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Commit cd4031f9 authored by Robert T. McGibbon's avatar Robert T. McGibbon
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Merge branch 'master' of github.com:pandegroup/openmm into sphinx

parents 9af3e56b 4d32047c
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CMakeLists.txt
View file @ cd4031f9
...@@ -87,7 +87,7 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}) ...@@ -87,7 +87,7 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
# The source is organized into subdirectories, but we handle them all from # The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS. # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/validate libraries/irrxml libraries/vecmath) SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/irrxml libraries/vecmath)
IF(WIN32) IF(WIN32)
SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads) SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads)
ELSE(WIN32) ELSE(WIN32)
...@@ -316,14 +316,14 @@ ENDIF (MSVC) ...@@ -316,14 +316,14 @@ ENDIF (MSVC)
IF(OPENMM_BUILD_SHARED_LIB) IF(OPENMM_BUILD_SHARED_LIB)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES}) ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY") SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY")
ENDIF(OPENMM_BUILD_SHARED_LIB) ENDIF(OPENMM_BUILD_SHARED_LIB)
SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries") SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES}) ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB") SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY -DPTHREAD_BUILDING_STATIC_LIBRARY") SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DPTHREAD_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS) IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
......
devtools/forcefield-scripts/processTinkerForceField.py
View file @ cd4031f9
...@@ -35,16 +35,16 @@ import os.path ...@@ -35,16 +35,16 @@ import os.path
# biotype 2006 CA "Calcium Ion" 256 # biotype 2006 CA "Calcium Ion" 256
# biotype 2007 CL "Chloride Ion" 258 # biotype 2007 CL "Chloride Ion" 258
ions = { 'Li+' : [ 'LI', 249, 249 ], ions = { 'Li+' : ['LI', 249],
'Na+' : [ 'NA', 250, 2003 ], 'Na+' : ['NA', 250],
'K+' : [ 'K', 251, 2004 ], 'K+' : ['K', 251],
'Rb+' : [ 'RB', 252, 252 ], 'Rb+' : ['RB', 252],
'Cs+' : [ 'CS', 253, 253 ], 'Cs+' : ['CS', 253],
'Be+' : [ 'BE', 254, 254 ], 'Be+' : ['BE', 254],
'Mg+' : [ 'MG', 255, 2005 ], 'Mg+' : ['MG', 255],
'Ca+' : [ 'CA', 256, 2006 ], 'Ca+' : ['CA', 256],
'Zn+' : [ 'ZN', 257, 257 ], 'Zn+' : ['ZN', 257],
'Cl-' : [ 'Cl', 258, 2007 ] 'Cl-' : ['Cl', 258]
} }
atomTypes = {} atomTypes = {}
...@@ -58,7 +58,6 @@ def getDefaultAtom( ): ...@@ -58,7 +58,6 @@ def getDefaultAtom( ):
atom = dict(); atom = dict();
atom['tinkerLookupName'] = 'XXX' atom['tinkerLookupName'] = 'XXX'
atom['numberOfBonds'] = -1
atom['type'] = -1 atom['type'] = -1
atom['bonds'] = dict() atom['bonds'] = dict()
...@@ -89,7 +88,6 @@ def getXmlAtoms( atoms ): ...@@ -89,7 +88,6 @@ def getXmlAtoms( atoms ):
name = atom.attrib['name'] name = atom.attrib['name']
atomInfo[name] = getDefaultAtom() atomInfo[name] = getDefaultAtom()
atomInfo[name]['tinkerLookupName'] = atom.attrib['tinkerLookupName'] atomInfo[name]['tinkerLookupName'] = atom.attrib['tinkerLookupName']
atomInfo[name]['numberOfBonds'] = atom.attrib['bonds']
return atomInfo return atomInfo
...@@ -113,166 +111,6 @@ def getXmlBonds( bonds ): ...@@ -113,166 +111,6 @@ def getXmlBonds( bonds ):
return bondInfo return bondInfo
#=============================================================================================
# Read residue xml file
#=============================================================================================
def buildResidueDict( residueXmlFileName ):
residueTree = etree.parse(residueXmlFileName)
root = residueTree.getroot()
residueDict = dict()
# residueDict[residueName] = dict()
# ['loc']
# ['type']
# ['atoms'] = dict()
# [atomName] = dict()
# ['bonds'] = dict{}
for residue in root.findall('Residue'):
residueName = residue.attrib['name']
type = residue.attrib['type']
fullName = residue.attrib['fullName']
if( type == 'protein' ):
isProtein = 1
else:
isProtein = 0
bondInfo = getXmlBonds( residue.findall('Bond') )
# if residue is an amino acid, then create CALA and NALA residues, in addition to non-termianal residue, and include approriate atoms
# HXT is excluded from all residues
if( isProtein ):
cResidueName = 'C' + residueName
nResidueName = 'N' + residueName
residueDict[residueName] = dict()
residueDict[cResidueName] = dict()
residueDict[nResidueName] = dict()
residueDict[residueName]['atoms'] = dict()
residueDict[residueName]['type'] = 'protein'
residueDict[residueName]['loc'] = 'middle'
residueDict[residueName]['tinkerLookupName'] = fullName
residueDict[residueName]['fullName'] = fullName
residueDict[residueName]['include'] = 1
residueDict[cResidueName]['atoms'] = dict()
residueDict[cResidueName]['type'] = 'protein'
residueDict[cResidueName]['loc'] = 'C-Terminal'
residueDict[cResidueName]['loc'] = 'C-Terminal'
residueDict[cResidueName]['tinkerLookupName'] = 'C-Terminal ' + residueName
residueDict[cResidueName]['fullName'] = fullName
residueDict[nResidueName]['atoms'] = dict()
residueDict[nResidueName]['type'] = 'protein'
residueDict[nResidueName]['loc'] = 'N-Terminal'
residueDict[cResidueName]['tinkerLookupName'] = 'N-Terminal ' + residueName
residueDict[cResidueName]['fullName'] = fullName
residueList = [ residueDict[residueName]['atoms'], residueDict[cResidueName]['atoms'] , residueDict[nResidueName]['atoms'] ]
for atom in bondInfo:
if( atom == 'OXT' ):
residueDict[cResidueName]['atoms'][atom] = dict()
elif( atom == 'H2' or atom == 'H3'):
residueDict[nResidueName]['atoms'][atom] = dict()
elif( atom != 'HXT' ):
residueDict[nResidueName]['atoms'][atom] = dict()
residueDict[cResidueName]['atoms'][atom] = dict()
residueDict[residueName]['atoms'][atom] = dict()
for atom1 in bondInfo:
for atom2 in bondInfo[atom1]:
for resDict in residueList:
if( atom1 in resDict and atom2 in resDict ):
if( 'bonds' not in resDict[atom1] ):
resDict[atom1]['bonds'] = dict()
if( 'bonds' not in resDict[atom2] ):
resDict[atom2]['bonds'] = dict()
resDict[atom1]['bonds'][atom2] = 1
resDict[atom2]['bonds'][atom1] = 1
else:
residueDict[residueName] = dict()
residueDict[residueName]['atoms'] = dict()
residueDict[residueName]['loc'] = 'unk'
residueDict[residueName]['type'] = 'unk'
residueDict[residueName]['include'] = 0
for atom in bondInfo:
if( atom not in residueDict[residueName]['atoms'] ):
residueDict[residueName]['atoms'][atom] = dict()
residueDict[residueName]['atoms'][atom]['bonds'] = dict()
for atom2 in bondInfo[atom]:
if( atom2 not in residueDict[residueName]['atoms'] ):
residueDict[residueName]['atoms'][atom2] = dict()
residueDict[residueName]['atoms'][atom2]['bonds'] = dict()
residueDict[residueName]['atoms'][atom2]['bonds'][atom] = 1
residueDict[residueName]['atoms'][atom]['bonds'][atom2] = 1
else:
print "File=%s does not have Residues tag." % (residueXmlFileName)
all = list( root.iter() )
for i in all:
print "Tag <%s>" % (i.tag)
etree.dump( root )
printMap = 0
if( printMap ):
print "Residue Map"
for resName in sorted( residueDict.keys() ):
residueInfo = residueDict[resName]['atoms']
print "\nResidue %s %s %s" % (resName, residueDict[resName]['type'], residueDict[resName]['loc'])
for atomName in sorted( residueInfo.keys() ):
bondInfo = residueInfo[atomName]['bonds']
outputString = atomName + ' { '
for bondedAtom in sorted( bondInfo.keys() ):
outputString += bondedAtom + ' '
outputString += ' }'
print "%s" % outputString
print "Start Lookup XML\n\n"
printXml = 1
if( printXml ):
print "<Residues>"
for resName in sorted( residueDict.keys() ):
if( 'include' in residueDict[resName] and residueDict[resName]['include'] ):
type = residueDict[resName]['type']
loc = residueDict[resName]['loc']
tinkerLookupName = residueDict[resName]['tinkerLookupName']
fullName = residueDict[resName]['fullName']
outputString = """ <Residue abbreviation="%s" loc="%s" type="%s" tinkerLookupName="%s" fullName="%s">""" % (resName, loc, type, tinkerLookupName, fullName )
print "%s" % outputString
atomsInfo = residueDict[resName]['atoms']
for atomName in sorted( atomsInfo.keys() ):
numberOfBonds = len( atomsInfo[atomName]['bonds'] )
outputString = """ <Atom name="%s" tinkerLookupName="%s" bonds=%d />""" % (atomName, atomName, numberOfBonds )
print "%s" % outputString
includedBonds = dict()
for atomName in sorted( atomsInfo.keys() ):
bondsInfo = atomsInfo[atomName]['bonds']
for bondedAtom in bondsInfo:
if( bondedAtom not in includedBonds or atomName not in includedBonds[bondedAtom] ):
outputString = """ <Bond from="%s" to="%s" />""" % (atomName, bondedAtom)
if( atomName not in includedBonds ):
includedBonds[atomName] = dict()
if( bondedAtom not in includedBonds ):
includedBonds[bondedAtom] = dict()
includedBonds[atomName][bondedAtom] = 1
includedBonds[bondedAtom][atomName] = 1
print "%s" % outputString
print "</Residue>"
print "</Residues>"
sys.exit(0)
return residueDict
#============================================================================================= #=============================================================================================
# Build entry for protein residue # Build entry for protein residue
#============================================================================================= #=============================================================================================
...@@ -363,7 +201,7 @@ def copyProteinResidue( residue ): ...@@ -363,7 +201,7 @@ def copyProteinResidue( residue ):
# Build residue hash based on xml file # Build residue hash based on xml file
#============================================================================================= #=============================================================================================
def buildResidueDictFinal( residueXmlFileName ): def buildResidueDict( residueXmlFileName ):
residueTree = etree.parse(residueXmlFileName) residueTree = etree.parse(residueXmlFileName)
print "Read %s" % (residueXmlFileName) print "Read %s" % (residueXmlFileName)
...@@ -384,12 +222,18 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -384,12 +222,18 @@ def buildResidueDictFinal( residueXmlFileName ):
type = residue.attrib['type'] type = residue.attrib['type']
tinkerName = residue.attrib['tinkerLookupName'] tinkerName = residue.attrib['tinkerLookupName']
residueName = residue.attrib['fullName'] residueName = residue.attrib['fullName']
isProtein = 0 isProtein = False
isWater = 0 isWater = False
if( type == 'protein' ): isDNA = False
isProtein = 1 isRNA = False
elif( type == 'AmoebaWater' ): if type == 'protein':
isWater = 1 isProtein = True
elif type == 'AmoebaWater':
isWater = True
elif type == 'dna':
isDNA = True
elif type == 'rna':
isRNA = True
else: else:
continue continue
...@@ -448,6 +292,10 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -448,6 +292,10 @@ def buildResidueDictFinal( residueXmlFileName ):
residueDict[nResidueName]['atoms']['H2'] = copyAtom( residueDict[abbr]['atoms']['H'] ) residueDict[nResidueName]['atoms']['H2'] = copyAtom( residueDict[abbr]['atoms']['H'] )
residueDict[nResidueName]['atoms']['H3'] = copyAtom( residueDict[abbr]['atoms']['H'] ) residueDict[nResidueName]['atoms']['H3'] = copyAtom( residueDict[abbr]['atoms']['H'] )
elif isDNA or isRNA:
buildProteinResidue( residueDict, atoms, bondInfo, abbr, loc, tinkerName, 1, residueName, type )
print "Start Lookup XML FFFFinal\n\n" print "Start Lookup XML FFFFinal\n\n"
printXml = 1 printXml = 1
if( printXml ): if( printXml ):
...@@ -463,9 +311,8 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -463,9 +311,8 @@ def buildResidueDictFinal( residueXmlFileName ):
atomsInfo = residueDict[resName]['atoms'] atomsInfo = residueDict[resName]['atoms']
for atomName in sorted( atomsInfo.keys() ): for atomName in sorted( atomsInfo.keys() ):
numberOfBonds = atomsInfo[atomName]['numberOfBonds']
tinkerLookupName = atomsInfo[atomName]['tinkerLookupName'] tinkerLookupName = atomsInfo[atomName]['tinkerLookupName']
outputString = """ <Atom name="%s" tinkerLookupName="%s" bonds="%s" />""" % (atomName, tinkerLookupName, numberOfBonds ) outputString = """ <Atom name="%s" tinkerLookupName="%s" />""" % (atomName, tinkerLookupName)
print "%s" % outputString print "%s" % outputString
includedBonds = dict() includedBonds = dict()
...@@ -492,18 +339,35 @@ def buildResidueDictFinal( residueXmlFileName ): ...@@ -492,18 +339,35 @@ def buildResidueDictFinal( residueXmlFileName ):
def setBioTypes( bioTypes, residueDict ): def setBioTypes( bioTypes, residueDict ):
for res in residueDict: for resname, res in residueDict.items():
for atom in residueDict[res]['atoms']: for atom in res['atoms']:
lookupName = residueDict[res]['atoms'][atom]['tinkerLookupName'] + '_' + residueDict[res]['tinkerLookupName'] atomLookup = res['atoms'][atom]['tinkerLookupName']
if( lookupName in bioTypes ): resLookup = []
residueDict[res]['atoms'][atom]['type'] = bioTypes[lookupName][3] if res['type'] == 'dna':
if res['loc'] in ('5', 'N'):
resLookup.append("5'-Hydroxyl DNA")
if res['loc'] in ('3', 'N'):
resLookup.append("3'-Hydroxyl DNA")
resLookup.append("Phosphodiester DNA")
if res['type'] == 'rna':
if res['loc'] in ('5', 'N'):
resLookup.append("5'-Hydroxyl RNA")
if res['loc'] in ('3', 'N'):
resLookup.append("3'-Hydroxyl RNA")
resLookup.append("Phosphodiester RNA")
resLookup.append(res['tinkerLookupName'])
for suffix in resLookup:
lookupName = atomLookup+'_'+suffix
if lookupName in bioTypes:
break
if lookupName in bioTypes:
res['atoms'][atom]['type'] = bioTypes[lookupName][3]
else: else:
print "For %s lookupName=%s not in biotype" % (atom,lookupName) print "For %s lookupName=%s not in biotype" % (atom,lookupName)
if( 'parent' in residueDict[res] ): if( 'parent' in res ):
lookupName = residueDict[res]['atoms'][atom]['tinkerLookupName'] + '_' + residueDict[res]['parent']['tinkerLookupName'] lookupName = res['atoms'][atom]['tinkerLookupName'] + '_' + res['parent']['tinkerLookupName']
if( lookupName in bioTypes ): if( lookupName in bioTypes ):
residueDict[res]['atoms'][atom]['type'] = bioTypes[lookupName][3] res['atoms'][atom]['type'] = bioTypes[lookupName][3]
else: else:
print "Missing lookupName=%s from biotype" % (lookupName) print "Missing lookupName=%s from biotype" % (lookupName)
return 0 return 0
...@@ -584,14 +448,8 @@ def addTorTor( lineIndex, allLines, forces ): ...@@ -584,14 +448,8 @@ def addTorTor( lineIndex, allLines, forces ):
#============================================================================================= #=============================================================================================
old = 0 residueXmlFileName = 'residuesFinal.xml'
if( old ): residueDict = buildResidueDict( residueXmlFileName )
residueXmlFileName = '/home/friedrim/source/pyTinker/residues.xml'
residueXmlFileName = '/home/friedrim/source/pyTinker/residues.xml'
residueDict = buildResidueDict( residueXmlFileName )
else:
residueXmlFileName = 'residuesFinal.xml'
residueDict = buildResidueDictFinal( residueXmlFileName )
#============================================================================================= #=============================================================================================
...@@ -687,6 +545,7 @@ while lineIndex < len( allLines ): ...@@ -687,6 +545,7 @@ while lineIndex < len( allLines ):
if( fields[3] in ions ): if( fields[3] in ions ):
ionInfo = ions[fields[3]] ionInfo = ions[fields[3]]
element = ionInfo[0] element = ionInfo[0]
ionInfo[1] = int(fields[1])
else: else:
element = fields[3][0] element = fields[3][0]
atomTypes[int(fields[1])] = (fields[2], element, fields[6]) atomTypes[int(fields[1])] = (fields[2], element, fields[6])
...@@ -695,6 +554,9 @@ while lineIndex < len( allLines ): ...@@ -695,6 +554,9 @@ while lineIndex < len( allLines ):
elif fields[0] == 'biotype': elif fields[0] == 'biotype':
lookUp = fields[2] + '_' + fields[3] lookUp = fields[2] + '_' + fields[3]
if lookUp in bioTypes:
# Workaround for Tinker using the same name but different types for H2', H2'', and for H5', H5''
lookUp = fields[2]+'*_'+fields[3]
bioTypes[lookUp] = fields[1:] bioTypes[lookUp] = fields[1:]
lineIndex += 1 lineIndex += 1
...@@ -736,12 +598,17 @@ print "Opened %s." % (gkXmlFileName) ...@@ -736,12 +598,17 @@ print "Opened %s." % (gkXmlFileName)
today = datetime.date.today().isoformat() today = datetime.date.today().isoformat()
sourceFile = os.path.basename(sys.argv[1]) sourceFile = os.path.basename(sys.argv[1])
header = "<!-- Generated on %s from %s -->\n\n" % (today, sourceFile) header = """ <Info>
tinkerXmlFile.write(header) <Source>%s</Source>
gkXmlFile.write(header) <DateGenerated>%s</DateGenerated>
<Reference></Reference>
</Info>
""" % (sourceFile, today)
gkXmlFile.write( "<ForceField>\n" ) gkXmlFile.write( "<ForceField>\n" )
gkXmlFile.write(header)
tinkerXmlFile.write( "<ForceField>\n" ) tinkerXmlFile.write( "<ForceField>\n" )
tinkerXmlFile.write(header)
tinkerXmlFile.write( " <AtomTypes>\n") tinkerXmlFile.write( " <AtomTypes>\n")
if( scalars['forcefield'].find( 'AMOEBA' ) > -1 ): if( scalars['forcefield'].find( 'AMOEBA' ) > -1 ):
...@@ -803,25 +670,25 @@ tinkerXmlFile.write( " </AtomTypes>\n") ...@@ -803,25 +670,25 @@ tinkerXmlFile.write( " </AtomTypes>\n")
# residues # residues
tinkerXmlFile.write( " <Residues>\n" ) tinkerXmlFile.write( " <Residues>\n" )
