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Commit 70ff98db authored by Peter Eastman's avatar Peter Eastman
Browse files

Removed lots of units code from AMBER file loader, which made it unnecessarily slow

parent 073e1a76
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Showing with 28 additions and 24 deletions
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
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......@@ -12,7 +12,7 @@ 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) 2012 Stanford University and the Authors.
Portions copyright (c) 2012-2013 Stanford University and the Authors.
Authors: Randall J. Radmer, John D. Chodera, Peter Eastman
Contributors: Christoph Klein, Michael R. Shirts
......@@ -217,7 +217,7 @@ class PrmtopLoader(object):
raw_masses=self._raw_data['MASS']
for ii in range(self.getNumAtoms()):
self._massList.append(float(raw_masses[ii]))
self._massList = units.Quantity(self._massList, units.amu)
self._massList = self._massList
return self._massList
def getCharges(self):
......@@ -231,7 +231,7 @@ class PrmtopLoader(object):
raw_charges=self._raw_data['CHARGE']
for ii in range(self.getNumAtoms()):
self._chargeList.append(float(raw_charges[ii])/18.2223)
self._chargeList = units.Quantity(self._chargeList, units.elementary_charge)
self._chargeList = self._chargeList
return self._chargeList
def getAtomName(self, iAtom):
......@@ -300,6 +300,8 @@ class PrmtopLoader(object):
except AttributeError:
pass
self._nonbondTerms=[]
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
energyConversionFactor = units.kilocalorie_per_mole.conversion_factor_to(units.kilojoule_per_mole)
for iAtom in range(self.getNumAtoms()):
numTypes=self.getNumTypes()
atomTypeIndexes=self._getAtomTypeIndexes()
......@@ -315,8 +317,8 @@ class PrmtopLoader(object):
except ZeroDivisionError:
rMin = 1.0
epsilon = 0.0
rVdw = units.Quantity(rMin/2.0, units.angstrom)
epsilon = units.Quantity(epsilon, units.kilocalorie_per_mole)
rVdw = rMin/2.0*lengthConversionFactor
epsilon = epsilon*energyConversionFactor
self._nonbondTerms.append( (rVdw, epsilon) )
return self._nonbondTerms
......@@ -324,6 +326,8 @@ class PrmtopLoader(object):
forceConstant=self._raw_data["BOND_FORCE_CONSTANT"]
bondEquil=self._raw_data["BOND_EQUIL_VALUE"]
returnList=[]
forceConstConversionFactor = (units.kilocalorie_per_mole/(units.angstrom*units.angstrom)).conversion_factor_to(units.kilojoule_per_mole/(units.nanometer*units.nanometer))
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
for ii in range(0,len(bondPointers),3):
if int(bondPointers[ii])<0 or \
int(bondPointers[ii+1])<0:
......@@ -331,11 +335,10 @@ class PrmtopLoader(object):
% ((bondPointers[ii],
bondPointers[ii+1]),))
iType=int(bondPointers[ii+2])-1
forceConstUnit=units.kilocalorie_per_mole/(units.angstrom*units.angstrom)
returnList.append((int(bondPointers[ii])/3,
int(bondPointers[ii+1])/3,
units.Quantity(float(forceConstant[iType]), forceConstUnit),
units.Quantity(float(bondEquil[iType]), units.angstrom)))
float(forceConstant[iType])*forceConstConversionFactor,
float(bondEquil[iType])*lengthConversionFactor))
return returnList
def getBondsWithH(self):
......@@ -370,6 +373,7 @@ class PrmtopLoader(object):
anglePointers = self._raw_data["ANGLES_INC_HYDROGEN"] \
+self._raw_data["ANGLES_WITHOUT_HYDROGEN"]
self._angleList=[]
forceConstConversionFactor = (units.kilocalorie_per_mole/(units.radian*units.radian)).conversion_factor_to(units.kilojoule_per_mole/(units.radian*units.radian))
for ii in range(0,len(anglePointers),4):
if int(anglePointers[ii])<0 or \
int(anglePointers[ii+1])<0 or \
......@@ -379,12 +383,11 @@ class PrmtopLoader(object):
anglePointers[ii+1],
anglePointers[ii+2]),))
iType=int(anglePointers[ii+3])-1
forceConstUnit=units.kilocalorie_per_mole/(units.radian*units.radian)
self._angleList.append((int(anglePointers[ii])/3,
int(anglePointers[ii+1])/3,
int(anglePointers[ii+2])/3,
units.Quantity(float(forceConstant[iType]), forceConstUnit),
units.Quantity(float(angleEquil[iType])*180/math.pi, units.degree)))
float(forceConstant[iType])*forceConstConversionFactor,
float(angleEquil[iType])))
return self._angleList
def getDihedrals(self):
......@@ -399,6 +402,7 @@ class PrmtopLoader(object):
dihedralPointers = self._raw_data["DIHEDRALS_INC_HYDROGEN"] \
