Python openmm.CustomGBForce类代码示例

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本文整理汇总了Python中simtk.openmm.CustomGBForce类的典型用法代码示例。如果您正苦于以下问题：Python CustomGBForce类的具体用法？Python CustomGBForce怎么用？Python CustomGBForce使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。

在下文中一共展示了CustomGBForce类的13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，您的评价将有助于我们的系统推荐出更棒的Python代码示例。

示例1: init

    def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
                 cutoff=None, kappa=0.0):

        CustomGBForce.__init__(self)

        self.addPerParticleParameter("q")
        self.addPerParticleParameter("or") # Offset radius
        self.addPerParticleParameter("sr") # Scaled offset radius
        self.addPerParticleParameter("alpha")
        self.addPerParticleParameter("beta")
        self.addPerParticleParameter("gamma")

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

        self.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=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)

        self.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
                                     "psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
        _createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)

开发者ID:PauloLira，项目名称:openmm，代码行数:27，代码来源:customgbforces.py

示例2: GBSAOBC2Force

def GBSAOBC2Force(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-tanh(psi-0.8*psi^2+4.85*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:17，代码来源:customgbforces.py

示例3: setParticleParameters

 def setParticleParameters(self, idx, params):
     params = copy.deepcopy(params)
     params[self.RADIUS_ARG_POSITION] = strip_unit(params[self.RADIUS_ARG_POSITION], u.nanometer) - self.OFFSET
     params[self.SCREEN_POSITION] *= params[self.RADIUS_ARG_POSITION]
     CustomGBForce.addParticle(self, params)
     return params

开发者ID:PauloLira，项目名称:openmm，代码行数:6，代码来源:customgbforces.py

示例4: GBSAGBn2Force

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("or") # Offset radius
    custom.addPerParticleParameter("sr") # Scaled offset radius
    custom.addPerParticleParameter("alpha")
    custom.addPerParticleParameter("beta")
    custom.addPerParticleParameter("gamma")

    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=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)

    custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
                                 "psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
    _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
    return custom

开发者ID:Bhattiasif，项目名称:openmm，代码行数:37，代码来源:customgbforces.py

示例5: GBSAOBC1Force

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:jchodera，项目名称:openmm-constph，代码行数:22，代码来源:cnstphgbforces.py

示例6: GBSAGBnForce

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("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.addGlobalParameter("neckScale", 0.361825)
    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(1.09511284*psi-1.907992938*psi^2+2.50798245*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:42，代码来源:customgbforces.py

示例7: GBSAGBn2Force

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", 0.0195141)
    custom.addGlobalParameter("neckScale", 0.826836)
    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:jchodera，项目名称:openmm-constph，代码行数:44，代码来源:cnstphgbforces.py

示例8: GBSAGBnForce

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:48，代码来源:customgbforces.py

示例9: GBSAOBC2Force

def GBSAOBC2Force(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-tanh(psi-0.8*psi^2+4.85*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:23，代码来源:customgbforces.py

示例10: GBSAOBC2Force

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:29，代码来源:customgbforces.py

示例11: GBSAHCTForce

def GBSAHCTForce(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-I);"
                                  "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:21，代码来源:customgbforces.py

示例12: _addParticles

 def _addParticles(self):
     for p in self.parameters:
         radIndex = self._radiusToIndex[p[self.RADIUS_ARG_POSITION]]
         CustomGBForce.addParticle(self, p + [radIndex])

开发者ID:andysim，项目名称:openmm，代码行数:4，代码来源:customgbforces.py

示例13: init

 def __init__(self):
     CustomGBForce.__init__(self)
     self.parameters = []

开发者ID:andysim，项目名称:openmm，代码行数:3，代码来源:customgbforces.py

注：本文中的simtk.openmm.CustomGBForce类示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，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。

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Python openmm.CustomGBForce类代码示例

示例1: init

示例2: GBSAOBC2Force

示例3: setParticleParameters

示例4: GBSAGBn2Force

示例5: GBSAOBC1Force

示例6: GBSAGBnForce

示例7: GBSAGBn2Force

示例8: GBSAGBnForce

示例9: GBSAOBC2Force

示例10: GBSAOBC2Force

示例11: GBSAHCTForce

示例12: _addParticles

示例13: init

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Python openmm.CustomGBForce类代码示例

示例1: __init__

示例2: GBSAOBC2Force

示例3: setParticleParameters

示例4: GBSAGBn2Force

示例5: GBSAOBC1Force

示例6: GBSAGBnForce

示例7: GBSAGBn2Force

示例8: GBSAGBnForce

示例9: GBSAOBC2Force

示例10: GBSAOBC2Force

示例11: GBSAHCTForce

示例12: _addParticles

示例13: __init__

请发表评论

全部评论

上一篇：

下一篇：

Python util.grid_equal函数代码示例

Python util.get_worker_name函数代码示例

Python util.get_webmention_target函数代

Python util.get_uuid函数代码示例

Python util.get_type_by_name函数代码示例

Python util.grid_equal函数代码示例

Python util.get_worker_name函数代码示例

Python util.get_webmention_target函数代

Python util.get_uuid函数代码示例

Python util.get_type_by_name函数代码示例

Python util.get_stdout函数代码示例

关于我们

产品与服务

解决方案

139-2527-9053

示例1: init

示例13: init