def test_9():
node = ET.fromstring('''
<detaileddescription>
<para>Get the force field parameters for an angle term.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>index</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the angle for which to get parameters </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="out">particle1</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the first particle forming the angle </para></parameterdescription>
</parameteritem>
</parameterlist>
</para>
</detaileddescription>''')
expected = '''
Get the force field parameters for an angle term.
:parameters:
* **index** -- the index of the angle for which to get parameters
* **particle1** -- [out] the index of the first particle forming the angle
'''
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_1():
node = ET.fromstring("""<detaileddescription>
<para>Get a reference to a tabulated function that may appear in the energy expression.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>index</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the function to get </para></parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>the <ref refid="classOpenMM_1_1TabulatedFunction" kindref="compound">TabulatedFunction</ref> object defining the function </para></simplesect>
</para> </detaileddescription>
""")
expected = """
Get a reference to a tabulated function that may appear in the energy expression.
:parameters:
* **index** -- the index of the function to get
:returns: the :cpp:any:`TabulatedFunction` object defining the function
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_9():
node = ET.fromstring('''
<detaileddescription>
<para>Get the force field parameters for an angle term.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>index</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the angle for which to get parameters </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="out">particle1</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the first particle forming the angle </para></parameterdescription>
</parameteritem>
</parameterlist>
</para>
</detaileddescription>''')
expected = '''
Get the force field parameters for an angle term.
:parameters:
* **index** -- the index of the angle for which to get parameters
* **particle1** -- [out] the index of the first particle forming the angle
'''
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_1():
node = ET.fromstring("""<detaileddescription>
<para>Get a reference to a tabulated function that may appear in the energy expression.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>index</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the function to get </para></parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>the <ref refid="classOpenMM_1_1TabulatedFunction" kindref="compound">TabulatedFunction</ref> object defining the function </para></simplesect>
</para> </detaileddescription>
""")
expected = """
Get a reference to a tabulated function that may appear in the energy expression.
:parameters:
* **index** -- the index of the function to get
:returns: the :cpp:any:`TabulatedFunction` object defining the function
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_7():
node = ET.fromstring('''<detaileddescription>
<para>Add an angle term to the force field.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>particle1</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the first particle connected by the angle </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>particle2</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the second particle connected by the angle </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>particle3</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the third particle connected by the angle </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>length</parametername>
</parameternamelist>
<parameterdescription>
<para>the equilibrium angle, measured in degrees </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>quadraticK</parametername>
</parameternamelist>
<parameterdescription>
<para>the quadratic force constant for the angle, measured in kJ/mol/radian^2 </para></parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>the index of the angle that was added </para></simplesect>
</para> </detaileddescription>''')
expected = """
Add an angle term to the force field.
:parameters:
* **particle1** -- the index of the first particle connected by the angle
* **particle2** -- the index of the second particle connected by the angle
* **particle3** -- the index of the third particle connected by the angle
* **length** -- the equilibrium angle, measured in degrees
* **quadraticK** -- the quadratic force constant for the angle, measured in kJ/mol/radian^2
:returns: the index of the angle that was added
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_7():
node = ET.fromstring('''<detaileddescription>
<para>Add an angle term to the force field.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>particle1</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the first particle connected by the angle </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>particle2</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the second particle connected by the angle </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>particle3</parametername>
</parameternamelist>
<parameterdescription>
<para>the index of the third particle connected by the angle </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>length</parametername>
</parameternamelist>
<parameterdescription>
<para>the equilibrium angle, measured in degrees </para></parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>quadraticK</parametername>
</parameternamelist>
<parameterdescription>
<para>the quadratic force constant for the angle, measured in kJ/mol/radian^2 </para></parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>the index of the angle that was added </para></simplesect>
</para> </detaileddescription>''')
expected = """
Add an angle term to the force field.
