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Commit ba5e21ff authored by peastman's avatar peastman
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Merge pull request #461 from swails/amber_restarts 

Rewrite Amber inpcrd file parsers
parents 49fe8122 90dfedb8
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Showing with 11989 additions and 157 deletions
wrappers/python/CMakeLists.txt
View file @ ba5e21ff
......@@ -55,8 +55,12 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.parm7"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rst7"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ncrst"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.par"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
)
......
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
View file @ ba5e21ff
......@@ -6,9 +6,9 @@ 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) 2012-2014 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Contributors: Jason Swails
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -31,87 +31,97 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
__author__ = "Peter Eastman"
__version__ = "1.0"
from functools import wraps
from simtk.openmm.app.internal import amber_file_parser
from simtk.unit import Quantity, nanometers, picoseconds
import warnings
try:
import numpy
import numpy as np
except:
pass
np = None
def numpy_protector(func):
"""
Decorator to emit useful error messages if users try to request numpy
processing if numpy is not available. Raises ImportError if numpy could not
be found
"""
@wraps(func)
def wrapper(self, asNumpy=False):
if asNumpy and np is None:
raise ImportError('Could not import numpy. Cannot set asNumpy=True')
return func(self, asNumpy=asNumpy)
return wrapper
class AmberInpcrdFile(object):
"""AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it."""
def __init__(self, file, loadVelocities=False, loadBoxVectors=False):
def __init__(self, file, loadVelocities=None, loadBoxVectors=None):
"""Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
Unfortunately, it is sometimes impossible to determine from the file itself exactly what data
it contains. You therefore must specify in advance what data to load. It is stored into this
object's "positions", "velocities", and "boxVectors" fields.
Parameters:
- file (string) the name of the file to load
- loadVelocities (boolean=False) whether to load velocities from the file
- loadBoxVectors (boolean=False) whether to load the periodic box vectors
- loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present
- loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present
"""
results = amber_file_parser.readAmberCoordinates(file, read_velocities=loadVelocities, read_box=loadBoxVectors)
if loadVelocities:
## The atom positions read from the inpcrd file
self.positions = results[0]
if loadBoxVectors:
## The periodic box vectors read from the inpcrd file
self.boxVectors = results[1]
## The atom velocities read from the inpcrd file
self.velocities = results[2]
else:
self.velocities = results[1]
elif loadBoxVectors:
self.positions = results[0]
self.boxVectors = results[1]
else:
self.positions = results
self.file = file
if loadVelocities is not None or loadBoxVectors is not None:
warnings.warn('loadVelocities and loadBoxVectors have been '
'deprecated. velocities and box information '
'is loaded automatically if the inpcrd file contains '
'them.', DeprecationWarning)
results = amber_file_parser.readAmberCoordinates(file)
self.positions, self.velocities, self.boxVectors = results
# Cached numpy arrays
self._numpyPositions = None
if loadVelocities:
self._numpyVelocities = None
if loadBoxVectors:
self._numpyBoxVectors = None
self._numpyVelocities = None
self._numpyBoxVectors = None
@numpy_protector
def getPositions(self, asNumpy=False):
"""Get the atomic positions.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
"""
"""
if asNumpy:
if self._numpyPositions is None:
self._numpyPositions = Quantity(numpy.array(self.positions.value_in_unit(nanometers)), nanometers)
self._numpyPositions = Quantity(np.array(self.positions.value_in_unit(nanometers)), nanometers)
return self._numpyPositions
return self.positions
@numpy_protector
def getVelocities(self, asNumpy=False):
"""Get the atomic velocities.
Parameters:
- asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s
"""
"""
if self.velocities is None:
raise AttributeError('velocities not found in %s' % self.file)
if asNumpy:
if self._numpyVelocities is None:
self._numpyVelocities = Quantity(numpy.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
self._numpyVelocities = Quantity(np.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
return self._numpyVelocities
return self.velocities
@numpy_protector
def getBoxVectors(self, asNumpy=False):
"""Get the periodic box vectors.
