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Commit 98d053d4 authored by Robert McGibbon's avatar Robert McGibbon
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Improve docstrings 

Swigged python docstrings now include documented return values and type
information or their arguments. They are generated in numpydoc format.
Furthermore, all of the Python app layer docstrings have been changed
to numpydoc format. The filterPythonFiles.py script which helps to
generate the Doxygen Python API docs has been updated to reflect these
changes.
parent 596a4197
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Showing with 333 additions and 332 deletions
openmmapi/include/openmm/CMAPTorsionForce.h
View file @ 98d053d4
......@@ -85,8 +85,8 @@ public:
* Get the energy values of a map.
*
* @param index the index of the map for which to get energy values
* @param size the size of the map along each dimension
* @param energy the energy values for the map. This must be of length size*size.
* @param[out] size the size of the map along each dimension
* @param[out] energy the energy values for the map. This must be of length size*size.
* The element energy[i+size*j] contains the energy when the first
* torsion angle equals i*2*PI/size and the second torsion angle
* equals j*2*PI/size.
......@@ -122,15 +122,15 @@ public:
* Get the force field parameters for a CMAP torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param map the index of the map to use for this term
* @param a1 the index of the first particle forming the first torsion
* @param a2 the index of the second particle forming the first torsion
* @param a3 the index of the third particle forming the first torsion
* @param a4 the index of the fourth particle forming the first torsion
* @param b1 the index of the first particle forming the second torsion
* @param b2 the index of the second particle forming the second torsion
* @param b3 the index of the third particle forming the second torsion
* @param b4 the index of the fourth particle forming the second torsion
* @param[out] map the index of the map to use for this term
* @param[out] a1 the index of the first particle forming the first torsion
* @param[out] a2 the index of the second particle forming the first torsion
* @param[out] a3 the index of the third particle forming the first torsion
* @param[out] a4 the index of the fourth particle forming the first torsion
* @param[out] b1 the index of the first particle forming the second torsion
* @param[out] b2 the index of the second particle forming the second torsion
* @param[out] b3 the index of the third particle forming the second torsion
* @param[out] b4 the index of the fourth particle forming the second torsion
*/
void getTorsionParameters(int index, int& map, int& a1, int& a2, int& a3, int& a4, int& b1, int& b2, int& b3, int& b4) const;
/**
......
openmmapi/include/openmm/CustomAngleForce.h
View file @ 98d053d4
......@@ -159,7 +159,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -176,10 +176,10 @@ public:
* Get the force field parameters for an angle term.
*
* @param index the index of the angle for which to get parameters
* @param particle1 the index of the first particle connected by the angle
* @param particle2 the index of the second particle connected by the angle
* @param particle3 the index of the third particle connected by the angle
* @param parameters the list of parameters for the angle
* @param[out] particle1 the index of the first particle connected by the angle
* @param[out] particle2 the index of the second particle connected by the angle
* @param[out] particle3 the index of the third particle connected by the angle
* @param[out] parameters the list of parameters for the angle
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomBondForce.h
View file @ 98d053d4
......@@ -159,7 +159,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -175,9 +175,9 @@ public:
* Get the force field parameters for a bond term.
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param parameters the list of parameters for the bond
* @param[out] particle1 the index of the first particle connected by the bond
* @param[out] particle2 the index of the second particle connected by the bond
* @param[out] parameters the list of parameters for the bond
*/
void getBondParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomCentroidBondForce.h
View file @ 98d053d4
......@@ -226,7 +226,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -242,8 +242,8 @@ public:
* Get the properties of a group.
*
* @param index the index of the group to get
* @param particles the indices of the particles in the group
* @param weights the weight used for each particle when computing the center position.
* @param[out] particles the indices of the particles in the group
* @param[out] weights the weight used for each particle when computing the center position.
* If no weights were specified, this vector will be empty indicating that particle
* masses should be used as weights.
*/
......@@ -269,8 +269,8 @@ public:
* Get the properties of a bond.
*
* @param index the index of the bond to get
* @param groups the indices of the groups in the bond
* @param parameters the list of per-bond parameter values for the bond
* @param[out] groups the indices of the groups in the bond
* @param[out] parameters the list of per-bond parameter values for the bond
*/
void getBondParameters(int index, std::vector<int>& groups, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomCompoundBondForce.h
View file @ 98d053d4
......@@ -209,7 +209,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -224,8 +224,8 @@ public:
* Get the properties of a bond.
