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Commit a1953312 authored by Robert McGibbon's avatar Robert McGibbon
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Merge branch 'docstrings' of github.com:rmcgibbo/openmm into docstrings

parents d137b536 d74a4cc1
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openmmapi/include/openmm/System.h
View file @ a1953312
......@@ -153,9 +153,9 @@ public:
* Get the parameters defining a distance constraint.
*
* @param index the index of the constraint for which to get parameters
* @param particle1 the index of the first particle involved in the constraint
* @param particle2 the index of the second particle involved in the constraint
* @param distance the required distance between the two particles, measured in nm
* @param[out] particle1 the index of the first particle involved in the constraint
* @param[out] particle2 the index of the second particle involved in the constraint
* @param[out] distance the required distance between the two particles, measured in nm
*/
void getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const;
/**
......@@ -216,9 +216,9 @@ public:
* created Context will have its box vectors set to these. They will affect
* any Force added to the System that uses periodic boundary conditions.
*
* @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 getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ a1953312
......@@ -128,7 +128,7 @@ public:
* @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 length the equilibrium angle, measured in degrees
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @param quadraticK the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @return the index of the angle that was added
*/
int addAngle(int particle1, int particle2, int particle3, double length, double quadraticK);
......@@ -137,11 +137,11 @@ 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 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 length the equilibrium angle, measured in degrees
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @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] length the equilibrium angle, measured in degrees
* @param[out] quadraticK the quadratic force constant for the angle, measured in kJ/mol/radian^2
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length, double& quadraticK) const;
......@@ -153,7 +153,7 @@ public:
* @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 length the equilibrium angle, measured in degrees
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @param quadraticK the quadratic force constant for the angle, measured in kJ/mol/radian^2
*/
void setAngleParameters(int index, int particle1, int particle2, int particle3, double length, double quadraticK);
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ a1953312
......@@ -100,7 +100,7 @@ public:
* @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 quadratic force constant for the bond
* @param quadraticK the quadratic force constant for the bond
* @return the index of the bond that was added
*/
......@@ -110,10 +110,10 @@ 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 quadratic k the quadratic force constant 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] length the equilibrium length of the bond, measured in nm
* @param[out] quadraticK the quadratic force constant for the bond
*/
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK) const;
......@@ -125,7 +125,7 @@ public:
* @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 quadratic force constant for the bond
* @param quadraticK the quadratic force constant for the bond
*/
void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK);
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ a1953312
......@@ -80,9 +80,9 @@ 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 atomic radius of the particle, measured in nm
* @param scalingFactor the scaling factor for the particle
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] radius the atomic radius of the particle, measured in nm
* @param[out] scalingFactor the scaling factor for the particle
*/
void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ a1953312
......@@ -129,7 +129,7 @@ public:
* @param particle3 the index of the third particle connected by the angle
* @param particle4 the index of the fourth particle connected by the angle
* @param length the equilibrium angle, measured in radians
* @param quadratic k the quadratic force constant for the angle measured in kJ/mol/radian^2
* @param quadraticK the quadratic force constant for the angle measured in kJ/mol/radian^2
* @return the index of the angle that was added
*/
int addAngle(int particle1, int particle2, int particle3, int particle4, double length,
......@@ -139,12 +139,12 @@ 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 particle4 the index of the fourth particle connected by the angle
* @param length the equilibrium angle, measured in radians
* @param quadratic k the quadratic force constant for the angle measured in kJ/mol/radian^2
* @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] particle4 the index of the fourth particle connected by the angle
* @param[out] length the equilibrium angle, measured in radians
* @param[out] quadraticK the quadratic force constant for the angle measured in kJ/mol/radian^2
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& length,
double& quadraticK) const;
......@@ -158,7 +158,7 @@ public:
* @param particle3 the index of the third particle connected by the angle
* @param particle4 the index of the fourth particle connected by the angle
* @param length the equilibrium angle, measured in radians
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @param quadraticK the quadratic force constant for the angle, measured in kJ/mol/radian^2
*/
void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK);
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ a1953312
......@@ -148,7 +148,7 @@ public:
* Set the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically
* based on the Ewald error tolerance.
*
* @param Ewald alpha parameter
* @param aewald alpha parameter
*/
void setAEwald(double aewald);
......@@ -171,7 +171,7 @@ public:
* Set the PME grid dimensions. If Ewald alpha is 0 (the default), this is ignored and grid dimensions
* are chosen automatically based on the Ewald error tolerance.
