Cheminformatics¶

10/31/2023 🎃¶

print view

notebook

In [44]:
%%html
<script src="https://bits.csb.pitt.edu/preamble.js"></script>

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

No description has been provided for this image SMILES

3D

No description has been provided for this image 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.

In [45]:
%%html
<div id="chem1" style="width: 500px"></div>
<script>

    var divid = '#chem1';
	jQuery(divid).asker({
	    id: divid,
	    question: "What is a SMILES string for ethane?",
		answers: ['cc','CC','C=C','C#C','[Ca]-[Ca]'],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();


</script>

SMILES, cont.¶

No description has been provided for this image

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.

No description has been provided for this image

As long as rings are separate, digits can be reused.

SMILES, cont.¶

Disconnections¶

A period . separates nonbonded molecules.

[Na+].[Cl-]

Isomeric Smiles¶

Slashes (/ \) denote configuration around double bonds.

At (@) denotes configuration around chiral centers.

In [46]:
%%html
<div id="chem3" style="width: 500px"></div>
<script>

    var divid = '#chem3';
	jQuery(divid).asker({
	    id: divid,
	    question: "What is a SMILES expression for benzene?",
		answers: ['c1cccc1','cccccc1','c2ccccc2','1cccccc1','c1ccccc1c'],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();


</script>

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

In [47]:
from openbabel import pybel
mol = pybel.readstring('smi','CC(NC1=CC=C(O)C=C1)=O')
mol
Out[47]:
No description has been provided for this image
In [48]:
mol.draw(filename="imgs/accet.png",show=False)
No description has been provided for this image

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
In [49]:
%%html
<div id="chem4" style="width: 500px"></div>
<script>

    var divid = '#chem4';
	jQuery(divid).asker({
	    id: divid,
	    question: "What is the best SMARTS expression for matching a 6 carbon ring?",
		answers: ['[#6]1~[#6]~[#6]~[#6]~[#6]~[#6]1','c1ccccc1','[R][R][R][R][R][R]','[R]1[R][R][R][R][R]1','CCCCCC'],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();


</script>

Pybel Input/Output¶

pybel.readstring

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

In [50]:
mol = pybel.readstring('smi','CCCC')
len(mol.atoms)
Out[50]:
4

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

In [51]:
mol.write('sdf','output.sdf',overwrite=True) #write to file
print(mol.write('sdf')) #no filename - return string

 OpenBabel10302320482D

  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
$$$$


==============================
*** Open Babel Warning  in WriteMolecule
  No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D.

pybel.readfile¶

pybel.readfile

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

In [52]:
mols = list(pybel.readfile('smi','../files/results.smi')) #expand the iterator into a list
len(mols)
Out[52]:
14
In [53]:
mol = next(pybel.readfile('smi','../files/results.smi')) #get just first molecule
mol
Out[53]:
No description has been provided for this image
In [54]:
#of course, this is the most efficient way to read all
for mol in pybel.readfile('smi','../files/results.smi'): 
    print(mol.write('can').rstrip()) #canonical smiles

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

In [55]:
output = pybel.Outputfile('sdf','output.sdf',overwrite=True)
for m in mols:
    output.write(m)

Molecules¶

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

In [56]:
for atom in mol:
    print(atom.atomicnum,end=' ')

6 6 6 6 6 6 6 7 6 7

Atom properties in clude atomicmass, atomicnum, coords, formalcharge, hyb, isotope, partialcharge, degree, explicitvalence and totalvalence

Atoms can also be accessed in mol.atoms

In [57]:
%%html
<div id="chemval" style="width: 500px"></div>
<script>

    var divid = '#chemval';
	jQuery(divid).asker({
	    id: divid,
	    question: "What is the valence of the first atom of CC?",
		answers: ['0','1','2','3','4'],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();


</script>

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.

