scopy.ScoDruglikeness package


Created on Tue Jun 25 21:59:42 2019

A module used for calculating physicochemical properties.

You can freely use and distribute it. If you have any problem, you could contact with us timely.

@Author: Zhi-Jiang Yang, Dong-Sheng Cao.

@Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China.

@Homepage: http://www.scbdd.com

@Mail: kotori@cbdd.me and oriental-cds@163.com


Submodules

scopy.ScoDruglikeness.molproperty module

scopy.ScoDruglikeness.molproperty.CalculateAromaticProportion(mol)[source]

The proportion of heavy atoms in the molecule that are in an aromatic ring —>AP

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the proportion of heavy atoms in the molecule that are in an aromatic ring

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateFlexibility(mol)[source]

The flexibility (ration between rotatable and rigid bonds) —>Flex

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of ring

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateFsp3(mol)[source]

Fsp3 (carbon bond saturation) is defined as the number of sp3 hybridized carbons / total carbon count. —>FSP3

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the carbon bond saturation

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateHetCarbonRatio(mol)[source]

The ratio between the number of non carbon atoms and the number of carbon atoms. —>HetRatio

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the ratio between the number of non carbon atoms and the number of carbon atoms

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateLogD(mol)[source]

Calculation of molecular logD under pH=7.4 —>LogD

Note:

We have built a liner model with DNN to predict logD7.4.

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

molecular logD under pH=7.4

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateLogP(mol)[source]

Calculation of molecular LogP —>logP

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

molecular logP

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateLogSw(mol)[source]

The logSw represents the logarithm of compounds water solubility computed by the ESOL method —>logSw

Equation:

Log(Sw) = 0.16-0.638*clogP-0.0062*MWT+0.066*RB-0.74*AP where, MWT: Molecular Weight; RB: Rotatable bonds; AP: Aromatic proportion

Reference:
  1. Delaney, John S (2004).

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the molecular logSw

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateMaxSizeSystemRing(mol)[source]

Number of atoms involved in the biggest system ring —> maxring

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

number of atoms involved in the biggest system ring

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateMolDensity(mol)[source]

Calculation of density of molecule —>Dense

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

density of molecule

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateMolFCharge(mol)[source]

Calculation of formal charge of molecule —>fChar

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

formal charge of molecule

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateMolMR(mol)[source]

Cacluation of molecular refraction value based on Crippen method —>MR

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

molecular refraction value based on Crippen method

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateMolVolume(mol)[source]

Calculation of Van der Waals Volume of molecule —>MV

Equation:

for single atom: Vw = 4/3*pi*rw^3, the rw is the Van der Waals radius of atom VvdW = ∑(atom contributions)-5.92NB(Unit in Å^3), NB is the total number of bonds the Van der Waals radius of atom is derived from wikipedia.

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

Van der Waals Volume of molecule

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateMolWeight(mol)[source]

Calculation of molecular weight(contain hydrogen atoms) —>MW

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the weight of molecule(contain hydrogen atoms)

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateNPscore(mol)[source]

A function to calculate the natural product-likeness score —>NPscore

Reference:
  1. Ertl Peter (2008).

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

product-likeness score

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateNumAromaAtom(mol)[source]

Calculation of aromatic atom counts in a molecule —>nAAtom

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the aromatic atom counts in a molecule

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumAromaRing(mol)[source]
scopy.ScoDruglikeness.molproperty.CalculateNumAtoms(mol)[source]

Calculation of the number of atoms in molecular(contain hydrogen atoms) —>nAtom

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of atoms in molecular(contain hydrogen atoms)

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumBonds(mol)[source]

Calculation the number of bonds where between heavy atoms —>nBond

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of bonds where between heavy atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumBoron(mol)[source]

Calculation of Boron counts in a molecule —>nB

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of boron atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumBromine(mol)[source]

Calculation of Bromine counts in a molecule —>nBr

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of bromine atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumCarbon(mol)[source]

Calculation of Carbon number in a molecule —>nC

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of carbon atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumChlorin(mol)[source]

Calculation of Chlorin counts in a molecule —>nCl

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of chlorin atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumDouBond(mol)[source]