*
* @param the PME grid dimensions
* @param gridDimension the PME grid dimensions
*/
void setPmeGridDimensions(const std::vector<int>& gridDimension);
......@@ -182,10 +182,10 @@ 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;
......@@ -212,16 +212,16 @@ public:
* Get the multipole parameters for a particle.
*
* @param index the index of the atom for which to get parameters
* @param charge the particle's charge
* @param molecularDipole the particle's molecular dipole (vector of size 3)
* @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9)
* @param axisType the particle's axis type
* @param multipoleAtomZ index of first atom used in constructing lab<->molecular frames
* @param multipoleAtomX index of second atom used in constructing lab<->molecular frames
* @param multipoleAtomY index of second atom used in constructing lab<->molecular frames
* @param thole Thole parameter
* @param dampingFactor dampingFactor parameter
* @param polarity polarity parameter
* @param[out] charge the particle's charge
* @param[out] molecularDipole the particle's molecular dipole (vector of size 3)
* @param[out] molecularQuadrupole the particle's molecular quadrupole (vector of size 9)
* @param[out] axisType the particle's axis type
* @param[out] multipoleAtomZ index of first atom used in constructing lab<->molecular frames
* @param[out] multipoleAtomX index of second atom used in constructing lab<->molecular frames
* @param[out] multipoleAtomY index of second atom used in constructing lab<->molecular frames
* @param[out] thole Thole parameter
* @param[out] dampingFactor dampingFactor parameter
* @param[out] polarity polarity parameter
*/
void getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity) const;
......@@ -237,6 +237,8 @@ public:
* @param multipoleAtomZ index of first atom used in constructing lab<->molecular frames
* @param multipoleAtomX index of second atom used in constructing lab<->molecular frames
* @param multipoleAtomY index of second atom used in constructing lab<->molecular frames
* @param thole thole parameter
* @param dampingFactor damping factor parameter
* @param polarity polarity parameter
*/
void setMultipoleParameters(int index, double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole,
......@@ -256,7 +258,7 @@ public:
*
* @param index the index of the atom for which to set parameters
* @param typeId CovalentTypes type
* @param covalentAtoms output vector of covalent atoms associated w/ the specfied CovalentType
* @param[out] covalentAtoms output vector of covalent atoms associated w/ the specfied CovalentType
*/
void getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms) const;
......@@ -264,7 +266,7 @@ public:
* Get the CovalentMap for an atom
*
* @param index the index of the atom for which to set parameters
* @param covalentLists output vector of covalent lists of atoms
* @param[out] covalentLists output vector of covalent lists of atoms
*/
void getCovalentMaps(int index, std::vector < std::vector<int> >& covalentLists) const;
......@@ -278,7 +280,7 @@ public:
/**
* Set the max number of iterations to be used in calculating the mutual induced dipoles
*
* @param max number of iterations
* @param inputMutualInducedMaxIterations number of iterations
*/
void setMutualInducedMaxIterations(int inputMutualInducedMaxIterations);
......@@ -292,7 +294,7 @@ public:
/**
* Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
*
* @param target epsilon
* @param inputMutualInducedTargetEpsilon target epsilon
*/
void setMutualInducedTargetEpsilon(double inputMutualInducedTargetEpsilon);
......@@ -319,7 +321,7 @@ public:
* Get the induced dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
* @param[out] dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(Context& context, std::vector<Vec3>& dipoles);
......@@ -328,7 +330,7 @@ public:
*
* @param inputGrid input grid points over which the potential is to be evaluated
* @param context context
* @param outputElectrostaticPotential output potential
* @param[out] outputElectrostaticPotential output potential
*/
void getElectrostaticPotential(const std::vector< Vec3 >& inputGrid,
......@@ -344,7 +346,7 @@ public:
* the quadrupole moment is still undefined and should be ignored.
*
* @param context context
* @param outputMultipoleMoments (charge,
* @param[out] outputMultipoleMoments (charge,
dipole_x, dipole_y, dipole_z,
quadrupole_xx, quadrupole_xy, quadrupole_xz,
quadrupole_yx, quadrupole_yy, quadrupole_yz,
......
plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h
View file @ a1953312
......@@ -134,11 +134,11 @@ public:
* Get the force field parameters for an out-of-plane bend term.