for res in sorted(residueDict): for resname, res in sorted(residueDict.items()):
if( residueDict[res]['include'] ): if res['include']:
outputString = """ <Residue name="%s">""" % (res) outputString = """ <Residue name="%s">""" % (resname)
tinkerXmlFile.write( "%s\n" % (outputString) ) tinkerXmlFile.write( "%s\n" % (outputString) )
atomIndex = dict() atomIndex = dict()
atomCount = 0 atomCount = 0
for atom in sorted( residueDict[res]['atoms'].keys() ): for atom in sorted( res['atoms'].keys() ):
type = residueDict[res]['atoms'][atom]['type'] type = res['atoms'][atom]['type']
typeI = int( type ) typeI = int( type )
if( typeI < 0 ): if( typeI < 0 ):
print "Error: type=%s for atom=%s of residue=%s" % (type, atom, res) print "Error: type=%s for atom=%s of residue=%s" % (type, atom, resname)
tag = " <Atom name=\"%s\" type=\"%s\" />" % (atom, type) tag = " <Atom name=\"%s\" type=\"%s\" />" % (atom, type)
atomIndex[atom] = atomCount atomIndex[atom] = atomCount
atomCount += 1 atomCount += 1
tinkerXmlFile.write( "%s\n" % (tag) ) tinkerXmlFile.write( "%s\n" % (tag) )
includedBonds = dict() includedBonds = dict()
for atomName in sorted( residueDict[res]['atoms'].keys() ): for atomName in sorted( res['atoms'].keys() ):
bondsInfo = residueDict[res]['atoms'][atomName]['bonds'] bondsInfo = res['atoms'][atomName]['bonds']
for bondedAtom in bondsInfo: for bondedAtom in bondsInfo:
if( bondedAtom not in includedBonds or atomName not in includedBonds[bondedAtom] ): if( bondedAtom not in includedBonds or atomName not in includedBonds[bondedAtom] ):
outputString = """ <Bond from="%s" to="%s" />""" % (str(atomIndex[atomName]), str(atomIndex[bondedAtom])) outputString = """ <Bond from="%s" to="%s" />""" % (str(atomIndex[atomName]), str(atomIndex[bondedAtom]))
...@@ -834,15 +701,21 @@ for res in sorted(residueDict): ...@@ -834,15 +701,21 @@ for res in sorted(residueDict):
tinkerXmlFile.write( "%s\n" % (outputString) ) tinkerXmlFile.write( "%s\n" % (outputString) )
outputStrings = [] outputStrings = []
if( residueDict[res]['loc'] == 'm' ): if res['type'] in ('rna', 'dna'):
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) )) if res['loc'] in ('middle', '3'):
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) ) outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['P']) ))
if( residueDict[res]['loc'] == 'n' ): if res['loc'] in ('middle', '5'):
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) ) outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex["O3'"]) ))
if( residueDict[res]['loc'] == 'c' ): else:
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) ) ) if res['loc'] == 'm':
if( res.find('CYX') > -1 ): outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) ))
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['SG']) ) ) outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) )
if res['loc'] == 'n':
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['C']) ) )
if res['loc'] == 'c':
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['N']) ) )
if resname.find('CYX') > -1:
outputStrings.append( """ <ExternalBond from="%s" />""" % (str(atomIndex['SG']) ) )
for outputString in outputStrings: for outputString in outputStrings:
tinkerXmlFile.write( "%s\n" % (outputString) ) tinkerXmlFile.write( "%s\n" % (outputString) )
...@@ -960,24 +833,26 @@ if( isAmoeba ): ...@@ -960,24 +833,26 @@ if( isAmoeba ):
# AmoebaTorsionForce # AmoebaTorsionForce
torsionUnit = float(scalars['torsionunit']) torsionUnit = float(scalars['torsionunit'])
outputString = """ <AmoebaTorsionForce torsionUnit="%s">""" % ( torsionUnit ) outputString = """ <PeriodicTorsionForce>"""
tinkerXmlFile.write( "%s\n" % (outputString ) ) tinkerXmlFile.write( "%s\n" % (outputString ) )
torsions = forces['torsion'] torsions = forces['torsion']
conversion = 4.184*torsionUnit conversion = 4.184*torsionUnit
for torsion in torsions: for torsion in torsions:
outputString = """ <Torsion class1="%s" class2="%s" class3="%s" class4="%s" """ % (torsion[0], torsion[1], torsion[2], torsion[3]) outputString = """ <Proper class1="%s" class2="%s" class3="%s" class4="%s" """ % (torsion[0], torsion[1], torsion[2], torsion[3])
startIndex = 4 startIndex = 4
for ii in range(0,3): for ii in range(0,3):
torsionSuffix = str(ii+1) torsionSuffix = str(ii+1)
amplitudeAttributeName = 'amp' + torsionSuffix amplitudeAttributeName = 'k'+torsionSuffix
angleAttributeName = 'angle' + torsionSuffix angleAttributeName = 'phase'+torsionSuffix
periodicityAttributeName = 'periodicity'+torsionSuffix
amplitude = float(torsion[startIndex])*conversion amplitude = float(torsion[startIndex])*conversion
angle = float(torsion[startIndex+1])/radian angle = float(torsion[startIndex+1])/radian
outputString += """ %s="%s" %s="%s" """ % (amplitudeAttributeName, str(amplitude), angleAttributeName, str(angle) ) periodicity = int(torsion[startIndex+2])
outputString += """ %s="%s" %s="%s" %s="%s" """ % (amplitudeAttributeName, str(amplitude), angleAttributeName, str(angle), periodicityAttributeName, str(periodicity))
startIndex += 3 startIndex += 3
outputString += "/>" outputString += "/>"
tinkerXmlFile.write( "%s\n" % (outputString ) ) tinkerXmlFile.write( "%s\n" % (outputString ) )
tinkerXmlFile.write( " </AmoebaTorsionForce>\n" ) tinkerXmlFile.write( " </PeriodicTorsionForce>\n" )
#============================================================================================= #=============================================================================================
...@@ -1162,7 +1037,7 @@ if( isAmoeba ): ...@@ -1162,7 +1037,7 @@ if( isAmoeba ):
# radii are set in forcefield.py # radii are set in forcefield.py
for type in sorted( atomTypes ): for type in sorted( atomTypes ):
print "atoom type=%s %s" % ( str(type), str(atomTypes[type]) ) print "atom type=%s %s" % ( str(type), str(atomTypes[type]) )
for type in sorted( bioTypes ): for type in sorted( bioTypes ):
print "bio type=%s %s" % ( str(type), str(bioTypes[type]) ) print "bio type=%s %s" % ( str(type), str(bioTypes[type]) )
......
devtools/forcefield-scripts/residuesFinal.xml
View file @ cd4031f9
...@@ -942,4 +942,2124 @@ ...@@ -942,4 +942,2124 @@
<Bond from="CG2" to="HG22" /> <Bond from="CG2" to="HG22" />
<Bond from="H" to="N" /> <Bond from="H" to="N" />
</Residue> </Residue>
<Residue abbreviation="DA" loc="middle" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DA3" loc="3" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DA5" loc="5" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DAN" loc="N" type="dna" tinkerLookupName="Deoxyadenosine" fullName="Deoxyadenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DC" loc="middle" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DC3" loc="3" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DC5" loc="5" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DCN" loc="N" type="dna" tinkerLookupName="Deoxycytidine" fullName="Deoxycytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DG" loc="middle" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DG3" loc="3" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DG5" loc="5" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DGN" loc="N" type="dna" tinkerLookupName="Deoxyguanosine" fullName="Deoxyguanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DT" loc="middle" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DT3" loc="3" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="DT5" loc="5" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
</Residue>
<Residue abbreviation="DTN" loc="N" type="dna" tinkerLookupName="Deoxythymidine" fullName="Deoxythymidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C7" tinkerLookupName="C7"/>
<Atom name="H71" tinkerLookupName="H7"/>
<Atom name="H72" tinkerLookupName="H7"/>
<Atom name="H73" tinkerLookupName="H7"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="H2''" tinkerLookupName="H2**"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="C7"/>
<Bond from="C5" to="C4"/>
<Bond from="C7" to="H71"/>
<Bond from="C7" to="H72"/>
<Bond from="C7" to="H73"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="H2''"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RA" loc="middle" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RA3" loc="3" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RA5" loc="5" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RAN" loc="N" type="rna" tinkerLookupName="Adenosine" fullName="Adenosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="N6" tinkerLookupName="N6"/>
<Atom name="H61" tinkerLookupName="H61"/>
<Atom name="H62" tinkerLookupName="H62"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="H2" tinkerLookupName="H2"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="N6"/>
<Bond from="C6" to="N1"/>
<Bond from="N6" to="H61"/>
<Bond from="N6" to="H62"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="H2"/>
<Bond from="C2" to="N3"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RC" loc="middle" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RC3" loc="3" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RC5" loc="5" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RCN" loc="N" type="rna" tinkerLookupName="Cytidine" fullName="Cytidine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="N4" tinkerLookupName="N4"/>
<Atom name="H41" tinkerLookupName="H41"/>
<Atom name="H42" tinkerLookupName="H42"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="N4"/>
<Bond from="C4" to="N3"/>
<Bond from="N4" to="H41"/>
<Bond from="N4" to="H42"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RG" loc="middle" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RG3" loc="3" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RG5" loc="5" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RGN" loc="N" type="rna" tinkerLookupName="Guanosine" fullName="Guanosine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N9" tinkerLookupName="N9"/>
<Atom name="C8" tinkerLookupName="C8"/>
<Atom name="H8" tinkerLookupName="H8"/>
<Atom name="N7" tinkerLookupName="N7"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="O6" tinkerLookupName="O6"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="H1" tinkerLookupName="H1"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="N2" tinkerLookupName="N2"/>
<Atom name="H21" tinkerLookupName="H21"/>
<Atom name="H22" tinkerLookupName="H22"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N9" to="C8"/>
<Bond from="N9" to="C4"/>
<Bond from="C8" to="H8"/>
<Bond from="C8" to="N7"/>
<Bond from="N7" to="C5"/>
<Bond from="C5" to="C6"/>
<Bond from="C5" to="C4"/>
<Bond from="C6" to="O6"/>
<Bond from="C6" to="N1"/>
<Bond from="N1" to="H1"/>
<Bond from="N1" to="C2"/>
<Bond from="C2" to="N2"/>
<Bond from="C2" to="N3"/>
<Bond from="N2" to="H21"/>
<Bond from="N2" to="H22"/>
<Bond from="N3" to="C4"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RU" loc="middle" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RU3" loc="3" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="P" tinkerLookupName="P"/>
<Atom name="O1P" tinkerLookupName="OP"/>
<Atom name="O2P" tinkerLookupName="OP"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/>
<Bond from="P" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
<Residue abbreviation="RU5" loc="5" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
</Residue>
<Residue abbreviation="RUN" loc="N" type="rna" tinkerLookupName="Uridine" fullName="Uridine">
<Atom name="H5T" tinkerLookupName="H5T"/>
<Atom name="O5'" tinkerLookupName="O5*"/>
<Atom name="C5'" tinkerLookupName="C5*"/>
<Atom name="H5'" tinkerLookupName="H5*"/>
<Atom name="H5''" tinkerLookupName="H5**"/>
<Atom name="C4'" tinkerLookupName="C4*"/>
<Atom name="H4'" tinkerLookupName="H4*"/>
<Atom name="O4'" tinkerLookupName="O4*"/>
<Atom name="C1'" tinkerLookupName="C1*"/>
<Atom name="H1'" tinkerLookupName="H1*"/>
<Atom name="N1" tinkerLookupName="N1"/>
<Atom name="C6" tinkerLookupName="C6"/>
<Atom name="H6" tinkerLookupName="H6"/>
<Atom name="C5" tinkerLookupName="C5"/>
<Atom name="H5" tinkerLookupName="H5"/>
<Atom name="C4" tinkerLookupName="C4"/>
<Atom name="O4" tinkerLookupName="O4"/>
<Atom name="N3" tinkerLookupName="N3"/>
<Atom name="H3" tinkerLookupName="H3"/>
<Atom name="C2" tinkerLookupName="C2"/>
<Atom name="O2" tinkerLookupName="O2"/>
<Atom name="C3'" tinkerLookupName="C3*"/>
<Atom name="H3'" tinkerLookupName="H3*"/>
<Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/>
<Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/>
<Bond from="C5'" to="H5'"/>
<Bond from="C5'" to="H5''"/>
<Bond from="C5'" to="C4'"/>
<Bond from="C4'" to="H4'"/>
<Bond from="C4'" to="O4'"/>
<Bond from="C4'" to="C3'"/>
<Bond from="O4'" to="C1'"/>
<Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/>
<Bond from="C1'" to="C2'"/>
<Bond from="N1" to="C6"/>
<Bond from="N1" to="C2"/>
<Bond from="C6" to="H6"/>
<Bond from="C6" to="C5"/>
<Bond from="C5" to="H5"/>
<Bond from="C5" to="C4"/>
<Bond from="C4" to="O4"/>
<Bond from="C4" to="N3"/>
<Bond from="N3" to="H3"/>
<Bond from="N3" to="C2"/>
<Bond from="C2" to="O2"/>
<Bond from="C3'" to="H3'"/>
<Bond from="C3'" to="C2'"/>
<Bond from="C3'" to="O3'"/>
<Bond from="C2'" to="H2'"/>
<Bond from="C2'" to="O2'"/>
<Bond from="O2'" to="HO2'"/>
<Bond from="O3'" to="H3T"/>
</Residue>
</Residues> </Residues>
docs-source/usersguide/application.rst
View file @ cd4031f9
...@@ -1889,12 +1889,12 @@ The residue template definitions look like this: ...@@ -1889,12 +1889,12 @@ The residue template definitions look like this:
<Atom name="HH33" type="710"/> <Atom name="HH33" type="710"/>
<Atom name="C" type="712"/> <Atom name="C" type="712"/>
<Atom name="O" type="713"/> <Atom name="O" type="713"/>
<Bond from="0" to="1"/> <Bond atomName1="HH31" atomName2="CH3"/>
<Bond from="1" to="2"/> <Bond atomName1="CH3" atomName2="HH32"/>
<Bond from="1" to="3"/> <Bond atomName1="CH3" atomName2="HH33"/>
<Bond from="1" to="4"/> <Bond atomName1="CH3" atomName2="C"/>
<Bond from="4" to="5"/> <Bond atomName1="C" atomName2="O"/>
<ExternalBond from="4"/> <ExternalBond atomName="C"/>
</Residue> </Residue>
<Residue name="ALA"> <Residue name="ALA">
... ...
...@@ -1908,12 +1908,16 @@ contains the following tags: ...@@ -1908,12 +1908,16 @@ contains the following tags:
* An :code:`<Atom>` tag for each atom in the residue. This specifies the * An :code:`<Atom>` tag for each atom in the residue. This specifies the
name of the atom and its atom type. name of the atom and its atom type.
* A :code:`<Bond>` tag for each pair of atoms that are bonded to each * 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 other. The :code:`atomName1` and :code:`atomName2` attributes are the names
the two bonded atoms (starting from 0) in the order they were listed. For of the two bonded atoms. (Some older force fields use the alternate tags
example, :code:`<Bond from="1" to="3"/>` describes a bond between atom CH3 :code:`to` and :code:`from` to specify the atoms by index instead of name.
and atom HH33. 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 * An :code:`<ExternalBond>` tag for each atom that will be bonded to an
atom of a different residue. atom of a different residue. :code:`atomName` is the name of the atom.
(Alternatively, the deprecated :code:`from` tag may indicate the atom by
index instead of name.)
The :code:`<Residue>` tag may also contain :code:`<VirtualSite>` tags, The :code:`<Residue>` tag may also contain :code:`<VirtualSite>` tags,
...@@ -1926,21 +1930,24 @@ as in the following example: ...@@ -1926,21 +1930,24 @@ as in the following example:
<Atom name="H1" type="tip4pew-H"/> <Atom name="H1" type="tip4pew-H"/>
<Atom name="H2" type="tip4pew-H"/> <Atom name="H2" type="tip4pew-H"/>
<Atom name="M" type="tip4pew-M"/> <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"/> weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond from="0" to="1"/> <Bond atomName1="O" atomName2="H1"/>
<Bond from="0" to="2"/> <Bond atomName1="O" atomName2="H2"/>
</Residue> </Residue>
Each :code:`<VirtualSite>` tag indicates an atom in the residue that should Each :code:`<VirtualSite>` tag indicates an atom in the residue that should
be represented with a virtual site. The :code:`type` attribute may equal be represented with a virtual site. The :code:`type` attribute may equal
:code:`"average2"`\ , :code:`"average3"`\ , :code:`"outOfPlane"`\ , or :code:`"average2"`\ , :code:`"average3"`\ , :code:`"outOfPlane"`\ , or
:code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite, :code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite,
OutOfPlaneSite, and LocalCoordinatesSite classes respectively. The :code:`index` attribute gives the OutOfPlaneSite, and LocalCoordinatesSite classes respectively. The :code:`siteName`
index (starting from 0) of the atom to represent with a virtual site. The atoms attribute gives the name of the atom to represent with a virtual site. The atoms
it is calculated based on are specified by :code:`atom1`\ , :code:`atom2`\ , it is calculated based on are specified by :code:`atomName1`\ , :code:`atomName2`\ ,
and (for virtual site classes that involve three atoms) :code:`atom3`\ . The and (for virtual site classes that involve three atoms) :code:`atomName3`\ .
remaining attributes are specific to the virtual site class, and specify the (Some old force fields use the deprecated tags :code:`index`, :code:`atom1`,
:code:`atom2`, and :code:`atom3` to refer to them by index instead of name.)