Parameters:
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
"""
"""
if self.boxVectors is None:
raise AttributeError('Box information not found in %s' % self.file)
if asNumpy:
if self._numpyBoxVectors is None:
self._numpyBoxVectors = []
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[0].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[1].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[0].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[1].value_in_unit(nanometers)), nanometers))
self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
return self._numpyBoxVectors
return self.boxVectors
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ ba5e21ff
......@@ -40,15 +40,14 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
#=============================================================================================
import os
import os.path
import re
import math
from math import ceil, cos, sin, asin, sqrt, pi
import warnings
try:
import numpy
import numpy as np
except:
pass
np = None
import simtk.unit as units
import simtk.openmm
......@@ -74,6 +73,9 @@ POINTER_LABELS = """
# Pointer labels (above) as a list, not string.
POINTER_LABEL_LIST = POINTER_LABELS.replace(',', '').split()
VELSCALE = 20.455 # velocity conversion factor to angstroms/picosecond
TINY = 1.0e-8
class PrmtopLoader(object):
"""Parsed AMBER prmtop file.
......@@ -83,14 +85,14 @@ class PrmtopLoader(object):
Parse a prmtop file of alanine dipeptide in implicit solvent.
>>> import os, os.path
>>> import os
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-gbsa')
>>> prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop')
>>> prmtop = PrmtopLoader(prmtop_filename)
Parse a prmtop file of alanine dipeptide in explicit solvent.
>>> import os, os.path
>>> import os
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
>>> prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop')
>>> prmtop = PrmtopLoader(prmtop_filename)
......@@ -437,7 +439,7 @@ class PrmtopLoader(object):
(rVdwI, epsilonI) = nonbondTerms[iAtom]
(rVdwL, epsilonL) = nonbondTerms[lAtom]
rMin = (rVdwI+rVdwL)
epsilon = math.sqrt(epsilonI*epsilonL)
epsilon = sqrt(epsilonI*epsilonL)
try:
iScee = float(self._raw_data["SCEE_SCALE_FACTOR"][iidx])
except KeyError:
......@@ -708,7 +710,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
l2 = bond[1]
# Compute the distance between atoms and add a constraint
length = math.sqrt(l1*l1 + l2*l2 - 2*l1*l2*math.cos(aMin))
length = sqrt(l1*l1 + l2*l2 - 2*l1*l2*cos(aMin))
system.addConstraint(iAtom, kAtom, length)
if flexibleConstraints or not constrained:
force.addAngle(iAtom, jAtom, kAtom, aMin, 2*k)
......@@ -739,10 +741,17 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
# System is periodic.
# Set periodic box vectors for periodic system
(boxBeta, boxX, boxY, boxZ) = prmtop.getBoxBetaAndDimensions()
d0 = units.Quantity(0.0, units.angstroms)
xVec = units.Quantity((boxX, d0, d0))
yVec = units.Quantity((d0, boxY, d0))
zVec = units.Quantity((d0, d0, boxZ))
boxBeta = boxBeta.value_in_unit(units.degrees)
boxX = boxX.value_in_unit(units.angstroms)
boxY = boxY.value_in_unit(units.angstroms)
boxZ = boxZ.value_in_unit(units.angstroms)
tmp = [[0.0, 0.0, 0.0],[0.0, 0.0, 0.0],[0.0, 0.0, 0.0]]
_box_vectors_from_lengths_angles([boxX, boxY, boxZ],
[boxBeta, boxBeta, boxBeta],
tmp)
xVec = units.Quantity(tmp[0], units.angstroms)
yVec = units.Quantity(tmp[1], units.angstroms)
zVec = units.Quantity(tmp[2], units.angstroms)
system.setDefaultPeriodicBoxVectors(xVec, yVec, zVec)
# Set cutoff.
......@@ -848,13 +857,13 @@ 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]/math.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
weightH = distOE[res]/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]/math.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
angleHOH = 2*math.asin(0.5*distHH[res]/distOH[res])
lenCross = (distOH[res]**2)*math.sin(angleHOH)
weightH = cosOOP*distOE[res]/sqrt(distOH[res]**2-(0.5*distHH[res])**2)
angleHOH = 2*asin(0.5*distHH[res]/distOH[res])
lenCross = (distOH[res]**2)*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))
......@@ -917,134 +926,395 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
return system
#=============================================================================================
# AMBER INPCRD loader
# AMBER INPCRD loader classes
#=============================================================================================
def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbose=False, asNumpy=False):
class AmberAsciiRestart(object):
"""
Class responsible for parsing Amber coordinates in the ASCII format.