In [59]:
mol
Out[59]:
No description has been provided for this image
In [60]:
aromatic_ring = pybel.Smarts('a1aaaaa1')
aromatic_ring.findall(mol) #returns all _unique_ matches
Out[60]:
[(1, 6, 5, 4, 3, 2)]

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

In [61]:
double_ring = pybel.Smarts('a1aaaa2a1aaaa2')
for (i,m) in enumerate(mols):
    if double_ring.findall(m):
        print(i)
        m.draw(filename="r%d.png"%i,show=False) 

5
8
In [62]:
mols[5]
Out[62]:
No description has been provided for this image
In [63]:
mols[8]
Out[63]:
No description has been provided for this image

Molecular Properties¶

In [64]:
print(mol.molwt) #molecular weight

128.13076
In [65]:
desc = mol.calcdesc()
print(desc)

{'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, 'MP': 79.79220000000001, '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}
In [66]:
desc['logP'] #calculated partition coefficient between octanol/water
Out[66]:
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
In [67]:
def lipinski(mol):
    desc = mol.calcdesc()
    return desc['HBD'] <= 5 and desc['HBA1'] <= 10 and desc['MW'] <= 500 and desc['logP'] <= 5
In [68]:
for m in mols:
    print(lipinski(m))

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.

No description has been provided for this image

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).

In [69]:
fp = mol.calcfp()
type(fp)
Out[69]:
openbabel.pybel.Fingerprint
In [70]:
print(fp.bits)

[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

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

In [71]:
fp = mol.calcfp()
for m in mols:
    f = m.calcfp()
    print(f | fp)

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
In [72]:
%%html
<div id="chemsim" style="width: 500px"></div>
<script>

    var divid = '#chemsim';
	jQuery(divid).asker({
	    id: divid,
	    question: "What is the Tanimoto coefficient of the bitstrings 1001 and 0011?",
		answers: ['0','0.25','0.33','0.5','0.66','0.75','1.0'],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();


</script>

2D -> 3D¶

In [73]:
mol.make3D() #this makes a reasonable 3D structure
print(mol.atoms[0].coords)
mol.localopt() #this further optimizes the structure
print(mol.atoms[0].coords)

(2.468272539514969, 0.6349880847110817, -0.018730053230247772)
(2.46371187360455, 0.6341729709888883, -0.010376048284164541)
In [74]:
sdf = mol.write('sdf')
In [75]:
import py3Dmol
view = py3Dmol.view()
view.addModel(sdf)
view.setStyle({'stick':{}})
view.zoomTo()
view.show()

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¶

In [76]:
mols = list(pybel.readfile('sdf','../files/best.sdf'))
len(mols)
Out[76]:
10
In [77]:
atom = mols[0].atoms[0]
print(atom.coords)

(-0.5939, -56.8911, 14.3139)
In [78]:
!cat ../files/best.sdf

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
   -4.0156  -58.3341   11.8081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0030  -58.0395   14.0758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7918  -58.3829   13.5703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6256  -58.7300   12.1163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7497  -58.6825   11.3283 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5225  -59.0404   11.6676 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6589  -58.9060   10.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5198  -58.6843   16.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8163  -56.4211   15.9438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6259  -58.3704   17.7678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9225  -56.1072   17.2987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1149  -57.7096   15.5009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3273  -57.0819   18.2108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4433  -56.7463   19.6592 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8030  -59.9702   14.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737  -60.8749   13.8173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3083  -61.4219   16.0936 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1631  -64.0341   14.7974 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4366  -64.3052   15.9262 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0669  -60.2450   15.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0225  -62.0537   14.5162 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2759  -62.3324   15.6757 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9642  -62.9109   14.0844 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4901  -63.4609   16.3744 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2882  -54.7944   15.8358 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6925  -55.1298   15.1839 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2860  -55.7119   15.1441 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>
-7.60183

> <minimizedRMSD>
2.26383

> <molecular weight>
475.372

$$$$
ZINC78996542


 39 44  0  0  0  0  0  0  0  0999 V2000
   -1.1562  -57.7105   14.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0859  -57.6546   15.8298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1390  -56.2126   14.7797 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392  -55.9873   15.0720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0584  -58.3149   14.9816 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8469  -57.3439   15.3020 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9188  -56.8145   16.1731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8917  -60.1405   14.9063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9219  -60.5932   13.5908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7606  -59.4813   15.3968 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8212  -60.3875   12.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6396  -59.2637   14.5786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6919  -59.7269   13.2610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4188  -58.5636   15.0722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3780  -58.3922   14.2190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4425  -58.8944   12.8026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5968  -59.5297   12.4148 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4927  -58.7341   12.0364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6562  -59.8644   11.4908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7756  -58.8669   17.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7367  -56.7639   16.7466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6706  -58.3845   18.7515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6320  -56.2815   18.0513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3085  -58.0565   16.4443 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0988  -57.0919   19.0536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9885  -56.5777   20.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6434  -55.4303   12.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3219  -54.7691   11.6131 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1612  -54.4616   14.2263 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1096  -52.5500   11.1925 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5256  -52.3975   12.4883 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0650  -55.2760   13.9477 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4186  -53.9532   11.8808 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8462  -53.7965   13.2121 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0567  -53.3258   10.8773 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9009  -53.0163   13.5062 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4158  -59.7838   14.5992 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6872  -59.3395   16.7216 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3789  -59.1280   15.9719 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>
-7.58798