*
* @param index the index of the bond to get
* @param particles the indices of the particles in the bond
* @param parameters the list of per-bond parameter values for the bond
* @param[out] particles the indices of the particles in the bond
* @param[out] parameters the list of per-bond parameter values for the bond
*/
void getBondParameters(int index, std::vector<int>& particles, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomExternalForce.h
View file @ 98d053d4
......@@ -170,7 +170,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -185,8 +185,8 @@ public:
* Get the force field parameters for a force field term.
*
* @param index the index of the particle term for which to get parameters
* @param particle the index of the particle this term is applied to
* @param parameters the list of parameters for the force field term
* @param[out] particle the index of the particle this term is applied to
* @param[out] parameters the list of parameters for the force field term
*/
void getParticleParameters(int index, int& particle, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/CustomGBForce.h
View file @ 98d053d4
......@@ -309,7 +309,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -324,7 +324,7 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param[out] parameters the list of parameters for the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters) const;
/**
......@@ -355,8 +355,8 @@ public:
* Get the properties of a computed value.
*
* @param index the index of the computed value for which to get parameters
* @param name the name of the value
* @param expression an algebraic expression to evaluate when calculating the computed value. If the
* @param[out] name the name of the value
* @param[out] expression an algebraic expression to evaluate when calculating the computed value. If the
* ComputationType is SingleParticle, the expression is evaluated independently
* for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle
* parameters and previous computed values for that particle. If the ComputationType is ParticlePair
......@@ -366,7 +366,7 @@ public:
* the per-particle parameters and previous computed values for each of them.
* Append "1" to a variable name to indicate the parameter for the particle whose
* value is being calculated, and "2" to indicate the particle it is interacting with.
* @param type the method to use for computing this value
* @param[out] type the method to use for computing this value
*/
void getComputedValueParameters(int index, std::string& name, std::string& expression, ComputationType& type) const;
/**
......@@ -407,7 +407,7 @@ public:
* Get the properties of a term to the energy computation.
*
* @param index the index of the term for which to get parameters
* @param expression an algebraic expression to evaluate when calculating the energy. If the
* @param[out] expression an algebraic expression to evaluate when calculating the energy. If the
* ComputationType is SingleParticle, the expression is evaluated once
* for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle
* parameters and computed values for that particle. If the ComputationType is ParticlePair or
......@@ -417,7 +417,7 @@ public:
* the per-particle parameters and computed values for each of them.
* Append "1" to a variable name to indicate the parameter for the first particle
* in the pair and "2" to indicate the second particle in the pair.
* @param type the method to use for computing this value
* @param[out] type the method to use for computing this value
*/
void getEnergyTermParameters(int index, std::string& expression, ComputationType& type) const;
/**
......@@ -449,8 +449,8 @@ public:
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @param[out] particle1 the index of the first particle in the pair
* @param[out] particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
......
openmmapi/include/openmm/CustomHbondForce.h
View file @ 98d053d4
......@@ -282,7 +282,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -301,12 +301,12 @@ public:
* Get the properties of a donor group.
*
* @param index the index of the donor group to get
* @param d1 the index of the first particle for this donor group
* @param d2 the index of the second particle for this donor group. If the group only
* @param[out] d1 the index of the first particle for this donor group
* @param[out] d2 the index of the second particle for this donor group. If the group only
* includes one particle, this will be -1.
* @param d3 the index of the third particle for this donor group. If the group includes
* @param[out] d3 the index of the third particle for this donor group. If the group includes
* less than three particles, this will be -1.
* @param parameters the list of per-donor parameter values for the donor
* @param[out] parameters the list of per-donor parameter values for the donor
*/
void getDonorParameters(int index, int& d1, int& d2, int& d3, std::vector<double>& parameters) const;
/**
......@@ -337,12 +337,12 @@ public:
* Get the properties of an acceptor group.