:parameters:
* **particle1** -- the index of the first particle connected by the angle
* **particle2** -- the index of the second particle connected by the angle
* **particle3** -- the index of the third particle connected by the angle
* **length** -- the equilibrium angle, measured in degrees
* **quadraticK** -- the quadratic force constant for the angle, measured in kJ/mol/radian^2
:returns: the index of the angle that was added
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_8():
node = ET.fromstring('''<detaileddescription>
<para>This is a <ref refid="classOpenMM_1_1VirtualSite" kindref="compound">VirtualSite</ref> that computes the particle location based on three other particles' locations. If r<subscript>1</subscript> is the location of particle 1, r<subscript>12</subscript> is the vector from particle 1 to particle 2, and r<subscript>13</subscript> is the vector from particle 1 to particle 3, then the virtual site location is given by</para><para>r<subscript>1</subscript> + w<subscript>12</subscript>r<subscript>12</subscript> + w<subscript>13</subscript>r<subscript>13</subscript> + w<subscript>cross</subscript>(r<subscript>12</subscript> x r<subscript>13</subscript>)</para><para>The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles. </para> </detaileddescription>''')
expected = '''
This is a :cpp:any:`VirtualSite` that computes the particle location based on three other particles' locations. If r\ :sub:`1` is the location of particle 1, r\ :sub:`12` is the vector from particle 1 to particle 2, and r\ :sub:`13` is the vector from particle 1 to particle 3, then the virtual site location is given by
r\ :sub:`1` + w\ :sub:`12` r\ :sub:`12` + w\ :sub:`13` r\ :sub:`13` + w\ :sub:`cross` (r\ :sub:`12` x r\ :sub:`13` )
The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles.
'''
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_5():
node = ET.fromstring("""<detaileddescription>
<para>Add a tabulated function that may appear in the energy expression.</para><para><xrefsect id="deprecated_1_deprecated000015"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This method exists only for backward compatibility. Use <ref refid="classOpenMM_1_1CustomNonbondedForce_1ac7c24d607916cca0d0980956de03cd15" kindref="member">addTabulatedFunction()</ref> instead. </para></xrefdescription></xrefsect></para> </detaileddescription>""")
expected = """
Add a tabulated function that may appear in the energy expression.
.. admonition:: Deprecated
This method exists only for backward compatibility. Use :cpp:any:`addTabulatedFunction()` instead.
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_4():
node = ET.fromstring("""<detaileddescription>
<para>As an example, the following code creates a <ref refid="classOpenMM_1_1CustomNonbondedForce" kindref="compound">CustomNonbondedForce</ref> that implements a 12-6 Lennard-Jones potential:</para><para><computeroutput>CustomNonbondedForce* force = new <ref refid="classOpenMM_1_1CustomNonbondedForce" kindref="compound">CustomNonbondedForce</ref>("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");</computeroutput></para>
</detaileddescription>""")
expected = '''
As an example, the following code creates a :cpp:any:`CustomNonbondedForce` that implements a 12-6 Lennard-Jones potential:
.. code-block:: C++
CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");
'''
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_2():
node = ET.fromstring(
"""<detaileddescription><para><computeroutput><preformatted>
<ref refid="classOpenMM_1_1CustomIntegrator" kindref="compound">CustomIntegrator</ref> integrator(0.001);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
</preformatted></computeroutput></para><para>The first step updates the velocities based on the current forces. The second step updates the positions based on the new velocities, and the third step updates the velocities again. Although the first and third steps look identical, the forces used in them are different. You do not need to tell the integrator that; it will recognize that the positions have changed and know to recompute the forces automatically.</para><para>The above example has two problems. First, it does not respect distance constraints. To make the integrator work with constraints, you need to add extra steps to tell it when and how to apply them. Second, it never gives Forces an opportunity to update the context state. This should be done every time step so that, for example, an <ref refid="classOpenMM_1_1AndersenThermostat" kindref="compound">AndersenThermostat</ref> can randomize velocities or a <ref refid="classOpenMM_1_1MonteCarloBarostat" kindref="compound">MonteCarloBarostat</ref> can scale particle positions. You need to add a step to tell the integrator when to do this. The following example corrects both these problems, using the RATTLE algorithm to apply constraints:</para><para><computeroutput><preformatted>
<ref refid="classOpenMM_1_1CustomIntegrator" kindref="compound">CustomIntegrator</ref> integrator(0.001);
integrator.addPerDofVariable("x1", 0);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();
</preformatted></computeroutput></para></detaileddescription>""")
#print(node)
#print(format_xml_paragraph((node)))
#print()
expected = """
.. code-block:: C++
CustomIntegrator integrator(0.001);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
The first step updates the velocities based on the current forces. The second step updates the positions based on the new velocities, and the third step updates the velocities again. Although the first and third steps look identical, the forces used in them are different. You do not need to tell the integrator that; it will recognize that the positions have changed and know to recompute the forces automatically.