Calculation of double bond number of molecule —>nDouble

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of double bond

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumFluorin(mol)[source]

Calculation of Fluorin counts in a molecule —>nF

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of fluori atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumHAcceptors(mol)[source]

Caculation of the number of Hydrogen Bond Acceptors —>nHA

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of Hydrogen Bond Acceptors

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumHDonors(mol)[source]

Caculation of the number of Hydrogen Bond Donors —>nHD

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of Hydrogen Bond Donors

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumHeavyAtom(mol)[source]

Calculation of Heavy atom counts in a molecule —>nHev

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of heavy atom counts in a molecule

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumHetero(mol)[source]

Calculation of the number of heteroatom in a molecule —>nHet

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of heteroatom in a molecule

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumHyBond(mol)[source]

Sum of Hydrogen Bond Donnors and Acceptors —>nHB

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

sum of Hydrogen Bond Donnors and Acceptors

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumIodine(mol)[source]

Calculation of Iodine counts in a molecule —>nI

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of bromine atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumNitrogen(mol)[source]

Calculation of Nitrogen counts in a molecule —>nN

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of nitrogen atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumOxygen(mol)[source]

Calculation of Oxygen counts in a molecule —>nO

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of oxygen atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumPhosphor(mol)[source]

Calcualtion of Phosphor number in a molecule —>nP

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of phosphor atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumRigidBonds(mol)[source]

Number of non-flexible bonds, in opposite to rotatable bonds —>nRig

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of non-flexible bonds

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumRing(mol)[source]

Calculation of the number of ring —>nRing

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of ring

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumRotatableBonds(mol)[source]

Calculation of the number of rotatableBonds —>nRot

Note:

In some situaion Amide C-N bonds are not considered because of their high rotational energy barrier

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of rotatableBond

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumSinBond(mol)[source]

Calculation of single bond number of molecule —> nSingle

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of single bond

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumStereocenters(mol)[source]

the number of stereo centers —>nStereo

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of stereo centers

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumSulfur(mol)[source]

Calculation of Sulfur counts in a molecule —>nS

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of sulfur atoms

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateNumTriBond(mol, btype='TRIPLE')[source]

Calculation of triple bond number of molecule —> nTriple

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

the number of triple bond

Return type

int

scopy.ScoDruglikeness.molproperty.CalculateQEDmax(mol)[source]

Calculation QED descriptor under different weights A descriptor a measure of drug-likeness based on the concept of desirability Here, calculating the QED descriptor using maximal descriptor weights. —>QEDmax

Reference:
  1. Bickerton, G. Richard (2012).

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

QED descriptor using maximal descriptor weights

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateQEDmean(mol)[source]

Calculation QED descriptor under different weights A descriptor a measure of drug-likeness based on the concept of desirability Here, calculating the QED descriptor using average descriptor weights. —>QEDmean

Reference:
  1. Bickerton, G. Richard (2012).

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

QED descriptor using average descriptor weights

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateQEDnone(mol)[source]

Calculation QED descriptor under different weights A descriptor a measure of drug-likeness based on the concept of desirability Here, calculating the QED descriptor using unit weights. —>QEDnone

Reference:
  1. Bickerton, G. Richard (2012).

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

QED descriptor using unit weights

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateSAscore(mol)[source]

A function to estimate ease of synthesis (synthetic accessibility) of drug-like molecules —>SAscore

Reference:
  1. Ertl Peter (2009).

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

ease of synthesis

Return type

float

scopy.ScoDruglikeness.molproperty.CalculateTPSA(mol)[source]

Calculation of TPSA —>TPSA

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

TPSA

Return type

float

scopy.ScoDruglikeness.molproperty.CalculatepKa(mol)[source]
scopy.ScoDruglikeness.molproperty.CheckAcid(mol)[source]

Judge a molecular whether is acid via SMARTS. These SMARTS retrived from https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html —>ab