Automatically detects the presence of velocities or box parameters in the
file.
Parameters
----------
filename : str
Name of the restart file
asNumpy : bool (False)
Load the coordinates, velocities, and box as numpy ndarray objects
Attributes
----------
coordinates : natom x 3 array, Quantity
Particle positions with units of length
velocities : natom x 3 array, Quantity
Particle velocities with units of length per time (None if velocities
are not present in the inpcrd file)
boxVectors : 3 x 3 array, Quantity
Box vectors with units of length (None if no box is present in the
inpcrd file)
time : float, Quantity
Simulation time (None if not present) with units of time
title : str
Title of the inpcrd file
filename : str
Name of the file we are parsing
natom : int
Number of atoms in the inpcrd file
Raises
------
`IOError' if the file does not exist
`TypeError' if the format of the file is not recognized
`ValueError' if not all fields are numbers (for example, if a field is
filled with ****'s)
`IndexError' if the file is empty
`ImportError' if numpy is requested but could not be imported
Example
-------
>>> f = AmberAsciiRestart('alanine-dipeptide.inpcrd')
>>> coordinates = f.coordinates
"""
def __init__(self, filename, asNumpy=False):
# Make sure numpy is available if requested
if asNumpy and np is None:
raise ImportError('asNumpy=True: numpy is not available')
self._asNumpy = asNumpy
self.filename = filename
with open(filename, 'r') as f:
lines = f.readlines()
# Get rid of trailing blank lines
while lines and not lines[-1].strip():
lines.pop()
self._parse(lines)
def __str__(self):
return self.filename
def _parse(self, lines):
""" Parses through the inpcrd file """
global VELSCALE
self.title = lines[0].strip()
self.time = None
try:
words = lines[1].split()
self.natom = int(words[0])
except (IndexError, ValueError):
raise TypeError('Unrecognized file type [%s]' % self.filename)
if len(words) >= 2:
self.time = float(words[1]) * units.picoseconds
if len(lines) == int(ceil(self.natom / 2.0) + 2):
hasbox = hasvels = False
self.boxVectors = self.velocities = None
elif self.natom in (1, 2) and len(lines) == 4:
# This is the _only_ case where line counting does not work -- there
# is either 1 or 2 atoms and there are 4 lines. The 1st 3 lines are
# the title, natom/time, and coordinates. The 4th are almost always
# velocities since Amber does not make it easy to make a periodic
# system with only 2 atoms. If natom is 1, the 4th line is either a
# velocity (3 #'s) or a box (6 #'s). If natom is 2, it is a bit
# ambiguous. However, velocities (which are scaled by 20.445) have a
# ~0% chance of being 60+, so we can pretty easily tell if the last
# line has box dimensions and angles or velocities. I cannot
# envision a _plausible_ scenario where the detection here will fail
# in real life.
line = lines[3]
if self.natom == 1:
tmp = [line[i:i+12] for i in range(0, 72, 12) if line[i:i+12]]
if len(tmp) == 3:
hasvels = True
hasbox = False
self.boxVectors = False
elif len(tmp) == 6:
hasbox = True
hasvels = False
self.velocities = None
else:
raise TypeError('Unrecognized line in restart file %s' %
self.filename)
else:
# Ambiguous case
tmp = [float(line[i:i+12]) >= 60.0 for i in range(0, 72, 12)]
if any(tmp):
hasbox = True
hasvels = False
self.velocities = False
else:
hasvels = True
hasbox = False
self.boxVectors = False
elif len(lines) == int(ceil(self.natom / 2.0) + 3):
hasbox = True
hasvels = False
self.velocities = None
elif len(lines) == int(2 * ceil(self.natom / 2.0) + 2):
hasbox = False
self.boxVectors = None
hasvels = True
elif len(lines) == int(2 * ceil(self.natom / 2.0) + 3):
hasbox = hasvels = True
else:
raise TypeError('Badly formatted restart file. Has %d lines '
'for %d atoms.' % (len(self.lines), self.natom))
if self._asNumpy:
coordinates = np.zeros((self.natom, 3), np.float32)
if hasvels:
velocities = np.zeros((self.natom, 3), np.float32)
if hasbox:
boxVectors = np.zeros((3, 3), np.float32)
else:
coordinates = [[0.0, 0.0, 0.0] for i in range(self.natom)]
if hasvels:
velocities = [[0.0, 0.0, 0.0] for i in range(self.natom)]
if hasbox:
boxVectors = [[0.0, 0.0, 0.0] for i in range(3)]
# Now it's time to parse. Coordinates first
startline = 2
endline = startline + int(ceil(self.natom / 2.0))
idx = 0
for i in range(startline, endline):
line = lines[i]
coordinates[idx][0] = float(line[ 0:12])
coordinates[idx][1] = float(line[12:24])
coordinates[idx][2] = float(line[24:36])
idx += 1
if idx < self.natom:
coordinates[idx][0] = float(line[36:48])
coordinates[idx][1] = float(line[48:60])
coordinates[idx][2] = float(line[60:72])
idx += 1
self.coordinates = units.Quantity(coordinates, units.angstroms)
startline = endline
# Now it's time to parse velocities if we have them
if hasvels:
endline = startline + int(ceil(self.natom / 2.0))
idx = 0
for i in range(startline, endline):
line = lines[i]
velocities[idx][0] = float(line[ 0:12]) * VELSCALE
velocities[idx][1] = float(line[12:24]) * VELSCALE
velocities[idx][2] = float(line[24:36]) * VELSCALE
idx += 1
if idx < self.natom:
velocities[idx][0] = float(line[36:48]) * VELSCALE
velocities[idx][1] = float(line[48:60]) * VELSCALE
velocities[idx][2] = float(line[60:72]) * VELSCALE
idx += 1
startline = endline
self.velocities = units.Quantity(velocities,
units.angstroms/units.picoseconds)
if hasbox:
line = lines[startline]
try:
tmp = [float(line[i:i+12]) for i in range(0, 72, 12)]
except (IndexError, ValueError):
raise ValueError('Could not parse box line in %s' %
self.filename)
lengths = tmp[:3]
angles = tmp[3:]
_box_vectors_from_lengths_angles(lengths, angles, boxVectors)
self.boxVectors = units.Quantity(boxVectors, units.angstroms)
class AmberNetcdfRestart(object):
"""
Amber restart/inpcrd file in the NetCDF format (full double-precision
coordinates, velocities, and unit cell parameters). Reads NetCDF restarts
written by LEaP and pmemd/sander. Requires scipy to parse NetCDF files.