The above example has two problems. First, it does not respect distance constraints. To make the integrator work with constraints, you need to add extra steps to tell it when and how to apply them. Second, it never gives Forces an opportunity to update the context state. This should be done every time step so that, for example, an :cpp:any:`AndersenThermostat` can randomize velocities or a :cpp:any:`MonteCarloBarostat` can scale particle positions. You need to add a step to tell the integrator when to do this. The following example corrects both these problems, using the RATTLE algorithm to apply constraints:
.. code-block:: C++
CustomIntegrator integrator(0.001);
integrator.addPerDofVariable("x1", 0);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_8():
node = ET.fromstring('''<detaileddescription>
<para>This is a <ref refid="classOpenMM_1_1VirtualSite" kindref="compound">VirtualSite</ref> that computes the particle location based on three other particles' locations. If r<subscript>1</subscript> is the location of particle 1, r<subscript>12</subscript> is the vector from particle 1 to particle 2, and r<subscript>13</subscript> is the vector from particle 1 to particle 3, then the virtual site location is given by</para><para>r<subscript>1</subscript> + w<subscript>12</subscript>r<subscript>12</subscript> + w<subscript>13</subscript>r<subscript>13</subscript> + w<subscript>cross</subscript>(r<subscript>12</subscript> x r<subscript>13</subscript>)</para><para>The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles. </para> </detaileddescription>'''
)
expected = '''
This is a :cpp:any:`VirtualSite` that computes the particle location based on three other particles' locations. If r\ :sub:`1` is the location of particle 1, r\ :sub:`12` is the vector from particle 1 to particle 2, and r\ :sub:`13` is the vector from particle 1 to particle 3, then the virtual site location is given by
r\ :sub:`1` + w\ :sub:`12` r\ :sub:`12` + w\ :sub:`13` r\ :sub:`13` + w\ :sub:`cross` (r\ :sub:`12` x r\ :sub:`13` )
The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles.
'''
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_4():
node = ET.fromstring("""<detaileddescription>
<para>As an example, the following code creates a <ref refid="classOpenMM_1_1CustomNonbondedForce" kindref="compound">CustomNonbondedForce</ref> that implements a 12-6 Lennard-Jones potential:</para><para><computeroutput>CustomNonbondedForce* force = new <ref refid="classOpenMM_1_1CustomNonbondedForce" kindref="compound">CustomNonbondedForce</ref>("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");</computeroutput></para>
</detaileddescription>""")
expected = '''
As an example, the following code creates a :cpp:any:`CustomNonbondedForce` that implements a 12-6 Lennard-Jones potential:
.. code-block:: C++
CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");
'''
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_5():
node = ET.fromstring("""<detaileddescription>
<para>Add a tabulated function that may appear in the energy expression.</para><para><xrefsect id="deprecated_1_deprecated000015"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This method exists only for backward compatibility. Use <ref refid="classOpenMM_1_1CustomNonbondedForce_1ac7c24d607916cca0d0980956de03cd15" kindref="member">addTabulatedFunction()</ref> instead. </para></xrefdescription></xrefsect></para> </detaileddescription>"""
)
expected = """
Add a tabulated function that may appear in the energy expression.
.. admonition:: Deprecated
This method exists only for backward compatibility. Use :cpp:any:`addTabulatedFunction()` instead.
