#634 Calculation of autoCorrelationPolarizability affects TPSA

cdk-1.2.x
closed
nobody
9
2012-11-03
2008-05-01
No

The following program shows that the TPSA of the molecule with SMILES "CCCN" changes when you calculate the value of the autoCorrelationPolarizability descriptor. I note that there is no problem if you add explicit hydrogens. However, TPSA should be independent of explicit hydrogens (according to the JavaDoc for CDK1.0.2). Is there any explanation for this?

from cinfony.cdk import *
mol = readstring("smi", "CCCN")
tpsa = mol.calcdesc(['tpsa'])['tpsa']
print tpsa

26.02

pol = mol.calcdesc(['autoCorrelationPolarizability'])
tpsa = mol.calcdesc(['tpsa'])['tpsa']
print tpsa

0.00

Regards,
Noel

Discussion

  • Noel O'Boyle

    Noel O'Boyle - 2008-05-01

    Logged In: YES
    user_id=850620
    Originator: YES

    To find out the interdependencies I've used the following code (note: doesn't check the 3D descriptors...I think 2D is a good place to start :-):

    from cinfony.cdk import *

    Get the correct values of each descriptor

    correctans = {}
    for descriptor in descriptors:
    mol = readstring("smi", "CCCN")
    res = sorted(list(mol.calcdesc([descriptor]).iteritems()))
    correctans[descriptor] = res

    For each descriptor, calculate all other descriptors one-by-one and

    see whether it's value has changed

    newans = {}
    for descriptor in descriptors:
    print "Investigating", descriptor
    otherdescs = descriptors[:]
    otherdescs.remove(descriptor)
    for testdesc in otherdescs:
    mol = readstring("smi", "CCCN")
    mol.calcdesc([testdesc])
    testans = sorted(list(mol.calcdesc([descriptor]).iteritems()))
    if correctans[descriptor] != testans:
    print testdesc + " affects " + descriptor, "(the evidence follows...)"
    if descriptor!="CPSA" or testdesc=="hBondacceptors":
    print "Before", correctans[descriptor]
    print "After ", testans

    The result is:

    Investigating hBondacceptors
    Investigating weight
    autoCorrelationPolarizability affects weight (the evidence follows...)
    Before [(u'weight', 59.07349936)]
    After [(u'weight', 50.003073999999998)]
    Investigating ip
    Investigating CPSA
    hBondacceptors affects CPSA (the evidence follows...)
    Before [(u'CPSA.0', 1.#QNAN), (u'CPSA.1', 1.#QNAN), (u'CPSA.10', 1.#QNAN), (u'CPSA.11', 1.#QNAN), (u'CPSA.12', 1.#QNAN), (u'CPSA.13', 1.#QNAN), (u'CPSA.14', 1.#QNAN), (u'CPSA.15', 1.#QNAN), (u'CPSA.16', 1.#QNAN), (u'CPSA.17', 1.#QNAN), (u'CPSA.18', 1.#QNAN), (u'CPSA.19', 1.#QNAN), (u'CPSA.2', 1.#QNAN), (u'CPSA.20', 1.#QNAN), (u'CPSA.21', 1.#QNAN), (u'CPSA.22', 1.#QNAN), (u'CPSA.23', 1.#QNAN), (u'CPSA.24', 1.#QNAN), (u'CPSA.25', 1.#QNAN), (u'CPSA.26', 1.#QNAN), (u'CPSA.27', 1.#QNAN), (u'CPSA.28', 1.#QNAN), (u'CPSA.3', 1.#QNAN), (u'CPSA.4', 1.#QNAN), (u'CPSA.5', 1.#QNAN), (u'CPSA.6', 1.#QNAN), (u'CPSA.7', 1.#QNAN), (u'CPSA.8', 1.#QNAN), (u'CPSA.9', 1.#QNAN)]
    After [(u'CPSA.0', 1.#QNAN), (u'CPSA.1', 1.#QNAN), (u'CPSA.10', 1.#QNAN), (u'CPSA.11', 1.#QNAN), (u'CPSA.12', 1.#QNAN), (u'CPSA.13', 1.#QNAN), (u'CPSA.14', 1.#QNAN), (u'CPSA.15', 1.#QNAN), (u'CPSA.16', 1.#QNAN), (u'CPSA.17', 1.#QNAN), (u'CPSA.18', 1.#QNAN), (u'CPSA.19', 1.#QNAN), (u'CPSA.2', 1.#QNAN), (u'CPSA.20', 1.#QNAN), (u'CPSA.21', 1.#QNAN), (u'CPSA.22', 1.#QNAN), (u'CPSA.23', 1.#QNAN), (u'CPSA.24', 1.#QNAN), (u'CPSA.25', 1.#QNAN), (u'CPSA.26', 1.#QNAN), (u'CPSA.27', 1.#QNAN), (u'CPSA.28', 1.#QNAN), (u'CPSA.3', 1.#QNAN), (u'CPSA.4', 1.#QNAN), (u'CPSA.5', 1.#QNAN), (u'CPSA.6', 1.#QNAN), (u'CPSA.7', 1.#QNAN), (u'CPSA.8', 1.#QNAN), (u'CPSA.9', 1.#QNAN)]
    weight affects CPSA (the evidence follows...)
    ip affects CPSA (the evidence follows...)
    autoCorrelationPolarizability affects CPSA (the evidence follows...)
    chi0vC affects CPSA (the evidence follows...)
    wienerNumbers affects CPSA (the evidence follows...)
    chi1vC affects CPSA (the evidence follows...)
    NilaComplexity affects CPSA (the evidence follows...)
    atomCount affects CPSA (the evidence follows...)
    rotatableBondsCount affects CPSA (the evidence follows...)
    BCUT affects CPSA (the evidence follows...)
    autoCorrelationMass affects CPSA (the evidence follows...)
    apol affects CPSA (the evidence follows...)
    xlogP affects CPSA (the evidence follows...)
    chi0C affects CPSA (the evidence follows...)
    lengthOverBreadth affects CPSA (the evidence follows...)
    petitjeanShapeIndex affects CPSA (the evidence follows...)
    largestPiSystem affects CPSA (the evidence follows...)
    gravitationalIndex affects CPSA (the evidence follows...)
    tpsa affects CPSA (the evidence follows...)
    weightedPath affects CPSA (the evidence follows...)
    WHIM affects CPSA (the evidence follows...)
    petitjeanNumber affects CPSA (the evidence follows...)
    zagrebIndex affects CPSA (the evidence follows...)
    momentOfInertia affects CPSA (the evidence follows...)
    chiPathCluster affects CPSA (the evidence follows...)
    vAdjMa affects CPSA (the evidence follows...)
    mde affects CPSA (the evidence follows...)
    kierValues affects CPSA (the evidence follows...)
    autoCorrelationCharge affects CPSA (the evidence follows...)
    bondCount affects CPSA (the evidence follows...)
    chiCluster affects CPSA (the evidence follows...)
    aromaticBondsCount affects CPSA (the evidence follows...)
    eccentricConnectivityIndex affects CPSA (the evidence follows...)
    hBondDonors affects CPSA (the evidence follows...)
    longestAliphaticChain affects CPSA (the evidence follows...)
    chi1C affects CPSA (the evidence follows...)
    bpol affects CPSA (the evidence follows...)
    chiPath affects CPSA (the evidence follows...)
    chiChain affects CPSA (the evidence follows...)
    aromaticAtomsCount affects CPSA (the evidence follows...)
    lipinskifailures affects CPSA (the evidence follows...)