*
* @param index the index of the outOfPlaneBend for which to get parameters
* @param particle1 the index of the first particle connected by the outOfPlaneBend
* @param particle2 the index of the second particle connected by the outOfPlaneBend
* @param particle3 the index of the third particle connected by the outOfPlaneBend
* @param particle4 the index of the fourth particle connected by the outOfPlaneBend
* @param k the force constant for the out-of-plane bend
* @param[out] particle1 the index of the first particle connected by the outOfPlaneBend
* @param[out] particle2 the index of the second particle connected by the outOfPlaneBend
* @param[out] particle3 the index of the third particle connected by the outOfPlaneBend
* @param[out] particle4 the index of the fourth particle connected by the outOfPlaneBend
* @param[out] k the force constant for the out-of-plane bend
*/
void getOutOfPlaneBendParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& k) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h
View file @ a1953312
......@@ -80,13 +80,13 @@ 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 particle5 the index of the fifth particle connected by the torsion
* @param particle6 the index of the sixth particle connected by the torsion
* @param k the force constant 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] particle5 the index of the fifth particle connected by the torsion
* @param[out] particle6 the index of the sixth particle connected by the torsion
* @param[out] k the force constant for the torsion
*/
void getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ a1953312
......@@ -82,14 +82,14 @@ public:
* Get the force field parameters for a stretch-bend term.
*
* @param index the index of the stretch-bend for which to get parameters
* @param particle1 the index of the first particle connected by the stretch-bend
* @param particle2 the index of the second particle connected by the stretch-bend
* @param particle3 the index of the third particle connected by the stretch-bend
* @param lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
* @param lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
* @param angle the equilibrium angle in radians
* @param k1 the force constant of the product of bond ab and angle a-b-c
* @param k2 the force constant of the product of bond bc and angle a-b-c
* @param[out] particle1 the index of the first particle connected by the stretch-bend
* @param[out] particle2 the index of the second particle connected by the stretch-bend
* @param[out] particle3 the index of the third particle connected by the stretch-bend
* @param[out] lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
* @param[out] lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
* @param[out] angle the equilibrium angle in radians
* @param[out] k1 the force constant of the product of bond ab and angle a-b-c
* @param[out] k2 the force constant of the product of bond bc and angle a-b-c
*/
void getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3, double& lengthAB,
double& lengthCB, double& angle, double& k1, double& k2) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h
View file @ a1953312
......@@ -90,13 +90,13 @@ public:
* Get the force field parameters for a torsion-torsion term.
*
* @param index the index of the torsion-torsion for which to get parameters
* @param particle1 the index of the first particle connected by the torsion-torsion
* @param particle2 the index of the second particle connected by the torsion-torsion
* @param particle3 the index of the third particle connected by the torsion-torsion
* @param particle4 the index of the fourth particle connected by the torsion-torsion
* @param particle5 the index of the fifth particle connected by the torsion-torsion
* @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
* @param gridIndex the grid index
* @param[out] particle1 the index of the first particle connected by the torsion-torsion
* @param[out] particle2 the index of the second particle connected by the torsion-torsion
* @param[out] particle3 the index of the third particle connected by the torsion-torsion
* @param[out] particle4 the index of the fourth particle connected by the torsion-torsion
* @param[out] particle5 the index of the fifth particle connected by the torsion-torsion
* @param[out] chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
* @param[out] gridIndex the grid index
*/
void getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const;
......@@ -117,7 +117,7 @@ public:
/**
* Get the torsion-torsion grid at the specified index
*
* @param gridIndex the grid index
* @param index the grid index
* @return grid return grid reference
*/
const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid(int index) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ a1953312
......@@ -98,10 +98,10 @@ public:
* Get the force field parameters for a vdw particle.
*
* @param particleIndex the particle index
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* @param[out] parentIndex the index of the parent particle
* @param[out] sigma vdw sigma
* @param[out] epsilon vdw epsilon
* @param[out] reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
*/
void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
......@@ -179,7 +179,7 @@ public:
* Get exclusions for specified particle
*
* @param particleIndex particle index
* @param exclusions vector of exclusions
* @param[out] exclusions vector of exclusions
*/
void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h
View file @ a1953312
......@@ -76,8 +76,8 @@ public:
* Get the force field parameters for a WCA dispersion particle.