The remaining attributes are specific to the virtual site class, and specify the
parameters for calculating the site position. For a TwoParticleAverageSite, parameters for calculating the site position. For a TwoParticleAverageSite,
they are :code:`weight1` and :code:`weight2`\ . For a they are :code:`weight1` and :code:`weight2`\ . For a
ThreeParticleAverageSite, they are :code:`weight1`\ , :code:`weight2`\ , and ThreeParticleAverageSite, they are :code:`weight1`\ , :code:`weight2`\ , and
......
libraries/validate/include/ValidateOpenMM.h deleted 100644 → 0
View file @ 9af3e56b
#ifndef VALIDATE_OPENMM_H_
#define VALIDATE_OPENMM_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "OpenMM.h"
#include "../../../platforms/reference/include/ReferencePlatform.h"
#include "openmm/Context.h"
#include "openmm/System.h"
#include "ValidateWindowsIncludes.h"
// free-energy plugin includes
//#define INCLUDE_FREE_ENERGY_PLUGIN
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
#include "../../../plugins/freeEnergy/openmmapi/include/OpenMMFreeEnergy.h"
#include "../../../plugins/freeEnergy/openmmapi/include/openmm/freeEnergyKernels.h"
//#include "../../../plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyPlatform.h"
#include "../../../plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyKernelFactory.h"
#endif
#include <sstream>
#include <typeinfo>
#include <limits>
#include <cstdlib>
#include <cstring>
#include <cstdio>
namespace OpenMM {
typedef std::map< std::string, int > StringIntMap;
typedef StringIntMap::iterator StringIntMapI;
typedef StringIntMap::const_iterator StringIntMapCI;
typedef std::map< std::string, double > StringDoubleMap;
typedef StringDoubleMap::iterator StringDoubleMapI;
typedef StringDoubleMap::const_iterator StringDoubleMapCI;
typedef std::map< std::string, unsigned int > StringUIntMap;
typedef StringUIntMap::iterator StringUIntMapI;
typedef StringUIntMap::const_iterator StringUIntMapCI;
typedef std::vector< std::string > StringVector;
typedef StringVector::iterator StringVectorI;
typedef StringVector::const_iterator StringVectorCI;
typedef std::vector< int > IntVector;
typedef IntVector::iterator IntVectorI;
typedef IntVector::const_iterator IntVectorCI;
typedef std::map< std::string, std::vector<std::string> > StringStringVectorMap;
typedef StringStringVectorMap::iterator StringStringVectorMapI;
typedef StringStringVectorMap::const_iterator StringStringVectorMapCI;
/**
* Base class w/ common functionality
*/
class ValidateOpenMM {
public:
ValidateOpenMM();
~ValidateOpenMM();
// force names
static const std::string HARMONIC_BOND_FORCE;
static const std::string HARMONIC_ANGLE_FORCE;
static const std::string PERIODIC_TORSION_FORCE;
static const std::string RB_TORSION_FORCE;
static const std::string NB_FORCE;
static const std::string NB_SOFTCORE_FORCE;
static const std::string NB_EXCEPTION_FORCE;
static const std::string NB_EXCEPTION_SOFTCORE_FORCE;
static const std::string GBSA_OBC_FORCE;
static const std::string GBSA_OBC_SOFTCORE_FORCE;
static const std::string GBVI_FORCE;
static const std::string GBVI_SOFTCORE_FORCE;
static const std::string CM_MOTION_REMOVER;
static const std::string ANDERSEN_THERMOSTAT;
static const std::string CUSTOM_BOND_FORCE;
static const std::string CUSTOM_EXTERNAL_FORCE;
static const std::string CUSTOM_NONBONDED_FORCE;
/**
* Return true if input number is nan or infinity
*
* @param number number to test
*
* @return true if number is nan or infinity
*/
static int isNanOrInfinity( double number );
/**
* Get force name
*
* @param force OpenMM system force
*
* @return force name or "NA" if force is not recognized
*/
std::string getForceName(const Force& force ) const;
/**
* Copy force
*
* @param force OpenMM system force to copy
*
* @return force or NULL if not recognized
*/
Force* copyForce(const Force& force) const;
/**
* Get copy of input system, but omit forces
*
* @param systemToCopy system to copy
*
* @return copy of system but w/o forces
*/
System* copySystemExcludingForces( const System& systemToCopy ) const;
/**
*
* Set the velocities/positions of context2 to those of context1
*
* @param context1 context1
* @param context2 context2
*
* @return 0
*/
void synchContexts( const Context& context1, Context& context2 ) const;
/**
*
* Get log FILE* reference
*
* @return log
*
*/
FILE* getLog() const;
/**
*
* Set log FILE* reference
*
* @param log log
*
*/
void OPENMM_VALIDATE_EXPORT setLog( FILE* log );
/**---------------------------------------------------------------------------------------
Copy constraints
@param systemToCopy system whose constraints are to be copied
@param system system to add constraints to
@param log log file pointer -- may be NULL
--------------------------------------------------------------------------------------- */
void copyConstraints( const System& systemToCopy, System* system, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Get force dependencies
@param forceName force to check if there exist any dependencies
@param returnVector vector of forces the input force is dependent on (example: GBSAOBC force requires Nonbonded force since
on Cuda platofrm they are computed in same loop and hence are inseparable)
--------------------------------------------------------------------------------------- */
void getForceDependencies( std::string forceName, StringVector& returnVector ) const;
/**
* Write masses to parameter file
*
* @param filePtr file to write masses to
* @param system write masses in system
*/
void writeMasses( FILE* filePtr, const System& system ) const;
/**
* Write constraints to parameter file
*
* @param filePtr file to write constraints to
* @param system write constraints in system
*
*/
void writeConstraints( FILE* filePtr, const System& system ) const;
/**
* Write harmonicBondForce parameters to file
*
* @param filePtr file to write forces to
* @param harmonicBondForce write harmonicBondForce parameters
*
*/
void writeHarmonicBondForce( FILE* filePtr, const HarmonicBondForce& harmonicBondForce ) const;
/**
* Write harmonicAngleForce parameters to file
*
* @param filePtr file to write forces to
* @param harmonicAngleForce write harmonicAngleForce parameters
*
*/
void writeHarmonicAngleForce( FILE* filePtr, const HarmonicAngleForce& harmonicAngleForce ) const;
/**
* Write rbTorsionForce parameters to file
*
* @param filePtr file to write forces to
* @param rbTorsionForce write rbTorsionForce parameters
*
*/
void writeRbTorsionForce( FILE* filePtr, const RBTorsionForce& rbTorsionForce ) const;
/**
* Write periodicTorsionForce parameters to file
*
* @param filePtr file to write forces to
* @param periodicTorsionForce write periodicTorsionForce parameters
*
*/
void writePeriodicTorsionForce( FILE* filePtr, const PeriodicTorsionForce& periodicTorsionForce ) const;
/**
* Write nonbonded parameters to file
*
* @param filePtr file to write forces to
* @param nonbondedForce write nonbondedForce parameters
*
*/
void writeNonbondedForce( FILE* filePtr, const NonbondedForce & nonbondedForce ) const;
/**
* Write GBSAOBCForce parameters to file
*
* @param filePtr file to write forces to
* @param gbsaObcForce write gbsaObcForce parameters
*
*/
void writeGbsaObcForce( FILE* filePtr, const GBSAOBCForce& gbsaObcForce ) const;
/**
* Write GBSA GB/VI Force parameters to file
*
* @param filePtr file to write forces to
* @param gbviObcForce write gbviObcForce parameters
*
*/
void writeGBVIForce( FILE* filePtr, const GBVIForce& gbviForce ) const;
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
/**
* Write nonbonded softcore parameters to file
*
* @param filePtr file to write forces to
* @param nonbondedForce write nonbondedForce parameters
*/
void writeNonbondedSoftcoreForce( FILE* filePtr, const NonbondedSoftcoreForce & nonbondedSoftcoreForce ) const;
/**
* Write GBSAOBCSoftcoreForce parameters to file
*
* @param filePtr file to write forces to
* @param gbsaObcForce write gbsaObcForce parameters
*
*/
void writeGbsaObcSoftcoreForce( FILE* filePtr, const GBSAOBCSoftcoreForce& gbsaObcForce ) const;
/**
* Write GBSA GB/VI softcore force parameters to file
*
* @param filePtr file to write forces to
* @param gbviObcForce write gbviObcForce parameters
*
*/
void writeGBVISoftcoreForce( FILE* filePtr, const GBVISoftcoreForce& gbviSoftcoreForce ) const;
#endif
/**
* Write coordinates, velocities, ... to file
*
* @param filePtr file to write Vec3 entries to
* @param vect3Array write array of Vec3
*
*/
void writeVec3( FILE* filePtr, const std::vector<Vec3>& vect3Array ) const;
/**
* Write context info to file (positions, velocities, forces, energies)
*
* @param filePtr file to write entries to
* @param context write context positions, velocities, forces, energies to file
*
*/
void writeContext( FILE* filePtr, const Context& context ) const;
/**
* Write integrator
*
* @param filePtr file to write integrator info to
* @param integrator write integrator info (time step, seed, ... as applicable)
*
*/
void writeIntegrator( FILE* filePtr, const Integrator& integrator ) const;
/**
* Write parameter file
* @param context context whose entries are to be written to file
* @param parameterFileName file name
*
*/
void writeParameterFile( const Context& context, const std::string& parameterFileName ) const;
private:
FILE* _log;
// map of force dependencies (e.g., GBSAObc requires NB force on CudaPlatform)
StringStringVectorMap _forceDependencies;
};
} // namespace OpenMM
#endif /*VALIDATE_OPENMM_H_*/
libraries/validate/include/ValidateOpenMMForces.h deleted 100644 → 0
View file @ 9af3e56b
#ifndef VALIDATE_OPENMM_FORCES_H_
#define VALIDATE_OPENMM_FORCES_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "ValidateOpenMM.h"
namespace OpenMM {
typedef std::map< int, int > MapIntInt;
typedef MapIntInt::iterator MapIntIntI;
typedef MapIntInt::const_iterator MapIntIntCI;
// Helper class for ValidateOpenMMForces class used to store force results and facitilitate comparisons of
// resulting forces
class ForceValidationResult {
public:
ForceValidationResult(const Context& context1, const Context& context2, StringUIntMap& forceNamesMap);
~ForceValidationResult();
/**
* Get potential energy at specified platform index (0 || 1)
*
* @return potential energy for spercifed platform
*
* @throws OpenMMException if energyIndex is not 0 or 1
*/
double getPotentialEnergy(int energyIndex) const;
/**
* Get array of forces at specified platform index (0 || 1)
*
* @return array of force norms
*
* @throws OpenMMException if forceIndex is not 0 or 1
*/
std::vector<double> getForceNorms(int forceIndex) const;
/**
* Get array of forces at platform index (0 || 1)
*
* @return force array
*
* @throws OpenMMException if forceIndex is not 0 or 1
*/
std::vector<Vec3> getForces(int forceIndex) const;
/**
* Get maximum delta in force norm
*
* @param maxIndex return atom index of entry with maximum delta norm (optional)
*
* @return max delta in norm of forces
*/
double getMaxDeltaForceNorm(int* maxIndex = NULL) const;
/**
* Get maximum relative delta in force norm
*
* @param maxIndex return atom index of entry w/ maximum relative delta norm (optional)
*
* @return max relative delta in norm of forces
*/
double getMaxRelativeDeltaForceNorm(int* maxIndex = NULL) const;
/**
* Get maximum dot product between forces
*
* @param maxIndex return atom index of entry w/ maximum dot product between forces (optional)
*
* @return max dot product between forces
*/
double getMaxDotProduct(int* maxIndex = NULL) const;
/**
* Get name of force associated w/ computed results
*
* @return force name(s); if more than one force active in computation,
* then names are concatenated and separated by '::' (e.g., 'NB_FORCE::GBSA_OBC_FORCE')
*/
std::string getForceName() const;
/**
* Get platform name
*
* @param index index of platform (0 or 1)
*
* @return platform name
*
* @throws OpenMMException if index is not 0 or 1
*/
std::string getPlatformName(int index) const;
/**
* Register index of two entries that differ by a specified tolerance
*
* @param index inconsistent index
*
*/
void registerInconsistentForceIndex(int index, int value = 1);
/**
* Clear list of entries that differ by a specified tolerance
*
*/
void clearInconsistentForceIndexList();
/**
* Get list of entries that differ by a specified tolerance
*
*/
void getInconsistentForceIndexList(std::vector<int>& inconsistentIndices) const;
/**
* Get number of entries in inconsistent index list
*
*/
int getNumberOfInconsistentForceEntries() const;
/**
* Return true if nans were detected
*
* @return true if nans were detected
*/
int nansDetected() const;
/**
* Determine if force norms are valid
*
* @param tolerance tolerance
*/
void compareForceNorms(double tolerance);
/**
* Determine if forces are valid
*
* @param tolerance tolerance
*/
void compareForces(double tolerance);
private:
// computed potential energies and forces fror two platforms
double _potentialEnergies[2];
std::vector<Vec3> _forces[2];
// platform and force names
std::string _platforms[2];
std::vector<std::string> _forceNames;
// force norms and stat entries
std::vector<double> _norms[2];
std::vector<double> _normStatVectors[2];
// map of indicies w/ inconsistent force entries
std::map<int, int> _inconsistentForceIndicies;
// if set, then nans detected
int _nansDetected;
/**
* Calculate norms of vectors
*
*/
void _calculateNorms();
/**
* Calculate norms of specified vector
*
*/
void _calculateNormOfForceVector(int forceIndex);
// stat indices
static const int STAT_AVG = 0;
static const int STAT_STD = 1;
static const int STAT_MIN = 2;
static const int STAT_ID1 = 3;
static const int STAT_MAX = 4;
static const int STAT_ID2 = 5;
static const int STAT_CNT = 6;
static const int STAT_END = 7;
/**
* Find vector stats
*
*/
void _findStatsForDouble(const std::vector<double>& array, std::vector<double>& statVector) const;
};
// Class used to compare forces/potential energies on two platforms
class ValidateOpenMMForces : public ValidateOpenMM {
public:
OPENMM_VALIDATE_EXPORT ValidateOpenMMForces();
OPENMM_VALIDATE_EXPORT ~ValidateOpenMMForces();
/**
* Validate force/energy by comparing the results between the forces/energies computed on user-provided context platform
* with Reference platform
*
* @param context context reference
* @param summaryString output summary string of results of comparison (optional)
*
* @return number of inconsistent entries
*/
int OPENMM_VALIDATE_EXPORT compareWithReferencePlatform(Context& context, std::string* summaryString = NULL);
/**
* Validate force/energy by comparing the results between the forces/energies computed on two different platforms
*
* @param context context reference
* @param compareForces indices of force to be tested
* @param platform1 first platform to compute forces
* @param platform2 second platform to compute forces
*
* @return ForceValidationResult reference containing results of force/energy computations
* on the two input platforms
*/
ForceValidationResult* compareForce(Context& context, std::vector<int>& compareForces,
Platform& platform1, Platform& platform2) const;
/**
* Compare individual forces by comparing calculations across two platforms (platform associated w/ input context and
* comparisonPlatform)
*
* @param context context reference
* @param platform comparsion platform reference
* @param forceValidationResults output vector of ForceValidationResult ptrs (user is responsible for deleting
* individual ForceValidationResult objects)
*/
void compareOpenMMForces(Context& context, Platform& comparisonPlatform, std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Determine if results are consistent
*
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent
*/
void checkForInconsistentForceEntries(std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Get total number of force entries that are inconsistent
*
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent
*/
int getTotalNumberOfInconsistentForceEntries(std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Get summary string of results
*
* @param forceValidationResults vector of ForceValidationResult ptrs
*/
std::string getSummary(std::vector<ForceValidationResult*>& forceValidationResults) const;
/**
* Set force tolerance
*
* @param tolerance force tolerance
*/
void setForceTolerance(double tolerance);
/**
* Get force tolerance
*
* @return force tolerance
*/
double getForceTolerance() const;
/*
* Get force tolerance for specified force
*
* @param forceName name of force
*
* @return force tolerance
*
* */
double getForceTolerance(const std::string& forceName) const;
/*
* Get max errors to print in summary string
*
* @return max errors to print
*
* */
int getMaxErrorsToPrint() const;
/*
* Set max errors to print in summary string
*
* @param maxErrorsToPrint max errors to print
*
* */
void setMaxErrorsToPrint(int maxErrorsToPrint);
/*
* Return true if force is not to be validated (Andersen thermostat, CM motion remover, ...)
*
* @param forceName force name
*
* @return true if force is not currently validated
**/
int isExcludedForce(std::string forceName) const;
private:
// initialize class entries
void _initialize();
/*
* Format output line
*
* @param tab tab
* @param description description
* @param value value
*
* @return string containing contents
*
* */
std::string _getLine(const std::string& tab,
const std::string& description,
const std::string& value) const;
std::vector<ForceValidationResult*> _forceValidationResults;
// max errors to print
int _maxErrorsToPrint;
// tolerence
double _forceTolerance;
// map of force tolerances to type (name)
StringDoubleMap _forceTolerances;
// forces to be excluded from validation
StringIntMap _forcesToBeExcluded;
};
} // namespace OpenMM
#endif /*VALIDATE_OPENMM_FORCES_H_*/
libraries/validate/include/ValidateWindowsIncludes.h deleted 100644 → 0
View file @ 9af3e56b
#ifndef OPENMM_VALIDATE_WINDOW_INCLUDE_H_
#define OPENMM_VALIDATE_WINDOW_INCLUDE_H_
/*
* Shared libraries are messy in Visual Studio. We have to distinguish three
* cases:
* (1) this header is being used to build the OpenMMValidate shared library
* (dllexport)
* (2) this header is being used by a *client* of the OpenMMValidate shared
* library (dllimport)
* (3) we are building the OpenMMValidate static library, or the client is
* being compiled with the expectation of linking with the
* OpenMMValidate static library (nothing special needed)
* In the CMake script for building this library, we define one of the symbols
* OpenMMValidate_BUILDING_{SHARED|STATIC}_LIBRARY
* Client code normally has no special symbol defined, in which case we'll
* assume it wants to use the shared library. However, if the client defines
* the symbol OPENMM_VALIDATE_USE_STATIC_LIBRARIES we'll suppress the dllimport so
* that the client code can be linked with static libraries. Note that
* the client symbol is not library dependent, while the library symbols
* affect only the OpenMMValidate library, meaning that other libraries can
* be clients of this one. However, we are assuming all-static or all-shared.
*/
#ifdef _MSC_VER
// We don't want to hear about how sprintf is "unsafe".
#pragma warning(disable:4996)
#if defined(OPENMM_VALIDATE_BUILDING_SHARED_LIBRARY)
#define OPENMM_VALIDATE_EXPORT __declspec(dllexport)
// Keep MS VC++ quiet about lack of dll export of private members.