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecule

Returns

classification to acid or base

Return type

str

scopy.ScoDruglikeness.molproperty.GetProperties(mol, items=['MW', 'Vol', 'Dense', 'fChar', 'nBond', 'nAtom', 'nHD', 'nHA', 'nHB', 'nHet', 'nStereo', 'nHev', 'nRot', 'nRig', 'Flex', 'nRing', 'logP', 'logD', 'pKa', 'logSw', 'ab', 'MR', 'TPSA', 'AP', 'HetRatio', 'Fsp3', 'MaxRing', 'QEDmean', 'QEDmax', 'QEDnone', 'SAscore', 'NPscore', 'nSingle', 'nDouble', 'nTriple', 'nC', 'nB', 'nF', 'nCl', 'nBr', 'nI', 'nP', 'nS', 'nO', 'nN'])[source]

Get all properties in scopy

scopy.ScoDruglikeness.molproperty_Lib module

class scopy.ScoDruglikeness.molproperty_Lib.PC_properties(mols, n_jobs=1)[source]

Bases: object

Here, we comdat the whole function that computing property retrieved from module molproperty

Parameters
  • mols (Iterable object, each element is rdkit.Chem.rdchem.Mol) – The molecule to be scanned.

  • n_jobs (int, optional) – The number of CPUs to use to do the computation, defaults to 1

CalculateAromaticProportion()[source]

The proportion of heavy atoms in the molecule that are in an aromatic ring —>AP

Parameters

mols (Iterable) – molecules

Returns

the proportion of heavy atoms in the molecule that are in an aromatic ring

Return type

list

CalculateFlexibility()[source]

The flexibility (ration between rotatable and rigid bonds) —>Flex

Parameters

mol (rdkit.Chem.rdchem.Mol) – molecules

Returns

the number of ring

Return type

list

CalculateFsp3()[source]

Fsp3 (carbon bond saturation) is defined as the number of sp3 hybridized carbons / total carbon count. —>FSP3

Parameters

mols (Iterable) – molecules

Returns

the carbon bond saturation

Return type

list

CalculateHetCarbonRatio()[source]

The ratio between the number of non carbon atoms and the number of carbon atoms. —>HetRatio

Parameters

mols (Iterable) – molecules

Returns

the ratio between the number of non carbon atoms and the number of carbon atoms

Return type

list

CalculateLogD()[source]

Calculation of molecular logD under pH=7.4 —>LogD

Note:

We have built a liner model with DNN to predict logD7.4.

Parameters

mols (Iterable) – molecules

Returns

molecular logD under pH=7.4

Return type

list

CalculateLogP()[source]

Calculation of molecular LogP —>logP

Parameters

mols (Iterable) – molecules

Returns

molecular logP

Return type

float

CalculateLogSw()[source]

The logSw represents the logarithm of compounds water solubility computed by the ESOL method —>logSw

Equation:

Log(Sw) = 0.16-0.638*clogP-0.0062*MWT+0.066*RB-0.74*AP where, MWT: Molecular Weight; RB: Rotatable bonds; AP: Aromatic proportion

Reference:
  1. Delaney, John S (2004).

Parameters

mols (Iterable) – molecules

Returns

the molecular logSw

Return type

list

CalculateMaxSizeSystemRing()[source]

Number of atoms involved in the biggest system ring —> maxring

Parameters

mols (Iterable) – molecules

Returns

number of atoms involved in the biggest system ring

Return type

list

CalculateMolDensity()[source]

Calculation of density of molecule —>Dense

Parameters

mols (Iterable) – molecules

Returns

density of molecule

Return type

list

CalculateMolFCharge()[source]

Calculation of formal charge of molecule —>fChar

Parameters

mols (Iterable) – molecules

Returns

formal charge of molecule

Return type

list

CalculateMolMR()[source]

Cacluation of molecular refraction value based on Crippen method —>MR

Parameters

mols (Iterable) – molecules

Returns

molecular refraction value based on Crippen method

Return type

list

CalculateMolVolume()[source]

Calculation of Van der Waals Volume of molecule —>MV

Equation:

for single atom: Vw = 4/3*pi*rw^3, the rw is the Van der Waals radius of atom VvdW = ∑(atom contributions)-5.92NB(Unit in Å^3), NB is the total number of bonds the Van der Waals radius of atom is derived from wikipedia.

Parameters

mols (Iterable) – molecules

Returns

Van der Waals Volume of molecule

Return type

list

CalculateMolWeight()[source]

Calculation of molecular weight(contain hydrogen atoms) —>MW

Parameters

mols (Iterable) – molecules

Returns

the weight of molecule(contain hydrogen atoms)

Return type

list

CalculateNPscore()[source]

A function to calculate the natural product-likeness score —>NPscore

Reference:
  1. Ertl (2008).