*
* @param particleIndex the particle index
* @param radius radius
* @param epsilon epsilon
* @param[out] radius radius
* @param[out] epsilon epsilon
*/
void getParticleParameters(int particleIndex, double& radius, double& epsilon) const;
......
plugins/drude/openmmapi/include/openmm/DrudeForce.h
View file @ a1953312
......@@ -92,18 +92,18 @@ public:
* Get the parameters for a Drude particle.
*
* @param index the index of the Drude particle for which to get parameters
* @param particle the index within the System of the Drude particle
* @param particle1 the index within the System of the particle to which the Drude particle is attached
* @param particle2 the index within the System of the second particle used for defining anisotropic polarizability.
* @param[out] particle the index within the System of the Drude particle
* @param[out] particle1 the index within the System of the particle to which the Drude particle is attached
* @param[out] particle2 the index within the System of the second particle used for defining anisotropic polarizability.
* This may be set to -1, in which case aniso12 will be ignored.
* @param particle3 the index within the System of the third particle used for defining anisotropic polarizability.
* @param[out] particle3 the index within the System of the third particle used for defining anisotropic polarizability.
* This may be set to -1, in which case aniso34 will be ignored.
* @param particle4 the index within the System of the fourth particle used for defining anisotropic polarizability.
* @param[out] particle4 the index within the System of the fourth particle used for defining anisotropic polarizability.
* This may be set to -1, in which case aniso34 will be ignored.
* @param charge The charge on the Drude particle
* @param polarizability The isotropic polarizability
* @param aniso12 The scale factor for the polarizability along the direction defined by particle1 and particle2
* @param aniso34 The scale factor for the polarizability along the direction defined by particle3 and particle4
* @param[out] charge The charge on the Drude particle
* @param[out] polarizability The isotropic polarizability
* @param[out] aniso12 The scale factor for the polarizability along the direction defined by particle1 and particle2
* @param[out] aniso34 The scale factor for the polarizability along the direction defined by particle3 and particle4
*/
void getParticleParameters(int index, int& particle, int& particle1, int& particle2, int& particle3, int& particle4, double& charge, double& polarizability, double& aniso12, double& aniso34) const;
/**
......@@ -137,9 +137,9 @@ public:
* Get the force field parameters for screened pair.
*
* @param index the index of the pair for which to get parameters
* @param particle1 the index within this Force of the first particle involved in the interaction
* @param particle2 the index within this Force of the second particle involved in the interaction
* @param thole the Thole screening factor
* @param[out] particle1 the index within this Force of the first particle involved in the interaction
* @param[out] particle2 the index within this Force of the second particle involved in the interaction
* @param[out] thole the Thole screening factor
*/
void getScreenedPairParameters(int index, int& particle1, int& particle2, double& thole) const;
/**
......
serialization/include/openmm/serialization/SerializationNode.h
View file @ a1953312
......@@ -105,7 +105,7 @@ public:
/**
* Determine whether this node has a property with a particular node.
*
* @param the name of the property to check for
* @param name the name of the property to check for
*/
bool hasProperty(const std::string& name) const;
/**
......
wrappers/python/filterPythonFiles.py
View file @ a1953312
from __future__ import print_function
import re
import sys
import textwrap
from inspect import cleandoc
from numpydoc.docscrape import NumpyDocString
# Doxygen does a bad job of generating documentation based on docstrings. This script is run as a filter
# on each file, and converts the docstrings into Doxygen style comments so we get better documentation.
# Doxygen does a bad job of generating documentation based on docstrings.
# This script is run as a filter
# on each file, and converts the docstrings into Doxygen style comments
# so we get better documentation.
input = open(sys.argv[1])
while True:
line = input.readline()
if len(line) == 0:
......@@ -15,10 +24,10 @@ while True:
split = stripped.split()
if split[0] == 'class' and split[1][0].islower():
# Classes that start with a lowercase letter were defined by SWIG. We want to hide them.
print("%s## @private" % prefix)
print("%s## @private" % prefix, end='')
if split[1][0] == '_' and split[1][1] != '_':
# Names starting with a single _ are assumed to be private.
print("%s## @private" % prefix)
print("%s## @private" % prefix, end='')