#pragma warning(disable:4251)
#elif defined(OPENMM_VALIDATE_BUILDING_STATIC_LIBRARY) || defined(OPENMM_VALIDATE_USE_STATIC_LIBRARIES)
#define OPENMM_VALIDATE_EXPORT
#else
#define OPENMM_VALIDATE_EXPORT __declspec(dllimport) // i.e., a client of a shared library
#endif
#else
#define OPENMM_VALIDATE_EXPORT // Linux, Mac
#endif
#endif // OPENMM_VALIDATE_WINDOW_INCLUDE_H_
libraries/validate/src/ValidateOpenMM.cpp deleted 100644 → 0
View file @ 9af3e56b
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "ValidateOpenMM.h"
using namespace OpenMM;
// fixed force names
const std::string ValidateOpenMM::HARMONIC_BOND_FORCE = "HarmonicBond";
const std::string ValidateOpenMM::HARMONIC_ANGLE_FORCE = "HarmonicAngle";
const std::string ValidateOpenMM::PERIODIC_TORSION_FORCE = "PeriodicTorsion";
const std::string ValidateOpenMM::RB_TORSION_FORCE = "RbTorsion";
const std::string ValidateOpenMM::NB_FORCE = "Nb";
const std::string ValidateOpenMM::NB_SOFTCORE_FORCE = "NbSoftcore";
const std::string ValidateOpenMM::NB_EXCEPTION_FORCE = "NbException";
const std::string ValidateOpenMM::NB_EXCEPTION_SOFTCORE_FORCE = "NbSoftcoreException";
const std::string ValidateOpenMM::GBSA_OBC_FORCE = "GBSAOBC";
const std::string ValidateOpenMM::GBSA_OBC_SOFTCORE_FORCE = "GBSAOBCSoftcore";
const std::string ValidateOpenMM::GBVI_FORCE = "GBVI";
const std::string ValidateOpenMM::GBVI_SOFTCORE_FORCE = "GBVISoftcore";
const std::string ValidateOpenMM::CM_MOTION_REMOVER = "CMMotionRemover";
const std::string ValidateOpenMM::ANDERSEN_THERMOSTAT = "AndersenThermostat";
const std::string ValidateOpenMM::CUSTOM_BOND_FORCE = "CustomBond";
const std::string ValidateOpenMM::CUSTOM_EXTERNAL_FORCE = "CustomExternal";
const std::string ValidateOpenMM::CUSTOM_NONBONDED_FORCE = "CustomNonBonded";
ValidateOpenMM::ValidateOpenMM() {
_log = NULL;
// force dependencies
// these may need to specialized depending on platform since
// currently apply to Cuda platform, but may not apply to OpenCL platform
std::vector< std::string > nbVector;
nbVector.push_back( NB_FORCE );
_forceDependencies[GBSA_OBC_FORCE] = nbVector;
_forceDependencies[GBVI_FORCE] = nbVector;
std::vector< std::string > nbSoftcoreVector;
nbSoftcoreVector.push_back( NB_SOFTCORE_FORCE );
_forceDependencies[GBSA_OBC_SOFTCORE_FORCE] = nbSoftcoreVector;
_forceDependencies[GBVI_SOFTCORE_FORCE] = nbSoftcoreVector;
}
ValidateOpenMM::~ValidateOpenMM() {
}
int ValidateOpenMM::isNanOrInfinity( double number ){
return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0;
}
FILE* ValidateOpenMM::getLog() const {
return _log;
}
void ValidateOpenMM::setLog( FILE* log ){
_log = log;
}
std::string ValidateOpenMM::getForceName(const Force& force) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ValidateForce::getForceName";
// ---------------------------------------------------------------------------------------
std::string forceName = "NA";
// bond force
try {
const HarmonicBondForce& harmonicBondForce = dynamic_cast<const HarmonicBondForce&>(force);
return HARMONIC_BOND_FORCE;
} catch( std::bad_cast ){
}
// angle force
try {
const HarmonicAngleForce& harmonicAngleForce = dynamic_cast<const HarmonicAngleForce&>(force);
return HARMONIC_ANGLE_FORCE;
} catch( std::bad_cast ){
}
// periodic torsion force
try {
const PeriodicTorsionForce & periodicTorsionForce = dynamic_cast<const PeriodicTorsionForce&>(force);
return PERIODIC_TORSION_FORCE;
} catch( std::bad_cast ){
}
// RB torsion force
try {
const RBTorsionForce& rBTorsionForce = dynamic_cast<const RBTorsionForce&>(force);
return RB_TORSION_FORCE;
} catch( std::bad_cast ){
}
// nonbonded force
try {
const NonbondedForce& nbForce = dynamic_cast<const NonbondedForce&>(force);
return NB_FORCE;
} catch( std::bad_cast ){
}
// GBSA OBC
try {
const GBSAOBCForce& obcForce = dynamic_cast<const GBSAOBCForce&>(force);
return GBSA_OBC_FORCE;
} catch( std::bad_cast ){
}
// GB/VI
try {
const GBVIForce& obcForce = dynamic_cast<const GBVIForce&>(force);
return GBVI_FORCE;
} catch( std::bad_cast ){
}
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
// free energy plugin forces
// nonbonded softcore
try {
const NonbondedSoftcoreForce& nbForce = dynamic_cast<const NonbondedSoftcoreForce&>(force);
return NB_SOFTCORE_FORCE;
} catch( std::bad_cast ){
}
// GBSA OBC softcore
try {
const GBSAOBCSoftcoreForce& obcForce = dynamic_cast<const GBSAOBCSoftcoreForce&>(force);
return GBSA_OBC_SOFTCORE_FORCE;
} catch( std::bad_cast ){
}
// GB/VI softcore
try {
const GBVISoftcoreForce& gbviForce = dynamic_cast<const GBVISoftcoreForce&>(force);
return GBVI_SOFTCORE_FORCE;
} catch( std::bad_cast ){
}
#endif
// CMMotionRemover
try {
const CMMotionRemover& cMMotionRemover = dynamic_cast<const CMMotionRemover&>(force);
return CM_MOTION_REMOVER;
} catch( std::bad_cast ){
}
// AndersenThermostat
try {
const AndersenThermostat & andersenThermostat = dynamic_cast<const AndersenThermostat&>(force);
return ANDERSEN_THERMOSTAT;
} catch( std::bad_cast ){
}
// CustomBondForce
try {
const CustomBondForce & customBondForce = dynamic_cast<const CustomBondForce&>(force);
return CUSTOM_BOND_FORCE;
} catch( std::bad_cast ){
}
// CustomExternalForce
try {
const CustomExternalForce& customExternalForce = dynamic_cast<const CustomExternalForce&>(force);
return CUSTOM_EXTERNAL_FORCE;
} catch( std::bad_cast ){
}
// CustomNonbondedForce
try {
const CustomNonbondedForce& customNonbondedForce = dynamic_cast<const CustomNonbondedForce&>(force);
return CUSTOM_NONBONDED_FORCE;
} catch( std::bad_cast ){
}
return forceName;
}
Force* ValidateOpenMM::copyForce(const Force& force) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ValidateForce::copyForce";
// ---------------------------------------------------------------------------------------
// bond force
try {
const HarmonicBondForce& harmonicBondForce = dynamic_cast<const HarmonicBondForce&>(force);
return new HarmonicBondForce( harmonicBondForce );
} catch( std::bad_cast ){
}
// angle force
try {
const HarmonicAngleForce& harmonicAngleForce = dynamic_cast<const HarmonicAngleForce&>(force);
return new HarmonicAngleForce( harmonicAngleForce );
} catch( std::bad_cast ){
}
// periodic torsion force
try {
const PeriodicTorsionForce & periodicTorsionForce = dynamic_cast<const PeriodicTorsionForce&>(force);
return new PeriodicTorsionForce( periodicTorsionForce );
} catch( std::bad_cast ){
}
// RB torsion force
try {
const RBTorsionForce& rBTorsionForce = dynamic_cast<const RBTorsionForce&>(force);
return new RBTorsionForce( rBTorsionForce );
} catch( std::bad_cast ){
}
// nonbonded force
try {
const NonbondedForce& nbForce = dynamic_cast<const NonbondedForce&>(force);
return new NonbondedForce( nbForce );
} catch( std::bad_cast ){
}
// GBSA OBC
try {
const GBSAOBCForce& obcForce = dynamic_cast<const GBSAOBCForce&>(force);
return new GBSAOBCForce( obcForce );
} catch( std::bad_cast ){
}
// GB/VI
try {
const GBVIForce& gbviForce = dynamic_cast<const GBVIForce&>(force);
return new GBVIForce( gbviForce );
} catch( std::bad_cast ){
}
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
// free energy plugin forces
// nonbonded softcore
try {
const NonbondedSoftcoreForce& nbForce = dynamic_cast<const NonbondedSoftcoreForce&>(force);
return new NonbondedSoftcoreForce( nbForce );
} catch( std::bad_cast ){
}
// GBSA OBC softcore
try {
const GBSAOBCSoftcoreForce& obcForce = dynamic_cast<const GBSAOBCSoftcoreForce&>(force);
return new GBSAOBCSoftcoreForce( obcForce );
} catch( std::bad_cast ){
}
// GB/VI softcore
try {
const GBVISoftcoreForce& gbviForce = dynamic_cast<const GBVISoftcoreForce&>(force);
return new GBVISoftcoreForce( gbviForce );
} catch( std::bad_cast ){
}
#endif
// CMMotionRemover
try {
const CMMotionRemover& cMMotionRemover = dynamic_cast<const CMMotionRemover&>(force);
return new CMMotionRemover( cMMotionRemover );
} catch( std::bad_cast ){
}
// AndersenThermostat
try {
const AndersenThermostat & andersenThermostat = dynamic_cast<const AndersenThermostat&>(force);
return new AndersenThermostat( andersenThermostat );
} catch( std::bad_cast ){
}
// CustomBondForce
try {
const CustomBondForce & customBondForce = dynamic_cast<const CustomBondForce&>(force);
return new CustomBondForce( customBondForce );
} catch( std::bad_cast ){
}
// CustomExternalForce
try {
const CustomExternalForce& customExternalForce = dynamic_cast<const CustomExternalForce&>(force);
return new CustomExternalForce( customExternalForce );
} catch( std::bad_cast ){
}
// CustomNonbondedForce
try {
const CustomNonbondedForce& customNonbondedForce = dynamic_cast<const CustomNonbondedForce&>(force);
return new CustomNonbondedForce( customNonbondedForce );
} catch( std::bad_cast ){
}
return NULL;
}
/**
* Get copy of input system, but leave out forces
*
* @param systemToCopy system to copy
* @return system w/o forces
*/
System* ValidateOpenMM::copySystemExcludingForces( const System& systemToCopy ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ValidateOpenMM::copySystemExcludingForces";
// ---------------------------------------------------------------------------------------
// create new system and add masses and box dimensions
System* system = new System();
for(int ii = 0; ii < systemToCopy.getNumParticles(); ii++ ){
double mass = systemToCopy.getParticleMass( ii );
system->addParticle( mass );
}
Vec3 a, b, c;
systemToCopy.getDefaultPeriodicBoxVectors( a, b, c );
system->setDefaultPeriodicBoxVectors( a, b, c );
copyConstraints( systemToCopy, system );
return system;
}
/**---------------------------------------------------------------------------------------
Set the velocities/positions of context2 to those of context1
@param context1 context1
@param context2 context2
@return 0
--------------------------------------------------------------------------------------- */
void ValidateOpenMM::synchContexts( const Context& context1, Context& context2 ) const {
// ---------------------------------------------------------------------------------------
//static const char* methodName = "ValidateOpenMM::synchContexts: ";
// ---------------------------------------------------------------------------------------
const State state = context1.getState(State::Positions | State::Velocities);
const std::vector<Vec3>& positions = state.getPositions();
const std::vector<Vec3>& velocities = state.getVelocities();
context2.setPositions( positions );
context2.setVelocities( velocities );
return;
}
/**---------------------------------------------------------------------------------------
Copy constraints
@param systemToCopy system whose constraints are to be copied
@param system system to add constraints to
@param log log file pointer -- may be NULL
--------------------------------------------------------------------------------------- */
void ValidateOpenMM::copyConstraints( const System& systemToCopy, System* system, FILE* log ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "copyConstraints";
// ---------------------------------------------------------------------------------------
for( int ii = 0; ii < systemToCopy.getNumConstraints(); ii++ ){
int particle1, particle2;
double distance;
systemToCopy.getConstraintParameters( ii, particle1, particle2, distance );
system->addConstraint( particle1, particle2, distance );
}
}
/**---------------------------------------------------------------------------------------
Get force dependencies
@param forceName force to check if there exist any dependencies
@param returnVector vector of forces the input force is dependent on (example: GBSAOBC force requires Nonbonded force)
--------------------------------------------------------------------------------------- */
void ValidateOpenMM::getForceDependencies( std::string forceName, StringVector& returnVector ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "getForceDependencies";
// ---------------------------------------------------------------------------------------
StringStringVectorMapCI dependencyVector = _forceDependencies.find( forceName );
if( dependencyVector != _forceDependencies.end() ){
StringVector dependices = (*dependencyVector).second;
for( unsigned int ii = 0; ii < dependices.size(); ii++ ){
returnVector.push_back( dependices[ii] );
}
}
}
/**
* Write masses and box dimensions to parameter file
*/
void ValidateOpenMM::writeMasses( FILE* filePtr, const System& system ) const {
(void) fprintf( filePtr, "Masses %d\n", system.getNumParticles() );
for(int ii = 0; ii < system.getNumParticles(); ii++ ){
double mass = system.getParticleMass( ii );
(void) fprintf( filePtr, "%8d %14.7e\n", ii, mass );
}
Vec3 a, b, c;
system.getDefaultPeriodicBoxVectors( a, b, c);
(void) fprintf( filePtr, "Box %14.6f %14.6f %14.6f %14.6f %14.6f %14.6f %14.6f %14.6f %14.6f\n",
a[0], a[1], a[2], b[0], b[1], b[2], c[0], c[1], c[2] );
}
/**
* Write constraints to parameter file
*/
void ValidateOpenMM::writeConstraints( FILE* filePtr, const System& system ) const {
(void) fprintf( filePtr, "Constraints %d\n", system.getNumConstraints() );
for(int ii = 0; ii < system.getNumConstraints(); ii++ ){
int particle1, particle2;
double distance;
system.getConstraintParameters( ii, particle1, particle2, distance );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e\n", ii, particle1, particle2, distance );
}
}
/**
* Write harmonicBondForce parameters to file
*/
void ValidateOpenMM::writeHarmonicBondForce( FILE* filePtr, const HarmonicBondForce& harmonicBondForce ) const {
(void) fprintf( filePtr, "HarmonicBondForce %d\n", harmonicBondForce.getNumBonds() );
for(int ii = 0; ii < harmonicBondForce.getNumBonds(); ii++ ){
int particle1, particle2;
double length, k;
harmonicBondForce.getBondParameters( ii, particle1, particle2, length, k );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e %14.7e\n", ii, particle1, particle2, length, k);
}
}
/**
* Write harmonicAngleForce parameters to file
*/
void ValidateOpenMM::writeHarmonicAngleForce( FILE* filePtr, const HarmonicAngleForce& harmonicAngleForce ) const {
(void) fprintf( filePtr, "HarmonicAngleForce %d\n", harmonicAngleForce.getNumAngles() );
for(int ii = 0; ii < harmonicAngleForce.getNumAngles(); ii++ ){
int particle1, particle2, particle3;
double angle, k;
harmonicAngleForce.getAngleParameters( ii, particle1, particle2, particle3, angle, k );
(void) fprintf( filePtr, "%8d %8d %8d %8d %14.7e %14.7e\n", ii, particle1, particle2, particle3, angle, k);
}
}
/**
* Write rbTorsionForce parameters to file
*/
void ValidateOpenMM::writeRbTorsionForce( FILE* filePtr, const RBTorsionForce& rbTorsionForce ) const {
(void) fprintf( filePtr, "RBTorsionForce %d\n", rbTorsionForce.getNumTorsions() );
for(int ii = 0; ii < rbTorsionForce.getNumTorsions(); ii++ ){
int particle1, particle2, particle3, particle4;
double c0, c1, c2, c3, c4, c5;
rbTorsionForce.getTorsionParameters( ii, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5 );
(void) fprintf( filePtr, "%8d %8d %8d %8d %8d %14.7e %14.7e %14.7e %14.7e %14.7e %14.7e\n", ii, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5 );
}
}
/**
* Write periodicTorsionForce parameters to file
*/
void ValidateOpenMM::writePeriodicTorsionForce( FILE* filePtr, const PeriodicTorsionForce& periodicTorsionForce ) const {
(void) fprintf( filePtr, "PeriodicTorsionForce %d\n", periodicTorsionForce.getNumTorsions() );
for(int ii = 0; ii < periodicTorsionForce.getNumTorsions(); ii++ ){
int particle1, particle2, particle3, particle4, periodicity;
double phase, k;
periodicTorsionForce.getTorsionParameters( ii, particle1, particle2, particle3, particle4, periodicity, phase, k );
(void) fprintf( filePtr, "%8d %8d %8d %8d %8d %8d %14.7e %14.7e\n", ii, particle1, particle2, particle3, particle4, periodicity, phase, k );
}
}
/**
* Write GBSAOBCForce parameters to file
*/
void ValidateOpenMM::writeGbsaObcForce( FILE* filePtr, const GBSAOBCForce& gbsaObcForce ) const {
(void) fprintf( filePtr, "GBSAOBCForce %d\n", gbsaObcForce.getNumParticles() );
for(int ii = 0; ii < gbsaObcForce.getNumParticles(); ii++ ){
double charge, radius, scalingFactor;
gbsaObcForce.getParticleParameters( ii, charge, radius, scalingFactor );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e\n", ii, charge, radius, scalingFactor );
}
(void) fprintf( filePtr, "SoluteDielectric %14.7e\n", gbsaObcForce.getSoluteDielectric() );
(void) fprintf( filePtr, "SolventDielectric %14.7e\n", gbsaObcForce.getSolventDielectric() );
}
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
/**
* Write GBSAOBCSoftcoreForce parameters to file
*/
void ValidateOpenMM::writeGbsaObcSoftcoreForce( FILE* filePtr, const GBSAOBCSoftcoreForce& gbsaObcForce ) const {
(void) fprintf( filePtr, "GBSAOBCSoftcoreForce %d\n", gbsaObcForce.getNumParticles() );
for(int ii = 0; ii < gbsaObcForce.getNumParticles(); ii++ ){
double charge, radius, scalingFactor;
double nonPolarScalingFactor;
gbsaObcForce.getParticleParameters( ii, charge, radius, scalingFactor, nonPolarScalingFactor );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e %14.7e\n", ii, charge, radius, scalingFactor, nonPolarScalingFactor );