Parameters

mols (Iterable) – molecules

Returns

product-likeness score

Return type

list

CalculateNumAtoms()[source]

Calculation of the number of atoms in molecular(contain hydrogen atoms) —>nAtom

Parameters

mols (Iterable) – molecules

Returns

the number of atoms in molecular(contain hydrogen atoms)

Return type

int

CalculateNumBonds()[source]

Calculation the number of bonds where between heavy atoms —>nBond

Parameters

mols (Iterable) – molecules

Returns

the number of bonds where between heavy atoms

Return type

list

CalculateNumBoron()[source]

Calculation of Boron counts in a molecule —>nB

Parameters

mols (Iterable) – molecules

Returns

the number of boron atoms

Return type

list

CalculateNumBromine()[source]

Calculation of Bromine counts in a molecule —>nBr

Parameters

mols (Iterable) – molecules

Returns

the number of bromine atoms

Return type

list

CalculateNumCarbon()[source]

Calculation of Carbon number in a molecule —>nC

Parameters

mols (Iterable) – molecules

Returns

the number of carbon atoms

Return type

list

CalculateNumChargedGroups()[source]

Number of Charged Groups —>nChar

Parameters

mols (Iterable) – molecules

Returns

the number of charged group

Return type

list

CalculateNumChlorin()[source]

Calculation of Chlorin counts in a molecule —>nCl

Parameters

mols (Iterable) – molecules

Returns

the number of chlorin atoms

Return type

list

CalculateNumDouBond()[source]

Calculation of double bond number of molecule —>nDouble

Parameters

mols (Iterable) – molecules

Returns

the number of double bond

Return type

list

CalculateNumFluorin()[source]

Calculation of Fluorin counts in a molecule —>nF

Parameters

mols (Iterable) – molecules

Returns

the number of fluori atoms

Return type

list

CalculateNumHAcceptors()[source]

Caculation of the number of Hydrogen Bond Acceptors —>nHA

Parameters

mols (Iterable) – molecules

Returns

the number of Hydrogen Bond Acceptors

Return type

list

CalculateNumHDonors()[source]

Caculation of the number of Hydrogen Bond Donors —>nHD

Parameters

mols (Iterable) – molecules

Returns

the number of Hydrogen Bond Donors

Return type

list

CalculateNumHeavyAtom()[source]

Calculation of Heavy atom counts in a molecule —>nHev

Parameters

mols (Iterable) – molecules

Returns

the number of heavy atom counts in a molecule

Return type

list

CalculateNumHetero()[source]

Calculation of the number of heteroatom in a molecule —>nHet

Parameters

mols (Iterable) – molecules

Returns

the number of heteroatom in a molecule

Return type

list

CalculateNumHyBond()[source]

Sum of Hydrogen Bond Donnors and Acceptors —>nHB

Parameters

mols (Iterable) – molecules

Returns

sum of Hydrogen Bond Donnors and Acceptors

Return type

list

CalculateNumIodine()[source]

Calculation of Iodine counts in a molecule —>nI

Parameters

mols (Iterable) – molecules

Returns

the number of bromine atoms

Return type

list

CalculateNumNitrogen()[source]

Calculation of Nitrogen counts in a molecule —>nN

Parameters

mols (Iterable) – molecules

Returns

the number of nitrogen atoms

Return type

list

CalculateNumOxygen()[source]

Calculation of Oxygen counts in a molecule —>nO

Parameters

mols (Iterable) – molecules

Returns

the number of oxygen atoms

Return type

list

CalculateNumPhosphor()[source]

Calcualtion of Phosphor number in a molecule —>nP

Parameters

mols (Iterable) – molecules

Returns

the number of phosphor atoms

Return type

list

CalculateNumRigidBonds()[source]

Number of non-flexible bonds, in opposite to rotatable bonds —>nRig

Parameters

mols (Iterable) – molecules

Returns

the number of non-flexible bonds

Return type

list

CalculateNumRing()[source]