Parameters
----------
filename : str
Name of the restart file
asNumpy : bool (False)
Load the coordinates, velocities, and box as numpy ndarray objects
Attributes
----------
coordinates : natom x 3 array, Quantity
Particle positions with units of length
velocities : natom x 3 array, Quantity
Particle velocities with units of length per time (None if velocities
are not present in the inpcrd file)
boxVectors : 3 x 3 array, Quantity
Box vectors with units of length (None if no box is present in the
inpcrd file)
time : float, Quantity
Simulation time (None if not present) with units of time
title : str
Title of the inpcrd file
filename : str
Name of the file we are parsing
natom : int
Number of atoms in the inpcrd file
Raises
------
`IOError' if the file does not exist
`TypeError' if the file is not a NetCDF v3 file
`ImportError' if scipy is not available
Example
-------
>>> f = AmberNetcdfRestart('alanine-dipeptide.ncrst')
>>> coordinates = f.coordinates
"""
def __init__(self, filename, asNumpy=False):
try:
from scipy.io.netcdf import NetCDFFile
except ImportError:
raise ImportError('scipy is necessary to parse NetCDF restarts')
self.filename = filename
self.velocities = self.boxVectors = self.time = None
# Extract the information from the NetCDF file. We need to make copies
# here because the NetCDF variables are mem-mapped, but is only mapped
# to valid memory while the file handle is open. Since the context
# manager GCs the ncfile handle, the memory for the original variables
# is no longer valid. So copy those arrays while the handle is still
# open. This is unnecessary in scipy v.0.12 and lower because NetCDFFile
# accidentally leaks the file handle, but that was 'fixed' in 0.13. This
# fix taken from MDTraj
ncfile = NetCDFFile(filename, 'r')
try:
self.natom = ncfile.dimensions['atom']
self.coordinates = np.array(ncfile.variables['coordinates'][:])
if 'velocities' in ncfile.variables:
vels = ncfile.variables['velocities']
self.velocities = np.array(vels[:]) * vels.scale_factor
if ('cell_lengths' in ncfile.variables and
'cell_angles' in ncfile.variables):
self.boxVectors = np.zeros((3,3), np.float32)
_box_vectors_from_lengths_angles(
ncfile.variables['cell_lengths'][:],
ncfile.variables['cell_angles'][:],
self.boxVectors,
)
if 'time' in ncfile.variables:
self.time = ncfile.variables['time'].getValue()
finally:
ncfile.close()
# They are already numpy -- convert to list if we don't want numpy
if not asNumpy:
self.coordinates = self.coordinates.tolist()
if self.velocities is not None:
self.velocities = self.velocities.tolist()
if self.boxVectors is not None:
self.boxVectors = self.boxVectors.tolist()
# Now add the units
self.coordinates = units.Quantity(self.coordinates, units.angstroms)
if self.velocities is not None:
self.velocities = units.Quantity(self.velocities,
units.angstroms/units.picoseconds)
if self.boxVectors is not None:
self.boxVectors = units.Quantity(self.boxVectors, units.angstroms)
self.time = units.Quantity(self.time, units.picosecond)
def _box_vectors_from_lengths_angles(lengths, angles, boxVectors):
"""
Converts lengths and angles into a series of box vectors and modifies
boxVectors in-place (it must be a mutable sequence)
Parameters
----------
lengths : 3-element array of floats
Lengths of the 3 periodic box vectors
angles : 3-element array of floats
Angles (in degrees) between the 3 periodic box vectors
boxVectors : mutable 3x3 sequence
"""
alpha = angles[0] * pi / 180.0
beta = angles[1] * pi / 180.0
gamma = angles[2] * pi / 180.0
boxVectors[0][0] = lengths[0]
boxVectors[1][0] = lengths[1] * cos(gamma)
boxVectors[1][1] = lengths[1] * sin(gamma)
boxVectors[2][0] = cx = lengths[2] * cos(beta)
boxVectors[2][1] = cy = lengths[2] * (cos(alpha) - cos(beta) * cos(gamma))
boxVectors[2][2] = sqrt(lengths[2]*lengths[2] - cx*cx - cy*cy)
boxVectors[0][1] = boxVectors[0][2] = boxVectors[1][2] = 0.0
# Now make sure any vector close to zero is zero exactly
for i in range(3):
for j in range(3):
if abs(boxVectors[i][j]) < TINY:
boxVectors[i][j] = 0.0
def readAmberCoordinates(filename, asNumpy=False):
"""
Read atomic coordinates (and optionally, box vectors) from Amber formatted coordinate file.
ARGUMENTS
filename (string) - name of Amber coordinates file to be read in
system (simtk.openmm.System) - System object for which coordinates are to be read
OPTIONAL ARGUMENTS
verbose (boolean) - if True, will print out verbose information about the file being read
asNumpy (boolean) - if True, results will be returned as Numpy arrays instead of lists of Vec3s
RETURNS
coordinates, velocities, boxVectors
The velocities and boxVectors will be None if they are not found in the
restart file
EXAMPLES
Read coordinates in vacuum.
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-gbsa')
>>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
>>> coordinates = readAmberCoordinates(crd_filename)
>>> coordinates, velocities, box_vectors = readAmberCoordinates(crd_filename)
Read coordinates in solvent.
