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Commit 6391f721 authored by Peter Eastman's avatar Peter Eastman
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Residue templates can specify atoms by name instead of index

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docs-source/usersguide/application.rst
View file @ 6391f721
......@@ -1889,12 +1889,12 @@ The residue template definitions look like this:
<Atom name="HH33" type="710"/>
<Atom name="C" type="712"/>
<Atom name="O" type="713"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="3"/>
<Bond from="1" to="4"/>
<Bond from="4" to="5"/>
<ExternalBond from="4"/>
<Bond atomName1="HH31" atomName2="CH3"/>
<Bond atomName1="CH3" atomName2="HH32"/>
<Bond atomName1="CH3" atomName2="HH33"/>
<Bond atomName1="CH3" atomName2="C"/>
<Bond atomName1="C" atomName2="O"/>
<ExternalBond atomName="C"/>
</Residue>
<Residue name="ALA">
...
......@@ -1908,10 +1908,12 @@ contains the following tags:
* An :code:`<Atom>` tag for each atom in the residue. This specifies the
name of the atom and its atom type.
* A :code:`<Bond>` tag for each pair of atoms that are bonded to each
other. The :code:`to` and :code:`from` attributes are the indices of
the two bonded atoms (starting from 0) in the order they were listed. For
example, :code:`<Bond from="1" to="3"/>` describes a bond between atom CH3
and atom HH33.
other. The :code:`atomName1` and :code:`atomName2` attributes are the names
of the two bonded atoms. (Some older force fields use the alternate tags
:code:`to` and :code:`from` to specify the atoms by index instead of name.
This is still supported for backward compatibility, but specifying atoms by
name is recommended, since it makes the residue definition much easier to
understand.)
* An :code:`<ExternalBond>` tag for each atom that will be bonded to an
atom of a different residue.
......@@ -1926,20 +1928,20 @@ as in the following example:
<Atom name="H1" type="tip4pew-H"/>
<Atom name="H2" type="tip4pew-H"/>
<Atom name="M" type="tip4pew-M"/>
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2"
<VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2"
weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
Each :code:`<VirtualSite>` tag indicates an atom in the residue that should
be represented with a virtual site. The :code:`type` attribute may equal
:code:`"average2"`\ , :code:`"average3"`\ , :code:`"outOfPlane"`\ , or
:code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite,
OutOfPlaneSite, and LocalCoordinatesSite classes respectively. The :code:`index` attribute gives the
index (starting from 0) of the atom to represent with a virtual site. The atoms
it is calculated based on are specified by :code:`atom1`\ , :code:`atom2`\ ,
and (for virtual site classes that involve three atoms) :code:`atom3`\ . The
OutOfPlaneSite, and LocalCoordinatesSite classes respectively. The :code:`siteName`
attribute gives the name of the atom to represent with a virtual site. The atoms
it is calculated based on are specified by :code:`atomName1`\ , :code:`atomName2`\ ,
and (for virtual site classes that involve three atoms) :code:`atomName3`\ . The
remaining attributes are specific to the virtual site class, and specify the
parameters for calculating the site position. For a TwoParticleAverageSite,
they are :code:`weight1` and :code:`weight2`\ . For a
......
wrappers/python/simtk/openmm/app/data/spce.xml
View file @ 6391f721
......@@ -8,8 +8,8 @@
<Atom name="O" type="spce-O"/>
<Atom name="H1" type="spce-H"/>
<Atom name="H2" type="spce-H"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
......
wrappers/python/simtk/openmm/app/data/tip3p.xml
View file @ 6391f721
......@@ -8,8 +8,8 @@
<Atom name="O" type="tip3p-O"/>
<Atom name="H1" type="tip3p-H"/>
<Atom name="H2" type="tip3p-H"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
......
wrappers/python/simtk/openmm/app/data/tip4pew.xml
View file @ 6391f721
......@@ -10,9 +10,9 @@
<Atom name="H1" type="tip4pew-H"/>
<Atom name="H2" type="tip4pew-H"/>
<Atom name="M" type="tip4pew-M"/>
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2" weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
......