Calculation of the number of ring —>nRing

Parameters

mols (Iterable) – molecules

Returns

the number of ring

Return type

list

CalculateNumRotatableBonds()[source]

Calculation of the number of rotatableBonds —>nRot

Note:

In some situaion Amide C-N bonds are not considered because of their high rotational energy barrier

Parameters

mols (Iterable) – molecules

Returns

the number of rotatableBond

Return type

list

CalculateNumSinBond()[source]

Calculation of single bond number of molecule —>nSingle

Parameters

mols (Iterable) – molecules

Returns

the number of single bond

Return type

list

CalculateNumStereocenters()[source]

This can not implement under multiprocessing The number of stereo centers —>nStereo

Parameters

mols (Iterable) – molecules

Returns

the number of stereo centers

Return type

list

CalculateNumSulfur()[source]

Calculation of Sulfur counts in a molecule —>nS

Parameters

mols (Iterable) – molecules

Returns

the number of sulfur atoms

Return type

list

CalculateNumTriBond()[source]

Calculation of triple bond number of molecule —> nTriple

Parameters

mols (Iterable) – molecules

Returns

the number of triple bond

Return type

list

CalculateQEDmax()[source]

Calculation QED descriptor under different weights A descriptor a measure of drug-likeness based on the concept of desirability Here, calculating the QED descriptor using maximal descriptor weights. —>QEDmax

Reference:
  1. Bickerton, G. Richard (2012).

Parameters

mols (Iterable) – molecules

Returns

QED descriptor using maximal descriptor weights

Return type

list

CalculateQEDmean()[source]

Calculation QED descriptor under different weights A descriptor a measure of drug-likeness based on the concept of desirability Here, calculating the QED descriptor using average descriptor weights. —>QEDmean

Reference:
  1. Bickerton, G. Richard (2012).

Parameters

mols (Iterable) – molecules

Returns

QED descriptor using average descriptor weights

Return type

list

CalculateQEDnone()[source]

Calculation QED descriptor under different weights A descriptor a measure of drug-likeness based on the concept of desirability Here, calculating the QED descriptor using unit weights. —>QEDnone

Reference:
  1. Bickerton, G. Richard (2012).

Parameters

mols (Iterable) – molecules

Returns

QED descriptor using unit weights

Return type

list

CalculateSAscore()[source]

A function to estimate ease of synthesis (synthetic accessibility) of drug-like molecules —>SAscore

Reference:
  1. Ertl, Peter, and Ansgar Schuffenhauer (2009).

Parameters

mols (Iterable) – molecules

Returns

ease of synthesis

Return type

list

CalculateTPSA()[source]

Calculation of TPSA —>TPSA

Parameters

mols (Iterable) – molecules

Returns

TPSA

Return type

list

CalculatepKa()[source]

This function should be revised Calculating pKa based on the ralation between logD and logP in specific pH. —>pKa

Eq.:

abs(pH-pKa) = log10(10^(logP-logD)-1) pKa = pH - log10(10^(logP-logD)-1) for acid pKa = log10(10^(logP-logD)-1) - pH for base

Parameters

mols (Iterable) – molecules

Returns

molecular pKa

Return type

list

CheckAcid()[source]

Judge a molecular whether is acid via SMARTS. These SMARTS retrived from https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html —>ab

Parameters

mols (Iterable) – molecules

Returns

classification to acid or base

Return type

list

GetProperties(items=['MW', 'Vol', 'Dense', 'fChar', 'nBond', 'nAtom', 'nHD', 'nHA', 'nHB', 'nHet', 'nStereo', 'nHev', 'nRot', 'nRig', 'nRing', 'Flex', 'logP', 'logD', 'pKa', 'logSw', 'ab', 'MR', 'TPSA', 'AP', 'HetRatio', 'Fsp3', 'MaxRing', 'QEDmean', 'QEDmax', 'QEDnone', 'SAscore', 'NPscore', 'nSingle', 'nDouble', 'nTriple', 'nC', 'nB', 'nF', 'nCl', 'nBr', 'nI', 'nP', 'nS', 'nO', 'nN'], showSMILES=False)[source]

Get all PC - properties in scopy

scopy.ScoDruglikeness.rulesfilter module

scopy.ScoDruglikeness.rulesfilter.CheckBeyondRo5(mol, detail=False, showSMILES=False)[source]

Check molecular under beyond Ro5

Reference:

Doak, Bradley C., et al. journal of medicinal chemistry 59.6 (2015): 2312-2327.