    largestChain affects CPSA (the evidence follows...)
    Investigating autoCorrelationPolarizability
    autoCorrelationCharge affects autoCorrelationPolarizability (the evidence follows...)
    Before [(u'autoCorrelationPolarizability.0', 106.08972826562506), (u'autoCorrelationPolarizability.1', 83.722304906250045), (u'autoCorrelationPolarizability.2', 51.966035187500026), (u'autoCorrelationPolarizability.3', 21.261128593750009), (u'autoCorrelationPolarizability.4', 0.0)]
    After [(u'autoCorrelationPolarizability.0', 105.97714276562508), (u'autoCorrelationPolarizability.1', 83.633041406250058), (u'autoCorrelationPolarizability.2', 51.909760687500039), (u'autoCorrelationPolarizability.3', 21.237589968750015), (u'autoCorrelationPolarizability.4', 0.0)]
    Investigating chi0vC
    autoCorrelationPolarizability affects chi0vC (the evidence follows...)
    Before [(u'chi0vC', 2.4142135623730949)]
    After [(u'chi0vC', 1.5)]
    Investigating wienerNumbers
    Investigating chi1vC
    autoCorrelationPolarizability affects chi1vC (the evidence follows...)
    Before [(u'chi1vC', 1.2071067811865475)]
    After [(u'chi1vC', 0.5)]
    Investigating NilaComplexity
    Investigating atomCount
    autoCorrelationPolarizability affects atomCount (the evidence follows...)
    Before [(u'atomCount', 13)]
    After [(u'atomCount', 4)]
    Investigating rotatableBondsCount
    Investigating BCUT
    Investigating autoCorrelationMass
    Investigating apol
    Investigating xlogP
    Investigating chi0C
    Investigating lengthOverBreadth
    Investigating petitjeanShapeIndex
    Investigating largestPiSystem
    Investigating gravitationalIndex
    Investigating tpsa
    autoCorrelationPolarizability affects tpsa (the evidence follows...)
    Before [(u'tpsa', 26.02)]
    After [(u'tpsa', 0.0)]
    Investigating weightedPath
    Investigating WHIM
    Investigating petitjeanNumber
    Investigating zagrebIndex
    Investigating momentOfInertia
    Investigating chiPathCluster
    Investigating vAdjMa
    Investigating mde
    momentOfInertia affects mde (the evidence follows...)
    Before [(u'mde.0', 0.0), (u'mde.1', 0.0), (u'mde.10', 0.0), (u'mde.11', 0.0), (u'mde.12', 0.0), (u'mde.13', 0.0), (u'mde.14', 0.0), (u'mde.15', 0.0), (u'mde.16', 0.0), (u'mde.17', 0.0), (u'mde.18', 0.0), (u'mde.2', 0.0), (u'mde.3', 0.0), (u'mde.4', 0.0), (u'mde.5', 0.0), (u'mde.6', 0.0), (u'mde.7', 0.0), (u'mde.8', 0.0), (u'mde.9', 0.0)]
    After [(u'mde.0', 0.0), (u'mde.1', 1.4142135623730951), (u'mde.10', 0.0), (u'mde.11', 0.0), (u'mde.12', 0.0), (u'mde.13', 0.0), (u'mde.14', 0.0), (u'mde.15', 0.0), (u'mde.16', 0.0), (u'mde.17', 0.0), (u'mde.18', 0.0), (u'mde.2', 0.0), (u'mde.3', 0.0), (u'mde.4', 1.0), (u'mde.5', 0.0), (u'mde.6', 0.0), (u'mde.7', 0.0), (u'mde.8', 0.0), (u'mde.9', 0.0)]
    Investigating kierValues
    Investigating autoCorrelationCharge
    Investigating bondCount
    Investigating chiCluster
    Investigating aromaticBondsCount
    Investigating eccentricConnectivityIndex
    Investigating hBondDonors
    autoCorrelationPolarizability affects hBondDonors (the evidence follows...)
    Before [(u'hBondDonors', 1)]
    After [(u'hBondDonors', 0)]
    Investigating longestAliphaticChain
    Investigating chi1C
    Investigating bpol
    Investigating chiPath
    Investigating chiChain
    Investigating aromaticAtomsCount
    Investigating lipinskifailures
    Investigating largestChain

     
  • Noel O'Boyle

    Noel O'Boyle - 2008-05-02

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    user_id=850620
    Originator: YES

    The CPSA stuff seems to be spurious. Why do I get all these 1.#QNAN values though?? Is this a known bug?

     
  • Rajarshi Guha

    Rajarshi Guha - 2008-10-19

    Should be fixed in 1.2.x and trunk

     
  • Egon Willighagen

    Bug is fixed: the current SVN version no longer has this
    problem.