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_2():
node = ET.fromstring("""<detaileddescription><para><computeroutput><preformatted>
<ref refid="classOpenMM_1_1CustomIntegrator" kindref="compound">CustomIntegrator</ref> integrator(0.001);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
</preformatted></computeroutput></para><para>The first step updates the velocities based on the current forces. The second step updates the positions based on the new velocities, and the third step updates the velocities again. Although the first and third steps look identical, the forces used in them are different. You do not need to tell the integrator that; it will recognize that the positions have changed and know to recompute the forces automatically.</para><para>The above example has two problems. First, it does not respect distance constraints. To make the integrator work with constraints, you need to add extra steps to tell it when and how to apply them. Second, it never gives Forces an opportunity to update the context state. This should be done every time step so that, for example, an <ref refid="classOpenMM_1_1AndersenThermostat" kindref="compound">AndersenThermostat</ref> can randomize velocities or a <ref refid="classOpenMM_1_1MonteCarloBarostat" kindref="compound">MonteCarloBarostat</ref> can scale particle positions. You need to add a step to tell the integrator when to do this. The following example corrects both these problems, using the RATTLE algorithm to apply constraints:</para><para><computeroutput><preformatted>
<ref refid="classOpenMM_1_1CustomIntegrator" kindref="compound">CustomIntegrator</ref> integrator(0.001);
integrator.addPerDofVariable("x1", 0);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();
</preformatted></computeroutput></para></detaileddescription>""")
#print(node)
#print(format_xml_paragraph((node)))
#print()
expected = """
.. code-block:: C++
CustomIntegrator integrator(0.001);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
The first step updates the velocities based on the current forces. The second step updates the positions based on the new velocities, and the third step updates the velocities again. Although the first and third steps look identical, the forces used in them are different. You do not need to tell the integrator that; it will recognize that the positions have changed and know to recompute the forces automatically.
The above example has two problems. First, it does not respect distance constraints. To make the integrator work with constraints, you need to add extra steps to tell it when and how to apply them. Second, it never gives Forces an opportunity to update the context state. This should be done every time step so that, for example, an :cpp:any:`AndersenThermostat` can randomize velocities or a :cpp:any:`MonteCarloBarostat` can scale particle positions. You need to add a step to tell the integrator when to do this. The following example corrects both these problems, using the RATTLE algorithm to apply constraints:
.. code-block:: C++
CustomIntegrator integrator(0.001);
integrator.addPerDofVariable("x1", 0);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_6():
node = ET.fromstring('''<detaileddescription>
<para>Set the force group this <ref refid="classOpenMM_1_1Force" kindref="compound">Force</ref> belongs to.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>group</parametername>
</parameternamelist>
<parameterdescription>
<para>the group index. Legal values are between 0 and 31 (inclusive). </para></parameterdescription>
</parameteritem>
</parameterlist>
</para> </detaileddescription>''')
expected = """
Set the force group this :cpp:any:`Force` belongs to.
:parameters:
* **group** -- the group index. Legal values are between 0 and 31 (inclusive).
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_6():
node = ET.fromstring('''<detaileddescription>
<para>Set the force group this <ref refid="classOpenMM_1_1Force" kindref="compound">Force</ref> belongs to.</para><para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>group</parametername>
</parameternamelist>
<parameterdescription>
<para>the group index. Legal values are between 0 and 31 (inclusive). </para></parameterdescription>
</parameteritem>
</parameterlist>
</para> </detaileddescription>''')
expected = """
Set the force group this :cpp:any:`Force` belongs to.
:parameters:
* **group** -- the group index. Legal values are between 0 and 31 (inclusive).
"""
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_3():
node = ET.fromstring("""
<type><ref refid="classOpenMM_1_1CustomHbondForce_1afefd9143292586209274d8e355d8cba1" kindref="member">NonbondedMethod</ref></type>""")
expected = ':cpp:any:`NonbondedMethod`'
assert '\n'.join(format_xml_paragraph(node)) == expected
def test_3():
node = ET.fromstring("""
<type><ref refid="classOpenMM_1_1CustomHbondForce_1afefd9143292586209274d8e355d8cba1" kindref="member">NonbondedMethod</ref></type>"""
)
expected = ':cpp:any:`NonbondedMethod`'
assert '\n'.join(format_xml_paragraph(node)) == expected