Rule details:

MW <= 1000 -2 <= logP <= 10 nHD <= 6 nHA <= 15 PSA <= 250 nRot <= 20

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckCNS(mol, detail=False, showSMILES=False)[source]

Check mol under CNS

Reference:

Jeffrey, Phil, and Scott Summerfield. Neurobiol Dis, 37.1 (2010): 33-37.

Rule details:

135 <= weight <= 582 -0.2 <= logP <= 6.1 nha <= 5 nhd <= 3 3 <= TPSA <= 118

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckCustomizeRule(mol, prop_kws, closed_interval=True, detail=False, showSMILES=False)[source]

You could customize the rule with mostly properties ypu want.

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • prop_kws (dict) – the keys of dict are properties you want to check; the values should be a tuple or list with two elements,present the left- and right-bounded respectively.

  • closed_interval (bool, optional) – control whether using closed interval, defaults to True

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckEganRule(mol, detail=False, showSMILES=False)[source]

Bad or Good oral biovailability rule

Reference:

Egan, William J., Kenneth M. Merz, and John J. Baldwin. J Med Chem, 43.21 (2000): 3867-3877.

Rule details:

0 <= TPSA <= 132 -1 <= logP <=6

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckGSKRule(mol, detail=False, showSMILES=False)[source]

Check molecular under GSK rule(4/400 Rule)

Reference:

Gleeson, M. Paul. Journal of medicinal chemistry 51.4 (2008): 817-834.

Rule details:

MW <= 400 logP <= 4

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckGhoseRule(mol, detail=False, showSMILES=False)[source]

Check molecular under Ghose rule

Reference.:

Ghose, Arup K., Vellarkad N. Viswanadhan, and John J. Wendoloski. Journal of combinatorial chemistry 1.1 (1999): 55-68.

Rules details:

-0.4 < logP < 5.6 160 < MW < 480 40 < MR< 130 20 < nAtom < 70

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckGoldenTriangle(mol, detail=False, showSMILES=False)[source]

Check molecular under ‘Golden Triangle’

Reference:

Johnson, Ted W., Klaus R. Dress, and Martin Edwards. Bioorg Med Chem Lett, 19.19 (2009): 5560-5564.

Rule details:

200 <= MW <= 500 -2 <= logD <= 5

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckLipinskiRule(mol, detail=False, showSMILES=False)[source]

Check molecular under Lipinski’s rule

Reference:

Lipinski, Christopher A., et al. Advanced drug delivery reviews 23.1-3 (1997): 3-25.

Rule details:

MW <= 500(Da) logP <= 5 nHD <= 5 nHA <= 10

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckOpreaRule(mol, detail=False, showSMILES=False)[source]
Reference:

Oprea, Tudor I. Journal of computer-aided molecular design 14.3 (2000): 251-264.

Rules details:

nRing >= 3 nRig >= 18 nRot >=6

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckOralMacrocycles(mol, detail=False, showSMILES=False)[source]

Check molecular under oral macrocycles rules

Reference:

Giordanetto, Fabrizio, and Jan Kihlberg. Journal of medicinal chemistry 57.2 (2013): 278-295.

Rule details:

MW < 1000 logP < 10 nHD < 5 TPSA < 250

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckPfizerRule(mol, detail=False, showSMILES=False)[source]

Check molecular under Rfizer Rule(3/75 Rule)

Reference:

Hughes, Jason D., et al. Bioorganic & medicinal chemistry letters 18.17 (2008): 4872-4875.

Rule details:

logp > 3 TPSA < 75

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckREOS(mol, detail=False, showSMILES=False)[source]

Check molecular under REOS program

Reference:

Walters, W. Patrick, and Mark Namchuk. Nat Rev Drug Discov, 2.4 (2003): 259.

Rule details:

200 <= MW <= 500 -5 <= logP <= 5 nHD <= 5 nHA <= 10 nRot <= 8 TPSA <= 150 -4 <= fChar <= 4

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckRespiratory(mol, detail=False, showSMILES=False)[source]

Check mol under Respiratory

Reference:

Ritchie, Timothy J., Christopher N. Luscombe, and Simon JF Macdonald. J Chem Inf Model, 49.4 (2009): 1025-1032.