> <minimizedRMSD>
1.876

> <molecular weight>
475.372

$$$$
ZINC35448294


 33 38  0  0  0  0  0  0  0  0999 V2000
    6.2193  -51.5392   13.7822 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5893  -51.9773   15.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1156  -52.0958   13.1259 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8703  -52.9821   15.7052 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3763  -53.1129   13.7626 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2347  -53.8835   13.4110 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7696  -53.5311   15.0379 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9678  -54.7425   14.4550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2954  -56.1404   13.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3853  -53.8636   12.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6865  -55.2195   12.0267 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8500  -55.7376   14.5366 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8912  -54.5146   15.4387 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0317  -55.6866   13.2732 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9662  -56.1848   12.1474 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9233  -54.9834   16.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9363  -58.4538   18.1389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3508  -57.1319   18.2899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1432  -58.8360   17.0510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9875  -56.1521   17.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9885  -57.8949   14.9095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643  -57.8655   16.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1944  -56.5486   16.2790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9633  -56.6191   14.3950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6932  -55.8143   15.2279 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8386  -54.8497   15.0945 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4658  -57.5272   16.2097 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6382  -58.0380   13.8546 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9083  -58.8130   16.5209 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0807  -59.3238   14.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3307  -57.1398   14.8765 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2157  -59.7112   15.4991 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7617  -61.2970   15.8834 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 17 18  1  0  0  0
  1  2  1  0  0  0
 19 22  1  0  0  0
  3  5  1  0  0  0
 27 31  1  0  0  0
 28 30  1  0  0  0
 20 23  1  0  0  0
  4  7  1  0  0  0
 29 32  1  0  0  0
 21 22  1  0  0  0
  5  6  1  0  0  0
 23 25  1  0  0  0
  7 13  1  0  0  0
 32 33  1  0  0  0
 24  9  1  0  0  0
 24 25  1  0  0  0
  8 13  1  0  0  0
  9 14  1  0  0  0
 10  6  1  0  0  0
 10 11  1  0  0  0
 11 14  1  0  0  0
 12 31  1  0  0  0
 12  8  1  0  0  0
 12 14  1  0  0  0
 17 19  2  0  0  0
  1  3  2  0  0  0
 18 20  2  0  0  0
  2  4  2  0  0  0
 27 29  2  0  0  0
 28 31  2  0  0  0
 30 32  2  0  0  0
 21 24  2  0  0  0
 22 23  2  0  0  0
  5  7  2  0  0  0
  6  8  2  0  0  0
  9 15  2  0  0  0
 25 26  1  0  0  0
 13 16  1  0  0  0
M  END
> <minimizedAffinity>
-7.52352