+self._raw_data["DIHEDRALS_WITHOUT_HYDROGEN"]
self._dihedralList=[]
forceConstConversionFactor = (units.kilocalorie_per_mole).conversion_factor_to(units.kilojoule_per_mole)
for ii in range(0,len(dihedralPointers),5):
if int(dihedralPointers[ii])<0 or int(dihedralPointers[ii+1])<0:
raise Exception("Found negative dihedral atom pointers %s"
......@@ -411,8 +415,8 @@ class PrmtopLoader(object):
int(dihedralPointers[ii+1])/3,
abs(int(dihedralPointers[ii+2]))/3,
abs(int(dihedralPointers[ii+3]))/3,
units.Quantity(float(forceConstant[iType]), units.kilocalorie_per_mole),
units.Quantity(float(phase[iType])*180/math.pi, units.degree),
float(forceConstant[iType])*forceConstConversionFactor,
float(phase[iType]),
int(0.5+float(periodicity[iType]))))
return self._dihedralList
......@@ -431,7 +435,7 @@ class PrmtopLoader(object):
(rVdwI, epsilonI) = nonbondTerms[iAtom]
(rVdwL, epsilonL) = nonbondTerms[lAtom]
rMin = (rVdwI+rVdwL)
epsilon = units.sqrt(epsilonI*epsilonL)
epsilon = math.sqrt(epsilonI*epsilonL)
returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon))
return returnList
......@@ -482,8 +486,9 @@ class PrmtopLoader(object):
screen[i] = 0.602256336067
else:
screen[i] = 0.5
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
for iAtom in range(len(radii)):
self._gb_List.append((float(radii[iAtom])*units.angstrom, float(screen[iAtom])))
self._gb_List.append((float(radii[iAtom])*lengthConversionFactor, float(screen[iAtom])))
return self._gb_List
def getBoxBetaAndDimensions(self):
......@@ -612,8 +617,9 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
atomConstraints = [[]]*system.getNumParticles()
for i in range(system.getNumConstraints()):
c = system.getConstraintParameters(i)
atomConstraints[c[0]].append((c[1], c[2]))
atomConstraints[c[1]].append((c[0], c[2]))
distance = c[2].value_in_units(units.nanometer)
atomConstraints[c[0]].append((c[1], distance))
atomConstraints[c[1]].append((c[0], distance))
for (iAtom, jAtom, kAtom, k, aMin) in prmtop.getAngles():
if shake == 'h-angles':
type1 = prmtop.getAtomType(iAtom)
......@@ -634,7 +640,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
l2 = bond[1]
# Compute the distance between atoms and add a constraint
length = units.sqrt(l1*l1 + l2*l2 - 2*l1*l2*units.cos(aMin))
length = math.sqrt(l1*l1 + l2*l2 - 2*l1*l2*math.cos(aMin))
system.addConstraint(iAtom, kAtom, length)
if flexibleConstraints or not constrained:
force.addAngle(iAtom, jAtom, kAtom, aMin, 2*k)
......@@ -715,7 +721,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
# Add Excluded Atoms
excludedAtoms=prmtop.getExcludedAtoms()
excludeParams = (0.0*units.elementary_charge**2, 1.0*units.angstroms, 0.0*units.kilocalories_per_mole)
excludeParams = (0.0, 0.1, 0.0)
for iAtom in range(prmtop.getNumAtoms()):
for jAtom in excludedAtoms[iAtom]:
if min((iAtom, jAtom), (jAtom, iAtom)) in excludedAtomPairs: continue
......@@ -771,13 +777,13 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if len(waterO[res]) == 1 and len(waterH[res]) == 2:
if len(waterEP[res]) == 1:
# Four point water
weightH = distOE[res]/units.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
weightH = distOE[res]/math.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
system.setVirtualSite(waterEP[res][0], mm.ThreeParticleAverageSite(waterO[res][0], waterH[res][0], waterH[res][1], 1-weightH, weightH/2, weightH/2))
elif len(waterEP[res]) == 2:
# Five point water
weightH = cosOOP*distOE[res]/units.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
weightH = cosOOP*distOE[res]/math.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
angleHOH = 2*math.asin(0.5*distHH[res]/distOH[res])
lenCross = (distOH[res].value_in_unit(units.nanometer)**2)*math.sin(angleHOH)*units.nanometer
lenCross = (distOH[res]**2)*math.sin(angleHOH)
weightCross = sinOOP*distOE[res]/lenCross
system.setVirtualSite(waterEP[res][0], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, weightCross))
system.setVirtualSite(waterEP[res][1], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, -weightCross))
......@@ -960,5 +966,3 @@ def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbos
if __name__ == "__main__":
import doctest
doctest.testmod()
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