}
(void) fprintf( filePtr, "SoluteDielectric %14.7e\n", gbsaObcForce.getSoluteDielectric() );
(void) fprintf( filePtr, "SolventDielectric %14.7e\n", gbsaObcForce.getSolventDielectric() );
}
#endif
/**
* Write GBSA GB/VI Force parameters to file
*/
void ValidateOpenMM::writeGBVIForce( FILE* filePtr, const GBVIForce& gbviForce ) const {
(void) fprintf( filePtr, "GBVIForce %d\n", gbviForce.getNumParticles() );
for(int ii = 0; ii < gbviForce.getNumParticles(); ii++ ){
double charge, radius, gamma;
gbviForce.getParticleParameters( ii, charge, radius, gamma );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e\n", ii, charge, radius, gamma );
}
(void) fprintf( filePtr, "GBVIBonds %d\n", gbviForce.getNumBonds() );
for(int ii = 0; ii < gbviForce.getNumBonds(); ii++ ){
int atomI, atomJ;
double bondLength;
gbviForce.getBondParameters( ii, atomI, atomJ, bondLength );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e\n", ii, atomI, atomJ, bondLength );
}
(void) fprintf( filePtr, "SoluteDielectric %14.7e\n", gbviForce.getSoluteDielectric() );
(void) fprintf( filePtr, "SolventDielectric %14.7e\n", gbviForce.getSolventDielectric() );
}
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
/**
* Write GBSA GB/VI softcore force parameters to file
*/
void ValidateOpenMM::writeGBVISoftcoreForce( FILE* filePtr, const GBVISoftcoreForce& gbviSoftcoreForce ) const {
(void) fprintf( filePtr, "GBVISoftcoreForce %d\n", gbviSoftcoreForce.getNumParticles() );
for(int ii = 0; ii < gbviSoftcoreForce.getNumParticles(); ii++ ){
double charge, radius, gamma;
double nonPolarScalingFactor;
gbviSoftcoreForce.getParticleParameters( ii, charge, radius, gamma, nonPolarScalingFactor );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e %14.7e\n", ii, charge, radius, gamma, nonPolarScalingFactor );
}
(void) fprintf( filePtr, "GBVISoftcoreBonds %d\n", gbviSoftcoreForce.getNumBonds() );
for(int ii = 0; ii < gbviSoftcoreForce.getNumBonds(); ii++ ){
int atomI, atomJ;
double bondLength;
gbviSoftcoreForce.getBondParameters( ii, atomI, atomJ, bondLength );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e\n", ii, atomI, atomJ, bondLength );
}
(void) fprintf( filePtr, "SoluteDielectric %14.7e\n", gbviSoftcoreForce.getSoluteDielectric() );
(void) fprintf( filePtr, "SolventDielectric %14.7e\n", gbviSoftcoreForce.getSolventDielectric() );
(void) fprintf( filePtr, "BornRadiusScalingMethod %d\n", gbviSoftcoreForce.getBornRadiusScalingMethod() );
(void) fprintf( filePtr, "QuinticLowerLimitFactor %14.7e\n", gbviSoftcoreForce.getQuinticLowerLimitFactor() );
(void) fprintf( filePtr, "QuinticUpperBornRadiusLimit %14.7e\n", gbviSoftcoreForce.getQuinticUpperBornRadiusLimit() );
}
#endif
/**
* Write coordinates to file
*/
void ValidateOpenMM::writeVec3( FILE* filePtr, const std::vector<Vec3>& vect3Array ) const {
for( unsigned int ii = 0; ii < vect3Array.size(); ii++ ){
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e\n", ii,
vect3Array[ii][0], vect3Array[ii][1], vect3Array[ii][2] );
}
}
/**
* Write context info to file
*/
void ValidateOpenMM::writeContext( FILE* filePtr, const Context& context ) const {
State state = context.getState( State::Positions | State::Velocities | State::Forces | State::Energy );
std::vector<Vec3> positions = state.getPositions();
std::vector<Vec3> velocities = state.getVelocities();
std::vector<Vec3> forces = state.getForces();
(void) fprintf( filePtr, "Positions %zu\n", positions.size() );
writeVec3( filePtr, positions );
(void) fprintf( filePtr, "Velocities %zu\n", velocities.size() );
writeVec3( filePtr, velocities );
(void) fprintf( filePtr, "Forces %zu\n", forces.size() );
writeVec3( filePtr, forces );
(void) fprintf( filePtr, "KineticEnergy %14.7e\n", state.getKineticEnergy() );
(void) fprintf( filePtr, "PotentialEnergy %14.7e\n", state.getPotentialEnergy() );
}
/**
* Write nonbonded parameters to file
*/
void ValidateOpenMM::writeNonbondedForce( FILE* filePtr, const NonbondedForce & nonbondedForce ) const {
// charge and vdw parameters
(void) fprintf( filePtr, "NonbondedForce %d\n", nonbondedForce.getNumParticles() );
for(int ii = 0; ii < nonbondedForce.getNumParticles(); ii++ ){
double charge, sigma, epsilon;
nonbondedForce.getParticleParameters( ii, charge, sigma, epsilon );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e\n", ii, charge, sigma, epsilon );
}
// cutoff, dielectric, Ewald tolerance
(void) fprintf( filePtr, "CutoffDistance %14.7e\n", nonbondedForce.getCutoffDistance() );
(void) fprintf( filePtr, "RFDielectric %14.7e\n", nonbondedForce.getReactionFieldDielectric() );
(void) fprintf( filePtr, "EwaldRTolerance %14.7e\n", nonbondedForce.getEwaldErrorTolerance() );
// cutoff mode
std::string nonbondedForceMethod;
switch( nonbondedForce.getNonbondedMethod() ){
case NonbondedForce::NoCutoff:
nonbondedForceMethod = "NoCutoff";
break;
case NonbondedForce::CutoffNonPeriodic:
nonbondedForceMethod = "CutoffNonPeriodic";
break;
case NonbondedForce::CutoffPeriodic:
nonbondedForceMethod = "CutoffPeriodic";
break;
case NonbondedForce::Ewald:
nonbondedForceMethod = "Ewald";
break;
case NonbondedForce::PME:
nonbondedForceMethod = "PME";
break;
default:
nonbondedForceMethod = "Unknown";
}
(void) fprintf( filePtr, "NonbondedForceMethod %s\n", nonbondedForceMethod.c_str() );
(void) fprintf( filePtr, "NonbondedForceExceptions %d\n", nonbondedForce.getNumExceptions() );
for(int ii = 0; ii < nonbondedForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd, sigma, epsilon;
nonbondedForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e %14.7e %14.7e\n", ii, particle1, particle2, chargeProd, sigma, epsilon );
}
}
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
/**
* Write nonbonded softcore parameters to file
*/
void ValidateOpenMM::writeNonbondedSoftcoreForce( FILE* filePtr, const NonbondedSoftcoreForce & nonbondedSoftcoreForce ) const {
(void) fprintf( filePtr, "NonbondedSoftcoreForce %d\n", nonbondedSoftcoreForce.getNumParticles() );
for(int ii = 0; ii < nonbondedSoftcoreForce.getNumParticles(); ii++ ){
double charge, sigma, epsilon, softCoreLJ;
nonbondedSoftcoreForce.getParticleParameters( ii, charge, sigma, epsilon, softCoreLJ );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e %14.7e\n", ii, charge, sigma, epsilon, softCoreLJ );
}
(void) fprintf( filePtr, "CutoffDistance %14.7e\n", nonbondedSoftcoreForce.getCutoffDistance() );
(void) fprintf( filePtr, "RFDielectric %14.7e\n", nonbondedSoftcoreForce.getReactionFieldDielectric() );
(void) fprintf( filePtr, "EwaldRTolerance %14.7e\n", nonbondedSoftcoreForce.getEwaldErrorTolerance() );
std::string nonbondedSoftcoreForceMethod;
switch( nonbondedSoftcoreForce.getNonbondedMethod() ){
case NonbondedSoftcoreForce::NoCutoff:
nonbondedSoftcoreForceMethod = "NoCutoff";
break;
/*
case NonbondedSoftcoreForce::CutoffNonPeriodic:
nonbondedSoftcoreForceMethod = "CutoffNonPeriodic";
break;
case NonbondedSoftcoreForce::CutoffPeriodic:
nonbondedSoftcoreForceMethod = "CutoffPeriodic";
break;
case NonbondedSoftcoreForce::Ewald:
nonbondedSoftcoreForceMethod = "Ewald";
break;
case NonbondedSoftcoreForce::PME:
nonbondedSoftcoreForceMethod = "PME";
break;
*/
default:
nonbondedSoftcoreForceMethod = "Unknown";
}
(void) fprintf( filePtr, "NonbondedSoftcoreForceMethod %s\n", nonbondedSoftcoreForceMethod.c_str() );
(void) fprintf( filePtr, "NonbondedSoftcoreForceExceptions %d\n", nonbondedSoftcoreForce.getNumExceptions() );
for(int ii = 0; ii < nonbondedSoftcoreForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd, sigma, epsilon, softCoreLJ;
nonbondedSoftcoreForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon, softCoreLJ );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e %14.7e %14.7e %14.7e\n", ii, particle1, particle2, chargeProd, sigma, epsilon, softCoreLJ );
}
return;
}
#endif
void ValidateOpenMM::writeIntegrator( FILE* filePtr, const Integrator& integrator ) const {
// LangevinIntegrator
try {
const LangevinIntegrator langevinIntegrator = dynamic_cast<const LangevinIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator LangevinIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", langevinIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", langevinIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "Temperature %14.7e\n", langevinIntegrator.getTemperature() );
(void) fprintf( filePtr, "Friction %14.7e\n", langevinIntegrator.getFriction() );
(void) fprintf( filePtr, "RandomNumberSeed %d\n", langevinIntegrator.getRandomNumberSeed() );
return;
} catch( std::bad_cast ){
}
// VariableLangevinIntegrator
try {
const VariableLangevinIntegrator& langevinIntegrator = dynamic_cast<const VariableLangevinIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator VariableLangevinIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", langevinIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", langevinIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "Temperature %14.7e\n", langevinIntegrator.getTemperature() );
(void) fprintf( filePtr, "Friction %14.7e\n", langevinIntegrator.getFriction() );
(void) fprintf( filePtr, "RandomNumberSeed %d\n", langevinIntegrator.getRandomNumberSeed() );
(void) fprintf( filePtr, "ErrorTolerance %14.7e\n", langevinIntegrator.getErrorTolerance() );
return;
} catch( std::bad_cast ){
}
// VerletIntegrator
try {
const VerletIntegrator& verletIntegrator = dynamic_cast<const VerletIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator VerletIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", verletIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", verletIntegrator.getConstraintTolerance() );
return;
} catch( std::bad_cast ){
}
// VariableVerletIntegrator
try {
const VariableVerletIntegrator & variableVerletIntegrator = dynamic_cast<const VariableVerletIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator VariableVerletIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", variableVerletIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", variableVerletIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "ErrorTolerance %14.7e\n", variableVerletIntegrator.getErrorTolerance() );
return;
} catch( std::bad_cast ){
}
// BrownianIntegrator
try {
const BrownianIntegrator& brownianIntegrator = dynamic_cast<const BrownianIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator BrownianIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", brownianIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", brownianIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "Temperature %14.7e\n", brownianIntegrator.getTemperature() );
(void) fprintf( filePtr, "Friction %14.7e\n", brownianIntegrator.getFriction() );
(void) fprintf( filePtr, "RandomNumberSeed %d\n", brownianIntegrator.getRandomNumberSeed() );
return;
} catch( std::bad_cast ){
}
if( getLog() ){
(void) fprintf( getLog(), "Integrator not recognized." );
(void) fflush( getLog() );
}
return;
}
/**
* Write parameter file: Custom forces not implemented
* Mesage is sent to stderr if a force is not recognized
*
*/
void ValidateOpenMM::writeParameterFile( const Context& context, const std::string& parameterFileName ) const {
// open file
FILE* filePtr = fopen( parameterFileName.c_str(), "w" );
const System& system = context.getSystem();
const Integrator& integrator = context.getIntegrator();
// (void) fprintf( filePtr, "Version %s\n", versionString.c_str() );
(void) fprintf( filePtr, "Particles %8d\n", system.getNumParticles() );
writeMasses( filePtr, system );
(void) fprintf( filePtr, "NumberOfForces %8d\n", system.getNumForces() );
// print active forces and relevant parameters
for(int i = 0; i < system.getNumForces(); ++i) {
int hit = 0;
const Force& force = system.getForce(i);
// bond
if( !hit ){
try {
const HarmonicBondForce& harmonicBondForce = dynamic_cast<const HarmonicBondForce&>(force);
writeHarmonicBondForce( filePtr, harmonicBondForce );
hit++;
} catch( std::bad_cast ){
}
}
// angle
if( !hit ){
try {
const HarmonicAngleForce& harmonicAngleForce = dynamic_cast<const HarmonicAngleForce&>(force);
writeHarmonicAngleForce( filePtr, harmonicAngleForce );
hit++;
} catch( std::bad_cast ){
}
}
// PeriodicTorsionForce
if( !hit ){
try {
const PeriodicTorsionForce & periodicTorsionForce = dynamic_cast<const PeriodicTorsionForce&>(force);
writePeriodicTorsionForce( filePtr, periodicTorsionForce );
hit++;
} catch( std::bad_cast ){
}
}
// RBTorsionForce
if( !hit ){
try {
const RBTorsionForce& rBTorsionForce = dynamic_cast<const RBTorsionForce&>(force);
writeRbTorsionForce( filePtr, rBTorsionForce );
hit++;
} catch( std::bad_cast ){
}
}
// nonbonded
if( !hit ){
try {
const NonbondedForce& nbForce = dynamic_cast<const NonbondedForce&>(force);
writeNonbondedForce( filePtr, nbForce );
hit++;
} catch( std::bad_cast ){
}
}
// nonbonded softcore
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
if( !hit ){
try {
const NonbondedSoftcoreForce& nbForce = dynamic_cast<const NonbondedSoftcoreForce&>(force);
writeNonbondedSoftcoreForce( filePtr, nbForce );
hit++;
} catch( std::bad_cast ){
}
}
#endif
// GBSA OBC
if( !hit ){
try {
const GBSAOBCForce& obcForce = dynamic_cast<const GBSAOBCForce&>(force);
writeGbsaObcForce( filePtr, obcForce );
hit++;
} catch( std::bad_cast ){
}
}
// GBSA OBC softcore
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
if( !hit ){
try {
const GBSAOBCSoftcoreForce& obcForce = dynamic_cast<const GBSAOBCSoftcoreForce&>(force);
writeGbsaObcSoftcoreForce( filePtr, obcForce );
hit++;
} catch( std::bad_cast ){
}
}
#endif
// GB/VI
if( !hit ){
try {
const GBVIForce& obcForce = dynamic_cast<const GBVIForce&>(force);
writeGBVIForce( filePtr, obcForce );
hit++;
} catch( std::bad_cast ){
}
}
// GB/VI softcore
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
if( !hit ){
try {
const GBVISoftcoreForce& obcForce = dynamic_cast<const GBVISoftcoreForce&>(force);
writeGBVISoftcoreForce( filePtr, obcForce );
hit++;
} catch( std::bad_cast ){
}
}
#endif
// COM
if( !hit ){
try {
const CMMotionRemover& cMMotionRemover = dynamic_cast<const CMMotionRemover&>(force);
(void) fprintf( filePtr, "CMMotionRemover %d\n", cMMotionRemover.getFrequency() );
hit++;
} catch( std::bad_cast ){
}
}
if( !hit ){
char buffer[1024];
(void) sprintf( buffer, " %2d force not recognized.\n", i );
(void) fprintf( stderr, "%s\n", buffer );
// throw OpenMMException( buffer );
}
}
// constraints
writeConstraints( filePtr, system );
// context
writeContext( filePtr, context );
// integrator
writeIntegrator( filePtr, integrator );
// close file
(void) fclose( filePtr );
}
libraries/validate/src/ValidateOpenMMForces.cpp deleted 100644 → 0
View file @ 9af3e56b
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include <iostream>
#include <sstream>
#include "openmm/OpenMMException.h"
#include "ValidateOpenMMForces.h"
using namespace OpenMM;
ForceValidationResult::ForceValidationResult( const Context& context1, const Context& context2, StringUIntMap& forceNamesMap ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::ForceValidationResult";
// ---------------------------------------------------------------------------------------
_nansDetected = 0;
// calculate forces/energies
int types = State::Forces | State::Energy;
State state1 = context1.getState( types );
State state2 = context2.getState( types );
_potentialEnergies[0] = state1.getPotentialEnergy();
_potentialEnergies[1] = state2.getPotentialEnergy();
if( ValidateOpenMM::isNanOrInfinity( _potentialEnergies[0] ) || ValidateOpenMM::isNanOrInfinity( _potentialEnergies[1] ) ){
_nansDetected++;
}
_forces[0] = state1.getForces();
_forces[1] = state2.getForces();
_platforms[0] = context1.getPlatform().getName();
_platforms[1] = context2.getPlatform().getName();
for( StringUIntMapI ii = forceNamesMap.begin(); ii != forceNamesMap.end(); ii++ ){
_forceNames.push_back( (*ii).first );
}
_calculateNorms();
}
ForceValidationResult::~ForceValidationResult( ){
}
void ForceValidationResult::_calculateNorms(){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::_calculateNorms";
// ---------------------------------------------------------------------------------------
for( int jj = 0; jj < 2; jj++ ){
if( _norms[jj].size() < 1 ){
_calculateNormOfForceVector( jj );
_findStatsForDouble( _norms[jj], _normStatVectors[jj] );
}
}
}
/**---------------------------------------------------------------------------------------
Find stats for double array
@param array array
@param statVector vector of stats
@return 0
--------------------------------------------------------------------------------------- */
void ForceValidationResult::_findStatsForDouble( const std::vector<double>& array, std::vector<double>& statVector ) const {
// ---------------------------------------------------------------------------------------
//static const char* methodName = "ForceValidationResult::_findStatsForDouble";
// ---------------------------------------------------------------------------------------