>>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
>>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
>>> [coordinates, box_vectors] = readAmberCoordinates(crd_filename, read_box=True)
>>> coordinates, velocities, box_vectors = readAmberCoordinates(crd_filename)
"""
# Open coordinate file for reading.
infile = open(filename, 'r')
# Read title
title = infile.readline().strip()
if verbose: print "title: '%s'" % title
# Read number of atoms
natoms = int(infile.readline().split()[0])
if verbose: print "%d atoms" % natoms
# Allocate storage for coordinates
coordinates = []
# Read coordinates
mm = simtk.openmm
natoms_read = 0
while (natoms_read < natoms):
line = infile.readline()
if len(line) == 0:
raise ValueError("Unexpected end of file while reading coordinates")
line = line.strip()
elements = line.split()
while (len(elements) > 0):
coordinates.append(mm.Vec3(float(elements.pop(0)), float(elements.pop(0)), float(elements.pop(0))))
natoms_read += 1
if asNumpy:
newcoords = numpy.zeros([natoms,3], numpy.float32)
for i in range(len(coordinates)):
for j in range(3):
newcoords[i,j] = coordinates[i][j]
coordinates = newcoords
# Assign units.
coordinates = units.Quantity(coordinates, units.angstroms)
# Read velocities if requested.
velocities = None
if (read_velocities):
# Read velocities
velocities = []
natoms_read = 0
while (natoms_read < natoms):
line = infile.readline()
if len(line) == 0:
raise ValueError("Unexpected end of file while reading velocities")
line = line.strip()
elements = line.split()
while (len(elements) > 0):
velocities.append(20.455*mm.Vec3(float(elements.pop(0)), float(elements.pop(0)), float(elements.pop(0))))
natoms_read += 1
if asNumpy:
newvel = numpy.zeros([natoms,3], numpy.float32)
for i in range(len(velocities)):
for j in range(3):
newvel[i,j] = velocities[i][j]
velocities = newvel
# Assign units.
velocities = units.Quantity(velocities, units.angstroms/units.picoseconds)
# Read box size if present
box_vectors = None
if (read_box):
line = infile.readline()
if len(line) == 0:
raise ValueError("Unexpected end of file while reading box vectors")
line = line.strip()
elements = line.split()
nelements = len(elements)
box_dimensions = [0.0]*nelements
for i in range(nelements):
box_dimensions[i] = float(elements[i])
# TODO: Deal with non-standard box sizes.
if nelements == 6:
if asNumpy:
a = units.Quantity(numpy.array([box_dimensions[0], 0.0, 0.0]), units.angstroms)
b = units.Quantity(numpy.array([0.0, box_dimensions[1], 0.0]), units.angstroms)
c = units.Quantity(numpy.array([0.0, 0.0, box_dimensions[2]]), units.angstroms)
else:
a = units.Quantity(mm.Vec3(box_dimensions[0], 0.0, 0.0), units.angstroms)
b = units.Quantity(mm.Vec3(0.0, box_dimensions[1], 0.0), units.angstroms)
c = units.Quantity(mm.Vec3(0.0, 0.0, box_dimensions[2]), units.angstroms)
box_vectors = [a,b,c]
else:
raise Exception("Don't know what to do with box vectors: %s" % line)
# Close file
infile.close()
if box_vectors and velocities:
return (coordinates, box_vectors, velocities)
if box_vectors:
return (coordinates, box_vectors)
if velocities:
return (coordinates, velocities)
return coordinates
try:
crdfile = AmberNetcdfRestart(filename)
except ImportError:
# See if it's an ASCII file. If so, no need to complain
try:
crdfile = AmberAsciiRestart(filename)
except TypeError:
raise TypeError('Problem parsing %s as an ASCII Amber restart file '
'and scipy could not be imported to try reading as '
'a NetCDF restart file.' % filename)
except (IndexError, ValueError):
raise TypeError('Could not parse Amber ASCII restart file %s' %
filename)
except ImportError:
raise ImportError('Could not find numpy; cannot use asNumpy=True')
except TypeError:
# We had scipy, but this is not a NetCDF v3 file. Try as ASCII now
try:
crdfile = AmberAsciiRestart(filename)
except TypeError:
raise TypeError('Problem parsing %s as an ASCII Amber restart file'
% filename)
except (IndexError, ValueError):
raise TypeError('Could not parse Amber ASCII restart file %s' %
filename)