*
* @param index the index of the acceptor group to get
* @param a1 the index of the first particle for this acceptor group
* @param a2 the index of the second particle for this acceptor group. If the group only
* @param[out] a1 the index of the first particle for this acceptor group
* @param[out] a2 the index of the second particle for this acceptor group. If the group only
* includes one particle, this will be -1.
* @param a3 the index of the third particle for this acceptor group. If the group includes
* @param[out] a3 the index of the third particle for this acceptor group. If the group includes
* less than three particles, this will be -1.
* @param parameters the list of per-acceptor parameter values for the acceptor
* @param[out] parameters the list of per-acceptor parameter values for the acceptor
*/
void getAcceptorParameters(int index, int& a1, int& a2, int& a3, std::vector<double>& parameters) const;
/**
......@@ -369,16 +369,16 @@ public:
* Get the donor and acceptor in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get donor and acceptor indices
* @param particle1 the index of the donor
* @param particle2 the index of the acceptor
* @param[out] particle1 the index of the donor
* @param[out] particle2 the index of the acceptor
*/
void getExclusionParticles(int index, int& donor, int& acceptor) const;
/**
* Get the donor and acceptor in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get donor and acceptor indices
* @param particle1 the index of the donor
* @param particle2 the index of the acceptor
* @param donor the index of the donor
* @param acceptor the index of the acceptor
*/
void setExclusionParticles(int index, int donor, int acceptor);
/**
......
openmmapi/include/openmm/CustomIntegrator.h
View file @ 98d053d4
......@@ -371,7 +371,7 @@ public:
* Get the value of a per-DOF variable, specified by name.
*
* @param name the name of the variable to get
* @param values the values of the variable for all degrees of freedom
* @param[out] values the values of the variable for all degrees of freedom
* are stored into this
*/
void getPerDofVariableByName(const std::string& name, std::vector<Vec3>& values) const;
......@@ -446,7 +446,7 @@ public:
/**
* Add a step which begins a new "if" block.
*
* @param expression a mathematical expression involving a comparison operator
* @param condition a mathematical expression involving a comparison operator
* and global variables. All steps between this one and
* the end of the block are executed only if the condition
* is true.
......@@ -457,7 +457,7 @@ public:
/**
* Add a step which begins a new "while" block.
*
* @param expression a mathematical expression involving a comparison operator
* @param condition a mathematical expression involving a comparison operator
* and global variables. All steps between this one and
* the end of the block are executed repeatedly as long as
* the condition remains true.
......@@ -476,12 +476,13 @@ public:
* Get the details of a computation step that has been added to the integration algorithm.
*
* @param index the index of the computation step to get
* @param type on exit, the type of computation this step performs
* @param variable on exit, the variable into which this step stores its result. If this
* step does not store a result in a variable, this will be an
* empty string.
* @param expression on exit, the expression this step evaluates. If this step does not
* evaluate an expression, this will be an empty string.
* @param[out] type the type of computation this step performs
* @param[out] variable the variable into which this step stores its
* result. If this step does not store a result in
* a variable, this will be an empty string.
* @param[out] expression the expression this step evaluates. If
* this step does not evaluate an expression, this
* will be an empty string.
*/
void getComputationStep(int index, ComputationType& type, std::string& variable, std::string& expression) const;
/**
......
openmmapi/include/openmm/CustomManyParticleForce.h
View file @ 98d053d4
......@@ -337,7 +337,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -353,8 +353,8 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param type the type of the specified particle
* @param[out] parameters the list of parameters for the specified particle
* @param[out] type the type of the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters, int& type) const;
/**
......@@ -379,8 +379,8 @@ public:
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @param[out] particle1 the index of the first particle in the pair
* @param[out] particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
......@@ -406,7 +406,7 @@ public:
* regardless of the type of the specified particle.
*
* @param index the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
* @param types the allowed types for the specified particle
* @param[out] types the allowed types for the specified particle
*/
void getTypeFilter(int index, std::set<int>& types) const;
/**
......
openmmapi/include/openmm/CustomNonbondedForce.h
View file @ 98d053d4
......@@ -318,7 +318,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -333,7 +333,7 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param[out] parameters the list of parameters for the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters) const;
/**
......@@ -357,8 +357,8 @@ public:
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @param[out] particle1 the index of the first particle in the pair
* @param[out] particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
......@@ -441,8 +441,8 @@ public:
* Get the parameters for an interaction group.