> <minimizedRMSD>
6.72818

> <molecular weight>
407.767

$$$$
ZINC72314638


 34 38  0  0  0  0  0  0  0  0999 V2000
   -6.9192  -60.0249   14.8267 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9224  -60.5532   13.5394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7591  -59.4408   15.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7655  -60.4981   12.7677 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5814  -59.3754   14.5808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6074  -59.9121   13.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3284  -58.7584   15.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2330  -58.7339   14.3037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2694  -59.3144   12.9167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4559  -59.8663   12.4993 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2700  -59.2872   12.1989 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4977  -60.2504   11.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9776  -58.1386   14.7709 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1138  -55.4726   15.4117 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0692  -59.0069   15.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2024  -57.9981   15.5499 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4884  -55.4636   16.0338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6963  -56.8766   14.7008 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5616  -56.7232   15.2099 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5532  -54.4163   15.1165 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3449  -58.4107   12.4428 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5462  -58.8702   12.9824 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2658  -58.1304   13.2810 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6683  -59.0498   14.3602 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3878  -58.3101   14.6587 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5892  -58.7698   15.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7434  -58.9704   16.6705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8700  -58.9787   17.5299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5363  -56.8305   16.6476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7893  -58.4284   18.8090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4557  -56.2801   17.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2435  -58.1798   16.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0821  -57.0791   19.0075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9979  -56.4920   20.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0
 21 22  1  0  0  0
  3  5  1  0  0  0
 28 32  1  0  0  0
 29 31  1  0  0  0
 23 25  1  0  0  0
 24 26  1  0  0  0
 30 33  1  0  0  0
  4  6  1  0  0  0
 32  7  1  0  0  0
  5  7  1  0  0  0
  6 10  1  0  0  0
  8 13  1  0  0  0
  8  9  1  0  0  0
  9 10  1  0  0  0
 14 19  1  0  0  0
 15 13  1  0  0  0
 15 16  1  0  0  0
 16 25  1  0  0  0
 16 19  1  0  0  0
 34 33  1  0  0  0
 27 26  1  0  0  0
 17 14  1  0  0  0
 19 18  1  0  0  0
  1  3  2  0  0  0
 21 23  2  0  0  0
 22 24  2  0  0  0
  2  4  2  0  0  0
 28 30  2  0  0  0
 29 32  2  0  0  0
 31 33  2  0  0  0
  5  6  2  0  0  0
 25 26  2  0  0  0
  7  8  2  0  0  0
 13 18  2  0  0  0
  9 11  2  0  0  0
 14 20  2  0  0  0
 10 12  1  0  0  0
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
   -2.2330  -58.7336   14.3037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2693  -59.3140   12.9166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4559  -59.8659   12.4992 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2700  -59.2867   12.1988 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4977  -60.2499   11.5936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9776  -58.1384   14.7708 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1137  -55.4723   15.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0691  -59.0065   15.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2024  -57.9977   15.5499 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4883  -55.4632   16.0337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6963  -56.8762   14.7006 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5616  -56.7229   15.2098 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5532  -54.4160   15.1161 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3452  -58.4103   12.4429 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5464  -58.8703   12.9827 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2660  -58.1300   13.2811 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6682  -59.0500   14.3606 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3879  -58.3098   14.6589 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5890  -58.7698   15.1986 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7431  -58.9706   16.6707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8702  -58.9787   17.5299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5360  -56.8304   16.6476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7895  -58.4286   18.8091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4554  -56.2801   17.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2434  -58.1797   16.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0819  -57.0792   19.0075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9978  -56.4922   20.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0
 21 22  1  0  0  0
  3  5  1  0  0  0
 28 32  1  0  0  0
 29 31  1  0  0  0
 23 25  1  0  0  0
 24 26  1  0  0  0
 30 33  1  0  0  0
  4  6  1  0  0  0
 32  7  1  0  0  0
  5  7  1  0  0  0
  6 10  1  0  0  0
  8 13  1  0  0  0
  8  9  1  0  0  0
  9 10  1  0  0  0
 14 19  1  0  0  0
 15 13  1  0  0  0
 15 16  1  0  0  0
 16 25  1  0  0  0
 16 19  1  0  0  0
 34 33  1  0  0  0
 27 26  1  0  0  0
 17 14  1  0  0  0
 19 18  1  0  0  0
  1  3  2  0  0  0
 21 23  2  0  0  0
 22 24  2  0  0  0
  2  4  2  0  0  0
 28 30  2  0  0  0
 29 32  2  0  0  0
 31 33  2  0  0  0
  5  6  2  0  0  0
 25 26  2  0  0  0
  7  8  2  0  0  0
 13 18  2  0  0  0
  9 11  2  0  0  0
 14 20  2  0  0  0
 10 12  1  0  0  0
M  END
> <minimizedAffinity>
-7.51156

