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Python CustomGBForce.addPerParticleParameter方法代码示例

本文整理汇总了Python中simtk.openmm.CustomGBForce.addPerParticleParameter方法的典型用法代码示例。如果您正苦于以下问题：Python CustomGBForce.addPerParticleParameter方法的具体用法？Python CustomGBForce.addPerParticleParameter怎么用？Python CustomGBForce.addPerParticleParameter使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类simtk.openmm.CustomGBForce的用法示例。


在下文中一共展示了CustomGBForce.addPerParticleParameter方法的10个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: GBSAGBnForce

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):


    """
    Indexing for tables:
        input: radius1, radius2
        index = (radius2*200-20)*21 + (radius1*200-20)
        output: index of desired value in row-by-row, 1D version of Tables 3 & 4
    """


    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("or") # Offset radius
    custom.addPerParticleParameter("sr") # Scaled offset radius

    custom.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
    custom.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))

    custom.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
                                  "Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
                                  "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2);"
                                  "radius1=or1+offset; radius2=or2+offset;"
                                  "neckScale=0.361825; neckCut=0.68; offset=0.009", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
                              "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
    return custom
开发者ID:Bhattiasif，项目名称:openmm，代码行数:36，代码来源:customgbforces.py

示例2: GBSAGBn2Force

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):

    """
    Indexing for tables:
        input: radius1, radius2
        index = (radius2*200-20)*21 + (radius1*200-20)
        output: index of desired value in row-by-row, 1D version of Tables 3 & 4
    """

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    custom.addPerParticleParameter("alpha")
    custom.addPerParticleParameter("beta")
    custom.addPerParticleParameter("gamma")

    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    custom.addGlobalParameter("offset", 0.019_514_1)
    custom.addGlobalParameter("neckScale", 0.826_836)
    custom.addGlobalParameter("neckCut", 0.68)

    custom.addFunction("getd0", d0, 0, 440)
    custom.addFunction("getm0", m0, 0, 440)

    custom.addComputedValue(
        "I",
        "Ivdw+neckScale*Ineck;"
        "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
        "index = (radius2*200-20)*21 + (radius1*200-20);"
        "Ivdw=step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
        "excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);"  # exclude pair where one atom is not charged
        "U=r+sr2;"
        "L=max(or1, D);"
        "D=abs(r-sr2);"
        "sr2 = scale2*or2;"
        "or1 = radius1-offset; or2 = radius2-offset",
        CustomGBForce.ParticlePairNoExclusions,
    )

    custom.addComputedValue(
        "B",
        "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
        "psi=I*or; or=radius-offset",
        CustomGBForce.SingleParticle,
    )
    _createEnergyTerms(custom, SA, cutoff)
    return custom
开发者ID:choderalab，项目名称:constph-openmm，代码行数:52，代码来源:cnstphgbforces.py

示例3: GBSAHCTForce

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
                 cutoff=None, kappa=0.0):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("or") # Offset radius
    custom.addPerParticleParameter("sr") # Scaled offset radius
    custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-I)", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
    return custom
开发者ID:Bhattiasif，项目名称:openmm，代码行数:18，代码来源:customgbforces.py

示例4: GBSAGBn2Force

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
                  cutoff=None, kappa=0.0):


    """
    Indexing for tables:
        input: radius1, radius2
        index = (radius2*200-20)*21 + (radius1*200-20)
        output: index of desired value in row-by-row, 1D version of Tables 3 & 4
    """


    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    custom.addPerParticleParameter("alpha")
    custom.addPerParticleParameter("beta")
    custom.addPerParticleParameter("gamma")

    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    custom.addGlobalParameter("offset", 0.0195141)
    custom.addGlobalParameter("neckScale", 0.826836)
    custom.addGlobalParameter("neckCut", 0.68)

    custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
    custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))

    custom.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
                                  "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
                                  "index = (radius2*200-20)*21 + (radius1*200-20);"
                                  "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2);"
                                  "sr2 = scale2*or2;"
                                  "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
                              "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff, kappa)
    return custom
开发者ID:MrBitKoin，项目名称:openmm，代码行数:47，代码来源:customgbforces.py

示例5: GBSAOBC2Force

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q");
    custom.addPerParticleParameter("radius");
    custom.addPerParticleParameter("scale");
    custom.addGlobalParameter("solventDielectric", solventDielectric);
    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
    custom.addGlobalParameter("offset", 0.009)
    custom.addComputedValue("I",  "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2);"
                                  "sr2 = scale2*or2;"
                                  "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
                                  "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)

    custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
    if SA=='ACE':
        custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
    elif SA is not None:
        raise ValueError('Unknown surface area method: '+SA)
    custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)

    return custom
开发者ID:rmcgibbo，项目名称:neb，代码行数:31，代码来源:customgbforces.py

示例6: GBSAOBC1Force

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    custom.addGlobalParameter("offset", 0.009)
    custom.addComputedValue(
        "I",
        "step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
        "excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);"  # exclude pair where one atom is not charged
        "U=r+sr2;"
        "L=max(or1, D);"
        "D=abs(r-sr2);"
        "sr2 = scale2*or2;"
        "or1 = radius1-offset; or2 = radius2-offset",
        CustomGBForce.ParticlePairNoExclusions,
    )

    custom.addComputedValue(
        "B",
        "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);" "psi=I*or; or=radius-offset",
        CustomGBForce.SingleParticle,
    )
    _createEnergyTerms(custom, SA, cutoff)
    return custom
开发者ID:choderalab，项目名称:constph-openmm，代码行数:31，代码来源:cnstphgbforces.py