# Import error cannot happen, since we had scipy which has numpy as a
# prereq. Do not catch that exception (only catch what you intend to
# catch...)
# We got here... one of the file types worked. Return the coordinates,
# velocities, and boxVectors
return crdfile.coordinates, crdfile.velocities, crdfile.boxVectors
#=============================================================================================
# MAIN AND TESTS
......
wrappers/python/tests/TestAmberInpcrdFile.py 0 → 100644
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import unittest
from validateConstraints import *
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.app.element as elem
def compareByElement(array1, array2, cmp):
for x, y in zip(array1, array2):
cmp(x, y)
class TestAmberInpcrdFile(unittest.TestCase):
"""Test the Amber inpcrd file parser"""
def test_CrdVelBox(self):
""" Test parsing ASCII restarts with crds, vels, and box """
cmp = self.assertAlmostEqual
inpcrd = AmberInpcrdFile('systems/crds_vels_box.rst7')
self.assertEqual(len(inpcrd.positions), 2101)
compareByElement(inpcrd.positions[-1].value_in_unit(angstroms),
[3.5958082, 8.4176792, -8.2954064], cmp)
compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picoseconds),
[0.3091332*20.455, 0.7355925*20.455, -0.1206961*20.455], cmp)
compareByElement(inpcrd.boxVectors[0].value_in_unit(angstroms),
[30.2642725, 0.0, 0.0], cmp)
def test_NetCDF(self):
""" Test NetCDF restart file parsing """
cmp = self.assertAlmostEqual
try:
from scipy.io import netcdf
except ImportError:
print('Not testing NetCDF file parser... scipy cannot be found')
else:
inpcrd = AmberInpcrdFile('systems/amber.ncrst')
self.assertEqual(len(inpcrd.positions), 2101)
compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
[6.82122492718229, 6.6276250662042, -8.51668999892245],
cmp)
compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picosecond),
[0.349702202733541*20.455, 0.391525333168534*20.455,
0.417941679767662*20.455], cmp)
self.assertAlmostEqual(inpcrd.boxVectors[0][0].value_in_unit(angstroms),
30.2642725, places=6)
def test_CrdBox(self):
""" Test parsing ASCII restarts with only crds and box """
inpcrd = AmberInpcrdFile('systems/crds_box.rst7')
self.assertEqual(len(inpcrd.positions), 18660)
self.assertTrue(inpcrd.velocities is None)
self.assertTrue(inpcrd.boxVectors is not None)
def test_CrdVel(self):
inpcrd = AmberInpcrdFile('systems/crds_vels.rst7')
self.assertTrue(inpcrd.boxVectors is None)
self.assertTrue(inpcrd.velocities is not None)
def test_CrdOnly(self):
inpcrd = AmberInpcrdFile('systems/crdsonly.rst7')
self.assertTrue(inpcrd.boxVectors is None)
self.assertTrue(inpcrd.velocities is None)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/crds_box.rst7 0 → 100644
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wrappers/python/tests/systems/crds_vels.rst7 0 → 100644
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wrappers/python/tests/systems/crds_vels_box.rst7 0 → 100644
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wrappers/python/tests/systems/crdsonly.rst7 0 → 100644
View file @ ba5e21ff
ACE
28
1.8662825 1.2455949 0.6672110 1.9626006 2.1938026 0.1396779
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wrappers/python/tests/systems/water-box-216.prmtop
View file @ ba5e21ff
......@@ -1054,7 +1054,7 @@ BLA BLA BLA BLA BLA BLA BLA BLA
3 3 3 3 3 3
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
5.15661795E+03 1.87743490E+01 1.87743490E+01 1.87743490E+01
9.00000000E+01 1.87743490E+01 1.87743490E+01 1.87743490E+01
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
......
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