> <minimizedRMSD>
2.07052

> <molecular weight>
411.326

$$$$
ZINC39912421


 35 39  0  0  0  0  0  0  0  0999 V2000
   -2.8637  -58.0485   14.3831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6591  -57.4567   14.0111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7718  -57.6110   13.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0742  -58.1435   13.6832 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4965  -58.9601   15.3604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8048  -56.6783   12.9233 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1200  -56.7955   12.6090 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8956  -58.9553   14.8275 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0866  -57.9453   13.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5472  -56.3394   11.8484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0881  -58.8830   14.9464 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1072  -57.9326   15.8719 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3763  -57.6028   14.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3300  -59.0479   15.5599 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6430  -56.6523   15.5704 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4011  -56.4874   14.9569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8249  -60.4168   15.8846 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4900  -55.4712   15.9138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0441  -55.2299   14.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4836  -54.4853   14.8788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9761  -58.9905   17.8000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6595  -56.9124   16.7746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8625  -58.3455   19.0315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5458  -56.2672   18.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3746  -58.2738   16.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1474  -56.9839   19.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0409  -56.3650   20.3177 F   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9715  -59.7155   15.4305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5076  -61.3824   13.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7831  -62.4617   12.6762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9064  -60.4967   14.0761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4575  -62.6553   13.0647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5808  -60.6902   14.4647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8563  -61.7695   13.9589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2144  -62.0410   14.4164 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 29 30  1  0  0  0
 21 25  1  0  0  0
 22 24  1  0  0  0
 31 33  1  0  0  0
 23 26  1  0  0  0
 32 34  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
 34 35  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
 17 14  1  0  0  0
 18 15  1  0  0  0
 28 33  1  0  0  0
 28  8  1  0  0  0
  7  6  1  0  0  0
 29 31  2  0  0  0
 30 32  2  0  0  0
 21 23  2  0  0  0
 22 25  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
 33 34  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>
-7.49363

> <minimizedRMSD>
1.94002

> <molecular weight>
442.764

$$$$
ZINC39912421


 35 39  0  0  0  0  0  0  0  0999 V2000
   -2.8637  -58.0484   14.3832 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6591  -57.4566   14.0111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7718  -57.6110   13.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0743  -58.1434   13.6832 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4964  -58.9600   15.3605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8048  -56.6783   12.9233 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1200  -56.7954   12.6090 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8956  -58.9552   14.8276 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0865  -57.9453   13.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5473  -56.3392   11.8484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0881  -58.8830   14.9464 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1074  -57.9325   15.8720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3763  -57.6028   14.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3299  -59.0479   15.5600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6428  -56.6523   15.5704 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4011  -56.4874   14.9569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8249  -60.4168   15.8846 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4900  -55.4712   15.9137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0441  -55.2299   14.6664 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4836  -54.4854   14.8789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9763  -58.9904   17.8002 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6592  -56.9122   16.7746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8627  -58.3454   19.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5455  -56.2671   18.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3746  -58.2738   16.6716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1473  -56.9838   19.1347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0408  -56.3649   20.3178 F   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9714  -59.7154   15.4306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5075  -61.3823   13.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7831  -62.4617   12.6762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9063  -60.4966   14.0762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4575  -62.6552   13.0648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5808  -60.6901   14.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8563  -61.7695   13.9591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2143  -62.0411   14.4166 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 29 30  1  0  0  0
 21 25  1  0  0  0
 22 24  1  0  0  0
 31 33  1  0  0  0
 23 26  1  0  0  0
 32 34  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
 34 35  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
 17 14  1  0  0  0
 18 15  1  0  0  0
 28 33  1  0  0  0
 28  8  1  0  0  0
  7  6  1  0  0  0
 29 31  2  0  0  0
 30 32  2  0  0  0
 21 23  2  0  0  0
 22 25  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
 33 34  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>
-7.49359

> <minimizedRMSD>
2.12367

> <molecular weight>
442.764

$$$$
ZINC39912344


 35 39  0  0  0  0  0  0  0  0999 V2000
   -2.9655  -58.0579   14.4075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7487  -57.5053   14.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8718  -57.6016   13.4941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1866  -58.0933   13.7357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6126  -58.9419   15.4006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8851  -56.7323   12.9225 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2070  -56.8131   12.6256 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0176  -58.9002   14.8849 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2006  -57.8708   13.0937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6301  -56.3508   11.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0185  -58.9767   14.9117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0258  -58.0767   15.8325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4630  -57.6840   14.6346 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2258  -59.1731   15.5107 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5813  -56.7838   15.5554 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3369  -56.5875   14.9564 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6995  -60.5554   15.8092 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524  -55.6234   15.9088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0884  -55.3180   14.6896 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4544  -54.5863   14.9086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0661  -58.9675   17.8345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6938  -56.8776   16.7976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9180  -58.3157   19.0588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5456  -56.2257   18.0218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4539  -58.2484   16.7039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1577  -56.9448   19.1524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0181  -56.3191   20.3285 F   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1077  -59.6230   15.5080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0602  -62.0396   13.3356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9663  -63.0767   13.9497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7088  -60.9008   14.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6148  -61.9379   14.6743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -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

$$$$

sdf files can have arbitrary data embedded in them:

M  END
> <minimizedAffinity>
-7.83433

> <minimizedRMSD>
1.45522

> <molecular weight>
475.372

$$$$
In [79]:
mols[0].data
Out[79]:
{'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'}

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).

In [80]:
obmol = mol.OBMol
vec = obmol.Center(0)
print(vec)

<openbabel.openbabel.vector3; proxy of <Swig Object of type 'OpenBabel::vector3 *' at 0x7f6af63aa610> >
In [81]:
print(vec.GetX(),vec.GetY(),vec.GetZ())

0.7085902947538542 -0.016861359909934506 -0.0005521894831451903
In [82]:
dir(obmol)
Out[82]:
['AddAtom',
 'AddBond',
 'AddConformer',
 'AddHydrogens',
 'AddNewHydrogens',
 'AddNonPolarHydrogens',
 'AddPolarHydrogens',
 'AddResidue',
 'Align',
 'AreInSameRing',
 'AssignSpinMultiplicity',
 'AssignTotalChargeToAtoms',
 'AutomaticFormalCharge',
 'AutomaticPartialCharge',
 'BeginAtom',
 'BeginAtoms',
 'BeginBond',
 'BeginBonds',
 'BeginConformer',
 'BeginData',
 'BeginInternalCoord',
 'BeginModify',
 'BeginResidue',
 'BeginResidues',
 'CBeginAtoms',
 'CEndAtoms',
 '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
In [ ]:
#fill in fps with fingerprint bits, yvals with title value
pca = PCA(n_components=2)
res = pca.fit_transform(fps)    

plt.scatter(res[:,0],res[:,1],c=yvals)
plt.gca().set_aspect('equal', adjustable='box');
In [41]:
!wget http://mscbio2025.csb.pitt.edu/files/er.smi

--2023-10-30 20:19:10--  http://mscbio2025.csb.pitt.edu/files/er.smi
Resolving mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)... 136.142.4.139
Connecting to mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)|136.142.4.139|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 20022 (20K) [application/smil+xml]
Saving to: ‘er.smi’

er.smi              100%[===================>]  19.55K  --.-KB/s    in 0s      

2023-10-30 20:19:10 (38.3 MB/s) - ‘er.smi’ saved [20022/20022]
In [22]:
import numpy as np
import matplotlib.pyplot as plt

yvals = []
fps = []
for mol in pybel.readfile('smi','er.smi'):
    yvals.append(float(mol.title))
    fpbits = mol.calcfp().bits
    fp = np.zeros(1024)
    fp[fpbits] = 1
    fps.append(fp)
    
pca = PCA(n_components=2)
res = pca.fit_transform(fps)    

plt.scatter(res[:,0],res[:,1],c=yvals)
plt.gca().set_aspect('equal', adjustable='box');
No description has been provided for this image
In [46]:
import numpy as np
from openbabel import pybel
from sklearn.linear_model import  LinearRegression
from sklearn.linear_model import  LassoCV
import matplotlib.pyplot as plt
%matplotlib inline

yvals = []
fps = []
for mol in pybel.readfile('smi','er.smi'):
    yvals.append(float(mol.title))
    fpbits = mol.calcfp().bits
    fp = np.zeros(1024)
    fp[fpbits] = 1
    fps.append(fp)
    
fps = np.array(fps)
yvals = np.array(yvals)
lin = LinearRegression()
lin.fit(fps,yvals)
pred = lin.predict(fps)
print(np.corrcoef(pred,yvals))
plt.plot(pred,yvals,'o')
plt.xlabel("Predicted")
plt.ylabel("Actual")
plt.show()

[[1.         0.97673441]
 [0.97673441 1.        ]]
No description has been provided for this image