statVector.resize( STAT_END );
double avgValue = 0.0;
double stdValue = 0.0;
double minValue = 1.0e+30;
double maxValue = -1.0e+30;
int minValueIndex = 0;
int maxValueIndex = 0;
for( unsigned int ii = 0; ii < array.size(); ii++ ){
double norm = array[ii];
avgValue += norm;
stdValue += norm*norm;
if( norm > maxValue ){
maxValue = norm;
maxValueIndex = ii;
}
if( norm < minValue ){
minValue = norm;
minValueIndex = ii;
}
}
double count = static_cast<double>(array.size());
double iCount = count > 0.0 ? 1.0/count : 0.0;
statVector[STAT_AVG] = avgValue*iCount;
statVector[STAT_STD] = stdValue - avgValue*avgValue*count;
if( count > 1.0 ){
statVector[STAT_STD] = std::sqrt( stdValue/( count - 1.0 ) );
}
statVector[STAT_MIN] = minValue;
statVector[STAT_ID1] = static_cast<double>(minValueIndex);
statVector[STAT_MAX] = maxValue;
statVector[STAT_ID2] = static_cast<double>(maxValueIndex);
statVector[STAT_CNT] = count;
return;
}
void ForceValidationResult::_calculateNormOfForceVector( int forceIndex ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::_calculateNormOfForceVector";
// ---------------------------------------------------------------------------------------
for( unsigned int ii = 0; ii < _forces[forceIndex].size(); ii++ ){
Vec3 f1 = _forces[forceIndex][ii];
_norms[forceIndex].push_back( std::sqrt( (f1[0]*f1[0]) + (f1[1]*f1[1]) + (f1[2]*f1[2]) ) );
if( ValidateOpenMM::isNanOrInfinity( f1[0] ) || ValidateOpenMM::isNanOrInfinity( f1[1] ) || ValidateOpenMM::isNanOrInfinity( f1[2] ) ){
_nansDetected++;
}
}
return;
}
double ForceValidationResult::getPotentialEnergy( int energyIndex ) const {
if( energyIndex == 0 || energyIndex == 1 ){
return _potentialEnergies[energyIndex];
} else {
char buffer[1024];
(void) sprintf( buffer, "getPotentialEnergy: energyIndex=%d is inconsistent.", energyIndex );
throw OpenMMException( buffer );
}
}
std::vector<Vec3> ForceValidationResult::getForces( int forceIndex ) const {
if( forceIndex == 0 || forceIndex == 1 ){
return _forces[forceIndex];
} else {
char buffer[1024];
(void) sprintf( buffer, "getForces: forceIndex=%d is inconsistent.", forceIndex );
throw OpenMMException( buffer );
}
}
std::vector<double> ForceValidationResult::getForceNorms( int forceIndex ) const {
if( forceIndex == 0 || forceIndex == 1 ){
return _norms[forceIndex];
} else {
char buffer[1024];
(void) sprintf( buffer, "getForceNorms: forceIndex=%d is inconsistent.", forceIndex );
throw OpenMMException( buffer );
}
}
int ForceValidationResult::nansDetected() const {
return _nansDetected;
}
void ForceValidationResult::registerInconsistentForceIndex( int index, int value ){
_inconsistentForceIndicies[index] = value;
}
void ForceValidationResult::clearInconsistentForceIndexList(){
_inconsistentForceIndicies.clear();
}
void ForceValidationResult::getInconsistentForceIndexList( std::vector<int>& inconsistentIndices ) const {
for( MapIntIntCI ii = _inconsistentForceIndicies.begin(); ii != _inconsistentForceIndicies.end(); ii++ ){
inconsistentIndices.push_back( (*ii).first );
}
}
int ForceValidationResult::getNumberOfInconsistentForceEntries() const {
return static_cast<int>(_inconsistentForceIndicies.size() );
}
double ForceValidationResult::getMaxDeltaForceNorm( int* maxIndex ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::calculateNorm";
// ---------------------------------------------------------------------------------------
double maxDelta = -1.0e+90;
int maxDeltaIndex = -1;
for( unsigned int ii = 0; ii < _forces[0].size(); ii++ ){
Vec3 f1 = _forces[0][ii];
double normF1 = _norms[0][ii];
Vec3 f2 = _forces[1][ii];
double normF2 = _norms[1][ii];
double delta = std::sqrt( (f1[0]-f2[0])*(f1[0]-f2[0]) + (f1[1]-f2[1])*(f1[1]-f2[1]) + (f1[2]-f2[2])*(f1[2]-f2[2]) );
if( maxDelta < delta ){
maxDelta = delta;
maxDeltaIndex = static_cast<int>(ii);
}
}
if( maxIndex ){
*maxIndex = maxDeltaIndex;
}
return maxDelta;
}
double ForceValidationResult::getMaxRelativeDeltaForceNorm( int* maxIndex ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::getMaxRelativeDeltaForceNorm";
// ---------------------------------------------------------------------------------------
double maxRelativeDelta = -1.0e+90;
int maxRelativeDeltaIndex = -1;
for( unsigned int ii = 0; ii < _forces[0].size(); ii++ ){
Vec3 f1 = _forces[0][ii];
double normF1 = _norms[0][ii];
Vec3 f2 = _forces[1][ii];
double normF2 = _norms[1][ii];
double delta = std::sqrt( (f1[0]-f2[0])*(f1[0]-f2[0]) + (f1[1]-f2[1])*(f1[1]-f2[1]) + (f1[2]-f2[2])*(f1[2]-f2[2]) );
double forceSum = 0.5*(normF1 + normF2);
if( forceSum > 0.0 ){
delta /= forceSum;
}
if( maxRelativeDelta < delta ){
maxRelativeDelta = delta;
maxRelativeDeltaIndex = static_cast<int>(ii);
}
}
if( maxIndex ){
*maxIndex = maxRelativeDeltaIndex;
}
return maxRelativeDelta;
}
double ForceValidationResult::getMaxDotProduct( int* maxIndex ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::getMaxDotProduct";
// ---------------------------------------------------------------------------------------
double maxDotProduct = -1.0e+90;
int maxDotProductIndex = -1;
for( unsigned int ii = 0; ii < _forces[0].size(); ii++ ){
Vec3 f1 = _forces[0][ii];
double normF1 = _norms[0][ii];
Vec3 f2 = _forces[1][ii];
double normF2 = _norms[1][ii];
double dotProduct = f1[0]*f2[0] + f1[1]*f2[1] + f1[2]*f2[2];
if( (normF1*normF2) > 0.0 ){
dotProduct /= (normF1*normF2);
dotProduct = 1.0 - dotProduct;
} else {
dotProduct = 0.0;
}
if( maxDotProduct < dotProduct ){
maxDotProduct = dotProduct;
maxDotProductIndex = static_cast<int>(ii);
}
}
if( maxIndex ){
*maxIndex = maxDotProductIndex;
}
return maxDotProduct;
}
std::string ForceValidationResult::getForceName() const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::getForceName";
// ---------------------------------------------------------------------------------------
std::stringstream forceName;
for( unsigned int ii = 0; ii < _forceNames.size(); ii++ ){
forceName << _forceNames[ii];
if( ii < (_forceNames.size()-1) )forceName << "::";
}
return forceName.str();
}
std::string ForceValidationResult::getPlatformName( int index ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ForceValidationResult::getPlatformName";
// ---------------------------------------------------------------------------------------
if( index == 0 || index == 1 ){
return _platforms[index];
} else {
char buffer[1024];
(void) sprintf( buffer, "getPlatformName: index=%d is inconsistent.", index );
throw OpenMMException( buffer );
}
}
void ForceValidationResult::compareForces( double tolerance ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = " ForceValidationResult::compareForces";
// ---------------------------------------------------------------------------------------
std::vector<Vec3> forces1 = getForces( 0 );
std::vector<double> forceNorms1 = getForceNorms( 0 );
std::vector<Vec3> forces2 = getForces( 1 );
std::vector<double> forceNorms2 = getForceNorms( 1 );
clearInconsistentForceIndexList();
for( unsigned int jj = 0; jj < forces1.size(); jj++ ){
if( ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms2[jj] ) ){
registerInconsistentForceIndex( jj );
} else {
double delta = std::sqrt( (forces1[jj][0]-forces2[jj][0])*(forces1[jj][0]-forces2[jj][0]) +
(forces1[jj][1]-forces2[jj][1])*(forces1[jj][1]-forces2[jj][1]) +
(forces1[jj][2]-forces2[jj][2])*(forces1[jj][2]-forces2[jj][2]) );
double sum = 0.5*( fabs( forceNorms1[jj] ) + fabs( forceNorms2[jj] ) );
double diff = delta > 0.0 ? delta/sum : 0.0;
if( diff > tolerance && sum > tolerance ){
registerInconsistentForceIndex( jj );
}
}
}
}
void ForceValidationResult::compareForceNorms( double tolerance ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "ForceValidationResult::compareForceNorms";
// ---------------------------------------------------------------------------------------
std::vector<double> forceNorms0 = getForceNorms( 0 );
std::vector<double> forceNorms1 = getForceNorms( 1 );
clearInconsistentForceIndexList();
for( unsigned int jj = 0; jj < forceNorms0.size(); jj++ ){
if( ValidateOpenMM::isNanOrInfinity( forceNorms0[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) ){
registerInconsistentForceIndex( jj );
} else {
double sum = 0.5*( fabs( forceNorms0[jj] ) + fabs( forceNorms1[jj] ) );
double diff = sum > 0.0 ? fabs( forceNorms0[jj] - forceNorms1[jj] )/sum : 0.0;
if( diff > tolerance && sum > tolerance ){
registerInconsistentForceIndex( jj );
}
}
}
}
ValidateOpenMMForces::ValidateOpenMMForces() {
_initialize();
}
void ValidateOpenMMForces::_initialize(){
_forceTolerance = 1.0e-02;
_maxErrorsToPrint = 25;
// force tolerances by name
_forceTolerances[HARMONIC_BOND_FORCE] = _forceTolerance;
_forceTolerances[HARMONIC_ANGLE_FORCE] = _forceTolerance;
//_forceTolerances[PERIODIC_TORSION_FORCE] = _forceTolerance;
_forceTolerances[PERIODIC_TORSION_FORCE] = 0.3;
//_forceTolerances[RB_TORSION_FORCE] = _forceTolerance;
_forceTolerances[RB_TORSION_FORCE] = 0.3;
_forceTolerances[NB_FORCE] = _forceTolerance;
_forceTolerances[NB_SOFTCORE_FORCE] = _forceTolerance;
_forceTolerances[GBSA_OBC_FORCE] = _forceTolerance;
_forceTolerances[GBSA_OBC_SOFTCORE_FORCE] = _forceTolerance;
_forceTolerances[GBVI_FORCE] = _forceTolerance;
_forceTolerances[GBVI_SOFTCORE_FORCE] = _forceTolerance;
// forces to be excluded from validation
_forcesToBeExcluded[CM_MOTION_REMOVER] = 1;
_forcesToBeExcluded[ANDERSEN_THERMOSTAT] = 1;
}
ValidateOpenMMForces::~ValidateOpenMMForces(){
for( unsigned int ii = 0; ii < _forceValidationResults.size(); ii++ ){
delete _forceValidationResults[ii];
}
_forceValidationResults.resize( 0 );
}
double ValidateOpenMMForces::getForceTolerance() const {
return _forceTolerance;
}
void ValidateOpenMMForces::setForceTolerance( double forceTolerance ){
_forceTolerance = forceTolerance;
}
int ValidateOpenMMForces::compareWithReferencePlatform( Context& context, std::string* summaryString ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "ValidateOpenMMForces::compareWithReferencePlatform";
// ---------------------------------------------------------------------------------------
ReferencePlatform referencePlatform;
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
ReferenceFreeEnergyKernelFactory* factory = new ReferenceFreeEnergyKernelFactory();
referencePlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
referencePlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
referencePlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
#endif
compareOpenMMForces( context, referencePlatform, _forceValidationResults );
checkForInconsistentForceEntries( _forceValidationResults );
if( summaryString ){
*summaryString = getSummary( _forceValidationResults );
}
return getTotalNumberOfInconsistentForceEntries( _forceValidationResults );
}
void ValidateOpenMMForces::compareOpenMMForces( Context& context, Platform& platform,
std::vector<ForceValidationResult*>& forceValidationResults ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "ValidateOpenMMForces::compareOpenMMForces";
// ---------------------------------------------------------------------------------------
// loop over forces
const System& system = context.getSystem();
std::vector<int> compareAllForces;
for( int ii = 0; ii < system.getNumForces(); ii++ ){
std::vector<int> compareForces;
std::string forceName = getForceName( system.getForce( ii ) );
if( isExcludedForce( forceName ) == 0 ){
compareForces.push_back( ii );
compareAllForces.push_back( ii );
ForceValidationResult* forceValidationResult = compareForce(context, compareForces, platform, context.getPlatform() );
forceValidationResults.push_back( forceValidationResult );
} else if( getLog() ){
(void) fprintf( getLog(), "Force %s is not being validated.\n", forceName.c_str() );
}
}
ForceValidationResult* forceValidationResult = compareForce(context, compareAllForces, platform, context.getPlatform() );
forceValidationResults.push_back( forceValidationResult );
}
ForceValidationResult* ValidateOpenMMForces::compareForce(Context& context, std::vector<int>& compareForces,
Platform& platform1, Platform& platform2 ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "ValidateOpenMMForces::compareForce";
// ---------------------------------------------------------------------------------------
// note if platforms are identical
if( getLog() && platform1.getName().compare( platform2.getName() ) == 0 ){
(void) fprintf( getLog(), "Note: Platforms to compares %s are identical.\n", platform1.getName().c_str() );
(void) fflush( getLog() );
}
const System& system = context.getSystem();
// collect systemForceNameMap[forceName] = index in system
// systemForceNameIndex[index] = force name
StringIntMap systemForceNameMap;
StringVector systemForceNameIndex;
systemForceNameIndex.resize( system.getNumForces() );
for( int ii = 0; ii < system.getNumForces(); ii++ ){
std::string forceName = getForceName( system.getForce( ii ) );
if( forceName.compare( "NA" ) == 0 ){
std::stringstream message;
message << "Force at index=" << ii << " not found -- aborting!";
std::cerr << message.str() << std::endl;
throw OpenMM::OpenMMException(message.str());
}
systemForceNameMap[forceName] = ii;
systemForceNameIndex[ii] = forceName;
}
// diagnostics
if( 0 && getLog() ){
for( StringIntMapI ii = systemForceNameMap.begin(); ii != systemForceNameMap.end(); ii++ ){
int index = (*ii).second;
(void) fprintf( getLog(), " System force map %s index=%d reverse map=%s\n", (*ii).first.c_str(), index, systemForceNameIndex[index].c_str() );
}
for( unsigned int ii = 0; ii < compareForces.size(); ii++ ){
(void) fprintf( getLog(), " ValidateOpenMMForces %u %s\n", ii, systemForceNameIndex[compareForces[ii]].c_str() );
}
(void) fflush( getLog() );
}
// get system copy and add forces to system
System* validationSystem = copySystemExcludingForces( system );
StringUIntMap forceNamesMap;
for( unsigned int ii = 0; ii < compareForces.size(); ii++ ){
const Force& forceToCopy = system.getForce( compareForces[ii] );
Force* force = copyForce( forceToCopy );
validationSystem->addForce( force );
forceNamesMap[systemForceNameIndex[compareForces[ii]]] = ii;
}
// include any missing dependencies (e.g, OBC force requires NB force for Cuda platform)
for( StringUIntMapI ii = forceNamesMap.begin(); ii != forceNamesMap.end(); ii++ ){
std::string forceName = (*ii).first;
StringVector dependencyVector;
getForceDependencies( forceName, dependencyVector );
for( unsigned int jj = 0; jj < dependencyVector.size(); jj++ ){
std::string dependentForceName = dependencyVector[jj];
StringUIntMapCI dependent = forceNamesMap.find( dependentForceName );
if( dependent == forceNamesMap.end() ){
forceNamesMap[dependentForceName] = 1;
int forceIndex = systemForceNameMap[dependentForceName];
const Force& forceToCopy = system.getForce( forceIndex );
validationSystem->addForce( copyForce( forceToCopy ) );
}
}
}
// create contexts
VerletIntegrator verletIntegrator( 0.001 );
Context* validationContext1 = new Context( *validationSystem, verletIntegrator, platform1);
Context* validationContext2 = new Context( *validationSystem, verletIntegrator, platform2);
// set positions
synchContexts( context, *validationContext1 );
synchContexts( context, *validationContext2 );
// diagnostics
if( 0 && getLog() ){
std::stringstream forceNames;
(void) fprintf( getLog(), " Validating system forces=%d\n", validationSystem->getNumForces() );
for( int ii = 0; ii < validationSystem->getNumForces(); ii++ ){
std::string forceName = getForceName( validationSystem->getForce( ii ) );
forceNames << forceName;
if( ii < (validationSystem->getNumForces()-1) ){
forceNames << "_";
} else {
forceNames << "Parameters.txt";
}
(void) fprintf( getLog(), " force %d %s\n", ii, forceName.c_str() );
}
writeParameterFile( *validationContext1, forceNames.str() );
(void) fflush( getLog() );
}
// calculate forces & build return result
ForceValidationResult* forceValidationResult = new ForceValidationResult( *validationContext1, *validationContext2, forceNamesMap );
delete validationContext1;
delete validationContext2;
delete validationSystem;
return forceValidationResult;
}
void ValidateOpenMMForces::checkForInconsistentForceEntries( std::vector<ForceValidationResult*>& forceValidationResults ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "ValidateOpenMMForces::checkForInconsistentForceEntries";
// ---------------------------------------------------------------------------------------
for( unsigned int ii = 0; ii < forceValidationResults.size(); ii++ ){
std::string forceName = forceValidationResults[ii]->getForceName();
double tolerance = getForceTolerance( forceName );
forceValidationResults[ii]->compareForces( tolerance );
}
}
int ValidateOpenMMForces::getTotalNumberOfInconsistentForceEntries( std::vector<ForceValidationResult*>& forceValidationResults ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "ValidateOpenMMForces::getTotalNumberOfInconsistentForceEntries";
// ---------------------------------------------------------------------------------------