*
* @param index the index of the interaction group for which to get parameters
* @param set1 the first set of particles forming the interaction group
* @param set2 the second set of particles forming the interaction group
* @param[out] set1 the first set of particles forming the interaction group
* @param[out] set2 the second set of particles forming the interaction group
*/
void getInteractionGroupParameters(int index, std::set<int>& set1, std::set<int>& set2) const;
/**
......
openmmapi/include/openmm/CustomTorsionForce.h
View file @ 98d053d4
......@@ -159,7 +159,7 @@ public:
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
* @param defaultValue the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
......@@ -177,11 +177,11 @@ public:
* Get the force field parameters for a torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param particle1 the index of the first particle connected by the torsion
* @param particle2 the index of the second particle connected by the torsion
* @param particle3 the index of the third particle connected by the torsion
* @param particle4 the index of the fourth particle connected by the torsion
* @param parameters the list of parameters for the torsion
* @param[out] particle1 the index of the first particle connected by the torsion
* @param[out] particle2 the index of the second particle connected by the torsion
* @param[out] particle3 the index of the third particle connected by the torsion
* @param[out] particle4 the index of the fourth particle connected by the torsion
* @param[out] parameters the list of parameters for the torsion
*/
void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, std::vector<double>& parameters) const;
/**
......
openmmapi/include/openmm/GBSAOBCForce.h
View file @ 98d053d4
......@@ -100,9 +100,9 @@ public:
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] radius the GBSA radius of the particle, measured in nm
* @param[out] scalingFactor the OBC scaling factor for the particle
*/
void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
/**
......
openmmapi/include/openmm/GBVIForce.h
View file @ 98d053d4
......@@ -110,9 +110,9 @@ public:
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param gamma the gamma parameter
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] radius the GBSA radius of the particle, measured in nm
* @param[out] gamma the gamma parameter
*/
void getParticleParameters(int index, double& charge, double& radius, double& gamma) const;
/**
......@@ -138,9 +138,9 @@ public:
* Get the parameters defining a bond
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle involved in the bond
* @param particle2 the index of the second particle involved in the bond
* @param distance the distance between the two particles, measured in nm
* @param[out] particle1 the index of the first particle involved in the bond
* @param[out] particle2 the index of the second particle involved in the bond
* @param[out] distance the distance between the two particles, measured in nm
*/
void getBondParameters(int index, int& particle1, int& particle2, double& distance) const;
/**
......
openmmapi/include/openmm/HarmonicAngleForce.h
View file @ 98d053d4
......@@ -74,11 +74,11 @@ public:
* Get the force field parameters for an angle term.
*
* @param index the index of the angle for which to get parameters
* @param particle1 the index of the first particle forming the angle
* @param particle2 the index of the second particle forming the angle
* @param particle3 the index of the third particle forming the angle
* @param angle the equilibrium angle, measured in radians
* @param k the harmonic force constant for the angle, measured in kJ/mol/radian^2
* @param[out] particle1 the index of the first particle forming the angle
* @param[out] particle2 the index of the second particle forming the angle
* @param[out] particle3 the index of the third particle forming the angle
* @param[out] angle the equilibrium angle, measured in radians
* @param[out] k the harmonic force constant for the angle, measured in kJ/mol/radian^2
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const;
/**
......
openmmapi/include/openmm/HarmonicBondForce.h
View file @ 98d053d4
......@@ -73,10 +73,10 @@ public:
* Get the force field parameters for a bond term.
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param length the equilibrium length of the bond, measured in nm
* @param k the harmonic force constant for the bond, measured in kJ/mol/nm^2
* @param[out] particle1 the index of the first particle connected by the bond
* @param[out] particle2 the index of the second particle connected by the bond
* @param[out] length the equilibrium length of the bond, measured in nm
* @param[out] k the harmonic force constant for the bond, measured in kJ/mol/nm^2
*/
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const;
/**
......
openmmapi/include/openmm/NonbondedForce.h
View file @ 98d053d4
......@@ -201,10 +201,10 @@ public:
* Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
* @param[out] alpha the separation parameter
* @param[out] nx the number of grid points along the X axis
* @param[out] ny the number of grid points along the Y axis
* @param[out] nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
......@@ -224,10 +224,10 @@ public:
* See the manual for details.