# We're at the start of a class or function definition. Find all lines that contain the declaration.
......@@ -28,33 +37,44 @@ while True:
declaration += line
# Now look for a docstring.
docstrings = []
docstringlines = []
line = input.readline()
stripped = line.lstrip()
if stripped.startswith('"""'):
line = stripped[3:]
readingParameters = False
while line.find('"""') == -1:
docstrings.append(line)
l = line.strip()
if l.startswith('"""') or l.startswith("'''"):
if l.count('"""') == 2 or l.count("'''") == 2:
docstringlines.append(l[3:-3])
else:
docstringlines.append(l[3:])
line = input.readline()
if line.strip() == 'Parameters:':
readingParameters = True
l = line.strip()
while l.find('"""') == -1 and l.find("'''") == -1:
docstringlines.append(line.rstrip())
line = input.readline()
stripped = line.lstrip()
if readingParameters and stripped.startswith('- '):
line = "@param %s" % stripped[2:]
elif stripped.startswith('Returns:'):
line = "@return %s" % stripped[8:]
line = line[:line.find('"""')]
docstrings.append(line)
l = line.strip()
if line.rstrip().endswith('"""') or line.rstrip().endswith("'''"):
# last line
docstringlines.append(line.rstrip()[:-3])
docstring = NumpyDocString(cleandoc('\n'.join(docstringlines)))
# print(docstringlines)
# Print out the docstring in Doxygen syntax, followed by the declaration.
for line in docstring['Summary']:
print('{prefix}## {line}'.format(prefix=prefix, line=line))
if len(docstring['Extended Summary']) > 0:
print('{prefix}##'.format(prefix=prefix))
for line in docstring['Extended Summary']:
print('{prefix}## {line}'.format(prefix=prefix, line=line.strip()))
print('{prefix}##'.format(prefix=prefix))
for name, type, descr in docstring['Parameters']:
print('{prefix}## @param {name} ({type}) {descr}'.format(prefix=prefix, type=type, name=name, descr=' '.join(descr)))
for name, type, descr in docstring['Returns']:
if type == '':
type = name
print('{prefix}## @return ({type}) {descr}'.format(prefix=prefix, type=type, name=name, descr=' '.join(descr)))
for s in docstrings:
print("%s##%s" % (prefix, s.strip()))
print(declaration)
if len(docstrings) == 0:
print(line)
print(declaration, end='')
if len(docstringlines) == 0:
print(line, end='')
else:
print(line)
\ No newline at end of file
print(line, end='')
wrappers/python/simtk/openmm/amd.py
View file @ a1953312
......@@ -49,10 +49,14 @@ class AMDIntegrator(CustomIntegrator):
def __init__(self, dt, alpha, E):
"""Create an AMDIntegrator.
Parameters:
- dt (time) The integration time step to use
- alpha (energy) The alpha parameter to use
- E (energy) The energy cutoff to use
Parameters
----------
dt : time
The integration time step to use
alpha : energy
The alpha parameter to use
E : energy
The energy cutoff to use
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alpha", alpha)
......@@ -104,11 +108,16 @@ class AMDForceGroupIntegrator(CustomIntegrator):
def __init__(self, dt, group, alphaGroup, EGroup):
"""Create a AMDForceGroupIntegrator.
Parameters:
- dt (time) The integration time step to use
- group (int) The force group to apply the boost to
- alphaGroup (energy) The alpha parameter to use for the boosted force group
- EGroup (energy) The energy cutoff to use for the boosted force group
Parameters
----------
dt : time
The integration time step to use
group : int
The force group to apply the boost to
alphaGroup : energy
The alpha parameter to use for the boosted force group
EGroup : energy
The energy cutoff to use for the boosted force group
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaGroup", alphaGroup)
......@@ -144,9 +153,14 @@ class AMDForceGroupIntegrator(CustomIntegrator):
def getEffectiveEnergy(self, groupEnergy):
"""Given the actual group energy of the system, return the value of the effective potential.
Parameters:
- groupEnergy (energy): the actual potential energy of the boosted force group
Returns: the value of the effective potential
Parameters
----------
groupEnergy : energy
the actual potential energy of the boosted force group
Returns
-------
the value of the effective potential
"""
alphaGroup = self.getAlphaGroup()
EGroup = self.getEGroup()
......@@ -172,13 +186,20 @@ class DualAMDIntegrator(CustomIntegrator):
def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup):
"""Create a DualAMDIntegrator.
