
  • Use sklearn.decomposition.PCA to transform the fingerprints into 2D coordinates
  • Plot the coordinates and color by specified property
[[1.         0.97673449]
 [0.97673449 1.        ]]