*
* @param context the Context for which to get the parameters
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
* @param[out] alpha the separation parameter
* @param[out] nx the number of grid points along the X axis
* @param[out] ny the number of grid points along the Y axis
* @param[out] nz the number of grid points along the Z axis
*/
void getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const;
/**
......@@ -247,9 +247,9 @@ public:
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param[out] epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
*/
void getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const;
/**
......@@ -284,11 +284,11 @@ public:
* Get the force field parameters for an interaction that should be calculated differently from others.
*
* @param index the index of the interaction for which to get parameters
* @param particle1 the index of the first particle involved in the interaction
* @param particle2 the index of the second particle involved in the interaction
* @param chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
* @param sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
* @param[out] particle1 the index of the first particle involved in the interaction
* @param[out] particle2 the index of the second particle involved in the interaction
* @param[out] chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
* @param[out] sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param[out] epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
*/
void getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
/**
......
openmmapi/include/openmm/PeriodicTorsionForce.h
View file @ 98d053d4
......@@ -76,13 +76,13 @@ public:
* Get the force field parameters for a periodic torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param particle1 the index of the first particle forming the torsion
* @param particle2 the index of the second particle forming the torsion
* @param particle3 the index of the third particle forming the torsion
* @param particle4 the index of the fourth particle forming the torsion
* @param periodicity the periodicity of the torsion
* @param phase the phase offset of the torsion, measured in radians
* @param k the force constant for the torsion
* @param[out] particle1 the index of the first particle forming the torsion
* @param[out] particle2 the index of the second particle forming the torsion
* @param[out] particle3 the index of the third particle forming the torsion
* @param[out] particle4 the index of the fourth particle forming the torsion
* @param[out] periodicity the periodicity of the torsion
* @param[out] phase the phase offset of the torsion, measured in radians
* @param[out] k the force constant for the torsion
*/
void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const;
/**
......
openmmapi/include/openmm/RBTorsionForce.h
View file @ 98d053d4
......@@ -79,16 +79,16 @@ public:
* Get the force field parameters for a Ryckaert-Bellemans torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param particle1 the index of the first particle forming the torsion
* @param particle2 the index of the second particle forming the torsion
* @param particle3 the index of the third particle forming the torsion
* @param particle4 the index of the fourth particle forming the torsion
* @param c0 the coefficient of the constant term, measured in kJ/mol
* @param c1 the coefficient of the 1st order term, measured in kJ/mol
* @param c2 the coefficient of the 2nd order term, measured in kJ/mol
* @param c3 the coefficient of the 3rd order term, measured in kJ/mol
* @param c4 the coefficient of the 4th order term, measured in kJ/mol
* @param c5 the coefficient of the 5th order term, measured in kJ/mol
* @param[out] particle1 the index of the first particle forming the torsion
* @param[out] particle2 the index of the second particle forming the torsion
* @param[out] particle3 the index of the third particle forming the torsion
* @param[out] particle4 the index of the fourth particle forming the torsion
* @param[out] c0 the coefficient of the constant term, measured in kJ/mol
* @param[out] c1 the coefficient of the 1st order term, measured in kJ/mol
* @param[out] c2 the coefficient of the 2nd order term, measured in kJ/mol
* @param[out] c3 the coefficient of the 3rd order term, measured in kJ/mol
* @param[out] c4 the coefficient of the 4th order term, measured in kJ/mol
* @param[out] c5 the coefficient of the 5th order term, measured in kJ/mol
*/
void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const;
/**
......
openmmapi/include/openmm/State.h
View file @ 98d053d4
......@@ -95,9 +95,9 @@ public:
/**
* Get the vectors defining the axes of the periodic box (measured in nm).
*
* @param a on exit, this contains the vector defining the first edge of the periodic box
* @param b on exit, this contains the vector defining the second edge of the periodic box
* @param c on exit, this contains the vector defining the third edge of the periodic box
* @param[out] a the vector defining the first edge of the periodic box
* @param[out] b the vector defining the second edge of the periodic box
* @param[out] c the vector defining the third edge of the periodic box
*/
void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
/**
......
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