int inconsistentEntries = 0;
for( unsigned int ii = 0; ii < forceValidationResults.size(); ii++ ){
inconsistentEntries += forceValidationResults[ii]->getNumberOfInconsistentForceEntries();
}
return inconsistentEntries;
}
int ValidateOpenMMForces::isExcludedForce( std::string forceName ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "ValidateOpenMMForces::isExcludedForce";
// ---------------------------------------------------------------------------------------
StringIntMapCI isPresent = _forcesToBeExcluded.find( forceName );
return isPresent != _forcesToBeExcluded.end() ? 1 : 0;
}
/*
* Get force tolerance for specified force
*
* @param forceName name of force
*
* @return force tolerance
*
* */
double ValidateOpenMMForces::getForceTolerance( const std::string& forceName ) const {
StringDoubleMapCI forceIsPresent = _forceTolerances.find( forceName );
if( forceIsPresent != _forceTolerances.end() ){
return (*forceIsPresent).second;
}
return _forceTolerance;
}
int ValidateOpenMMForces::getMaxErrorsToPrint() const {
return _maxErrorsToPrint;
}
void ValidateOpenMMForces::setMaxErrorsToPrint( int maxErrorsToPrint ){
_maxErrorsToPrint = maxErrorsToPrint;
}
/*
* Format line
*
* @param tab tab
* @param description description
* @param value value
*
* @return string containing contents
*
* */
std::string ValidateOpenMMForces::_getLine( const std::string& tab,
const std::string& description,
const std::string& value ) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "GromacsOpenMMTest::_getLine";
static const unsigned int MAX_LINE_CHARS = 256;
char line[MAX_LINE_CHARS];
// ---------------------------------------------------------------------------------------
std::stringstream message;
memset( line, ' ', MAX_LINE_CHARS );
#ifdef WIN32
(void) sprintf_s( line, MAX_LINE_CHARS, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
#else
(void) sprintf( line, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
#endif
message << std::string( line ) << std::endl;
return message.str();
}
std::string ValidateOpenMMForces::getSummary( std::vector<ForceValidationResult*>& forceValidationResults ) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "ValidateOpenMMForces::getSummary";
static const unsigned int MAX_LINE_CHARS = 256;
char value[MAX_LINE_CHARS];
// ---------------------------------------------------------------------------------------
#ifdef WIN32
#define LOCAL_SPRINTF0(a,b) sprintf_s( (a), MAX_LINE_CHARS, (b) );
#define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );
#define LOCAL_SPRINTF4(a,b,c,d) sprintf_s( (a), MAX_LINE_CHARS, (b), (c), (d) );
#define LOCAL_SPRINTF5(a,b,c,d,e) sprintf_s( (a), MAX_LINE_CHARS, (b), (c), (d), (e) );
#define LOCAL_SPRINTF6(a,b,c,d,e,f) sprintf_s( (a), MAX_LINE_CHARS, (b), (c), (d), (e), (f) );
#define LOCAL_SPRINTF12(a,b,c,d,e,f,g,h,i,j,k,l) sprintf_s( (a), MAX_LINE_CHARS, (b), (c), (d), (e), (f), (g), (h), (i), (j), (k), (l) );
#else
#define LOCAL_SPRINTF0(a,b) sprintf( (a), (b) );
#define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );
#define LOCAL_SPRINTF4(a,b,c,d) sprintf( (a), (b), (c), (d) );
#define LOCAL_SPRINTF5(a,b,c,d,e) sprintf( (a), (b), (c), (d), (e) );
#define LOCAL_SPRINTF6(a,b,c,d,e,f) sprintf( (a), (b), (c), (d), (e), (f) );
#define LOCAL_SPRINTF12(a,b,c,d,e,f,g,h,i,j,k,l) sprintf( (a), (b), (c), (d), (e), (f), (g), (h), (i), (j), (k), (l) );
#endif
unsigned int maxMissesToPrint = static_cast<unsigned int>(getMaxErrorsToPrint());
std::stringstream summary;
std::string tab = " ";
int useForces = 1;
for( unsigned int ii = 0; ii < forceValidationResults.size(); ii++ ){
// platforms
if( ii == 0 ){
std::string platform1 = forceValidationResults[ii]->getPlatformName( 0 );
std::string platform2 = forceValidationResults[ii]->getPlatformName( 1 );
(void) LOCAL_SPRINTF4( value, "%10s %10s\n", platform1.c_str(), platform2.c_str());
summary << _getLine( tab, "Platforms", value );
}
// force name
std::string forceName = forceValidationResults[ii]->getForceName();
double tolerance = getForceTolerance( forceName );
summary << _getLine( tab, "Force", forceName );
(void) LOCAL_SPRINTF( value, "%.3e ", tolerance );
summary << _getLine( tab, "Tolerance", value );
int index;
// delta
double delta = forceValidationResults[ii]->getMaxDeltaForceNorm( &index );
(void) LOCAL_SPRINTF4( value, "%.3e at index %6d", delta, index );
summary << _getLine( tab, "Max Delta", value );
// relative delta
delta = forceValidationResults[ii]->getMaxRelativeDeltaForceNorm( &index );
(void) LOCAL_SPRINTF4( value, "%.3e at index %6d", delta, index );
summary << _getLine( tab, "Max Relative Delta", value );
// PE delta
double pe1 = forceValidationResults[ii]->getPotentialEnergy( 0 );
double pe2 = forceValidationResults[ii]->getPotentialEnergy( 1 );
double sum = 0.5*(fabs( pe1 ) + fabs( pe2 ) );
delta = sum > 0.0 ? fabs( pe1 - pe2 )/sum : 0.0;
(void) LOCAL_SPRINTF5( value, "%10.4e PE[%14.6e %14.6e]", delta, pe1, pe2 );
summary << _getLine( tab, "Potential energies relative delta", value );
// misses
std::vector<int> inconsistentIndices;
forceValidationResults[ii]->getInconsistentForceIndexList( inconsistentIndices );
if( inconsistentIndices.size() > 0 ){
std::vector<Vec3> forces1 = forceValidationResults[ii]->getForces( 0 );
std::vector<Vec3> forces2 = forceValidationResults[ii]->getForces( 1 );
std::vector<double> forceNorms1 = forceValidationResults[ii]->getForceNorms( 0 );
std::vector<double> forceNorms2 = forceValidationResults[ii]->getForceNorms( 1 );
for( unsigned int kk = 0; kk < inconsistentIndices.size() && kk < maxMissesToPrint; kk++ ){
int jj = inconsistentIndices[kk];
if( isNanOrInfinity( forceNorms1[jj] ) || isNanOrInfinity( forceNorms2[jj] ) ){
(void) LOCAL_SPRINTF5( value, " nan at index %6d norms: [%12.5e %12.5e]", jj, forceNorms1[jj], forceNorms2[jj] );
summary << _getLine( tab, "Error", value );
} else {
double diff, sum;
if( useForces ){
double delta = std::sqrt( (forces1[jj][0]-forces2[jj][0])*(forces1[jj][0]-forces2[jj][0]) +
(forces1[jj][1]-forces2[jj][1])*(forces1[jj][1]-forces2[jj][1]) +
(forces1[jj][2]-forces2[jj][2])*(forces1[jj][2]-forces2[jj][2]) );
sum = 0.5*( fabs( forceNorms1[jj] ) + fabs( forceNorms2[jj] ) );
diff = delta > 0.0 ? delta/sum : 0.0;
} else {
sum = 0.5*( fabs( forceNorms1[jj] ) + fabs( forceNorms2[jj] ) );
diff = sum > 0.0 ? fabs( forceNorms1[jj] - forceNorms2[jj] )/sum : 0.0;
}
(void) LOCAL_SPRINTF12( value, "%11.5e at index %6d norms: [%11.5e %11.5e] forces: [%12.5e %12.5e %12.5e] [%12.5e %12.5e %12.5e]",
diff, jj, forceNorms1[jj], forceNorms2[jj],
forces1[jj][0], forces1[jj][1], forces1[jj][2],
forces2[jj][0], forces2[jj][1], forces2[jj][2] );
summary << _getLine( tab, "Error", value );
if( kk == (maxMissesToPrint-1) ){
value[0] = '\0';
summary << _getLine( tab, "No more errors will be printed: call ValidateOpenMMForces::setMaxErrorsToPrint() to modifiy this limit.", value );
}
}
}
}
(void) LOCAL_SPRINTF0( value, "\n" );
summary << _getLine( tab, " ", value );
if( inconsistentIndices.size() > 0 ){
(void) LOCAL_SPRINTF( value, "%u\n", static_cast<unsigned int>(inconsistentIndices.size()) );
summary << _getLine( tab, "Total errors", value );
}
if( forceValidationResults[ii]->nansDetected() ){
value[0] = '\0';
summary << _getLine( tab, "Nans detected.", value );
}
}
return summary.str();
}
olla/include/openmm/kernels.h
View file @ cd4031f9
...@@ -48,7 +48,6 @@ ...@@ -48,7 +48,6 @@
#include "openmm/CustomManyParticleForce.h" #include "openmm/CustomManyParticleForce.h"
#include "openmm/CustomTorsionForce.h" #include "openmm/CustomTorsionForce.h"
#include "openmm/GBSAOBCForce.h" #include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/HarmonicAngleForce.h" #include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h" #include "openmm/HarmonicBondForce.h"
#include "openmm/KernelImpl.h" #include "openmm/KernelImpl.h"
...@@ -667,35 +666,6 @@ public: ...@@ -667,35 +666,6 @@ public:
virtual void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force) = 0; virtual void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force) = 0;
}; };
/**
* This kernel is invoked by GBVIForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcGBVIForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcGBVIForce";
}
CalcGBVIForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the GBVIForce this kernel will be used for
* @param scaledRadii scaled radii
*/
virtual void initialize(const System& system, const GBVIForce& force, const std::vector<double>& scaledRadii) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/** /**
* This kernel is invoked by CustomGBForce to calculate the forces acting on the system and the energy of the system. * This kernel is invoked by CustomGBForce to calculate the forces acting on the system and the energy of the system.
*/ */
......
openmmapi/include/OpenMM.h
View file @ cd4031f9
...@@ -50,7 +50,6 @@ ...@@ -50,7 +50,6 @@
#include "openmm/CustomNonbondedForce.h" #include "openmm/CustomNonbondedForce.h"
#include "openmm/Force.h" #include "openmm/Force.h"
#include "openmm/GBSAOBCForce.h" #include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/HarmonicAngleForce.h" #include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h" #include "openmm/HarmonicBondForce.h"
#include "openmm/Integrator.h" #include "openmm/Integrator.h"
......
openmmapi/include/openmm/GBVIForce.h deleted 100644 → 0
View file @ 9af3e56b
#ifndef OPENMM_GBVIFORCEFIELD_H_
#define OPENMM_GBVIFORCEFIELD_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "Force.h"
#include <vector>
#include "internal/windowsExport.h"
namespace OpenMM {
/**
* This class implements an implicit solvation force using the GB/VI model.
* <p>
* To use this class, create a GBVIForce object, then call addParticle() once for each particle in the
* System to define its parameters. The number of particles for which you define GB/VI parameters must
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters().
*
* @deprecated This class is not supported by most platforms, and will eventually be removed. You can implement the same force with CustomGBForce.
*/
class OPENMM_EXPORT GBVIForce : public Force {
public:
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
/**
* No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/
NoCutoff = 0,
/**
* Interactions beyond the cutoff distance are ignored.
*/
CutoffNonPeriodic = 1,
/**
* Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
* each other particle. Interactions beyond the cutoff distance are ignored.
*/
CutoffPeriodic = 2,
};
/**
* This is an enumeration of the different methods that may be used for scaling of the Born radii.
*/
enum BornRadiusScalingMethod {
/**
* No scaling method is applied.
*/
NoScaling = 0,
/**
* Use quintic spline scaling function
*/
QuinticSpline = 1
};
/*
* Create a GBVIForce.
*/
GBVIForce();
/**
* Get the number of particles in the system.
*/
int getNumParticles() const {
return particles.size();
}
/**
* Add the GB/VI parameters for a particle. This should be called once for each particle
* in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
*
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GB/VI radius of the particle, measured in nm
* @param gamma the gamma parameter
* @return the index of the particle that was added
*/
int addParticle(double charge, double radius, double gamma);
/**
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @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;
/**
* Set the force field parameters for a particle.
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GB/VI radius of the particle, measured in nm
* @param gamma the gamma parameter
*/
void setParticleParameters(int index, double charge, double radius, double gamma);
/**
* Add a bond
*
* @param particle1 the index of the first particle
* @param particle2 the index of the second particle
* @param distance the distance between the two particles, measured in nm
* @return the index of the bond that was added
*/
int addBond(int particle1, int particle2, double distance);
/**
* Get the parameters defining a bond
*
* @param index the index of the bond for which to get parameters
* @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;
/**
* Set 1-2 bonds
*
* @param index index of the bond for which to set parameters
* @param particle1 index of first atom in bond
* @param particle2 index of second atom in bond
* @param bondLength bond length, measured in nm
*/
void setBondParameters( int index, int particle1, int particle2, double bondLength);
/**
* Get number of bonds
*
* @return number of bonds
*/
int getNumBonds() const;
/**
* Get the dielectric constant for the solvent.
*/
double getSolventDielectric() const {
return solventDielectric;
}
/**
* Set the dielectric constant for the solvent.
*/
void setSolventDielectric(double dielectric) {
solventDielectric = dielectric;
}
/**
* Get the dielectric constant for the solute.
*/
double getSoluteDielectric() const {
return soluteDielectric;
}
/**
* Set the dielectric constant for the solute.
*/
void setSoluteDielectric(double dielectric) {
soluteDielectric = dielectric;
}
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* Get Born radius scaling method
*/
BornRadiusScalingMethod getBornRadiusScalingMethod() const;
/**
* Set Born radius scaling method
*/
void setBornRadiusScalingMethod( BornRadiusScalingMethod method);
/**
* Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
double getQuinticLowerLimitFactor() const;
/**
* Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
void setQuinticLowerLimitFactor(double quinticLowerLimitFactor );
/**
* Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
double getQuinticUpperBornRadiusLimit() const;
/**
* Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
void setQuinticUpperBornRadiusLimit(double quinticUpperBornRadiusLimit);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == GBVIForce::CutoffPeriodic;
}
protected:
ForceImpl* createImpl() const;
private:
class ParticleInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, solventDielectric, soluteDielectric;
BornRadiusScalingMethod scalingMethod;
double quinticLowerLimitFactor, quinticUpperBornRadiusLimit;
class BondInfo;
std::vector<ParticleInfo> particles;
std::vector<BondInfo> bonds;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class GBVIForce::ParticleInfo {
public:
double charge, radius, gamma;
ParticleInfo() {
charge = radius = gamma = 0.0;
}
ParticleInfo(double charge, double radius, double gamma) :
charge(charge), radius(radius), gamma(gamma) {
}
};
/**
* This is an internal class used to record information about a bond.
* @private
*/
class GBVIForce::BondInfo {
public:
int particle1, particle2;
double bondLength;
BondInfo() {
bondLength = 0.0;
particle1 = -1;
particle2 = -1;
}
BondInfo(int atomIndex1, int atomIndex2, double bondLength) :
particle1(atomIndex1), particle2(atomIndex2), bondLength(bondLength) {
}
};
} // namespace OpenMM
#endif /*OPENMM_GBVIFORCEFIELD_H_*/
openmmapi/include/openmm/internal/GBVIForceImpl.h deleted 100644 → 0
View file @ 9af3e56b
#ifndef OPENMM_GBVIFORCEFIELDIMPL_H_
#define OPENMM_GBVIFORCEFIELDIMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ForceImpl.h"
#include "openmm/GBVIForce.h"
#include "openmm/Kernel.h"
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of GBVIForce.
*/
class GBVIForceImpl : public ForceImpl {
public:
GBVIForceImpl(const GBVIForce& owner);
void initialize(ContextImpl& context);
const GBVIForce& getOwner() const {
return owner;
}
// calculate scaled radii (Eq. 5 of Labute paper [JCC 29 1693-1698 2008])
void findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const;
// if bond info not set, then use bond forces/constraints
int getBondsFromForces(ContextImpl& context);
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
const GBVIForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_GBVIFORCEFIELDIMPL_H_*/
openmmapi/src/Context.cpp
View file @ cd4031f9
...@@ -115,9 +115,9 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const { ...@@ -115,9 +115,9 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
// Find the displacement to move it into the first periodic box. // Find the displacement to move it into the first periodic box.
Vec3 diff; Vec3 diff;
diff -= periodicBoxSize[0]*static_cast<int>(center[0]/periodicBoxSize[0][0]); diff += periodicBoxSize[2]*floor(center[2]/periodicBoxSize[2][2]);
diff -= periodicBoxSize[1]*static_cast<int>(center[1]/periodicBoxSize[1][1]); diff += periodicBoxSize[1]*floor((center[1]-diff[1])/periodicBoxSize[1][1]);
diff -= periodicBoxSize[2]*static_cast<int>(center[2]/periodicBoxSize[2][2]); diff += periodicBoxSize[0]*floor((center[0]-diff[0])/periodicBoxSize[0][0]);
// Translate all the particles in the molecule. // Translate all the particles in the molecule.
for (int j = 0; j < (int) molecules[i].size(); j++) { for (int j = 0; j < (int) molecules[i].size(); j++) {
......
