User Guide

User Guide for ChemoPy 1.0

Dongsheng Cao

Yizeng Liang

©2012 China Computational Biology Drug Design Group

Table of Contents

1. What is this?...........................................................................................................................................3

2. Install the ChemoPy package.................................................................................................................3

3. Read molecules......................................................................................................................................4

4. Download molecules from corresponding ID........................................................................................5

5.1.5. Burden descriptors.............................................................................................................9

5.1.6. E-state indices....................................................................................................................9

5.1.7. Basak information indices................................................................................................10

5.1.8. Autocorrelation descriptors..............................................................................................10

5.1.9. Molecular properties........................................................................................................10

5.1.10. Charge descriptors..........................................................................................................11

5.1.11. MOE-type descriptors....................................................................................................11

5.1.12. Using PyChem2d object.................................................................................................12

5.2. Calculating 3-D descriptors.......................................................................................................12

5.2.1. Geometric descriptors......................................................................................................12

5.3.1. Daylight-type fingerprints................................................................................................15

5.3.2. MACCS keys and FP4 fingerprints.................................................................................15

5.3.3. E-state fingerprints...........................................................................................................16

5.3.4. Atom pairs and topological torsions.................................................................................16

5.3.5. Morgan fingerprints.........................................................................................................16

5.3.6. Using PyChem2d object...................................................................................................17

5.3.7. fingerprint similarity........................................................................................................17

6. Calculating all descriptors....................................................................................................................18

Appendix:.................................................................................................................................................19

1. What is this?

ChemoPy package via: http://code.google.com/p/pychem/downloads/list (.zip and .tar.gz). The install

process of ChemoPy is very easy:

* You first need to install RDKit, Openbabel, MOPAC and pybel successfully.*

Openbabel and pybel can be downloaded via: http://openbabel.org/wiki/Main_Page

RDkit can be downloaded via: http://code.google.com/p/rdkit/

MOPAC can be downloaded via: http://openmopac.net/

Note: ChemoPy was tested in MOPAC 7.

On Windows:

(2): tar -zxf chemopy-1.0.tar.gz

(3): cd chemopy-1.0

(4): python setup.py install or sudo python setup.py install

3. Read molecules

The majority of the basic molecular functionality is found in module pychem:

Individual molecule can be constructed using a variety of approaches.

Because we have imported pybel module, all functionalities in pybel can be used to construct a Mol

object. Moreover, the transformation between any two molecular formats are allowed by using pybel.

Note: When computing 2-D descriptors by individual module, we used Mol object from RDKit. When

Using PyChem3d:

All of these functions return a Mol object on success:

4. Download molecules from corresponding ID

The PyDPI allows the user to download the molecules by providing their IDs such as CAS, NCBI,

KEGG, EBI and Drugbank.

By providing a aspirin IDs, we could download its SMILES format conveniently.

We can also download and read a molecule by constructing a PyChem2d or PyChem3d object, which

Using PyChem2d object:

5. Calculating molecular descriptors

The ChemoPy package could calculate a large number of molecular descriptors. These descriptors cap-

ture and magnify distinct aspects of chemical structures. Generally speaking, all descriptors could be

scriptors, molecular properties, kappa shape indices, MOE-type descriptors, and molecular fingerprints.

MOPAC program to optimize molecular structures by the AM1 method. The 3-D descriptors calculated

5.1. Calculating 2-D descriptors

We could import the corresponding module to calculate the molecular descriptors as need. There are 13

modules to compute 2-D descriptors. Moreover, a easier way to compute these descriptors is construct

a PyChem2d object, which encapsulates all methods for the calculation of 2-D descriptors.

5.1.1. Molecular constitutional descriptors

We could calculate any constitution descriptor by calling the corresponding functions. We could also

calculate all 30 descriptors by calling GetConstitution function. The result is given in the form of dic-

tionary.

5.1.2. Topology descriptors

35 topology descriptors can be calculated by the ChemoPy package. For detailed information of topol-

ogy descriptors, refer to Table S1 in Appendix and their introductions in Manual.

5.1.4. Kappa shape descriptors

Note that the input of MACCS and FP4 is different.

5.3.3. E-state fingerprints

5.3.4. Atom pairs and topological torsions

5.3.6. Using PyChem2d object

The convenient way to calculate the fingerprints is to generate a PyDrug object and call GetFingerprint

method.

6. Calculating all descriptors

Appendix:

1 Weight Molecular weight

2 nhyd Count of hydrogen atoms

3 nhal Count of halogen atoms

4 nhet Count of hetero atoms

5 nhev Count of heavy atoms

6 ncof Count of F atoms

7 ncocl Count of Cl atoms

8 ncobr Count of Br atoms

9 ncoi Count of I atoms

Topological descriptors (35)

Modified Zagreb index with order 1-2

6 IC5 Information content with order 5 proposed by Basak

proposed by Basak

4 S4 Sum of E-State of atom type: ssBH

matrix

7 Harary3D The 3D-Harary index

surface area

based on atomic charge

based on atomic polarizablity

atomic electronegativity

3 E-state 79 E-state fingerprints or fragments

4 FP4 307 FP4 fingerprints

6 Torsions Topological torsion fingerprints

7 Morgan/Circular Fingerprints based on the Morgan algorithm