Rule details:

240<=MW<= 520 -2.0<=logP<=4.7 6<=nHB<=12 51<=tPSA<=135 3<=nRot<=8 1<=nRing<=5

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckRo2(mol, detail=False, showSMILES=False)[source]

Check molecular under RO2

Ref.:

Goldberg, Frederick W., et al. Drug Discovery Today 20.1 (2015): 11-17.

Rule details:

MW <= 200 Logp <= 2 NHD <= 2 NHA <= 4

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckRo3(mol, detail=False, showSMILES=False)[source]

Check molecular under Ro3

Ref.:

Congreve, Miles, et al. Drug discovery today 19.8 (2003): 876-877.

Rule details:

MW <= 300 -3 <= logP <= 3 NHD <= 3 NHA <= 6 PSA <= 60 nRot <= 3

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckRo4(mol, detail=False, showSMILES=False)[source]

Referenece:

Rule details:

MW <= 400 logP <= 4 nHD <= 4 nHA <= 8 TPSA <= 120

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckVeberRule(mol, detail=False, showSMILES=False)[source]

Bad or Good oral biovailability rule

Reference:

Veber, Daniel F., et al. Journal of medicinal chemistry 45.12 (2002): 2615-2623.

Rule details:

nRot <= 10 TPSA <= 140 nHB <= 12

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter.CheckXuRule(mol, detail=False, showSMILES=False)[source]

Check molecular under Xu’s rule

Reference:

Rule details:

nhd <= 5 nha <= 10 3 <= rot <= 35 1 <= nring <= 7 10 <= nhev <= 50

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

scopy.ScoDruglikeness.rulesfilter_Lib module

class scopy.ScoDruglikeness.rulesfilter_Lib.PC_rules(mols, n_jobs=1, detail=False, showSMILES=False)[source]

Bases: object

Here, we comdat the whole function that analyse PC-drived rules

Parameters
  • mols (Iterable object, each element is rdkit.Chem.rdchem.Mol) – the molecule to be scanned.

  • n_jobs (int, optional) – The number of CPUs to use to do the computation, defaults to 1

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

CheckBeyondRo5()[source]

Check molecular under beyond Ro5

Reference:

Doak, Bradley C., et al. journal of medicinal chemistry 59.6 (2015): 2312-2327.

Rule details:

MW <= 1000 -2 <= logP <= 10 nHD <= 6 nHA <= 15 PSA <= 250 nRot <= 20

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckCNS()[source]

Check mol under CNS

Reference:

Jeffrey, Phil, and Scott Summerfield. Neurobiol Dis, 37.1 (2010): 33-37.

Rule details:

135 <= weight <= 582 -0.2 <= logP <= 6.1 nha <= 5 nhd <= 3 3 <= TPSA <= 118

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckCustomizeRule(prop_kws, closed_interval=True)[source]

You could customize the rule with mostly properties ypu want.

Parameters
  • prop_kws (dict) – the keys of dict are properties you want to check; the values should be a tuple or list with two elements,present the left- and right-bounded respectively.

  • closed_interval (bool, optional) – control whether using closed interval, defaults to True

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

dict

CheckEganRule()[source]

Bad or Good oral biovailability rule

Reference:

Egan, William J., Kenneth M. Merz, and John J. Baldwin. J Med Chem, 43.21 (2000): 3867-3877.

Rule details:

0 <= TPSA <= 132 -1 <= logP <=6

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

the weight of molecule(contain hydrogen atoms)

Return type

list

CheckGSKRule()[source]

Check molecular under GSK rule(4/400 Rule)

Reference:

Gleeson, M. Paul. Journal of medicinal chemistry 51.4 (2008): 817-834.

Rule details:

MW <= 400 logP <= 4

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckGhoseRule()[source]

Check molecular under Ghose rule

Reference.:

Ghose, Arup K., Vellarkad N. Viswanadhan, and John J. Wendoloski. Journal of combinatorial chemistry 1.1 (1999): 55-68.