openmmapi/src/GBVIForce.cpp deleted 100644 → 0
View file @ 9af3e56b
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/GBVIForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/internal/GBVIForceImpl.h"
#include <sstream>
using namespace OpenMM;
GBVIForce::GBVIForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), solventDielectric(78.3), soluteDielectric(1.0),
scalingMethod(QuinticSpline), quinticLowerLimitFactor(0.8), quinticUpperBornRadiusLimit(5.0) {
}
int GBVIForce::addParticle(double charge, double radius, double gamma) {
particles.push_back(ParticleInfo(charge, radius, gamma));
return particles.size()-1;
}
void GBVIForce::getParticleParameters(int index, double& charge, double& radius, double& gamma) const {
ASSERT_VALID_INDEX(index, particles);
charge = particles[index].charge;
radius = particles[index].radius;
gamma = particles[index].gamma;
}
void GBVIForce::setParticleParameters(int index, double charge, double radius, double gamma) {
ASSERT_VALID_INDEX(index, particles);
particles[index].charge = charge;
particles[index].radius = radius;
particles[index].gamma = gamma;
}
GBVIForce::NonbondedMethod GBVIForce::getNonbondedMethod() const {
return nonbondedMethod;
}
void GBVIForce::setNonbondedMethod(NonbondedMethod method) {
nonbondedMethod = method;
}
double GBVIForce::getCutoffDistance() const {
return cutoffDistance;
}
void GBVIForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod() const {
return scalingMethod;
}
void GBVIForce::setBornRadiusScalingMethod(BornRadiusScalingMethod method) {
scalingMethod = method;
}
double GBVIForce::getQuinticLowerLimitFactor() const {
return quinticLowerLimitFactor;
}
void GBVIForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor ){
quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
}
double GBVIForce::getQuinticUpperBornRadiusLimit() const {
return quinticUpperBornRadiusLimit;
}
void GBVIForce::setQuinticUpperBornRadiusLimit(double inputQuinticUpperBornRadiusLimit){
quinticUpperBornRadiusLimit = inputQuinticUpperBornRadiusLimit;
}
int GBVIForce::addBond(int particle1, int particle2, double bondLength) {
bonds.push_back(BondInfo(particle1, particle2, bondLength));
return bonds.size()-1;
}
void GBVIForce::setBondParameters( int index, int particle1, int particle2, double bondLength) {
ASSERT_VALID_INDEX(index, bonds);
bonds[index].particle1 = particle1;
bonds[index].particle2 = particle2;
bonds[index].bondLength = bondLength;
}
int GBVIForce::getNumBonds() const {
return (int) bonds.size();
}
void GBVIForce::getBondParameters(int index, int& bondIndex1, int& bondIndex2, double& bondLength) const {
ASSERT_VALID_INDEX(index, bonds);
bondIndex1 = bonds[index].particle1;
bondIndex2 = bonds[index].particle2;
bondLength = bonds[index].bondLength;
}
ForceImpl* GBVIForce::createImpl() const {
return new GBVIForceImpl(*this);
}
openmmapi/src/GBVIForceImpl.cpp deleted 100644 → 0
View file @ 9af3e56b
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/GBVIForceImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"
#include "openmm/kernels.h"
#include <vector>
#include <cmath>
#include <cstdio>
#include <sstream>
using namespace OpenMM;
using std::vector;
GBVIForceImpl::GBVIForceImpl(const GBVIForce& owner) : owner(owner) {
}
void GBVIForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcGBVIForceKernel::Name(), context);
if (owner.getNumParticles() != context.getSystem().getNumParticles())
throw OpenMMException("GBVIForce must have exactly as many particles as the System it belongs to.");
const System& system = context.getSystem();
int numberOfParticles = owner.getNumParticles();
int numberOfBonds = owner.getNumBonds();
// load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
// numberOfBonds < 1, indicating they were not set by the user
if( numberOfBonds < 1 && numberOfParticles > 1 ){
(void) fprintf( stderr, "Warning: no covalent bonds set for GB/VI force!\n" );
// getBondsFromForces( context );
// numberOfBonds = owner.getNumBonds();
}
std::vector< std::vector<int> > bondIndices;
bondIndices.resize( numberOfBonds );
std::vector<double> bondLengths;
bondLengths.resize( numberOfBonds );
for (int i = 0; i < numberOfBonds; i++) {
int particle1, particle2;
double bondLength;
owner.getBondParameters(i, particle1, particle2, bondLength);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
std::stringstream msg;
msg << "GBVISoftcoreForce: Illegal particle index: ";
msg << particle1;
throw OpenMMException(msg.str());
}
if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
std::stringstream msg;
msg << "GBVISoftcoreForce: Illegal particle index: ";
msg << particle2;
throw OpenMMException(msg.str());
}
if (bondLength < 0 ) {
std::stringstream msg;
msg << "GBVISoftcoreForce: negative bondlength: ";
msg << bondLength;
throw OpenMMException(msg.str());
}
bondIndices[i].push_back( particle1 );
bondIndices[i].push_back( particle2 );
bondLengths[i] = bondLength;
}
if (owner.getNonbondedMethod() == GBVIForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("GBVIForce: The cutoff distance cannot be greater than half the periodic box size.");
}
vector<double> scaledRadii;
scaledRadii.resize(numberOfParticles);
findScaledRadii( numberOfParticles, bondIndices, bondLengths, scaledRadii);
kernel.getAs<CalcGBVIForceKernel>().initialize(context.getSystem(), owner, scaledRadii);
}
/*
int GBVIForceImpl::getBondsFromForces(ContextImpl& context) {
// load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
const System& system = context.getSystem();
for (int i = 0; i < system.getNumForces(); i++) {
if (dynamic_cast<const HarmonicBondForce*>(&system.getForce(i)) != NULL) {
const HarmonicBondForce& force = dynamic_cast<const HarmonicBondForce&>(system.getForce(i));
for (int j = 0; j < force.getNumBonds(); ++j) {
int particle1, particle2;
double length, k;
force.getBondParameters(j, particle1, particle2, length, k);
owner.addBond( particle1, particle2, length );
}
break;
}
}
// Also treat constrained distances as bonds if mass of one particle is < (2 + epsilon) (~2=deuterium)
for (int j = 0; j < system.getNumConstraints(); j++) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
double mass1 = system.getParticleMass( particle1 );
double mass2 = system.getParticleMass( particle2 );
if( mass1 < 2.1 || mass2 < 2.1 ){
owner.addBond( particle1, particle2, distance );
}
}
return 0;
}
*/
void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const {
// load 1-2 indicies for each atom
std::vector<std::vector<int> > bonded12(numberOfParticles);
for (int i = 0; i < (int) bondIndices.size(); ++i) {
bonded12[bondIndices[i][0]].push_back(i);
bonded12[bondIndices[i][1]].push_back(i);
}
int errors = 0;
// compute scaled radii (Eq. 5 of Labute paper [JCC 29 p. 1693-1698 2008])
for (int j = 0; j < (int) bonded12.size(); ++j){
double charge;
double gamma;
double radiusJ;
double scaledRadiusJ;
owner.getParticleParameters(j, charge, radiusJ, gamma);
if( bonded12[j].size() == 0 && numberOfParticles > 1 ){
(void) fprintf( stderr, "Warning GBVIForceImpl::findScaledRadii atom %d has no covalent bonds; using atomic radius=%.3f.\n", j, radiusJ );
scaledRadiusJ = radiusJ;
// errors++;
} else {
double rJ2 = radiusJ*radiusJ;
// loop over bonded neighbors of atom j, applying Eq. 5 in Labute
scaledRadiusJ = 0.0;
for (int i = 0; i < (int) bonded12[j].size(); ++i){
int index = bonded12[j][i];
int bondedAtomIndex = (j == bondIndices[index][0]) ? bondIndices[index][1] : bondIndices[index][0];
double radiusI;
owner.getParticleParameters(bondedAtomIndex, charge, radiusI, gamma);
double rI2 = radiusI*radiusI;
double a_ij = (radiusI - bondLengths[index]);
a_ij *= a_ij;
a_ij = (rJ2 - a_ij)/(2.0*bondLengths[index]);
double a_ji = radiusJ - bondLengths[index];
a_ji *= a_ji;
a_ji = (rI2 - a_ji)/(2.0*bondLengths[index]);
scaledRadiusJ += a_ij*a_ij*(3.0*radiusI - a_ij) + a_ji*a_ji*( 3.0*radiusJ - a_ji );
}
scaledRadiusJ = (radiusJ*radiusJ*radiusJ) - 0.125*scaledRadiusJ;
if( scaledRadiusJ > 0.0 ){
scaledRadiusJ = 0.95*pow( scaledRadiusJ, (1.0/3.0) );
} else {
scaledRadiusJ = 0.0;
}
}
scaledRadii[j] = scaledRadiusJ;
}
// abort if errors
if( errors ){
throw OpenMMException("GBVIForceImpl::findScaledRadii errors -- aborting");
}
}
double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
if ((groups&(1<<owner.getForceGroup())) != 0)
return kernel.getAs<CalcGBVIForceKernel>().execute(context, includeForces, includeEnergy);
return 0.0;
}
std::vector<std::string> GBVIForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcGBVIForceKernel::Name());
return names;
}
platforms/reference/include/GBVIParameters.h deleted 100644 → 0
View file @ 9af3e56b
/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __GBVIParameters_H__
#define __GBVIParameters_H__
#include "RealVec.h"
#include <vector>
namespace OpenMM {
class GBVIParameters {
public:
/**
* This is an enumeration of the different methods that may be used for scaling of the Born radii.
*/
enum BornRadiusScalingMethod {
/**
* No scaling method is applied.
*/
NoScaling = 0,
/**
* Use quintic spline scaling function
*/
QuinticSpline = 1
};
private:
int _numberOfAtoms;
RealOpenMM _solventDielectric;
RealOpenMM _soluteDielectric;
RealOpenMM _electricConstant;
// parameter vectors
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _scaledRadii;
std::vector<RealOpenMM> _gammaParameters;
// cutoff and periodic boundary conditions
bool _cutoff;
bool _periodic;
OpenMM::RealVec _periodicBoxVectors[3];
RealOpenMM _cutoffDistance;
int _bornRadiusScalingMethod;
RealOpenMM _quinticLowerLimitFactor;
RealOpenMM _quinticUpperBornRadiusLimit;
public:
/**---------------------------------------------------------------------------------------
GBVIParameters constructor (Simbios)
@param numberOfAtoms number of atoms
--------------------------------------------------------------------------------------- */
GBVIParameters(int numberOfAtoms);
/**---------------------------------------------------------------------------------------
GBVIParameters destructor (Simbios)
--------------------------------------------------------------------------------------- */
~GBVIParameters();
/**---------------------------------------------------------------------------------------
Get number of atoms
@return number of atoms
--------------------------------------------------------------------------------------- */
int getNumberOfAtoms() const;
/**---------------------------------------------------------------------------------------
Get electric constant
@return electric constant
--------------------------------------------------------------------------------------- */
RealOpenMM getElectricConstant() const;
/**---------------------------------------------------------------------------------------
Get solvent dielectric
@return solvent dielectric
--------------------------------------------------------------------------------------- */
RealOpenMM getSolventDielectric() const;
/**---------------------------------------------------------------------------------------
Set solvent dielectric
@param solventDielectric solvent dielectric
--------------------------------------------------------------------------------------- */
void setSolventDielectric(RealOpenMM solventDielectric);
/**---------------------------------------------------------------------------------------
Get solute dielectric
@return soluteDielectric
--------------------------------------------------------------------------------------- */
RealOpenMM getSoluteDielectric() const;
/**---------------------------------------------------------------------------------------
Set solute dielectric
@param soluteDielectric solute dielectric
--------------------------------------------------------------------------------------- */
void setSoluteDielectric(RealOpenMM soluteDielectric);
/**---------------------------------------------------------------------------------------
Return scaled radii
@return array
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getScaledRadii() const;
/**---------------------------------------------------------------------------------------
Return scaled radii
@return array
--------------------------------------------------------------------------------------- */
void setScaledRadii(const std::vector<RealOpenMM>& scaledRadii);
/**---------------------------------------------------------------------------------------
Get AtomicRadii array w/ dielectric offset applied
@return array of atom volumes
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
@param atomicRadii vector of atomic radii
--------------------------------------------------------------------------------------- */
void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
/**---------------------------------------------------------------------------------------
Get GammaParameters array
@return array of gamma values
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getGammaParameters() const;
/**---------------------------------------------------------------------------------------
Set GammaParameters array
@param gammaParameters array of gamma parameters
--------------------------------------------------------------------------------------- */
void setGammaParameters(const std::vector<RealOpenMM>& gammaParameters);
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
--------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
Get whether to use a cutoff.
--------------------------------------------------------------------------------------- */
bool getUseCutoff();
/**---------------------------------------------------------------------------------------
Get the cutoff distance.
--------------------------------------------------------------------------------------- */
RealOpenMM getCutoffDistance();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get whether to use periodic boundary conditions.
--------------------------------------------------------------------------------------- */
bool getPeriodic();
/**---------------------------------------------------------------------------------------
Get the periodic box dimension
--------------------------------------------------------------------------------------- */
const OpenMM::RealVec* getPeriodicBox();
/**---------------------------------------------------------------------------------------
Get tau prefactor
@return (1/e1 - 1/e0), where e1 = solute dielectric, e0 = solvent dielectric
--------------------------------------------------------------------------------------- */
RealOpenMM getTau() const;
/**---------------------------------------------------------------------------------------
Get bornRadiusScalingMethod
@return bornRadiusScalingMethod
--------------------------------------------------------------------------------------- */
int getBornRadiusScalingMethod() const;
/**---------------------------------------------------------------------------------------
Set bornRadiusScalingMethod
@param bornRadiusScalingMethod bornRadiusScalingMethod
--------------------------------------------------------------------------------------- */
void setBornRadiusScalingMethod(int bornRadiusScalingMethod);
/**---------------------------------------------------------------------------------------
Get quinticLowerLimitFactor
@return quinticLowerLimitFactor
--------------------------------------------------------------------------------------- */
RealOpenMM getQuinticLowerLimitFactor() const;
/**---------------------------------------------------------------------------------------
Set quinticLowerLimitFactor
@param quinticLowerLimitFactor quinticLowerLimitFactor
--------------------------------------------------------------------------------------- */
void setQuinticLowerLimitFactor(RealOpenMM quinticLowerLimitFactor);
/**---------------------------------------------------------------------------------------
Get quinticUpperBornRadiusLimit
@return quinticUpperBornRadiusLimit
--------------------------------------------------------------------------------------- */
RealOpenMM getQuinticUpperBornRadiusLimit() const;
/**---------------------------------------------------------------------------------------
Set quinticUpperBornRadiusLimit
@param quinticUpperBornRadiusLimit quinticUpperBornRadiusLimit
--------------------------------------------------------------------------------------- */
void setQuinticUpperBornRadiusLimit(RealOpenMM quinticUpperSplineLimit);
};
} // namespace OpenMM
#endif // __GBVIParameters_H__
platforms/reference/include/ReferenceGBVI.h deleted 100644 → 0
View file @ 9af3e56b
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceGBVI_H__
#define __ReferenceGBVI_H__
#include <vector>
#include "RealVec.h"
#include "GBVIParameters.h"
namespace OpenMM {
class ReferenceGBVI {
private:
// GB/VI parameters
GBVIParameters* _gbviParameters;
std::vector<RealOpenMM> _switchDeriviative;
public:
/**---------------------------------------------------------------------------------------
Constructor
@param implicitSolventParameters ImplicitSolventParameters reference
@return CpuImplicitSolvent object
--------------------------------------------------------------------------------------- */
ReferenceGBVI(GBVIParameters* gbviParameters);
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceGBVI();
/**---------------------------------------------------------------------------------------
Return GBVIParameters
@return GBVIParameters
--------------------------------------------------------------------------------------- */
GBVIParameters* getGBVIParameters() const;
/**---------------------------------------------------------------------------------------
Set ImplicitSolventParameters
@param ImplicitSolventParameters
--------------------------------------------------------------------------------------- */
void setGBVIParameters(GBVIParameters* gbviParameters);
/**---------------------------------------------------------------------------------------
Get Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008])
@param atomCoordinates atomic coordinates
@param bornRadii output array of Born radii
@param gbviChain not used
--------------------------------------------------------------------------------------- */
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
/**---------------------------------------------------------------------------------------
Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return volume
--------------------------------------------------------------------------------------- */
static RealOpenMM getVolume(RealOpenMM r, RealOpenMM R, RealOpenMM S);
/**---------------------------------------------------------------------------------------
Get L (analytical solution for volume integrals)
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static RealOpenMM getL(RealOpenMM r, RealOpenMM x, RealOpenMM S);
/**---------------------------------------------------------------------------------------
Get partial derivative of L wrt r
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static RealOpenMM dL_dr(RealOpenMM r, RealOpenMM x, RealOpenMM S);
/**---------------------------------------------------------------------------------------
Get partial derivative of L wrt x
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static RealOpenMM dL_dx(RealOpenMM r, RealOpenMM x, RealOpenMM S);
/**---------------------------------------------------------------------------------------
Sgb function
@param t r*r*G_i*G_j
@return Sgb (p. 1694 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static RealOpenMM Sgb(RealOpenMM t);
/**---------------------------------------------------------------------------------------
Get GB/VI energy
@param atomCoordinates atomic coordinates
@param partialCharges partial charges
@return energy
--------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges);
/**---------------------------------------------------------------------------------------
Get GB/VI forces
@param atomCoordinates atomic coordinates
@param partialCharges partial charges
@param forces output forces
--------------------------------------------------------------------------------------- */
void computeBornForces(std::vector<OpenMM::RealVec>& atomCoordinates,
const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
/**---------------------------------------------------------------------------------------
Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return volume
--------------------------------------------------------------------------------------- */
static double getVolumeD(double r, double R, double S);
/**---------------------------------------------------------------------------------------
Get L (analytical solution for volume integrals)
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static double getLD(double r, double x, double S);
/**---------------------------------------------------------------------------------------
Get partial derivative of L wrt r
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static double dL_drD(double r, double x, double S);
/**---------------------------------------------------------------------------------------
Get partial derivative of L wrt x
@param r distance between atoms i & j
@param R atomic radius
@param S scaled atomic radius
@return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
--------------------------------------------------------------------------------------- */
static double dL_dxD(double r, double x, double S);
/**---------------------------------------------------------------------------------------
Return OBC chain derivative: size = _obcParameters->getNumberOfAtoms()
On first call, memory for array is allocated if not set
@return array
--------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& getSwitchDeriviative();
/**---------------------------------------------------------------------------------------
Compute quintic spline value and associated derviative
@param x value to compute spline at
@param rl lower cutoff value
@param ru upper cutoff value
@param outValue value of spline at x
@param outDerivative value of derivative of spline at x
--------------------------------------------------------------------------------------- */
void quinticSpline(RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
RealOpenMM* outValue, RealOpenMM* outDerivative);
/**---------------------------------------------------------------------------------------
Compute Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008])
and quintic splice switching function
@param atomicRadius3 atomic radius cubed
@param bornSum Born sum (volume integral)
@param gbviParameters Gbvi parameters (parameters used in spline
QuinticLowerLimitFactor & QuinticUpperBornRadiusLimit)
@param bornRadius output Born radius
@param switchDeriviative output switching function deriviative
--------------------------------------------------------------------------------------- */
void computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealOpenMM bornSum,
GBVIParameters* gbviParameters,
RealOpenMM* bornRadius, RealOpenMM* switchDeriviative);
};
} // namespace OpenMM
#endif // __ReferenceGBVI_H__
platforms/reference/include/ReferenceKernels.h
View file @ cd4031f9
...@@ -43,7 +43,6 @@ ...@@ -43,7 +43,6 @@
namespace OpenMM { namespace OpenMM {
class ReferenceObc; class ReferenceObc;
class ReferenceGBVI;
class ReferenceAndersenThermostat; class ReferenceAndersenThermostat;
class ReferenceCustomCentroidBondIxn; class ReferenceCustomCentroidBondIxn;
class ReferenceCustomCompoundBondIxn; class ReferenceCustomCompoundBondIxn;
...@@ -683,37 +682,6 @@ private: ...@@ -683,37 +682,6 @@ private:
bool isPeriodic; bool isPeriodic;
}; };
/**
* This kernel is invoked by GBVIForce to calculate the forces acting on the system.
*/
class ReferenceCalcGBVIForceKernel : public CalcGBVIForceKernel {
public:
ReferenceCalcGBVIForceKernel(std::string name, const Platform& platform) : CalcGBVIForceKernel(name, platform) {
}
~ReferenceCalcGBVIForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the GBVIForce this kernel will be used for
* @param scaled radii the scaled radii (Eq. 5 of Labute paper)
*/
void initialize(const System& system, const GBVIForce& force, const std::vector<double> & scaledRadii);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
ReferenceGBVI * gbvi;
std::vector<RealOpenMM> charges;
bool isPeriodic;
};
/** /**
* This kernel is invoked by CustomGBForce to calculate the forces acting on the system. * This kernel is invoked by CustomGBForce to calculate the forces acting on the system.
*/ */
......
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ cd4031f9
...@@ -70,8 +70,6 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla ...@@ -70,8 +70,6 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceCalcCustomTorsionForceKernel(name, platform); return new ReferenceCalcCustomTorsionForceKernel(name, platform);
if (name == CalcGBSAOBCForceKernel::Name()) if (name == CalcGBSAOBCForceKernel::Name())
return new ReferenceCalcGBSAOBCForceKernel(name, platform); return new ReferenceCalcGBSAOBCForceKernel(name, platform);
if (name == CalcGBVIForceKernel::Name())
return new ReferenceCalcGBVIForceKernel(name, platform);
if (name == CalcCustomGBForceKernel::Name()) if (name == CalcCustomGBForceKernel::Name())
return new ReferenceCalcCustomGBForceKernel(name, platform); return new ReferenceCalcCustomGBForceKernel(name, platform);
if (name == CalcCustomExternalForceKernel::Name()) if (name == CalcCustomExternalForceKernel::Name())
......
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