示例7: GBSAGBnForce

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):

    
    """
    Indexing for tables:
        input: radius1, radius2
        index = (radius2*200-20)*21 + (radius1*200-20)
        output: index of desired value in row-by-row, 1D version of Tables 3 & 4
    """
     
 
    custom = CustomGBForce()

    custom.addPerParticleParameter("q");
    custom.addPerParticleParameter("radius");
    custom.addPerParticleParameter("scale");
    
    custom.addGlobalParameter("solventDielectric", solventDielectric);
    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
    custom.addGlobalParameter("offset", 0.009)
    custom.addGlobalParameter("neckScale", 0.361825)
    custom.addGlobalParameter("neckCut", 0.68)
    
    custom.addFunction("getd0", d0, 0, 440)
    custom.addFunction("getm0", m0, 0, 440)

    custom.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
                                  "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
                                  "index = (radius2*200-20)*21 + (radius1*200-20);"
                                  "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2);"
                                  "sr2 = scale2*or2;"
                                  "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
    
    custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
                              "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
 
    custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
    if SA=='ACE':
        custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
    elif SA is not None:
        raise ValueError('Unknown surface area method: '+SA)
    custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)

    return custom
开发者ID:rmcgibbo，项目名称:neb，代码行数:50，代码来源:customgbforces.py

示例8: GBSAGBnForce

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):

    """
    Indexing for tables:
        input: radius1, radius2
        index = (radius2*200-20)*21 + (radius1*200-20)
        output: index of desired value in row-by-row, 1D version of Tables 3 & 4
    """

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")

    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    custom.addGlobalParameter("offset", 0.009)
    custom.addGlobalParameter("neckScale", 0.361825)
    custom.addGlobalParameter("neckCut", 0.68)

    custom.addFunction("getd0", d0, 0, 440)
    custom.addFunction("getm0", m0, 0, 440)

    custom.addComputedValue(
        "I",
        "Ivdw+neckScale*Ineck;"
        "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
        "index = (radius2*200-20)*21 + (radius1*200-20);"
        "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
        "U=r+sr2;"
        "L=max(or1, D);"
        "D=abs(r-sr2);"
        "sr2 = scale2*or2;"
        "or1 = radius1-offset; or2 = radius2-offset",
        CustomGBForce.ParticlePairNoExclusions,
    )

    custom.addComputedValue(
        "B",
        "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);" "psi=I*or; or=radius-offset",
        CustomGBForce.SingleParticle,
    )
    _createEnergyTerms(custom, SA, cutoff)
    return custom
开发者ID:jwagoner，项目名称:openmm，代码行数:47，代码来源:customgbforces.py

示例9: GBSAOBC2Force

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q");
    custom.addPerParticleParameter("radius");
    custom.addPerParticleParameter("scale");
    custom.addGlobalParameter("solventDielectric", solventDielectric);
    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
    custom.addGlobalParameter("offset", 0.009)
    custom.addComputedValue("I",  "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2);"
                                  "sr2 = scale2*or2;"
                                  "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
                                  "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff)
    return custom
开发者ID:jayavanth，项目名称:openmm，代码行数:23，代码来源:customgbforces.py

示例10: GBSAHCTForce

# 需要导入模块: from simtk.openmm import CustomGBForce [as 别名]
# 或者: from simtk.openmm.CustomGBForce import addPerParticleParameter [as 别名]
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
                 cutoff=None, kappa=0.0):

    custom = CustomGBForce()

    custom.addPerParticleParameter("q")
    custom.addPerParticleParameter("radius")
    custom.addPerParticleParameter("scale")
    if kappa > 0: custom.addGlobalParameter('kappa', kappa)
    custom.addGlobalParameter("solventDielectric", solventDielectric)
    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
    custom.addGlobalParameter("offset", 0.009)
    custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                  "U=r+sr2;"
                                  "L=max(or1, D);"
                                  "D=abs(r-sr2);"
                                  "sr2 = scale2*or2;"
                                  "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-I);"
                                  "or=radius-offset", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, SA, cutoff, kappa)
    return custom
开发者ID:MrBitKoin，项目名称:openmm，代码行数:25，代码来源:customgbforces.py


注：本文中的simtk.openmm.CustomGBForce.addPerParticleParameter方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。