Rules details:

-0.4 < logP < 5.6 160 < MW < 480 40 < MR< 130 20 < nAtom < 70

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckGoldenTriangle()[source]

Check molecular under ‘Golden Triangle’

Reference:

Johnson, Ted W., Klaus R. Dress, and Martin Edwards. Bioorg Med Chem Lett, 19.19 (2009): 5560-5564.

Rule details:

200 <= MW <= 500 -2 <= logD <= 5

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckLipinskiRule()[source]

Check molecular under Lipinski’s rule

Reference:

Lipinski, Christopher A., et al. Advanced drug delivery reviews 23.1-3 (1997): 3-25.

Rule details:

MW <= 500 logP <= 5 nHD <= 5 nHA <= 10

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckOpreaRule()[source]
Reference:

Oprea, Tudor I. Journal of computer-aided molecular design 14.3 (2000): 251-264.

Rules details:

nRing >= 3 nRig >= 18 nRot >=6

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckOralMacrocycles()[source]

Check molecular under oral macrocycles rules

Reference:

Giordanetto, Fabrizio, and Jan Kihlberg. Journal of medicinal chemistry 57.2 (2013): 278-295.

Rule details:

MW < 1000 logP < 10 nHD < 5 TPSA < 250

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckPfizerRule()[source]

Check molecular under Rfizer Rule(3/75 Rule)

Reference:

Hughes, Jason D., et al. Bioorganic & medicinal chemistry letters 18.17 (2008): 4872-4875.

Rule details:

logp > 3 TPSA < 75

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckREOS()[source]

Check molecular under REOS program

Reference:

Walters, W. Patrick, and Mark Namchuk. Nat Rev Drug Discov, 2.4 (2003): 259.

Rule details:

200 <= MW <= 500 -5 <= logP <= 5 nHD <= 5 nHA <= 10 nRot <= 8 TPSA <= 150 -4 <= fChar <= 4

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckRespiratory()[source]

Check mol under Respiratory

Reference:

Ritchie, Timothy J., Christopher N. Luscombe, and Simon JF Macdonald. J Chem Inf Model, 49.4 (2009): 1025-1032.

Rule details:

240<=MW<= 520 -2.0<=logP<=4.7 6<=nHB<=12 51<=tPSA<=135 3<=nRot<=8 1<=nRing<=5

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckRo2()[source]

Check molecular under RO2

Ref.:

Goldberg, Frederick W., et al. Drug Discovery Today 20.1 (2015): 11-17.

Rule details:

MW <= 200 Logp <= 2 NHD <= 2 NHA <= 4

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckRo3()[source]

Check molecular under Ro3

Ref.:

Congreve, Miles, et al. Drug discovery today 19.8 (2003): 876-877.

Rule details:

MW <= 300 -3 <= logP <= 3 NHD <= 3 NHA <= 6 PSA <= 60

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckRo4()[source]

Referenece:

Rule details:

MW <= 400 logP <= 4 nHD <= 4 nHA <= 8 TPSA <= 120

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckSchneiderRule()[source]

Check molecular under Schneider rule

Reference:

Schneider, Nadine, et al. J Chem Inf Model, 48.3 (2008): 613-628.

Rule details:

mw > 230 nhd > 0 nha > 0 nrot > 0 nring > 0 mr > 40 functional groups > 0 molecular volume > 191

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckVeberRule()[source]

Bad or Good oral biovailability rule

Reference:

Veber, Daniel F., et al. Journal of medicinal chemistry 45.12 (2002): 2615-2623.

Rule details:

nRot <= 10 TPSA <= 140 nHB <= 12

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

CheckXuRule()[source]

Check molecular under Xu’s rule

Reference:

Rule details:

nhd <= 5 nha <= 10 3 <= rot <= 35 1 <= nring <= 7 10 <= nhev <= 50

Parameters
  • mols (Iterable) – molecules

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘nViolate’, otherwise exrta returning each property

Return type

list

Module contents

Created on Tue Jun 25 21:59:42 2019

@Author: Zhi-Jiang Yang, Dong-Sheng Cao @Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China, @Homepage: http://www.scbdd.com @Mail: yzjkid9@gmail.com; oriental-cds@163.com @Blog: https://blog.moyule.me