Parameters:
- dt (time) The integration time step to use
- group (int) The force group to apply the second boost to
- alphaTotal (energy) The alpha parameter to use for the total energy
- ETotal (energy) The energy cutoff to use for the total energy
- alphaGroup (energy) The alpha parameter to use for the boosted force group
- EGroup (energy) The energy cutoff to use for the boosted force group
Parameters
----------
dt : time
The integration time step to use
group : int
The force group to apply the second boost to
alphaTotal : energy
The alpha parameter to use for the total energy
ETotal : energy
The energy cutoff to use for the total energy
alphaGroup : energy
The alpha parameter to use for the boosted force group
EGroup : energy
The energy cutoff to use for the boosted force group
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaTotal", alphaTotal)
......@@ -237,10 +258,16 @@ class DualAMDIntegrator(CustomIntegrator):
def getEffectiveEnergy(self, totalEnergy, groupEnergy):
"""Given the actual potential energy of the system, return the value of the effective potential.
Parameters:
- totalEnergy (energy): the actual potential energy of the whole system
- groupEnergy (energy): the actual potential energy of the boosted force group
Returns: the value of the effective potential
Parameters
----------
totalEnergy : energy
the actual potential energy of the whole system
groupEnergy : energy
the actual potential energy of the boosted force group
Returns
-------
the value of the effective potential
"""
alphaTotal = self.getAlphaTotal()
ETotal = self.getETotal()
......
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
View file @ a1953312
......@@ -60,12 +60,17 @@ class AmberInpcrdFile(object):
def __init__(self, file, loadVelocities=None, loadBoxVectors=None):
"""Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
Parameters:
- file (string) the name of the file to load
- loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present
- loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present
An inpcrd file contains atom positions and, optionally, velocities and
periodic box dimensions.
Parameters
----------
file : str
The name of the file to load
loadVelocities : bool
Deprecated. Velocities are loaded automatically if present
loadBoxVectors : bool
Deprecated. Box vectors are loaded automatically if present
"""
self.file = file
if loadVelocities is not None or loadBoxVectors is not None:
......@@ -84,8 +89,11 @@ class AmberInpcrdFile(object):
def getPositions(self, asNumpy=False):
"""Get the atomic positions.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
Parameters
----------
asNumpy : bool=False
if true, the values are returned as a numpy array instead of a list
of Vec3s
"""
if asNumpy:
if self._numpyPositions is None:
......@@ -97,8 +105,10 @@ class AmberInpcrdFile(object):
def getVelocities(self, asNumpy=False):
"""Get the atomic velocities.
Parameters:
- asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s
Parameters
----------
asNumpy : bool=False
if true, the vectors are returned as numpy arrays instead of Vec3s
"""
if self.velocities is None:
raise AttributeError('velocities not found in %s' % self.file)
......@@ -112,8 +122,11 @@ class AmberInpcrdFile(object):
def getBoxVectors(self, asNumpy=False):
"""Get the periodic box vectors.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
Parameters
----------
asNumpy : bool=False
if true, the values are returned as a numpy array instead of a list
of Vec3s
"""
if self.boxVectors is None:
raise AttributeError('Box information not found in %s' % self.file)
......
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ a1953312
......@@ -151,29 +151,52 @@ class AmberPrmtopFile(object):
implicitSolventKappa=None, temperature=298.15*unit.kelvin,
soluteDielectric=1.0, solventDielectric=78.5,
removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005):
"""Construct an OpenMM System representing the topology described by this prmtop file.
"""Construct an OpenMM System representing the topology described by this
prmtop file.
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are
Parameters
----------
nonbondedMethod : object=NoCutoff
The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
- constraints (object=None) Specifies which bonds angles should be implemented with constraints.
nonbondedCutoff : distance=1*nanometer
The cutoff distance to use for nonbonded interactions
constraints : object=None
Specifies which bonds angles should be implemented with constraints.
Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
- implicitSolventSaltConc (float=0.0*unit.moles/unit.liter) The salt concentration for GB
calculations (modelled as a debye screening parameter). It is converted to the debye length (kappa)
rigidWater : boolean=True
If true, water molecules will be fully rigid regardless of the value
passed for the constraints argument
implicitSolvent : object=None
If not None, the implicit solvent model to use. Allowed values are
HCT, OBC1, OBC2, GBn, or GBn2.
implicitSolventSaltConc : float=0.0*unit.moles/unit.liter
The salt concentration for GB calculations (modelled as a debye
screening parameter). It is converted to the debye length (kappa)
using the provided temperature and solventDielectric
- temperature (float=300*kelvin) Temperature of the system. Only used to compute the Debye length from
implicitSolventSoltConc
- implicitSolventKappa (float units of 1/length) If this value is set, implicitSolventSaltConc will be ignored.
- soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
- solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
- hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is
subtracted from the heavy atom to keep their total mass the same.
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
Returns: the newly created System
temperature : float=300*kelvin
Temperature of the system. Only used to compute the Debye length
from implicitSolventSoltConc
implicitSolventKappa : float units of 1/length
If this value is set, implicitSolventSaltConc will be ignored.
soluteDielectric : float=1.0
The solute dielectric constant to use in the implicit solvent model.
solventDielectric : float=78.5
The solvent dielectric constant to use in the implicit solvent
model.
removeCMMotion : boolean=True
If true, a CMMotionRemover will be added to the System
hydrogenMass : mass=None
The mass to use for hydrogen atoms bound to heavy atoms. Any mass
added to a hydrogen is subtracted from the heavy atom to keep their
total mass the same.
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald or PME.
Returns
-------
System
the newly created System
"""
if self._prmtop.chamber:
raise ValueError("CHAMBER-style topology file detected. CHAMBER "
......
wrappers/python/simtk/openmm/app/charmmcrdfiles.py
View file @ a1953312
......@@ -49,12 +49,17 @@ class CharmmCrdFile(object):
Reads and parses a CHARMM coordinate file (.crd) into its components,
namely the coordinates, CHARMM atom types, resid, resname, etc.
Main attributes:
- natom (int) : Number of atoms in the system
- resname (list) : Names of all residues
- positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...]
Example:
Attributes
----------
natom : int
Number of atoms in the system
resname : list
Names of all residues
positions : list
All cartesian coordinates [x1, y1, z1, x2, ...]
Examples
--------
>>> chm = CharmmCrdFile('testfiles/1tnm.crd')
>>> print '%d atoms; %d coords' % (chm.natom, len(chm.positions))
1414 atoms; 1414 coords
......@@ -131,14 +136,21 @@ class CharmmRstFile(object):
Reads and parses data, velocities and coordinates from a CHARMM restart
file (.rst) of file name 'fname' into class attributes
Main attributes:
- natom (int) : Number of atoms in the system
- resname (list) : Names of all residues
- positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...]
- positionsold (list) : Old cartesian coordinates
- velocities (list) : List of all cartesian velocities
Example:
Attributes
----------
natom : int
Number of atoms in the system
resname : list
Names of all residues
positions : list
All cartesian coordinates [x1, y1, z1, x2, ...]
positionsold : list
Old cartesian coordinates
velocities : list
List of all cartesian velocities
Examples
--------
>>> chm = CharmmRstFile('testfiles/sample-charmm.rst')
>>> print chm.header[0]
REST 37 1
......
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ a1953312
......@@ -51,18 +51,19 @@ class CharmmParameterSet(object):
the information found in the MASS section of the CHARMM topology file
(TOP/RTF) and all of the information in the parameter files (PAR)
Parameters:
- filenames : List of topology, parameter, and stream files to load into
the parameter set. The following file type suffixes are recognized.
Unrecognized file types raise a TypeError
.rtf, .top -- Residue topology file
.par, .prm -- Parameter file
.str -- Stream file
.inp -- If "par" is in the file name, it is a parameter file. If
Parameters
----------
filenames : List of topology, parameter, and stream files to load into the parameter set.
The following file type suffixes are recognized. Unrecognized file types raise a TypeError
* .rtf, .top -- Residue topology file
* .par, .prm -- Parameter file
* .str -- Stream file
* .inp -- If "par" is in the file name, it is a parameter file. If
"top" is in the file name, it is a topology file. Otherwise,
raise TypeError
Attributes:
Attributes
----------
All type lists are dictionaries whose keys are tuples (with however
many elements are needed to define that type of parameter). The types
that can be in any order are SORTED.