wrappers/python/simtk/openmm/app/data/tip5p.xml
View file @ 6391f721
......@@ -11,10 +11,10 @@
<Atom name="H2" type="tip5p-H"/>
<Atom name="M1" type="tip5p-M"/>
<Atom name="M2" type="tip5p-M"/>
<VirtualSite type="outOfPlane" index="3" atom1="0" atom2="1" atom3="2" weight12="-0.34490826" weight13="-0.34490826" weightCross="-6.4437903"/>
<VirtualSite type="outOfPlane" index="4" atom1="0" atom2="1" atom3="2" weight12="-0.34490826" weight13="-0.34490826" weightCross="6.4437903"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<VirtualSite type="outOfPlane" siteName="M1" atomName1="O" atomName2="H1" atomName3="H2" weight12="-0.34490826" weight13="-0.34490826" weightCross="-6.4437903"/>
<VirtualSite type="outOfPlane" siteName="M2" atomName1="O" atomName2="H1" atomName3="H2" weight12="-0.34490826" weight13="-0.34490826" weightCross="6.4437903"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 6391f721
......@@ -149,17 +149,28 @@ class ForceField(object):
for residue in root.find('Residues').findall('Residue'):
resName = residue.attrib['name']
template = ForceField._TemplateData(resName)
atomIndices = {}
for atom in residue.findall('Atom'):
params = {}
for key in atom.attrib:
if key not in ('name', 'type'):
params[key] = _convertParameterToNumber(atom.attrib[key])
template.atoms.append(ForceField._TemplateAtomData(atom.attrib['name'], atom.attrib['type'], self._atomTypes[atom.attrib['type']][2], params))
atomName = atom.attrib['name']
if atomName in atomIndices:
raise ValueError('Residue '+resName+' contains multiple atoms named '+atomName)
atomIndices[atomName] = len(template.atoms)
template.atoms.append(ForceField._TemplateAtomData(atomName, atom.attrib['type'], self._atomTypes[atom.attrib['type']][2], params))
for site in residue.findall('VirtualSite'):
template.virtualSites.append(ForceField._VirtualSiteData(site))
template.virtualSites.append(ForceField._VirtualSiteData(site, atomIndices))
for bond in residue.findall('Bond'):
if 'atomName1' in bond.attrib:
template.addBond(atomIndices[bond.attrib['atomName1']], atomIndices[bond.attrib['atomName2']])
else:
template.addBond(int(bond.attrib['from']), int(bond.attrib['to']))
for bond in residue.findall('ExternalBond'):
if 'atomName' in bond.attrib:
b = atomIndices[bond.attrib['atomName']]
else:
b = int(bond.attrib['from'])
template.externalBonds.append(b)
template.atoms[b].externalBonds += 1
......@@ -316,27 +327,32 @@ class ForceField(object):
class _VirtualSiteData:
"""Inner class used to encapsulate data about a virtual site."""
def __init__(self, node):
def __init__(self, node, atomIndices):
attrib = node.attrib
self.index = int(attrib['index'])
self.type = attrib['type']
if self.type == 'average2':
self.atoms = [int(attrib['atom1']), int(attrib['atom2'])]
numAtoms = 2
self.weights = [float(attrib['weight1']), float(attrib['weight2'])]
elif self.type == 'average3':
self.atoms = [int(attrib['atom1']), int(attrib['atom2']), int(attrib['atom3'])]
numAtoms = 3
self.weights = [float(attrib['weight1']), float(attrib['weight2']), float(attrib['weight3'])]
elif self.type == 'outOfPlane':
self.atoms = [int(attrib['atom1']), int(attrib['atom2']), int(attrib['atom3'])]
numAtoms = 3
self.weights = [float(attrib['weight12']), float(attrib['weight13']), float(attrib['weightCross'])]
elif self.type == 'localCoords':
self.atoms = [int(attrib['atom1']), int(attrib['atom2']), int(attrib['atom3'])]
numAtoms = 3
self.originWeights = [float(attrib['wo1']), float(attrib['wo2']), float(attrib['wo3'])]
self.xWeights = [float(attrib['wx1']), float(attrib['wx2']), float(attrib['wx3'])]
self.yWeights = [float(attrib['wy1']), float(attrib['wy2']), float(attrib['wy3'])]
self.localPos = [float(attrib['p1']), float(attrib['p2']), float(attrib['p3'])]
else:
raise ValueError('Unknown virtual site type: %s' % self.type)
if 'siteName' in attrib:
self.index = atomIndices[attrib['siteName']]
self.atoms = [atomIndices[attrib['atomName%d'%(i+1)]] for i in range(numAtoms)]
else:
self.index = int(attrib['index'])
self.atoms = [int(attrib['atom%d'%(i+1)]) for i in range(numAtoms)]
if 'excludeWith' in attrib:
self.excludeWith = int(attrib['excludeWith'])
else:
......
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