Using class methods in a for loop

Question

I have an externally defined module which has a number of methods in it. I can get all the methods as a list with dir() like print(dir[Descriptors]) and I get a list ['BalabanJ', 'BertzCT',...]. Now I want to apply all the methods on a list of values [x1, x2, ...]. If I directly use Descriptors.BalabanJ(x1) it works. However, I want to do them in a loop like

from rdkit.Chem import Descriptors
for i in dir[Descriptors]:
    for x in [x1,x2,x3]:
        print(Descriptors.i(x))

, it says that Descriptors does not have method i in it. How can I implement this?

There is a type difference in 'BalabanJ' and .BalabanJ(). The first one is string while the latter is a function — mad_
– mad_, Commented Mar 14, 2019 at 15:33

sanyassh · Accepted Answer · 2019-03-14 17:33:49Z

4

I think that getattr is this for which you are looking

from rdkit.Chem import Descriptors
for i in dir(Descriptors):
    if callable(i):
        for x in [x1,x2,x3]:
            print(getattr(Descriptors ,i)(x))

edited Mar 14, 2019 at 17:33

sanyassh

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answered Mar 14, 2019 at 15:34

Grzegorz Bokota

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2 Comments

anotherone Over a year ago

Thanks! Can you explain it a bit?

Grzegorz Bokota Over a year ago

I think full explanation is in BlueSheepToken post. getattr function allows to get object attribute by name (string). It can be used on modules, objects etc.

sanyassh · Accepted Answer · 2019-03-14 17:38:35Z

2

I would recommend inspect:

from rdkit.Chem import Descriptors
import inspect

for i in inspect.getmembers(Descriptors, callable):
    for x in [1, 2, 3]:
        print(i[0], i[1](x))  # name of function of Descriptors module, result

edited Mar 14, 2019 at 17:38

answered Mar 14, 2019 at 15:41

sanyassh

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1 Comment

Grzegorz Bokota Over a year ago

This also will fail if signature of function needs 0 or more than 1 argument, or type of argument is invalid. So i remind about inspect.signature function.

BlueSheepToken · Accepted Answer · 2019-03-14 15:46:51Z

1

You can retrieve them with getattr

for instance

class Bar:
    def __init__(self, foo):
        self.foo = foo

    def p(self):
        print(self.foo)

bar = Bar('hello word')
getattr(bar, 'p')()

Be aware that if there is no method i, it will raise a value error, but you can set a default method

getattr(bar, 'pr', lambda :print('no such method: pr'))()

You need to define your class and pass it as a parameter as I did for bar if it is a class method

from rdkit.Chem import Descriptors
for i in dir[Descriptors]:
    for x in [x1,x2,x3]:
        print(getattr(Descriptors, i)(x))

you can take a look at getattr() official documentation

edited Mar 14, 2019 at 15:46

answered Mar 14, 2019 at 15:36

BlueSheepToken

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2 Comments

mad_ Over a year ago

More relevant here would be getattr(bar, 'p')()

BlueSheepToken Over a year ago

@mad_ Why so? (I mean why not, but why this one is more relevant?) (I fixed it)

rapelpy · Accepted Answer · 2019-03-15 17:46:34Z

1

For this the RDKit has the MolecularDescriptorCalculator.

from rdkit import Chem
from rdkit.ML.Descriptors import MoleculeDescriptors
from rdkit.Chem import Descriptors

descriptors = [d[0] for d in Descriptors._descList]

smiles = ['CCN','CCNC', 'CCN(C)C']

for d in descriptors[:3]: # just the first three descriptors
    print(d)
    calc = MoleculeDescriptors.MolecularDescriptorCalculator([d])
    for s in smiles:
        c = calc.CalcDescriptors(Chem.MolFromSmiles(s))
        print(s, c[0])

Output:

MaxEStateIndex
CCN 4.847222222222222
CCNC 2.9305555555555554
CCN(C)C 2.125
MinEStateIndex
CCN 0.75
CCNC 1.0694444444444444
CCN(C)C 1.1388888888888888
MaxAbsEStateIndex
CCN 4.847222222222222
CCNC 2.9305555555555554
CCN(C)C 2.125

answered Mar 15, 2019 at 17:46

rapelpy

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1 Comment

anotherone Over a year ago

Oh thanks! I was keeping the question answer on purpose :)

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