......@@ -85,7 +86,8 @@ class CharmmParameterSet(object):
when only the integer or string is available the other dictionaries are
helpful
Example:
Examples
--------
>>> params = CharmmParameterSet('charmm22.top', 'charmm22.par', 'file.str')
"""
......@@ -150,18 +152,25 @@ class CharmmParameterSet(object):
Instantiates a CharmmParameterSet from a Topology file and a Parameter
file (or just a Parameter file if it has all information)
Parameters:
- tfile (str) : Name of the Topology (RTF/TOP) file
- pfile (str) : Name of the Parameter (PAR) file
- sfiles (list of str) : List or tuple of stream (STR) file names.
- permissive (bool) : Accept non-bonbded parameters for undefined
atom types (default False)
Returns:
Parameters
-----------
tfile : str
Name of the Topology (RTF/TOP) file
pfile : str
Name of the Parameter (PAR) file
sfiles : list of str
List or tuple of stream (STR) file names.
permissive : bool=False
Accept non-bonbded parameters for undefined atom types
Returns
-------
CharmmParameterSet
New CharmmParameterSet populated with the parameters found in the
provided files.
Notes:
Notes
-----
The RTF file is read first (if provided), followed by the PAR file,
followed by the list of stream files (in the order they are
provided). Parameters in each stream file will overwrite those that
......@@ -183,21 +192,24 @@ class CharmmParameterSet(object):
return inst
def readParameterFile(self, pfile, permissive=False):
"""
Reads all of the parameters from a parameter file. Versions 36 and
later of the CHARMM force field files have an ATOMS section defining
all of the atom types. Older versions need to load this information
from the RTF/TOP files.
Parameters:
- pfile (str) : Name of the CHARMM PARameter file to read
- permissive (bool) : Accept non-bonbded parameters for undefined
atom types (default False)
Notes: The atom types must all be loaded by the end of this routine.
Either supply a PAR file with atom definitions in them or read in a
RTF/TOP file first. Failure to do so will result in a raised
RuntimeError.
"""Reads all of the parameters from a parameter file. Versions 36 and later
of the CHARMM force field files have an ATOMS section defining all of
the atom types. Older versions need to load this information from the
RTF/TOP files.
Parameters
----------
pfile : str
Name of the CHARMM PARameter file to read
permissive : bool
Accept non-bonbded parameters for undefined atom types (default:
False).
Notes
-----
The atom types must all be loaded by the end of this routine. Either
supply a PAR file with atom definitions in them or read in a RTF/TOP
file first. Failure to do so will result in a raised RuntimeError.
"""
conv = CharmmParameterSet._convert
if isinstance(pfile, str):
......@@ -518,14 +530,17 @@ class CharmmParameterSet(object):
if own_handle: f.close()
def readTopologyFile(self, tfile):
"""
Reads _only_ the atom type definitions from a topology file. This is
"""Reads _only_ the atom type definitions from a topology file. This is
unnecessary for versions 36 and later of the CHARMM force field.
Parameters:
- tfile (str) : Name of the CHARMM TOPology file to read
Parameters
----------
tfile : str
: Name of the CHARMM TOPology file to read
Note: The CHARMM TOPology file is also called a Residue Topology File
Notes
-----
The CHARMM TOPology file is also called a Residue Topology File
"""
conv = CharmmParameterSet._convert
if isinstance(tfile, str):
......@@ -564,12 +579,13 @@ class CharmmParameterSet(object):
if own_handle: f.close()
def readStreamFile(self, sfile):
"""
Reads RTF and PAR sections from a stream file and dispatches the
"""Reads RTF and PAR sections from a stream file and dispatches the
sections to readTopologyFile or readParameterFile
Parameters:
- sfile (str or CharmmStreamFile) : Stream file to parse
Parameters
----------
sfile : str or CharmmStreamFile
Stream file to parse
"""
if isinstance(sfile, CharmmStreamFile):
f = sfile
......@@ -594,14 +610,8 @@ class CharmmParameterSet(object):
bond, angle, dihedral, improper, or cmap type will pair with EVERY key
in the type mapping dictionaries that points to the equivalent type
Returns:
- Returns the instance that is being condensed.
Notes:
The return value allows you to condense the types at construction
time.
Example:
Example
-------
>>> params = CharmmParameterSet('charmm.prm').condense()
"""
# First scan through all of the bond types
......@@ -631,8 +641,10 @@ class CharmmParameterSet(object):
"""
Loops through the given dict and condenses all types.
Parameter:
- typedict : Type dictionary to condense
Parameters
----------
typedict
Type dictionary to condense
"""
keylist = list(typedict.keys())
for i in range(len(keylist) - 1):
......
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