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RMSD calculations (linking against mdtraj) in enspara #150

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RMSD calculations (linking against mdtraj) in enspara #150

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aad7c41
wip rmsd in enspara
justinrporter Dec 20, 2018
1387ed7
fix setup.py's adminition about installing cython.
justinrporter Dec 20, 2018
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57 changes: 55 additions & 2 deletions enspara/geometry/libdist.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -29,18 +29,26 @@ cdef extern from "math.h" nogil:
double fabs(double x)
float fabs(float x)

cdef extern from "theobald_rmsd.h":
cdef extern float msd_atom_major(
int nrealatoms, int npaddedatoms, float* a,
float* b, float G_a, float G_b, int computeRot, float rot[9]) nogil


def _check_is_2d(X):
if len(X.shape) != 2:
raise exception.DataInvalid(
"Data array dimension must be two, got shape %s." %
str(X.shape))


def _check_is_1d(x):
if len(x.shape) != 1:
raise exception.DataInvalid(
"Target point dimension must be one, got shape %s." %
str(x.shape))


def _prepare_for_2d_to_1d_distance(X, y, out):

_check_is_2d(X)
Expand Down Expand Up @@ -80,8 +88,10 @@ def _hamming(np.ndarray[INTEGRAL_TYPE_T, ndim=2] X,

cdef long n_samples = len(out)
cdef long n_features = len(y)
assert len(out) == X.shape[0], "Size of output array didn't match number of observations in X"
assert n_features == X.shape[1], "Number of features between X and y didn't match."
assert len(out) == X.shape[0], \
"Size of output array didn't match number of observations in X"
assert n_features == X.shape[1], \
"Number of features between X and y didn't match."

cdef long i, j = 0

Expand Down Expand Up @@ -145,6 +155,48 @@ def _euclidean(np.ndarray[FLOAT_TYPE_T, ndim=2] X,
return out.reshape(-1, 1)


cdef _rmsd(XA, XB):
cdef long i, j
cdef float[:, :, ::1] XA_xyz = XA.xyz
cdef float[:, :, ::1] XB_xyz = XB.xyz
cdef long XA_length = XA_xyz.shape[0]
cdef long XB_length = XB_xyz.shape[0]
cdef int n_atoms = XA_xyz.shape[1]
cdef float[::1] XA_trace, XB_trace
cdef double[:, ::1] out

if XA._rmsd_traces is None:
XA.center_coordinates()
if XB._rmsd_traces is None:
XB.center_coordinates()

if XA_xyz.shape[1] != XB_xyz.shape[1]:
raise ValueError('XA and XB must have the same number of atoms')

XA_trace = XA._rmsd_traces
XB_trace = XB._rmsd_traces

out = np.zeros((XA_length, XB_length), dtype=np.double)

for i in range(XA_length):
for j in range(XB_length):
rmsd = sqrt(msd_atom_major(n_atoms, n_atoms, &XA_xyz[i,0,0],
&XB_xyz[j,0,0], XA_trace[i], XB_trace[j], 0, NULL))
out[i,j] = rmsd

return np.array(out, copy=False)


def rmsd(X, y, out=None):

# out = _prepare_for_2d_to_1d_distance(XA, XB, out)
# _rmsd(X, y, out)
_rmsd(XA, AB, out)

return out



def euclidean(X, y, out=None):
"""Compute the euclidean distance between a point, `y`, and a group
of points `X`. Uses thread-parallelism with OpenMP.
Expand All @@ -163,6 +215,7 @@ def euclidean(X, y, out=None):
_euclidean(X, y, out)
return out


def manhattan(X, y, out=None):
"""Compute the Manhattan distance between a point `y` and a group of
points `X`. Thread-parallized using OpenMP.
Expand Down
16 changes: 13 additions & 3 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,19 @@
except ImportError:
sys.stderr.write('-' * 80)
sys.stderr.write('\n'.join([
'Error: building mdtraj requires numpy and cython>=0.19',
'Error: building enspara requires numpy and cython>=0.19',
'Try running the command ``pip install numpy cython`` or'
'``conda install numpy cython``.',

'or see http://docs.scipy.org/doc/numpy/user/install.html and'
'http://cython.org/ for more information.']))

try:
import mdtraj
mdtraj_capi = mdtraj.capi()
except (ImportError, AttributeError):
print('MDTraj>=1.1 is required')
sys.exit(1)

# this probably won't work for everyone. Works for me, though!
# they'll need gcc 7 installed. Unfortunately, I don't have any idea how
Expand All @@ -62,10 +68,14 @@
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
), Extension(
"enspara.geometry.libdist",
["enspara/geometry/libdist.pyx"],
name="enspara.geometry.libdist",
sources=["enspara/geometry/libdist.pyx"],
# msvc needs to be told "libtheobald", gcc wants just "theobald"
libraries=['theobald'],
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
include_dirs=[mdtraj_capi['include_dir'], np.get_include()],
library_dirs=[mdtraj_capi['lib_dir']],
), Extension(
"enspara.msm.libmsm",
["enspara/msm/libmsm.pyx"],
Expand Down