completed the oldnumeric removal

Examples/Forcefield/ElectricField/C/setup.py

@@ -10,15 +10,9 @@ import os, sys
 compile_args = []
 include_dirs = ['../../../../Include']
 
-from Scientific import N
-try:
-    num_package = N.package
-except AttributeError:
-    num_package = "Numeric"
-if num_package == "NumPy":
-    compile_args.append("-DNUMPY=1")
-    import numpy.distutils.misc_util
-    include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
+compile_args.append("-DNUMPY=1")
+import numpy.distutils.misc_util
+include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
 
 setup (name = "ElectricField",
        version = "1.0",

Examples/Forcefield/ElectricField/Cython/setup.py

@@ -11,15 +11,9 @@ import os, sys
 compile_args = []
 include_dirs = ['../../../../Include']
 
-from Scientific import N
-try:
-    num_package = N.package
-except AttributeError:
-    num_package = "Numeric"
-if num_package == "NumPy":
-    compile_args.append("-DNUMPY=1")
-    import numpy.distutils.misc_util
-    include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
+compile_args.append("-DNUMPY=1")
+import numpy.distutils.misc_util
+include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
 
 setup (name = "ElectricField",
        version = "1.0",

Examples/Forcefield/HarmonicOscillator/C/setup.py

@@ -10,15 +10,9 @@ import os, sys
 compile_args = []
 include_dirs = ['../../../../Include']
 
-from Scientific import N
-try:
-    num_package = N.package
-except AttributeError:
-    num_package = "Numeric"
-if num_package == "NumPy":
-    compile_args.append("-DNUMPY=1")
-    import numpy.distutils.misc_util
-    include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
+compile_args.append("-DNUMPY=1")
+import numpy.distutils.misc_util
+include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
 
 setup (name = "HarmonicOscillatorForceField",
        version = "1.0",

Examples/Forcefield/HarmonicOscillator/Cython/setup.py

@@ -11,15 +11,9 @@ import os, sys
 compile_args = []
 include_dirs = ['../../../../Include']
 
-from Scientific import N
-try:
-    num_package = N.package
-except AttributeError:
-    num_package = "Numeric"
-if num_package == "NumPy":
-    compile_args.append("-DNUMPY=1")
-    import numpy.distutils.misc_util
-    include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
+compile_args.append("-DNUMPY=1")
+import numpy.distutils.misc_util
+include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
 
 setup (name = "HarmonicOscillatorForceField",
        version = "1.0",

Examples/LangevinDynamics/setup.py

@@ -6,20 +6,14 @@ import os, sys
 compile_args = []
 include_dirs = ['.']
 
-from Scientific import N
-try:
-    num_package = N.package
-except AttributeError:
-    num_package = "Numeric"
-if num_package == "NumPy":
-    compile_args.append("-DNUMPY=1")
-    if sys.platform == 'win32':
-        include_dirs.append(os.path.join(sys.prefix,
-                            "Lib/site-packages/numpy/core/include"))
-    else:
-        include_dirs.append(os.path.join(sys.prefix,
-                            "lib/python%s.%s/site-packages/numpy/core/include"
-                             % sys.version_info [:2]))
+compile_args.append("-DNUMPY=1")
+if sys.platform == 'win32':
+    include_dirs.append(os.path.join(sys.prefix,
+                        "Lib/site-packages/numpy/core/include"))
+else:
+    include_dirs.append(os.path.join(sys.prefix,
+                        "lib/python%s.%s/site-packages/numpy/core/include"
+                         % sys.version_info [:2]))
 
 setup (name = "MMTK-LangevinDynamics",
        version = "2.7",

Examples/MDIntegrator/setup.py

@@ -8,9 +8,6 @@ import os, sys
 compile_args = ['-g', '-O0']
 include_dirs = ['.', '../../Include']
 
-from Scientific import N
-assert N.package == "NumPy"
-
 compile_args.append("-DNUMPY=1")
 include_dirs.extend(numpy.distutils.misc_util.get_numpy_include_dirs())
 

Examples/Miscellaneous/thermal_fluctuations.py

 # Retrieve atomic fluctuation information from a PDBConfiguration object.
 #
 
+import numpy
+
 from MMTK import *
 from MMTK.PDB import PDBConfiguration
-from Scientific import N
 
 # Read a PDB file containing ANISOU records.
 conf = PDBConfiguration('1G66.pdb')
@@ -37,4 +38,4 @@ for c in conf.peptide_chains:
             u_trace = pdb_atom.properties['u'].trace()/3. * Units.Ang**2
         except KeyError:
             u_trace = "[no ANISOU record]"
-        print atom, b_factor/(8*N.pi**2), u_trace
+        print atom, b_factor/(8*numpy.pi**2), u_trace

Examples/NormalModes/constrained_modes.py

 # A normal mode calculation in the subspace of residue rigid-body motion.
 #
 
+import numpy
+
 from MMTK import *
 from MMTK.Proteins import Protein
 from MMTK.ForceFields import Amber94ForceField
@@ -9,8 +11,6 @@ from MMTK.Subspace import RigidMotionSubspace
 from MMTK.Minimization import ConjugateGradientMinimizer
 from MMTK.Trajectory import StandardLogOutput
 
-from Scientific import N
-
 # Construct system
 universe = InfiniteUniverse(Amber94ForceField())
 universe.protein = Protein('bala1')
@@ -38,8 +38,8 @@ for i in range(6, len(modes)):
     overlap = []
     for m2 in full_modes:
 	o = m1.massWeightedDotProduct(m2) / \
-	    N.sqrt(m1.massWeightedDotProduct(m1)) / \
-	    N.sqrt(m2.massWeightedDotProduct(m2))
+	    numpy.sqrt(m1.massWeightedDotProduct(m1)) / \
+	    numpy.sqrt(m2.massWeightedDotProduct(m2))
 	overlap.append(abs(o))
-    best = N.argsort(overlap)[-1]
+    best = numpy.argsort(overlap)[-1]
     print m1.frequency, full_modes[best].frequency, overlap[best]

Examples/NormalModes/mode_analysis.py

+import numpy
+
 from MMTK import *
 from MMTK.Subspace import Subspace
 from Scientific.Statistics.Histogram import WeightedHistogram, Histogram
-from Scientific import N
 
 #
 # You ned to provide a mode file as input for this script; the
@@ -22,13 +23,13 @@ for chain in protein:
     dihedrals_with_index = zip(range(1, 1+len(dihedrals)), dihedrals)
     helix_indices = [index for index, (phi, psi) in dihedrals_with_index
                            if 4.5 < phi < 5.8 and 5. < psi < 6.]
-    helix_indices = N.array(helix_indices)
-    breaks = N.repeat(N.arange(len(helix_indices)-1),
+    helix_indices = numpy.array(helix_indices)
+    breaks = numpy.repeat(numpy.arange(len(helix_indices)-1),
                       (helix_indices[1:]-helix_indices[:-1]) > 1)
-    breaks = N.concatenate(([0], breaks + 1))
+    breaks = numpy.concatenate(([0], breaks + 1))
     backbone = chain.backbone()
     for i in range(len(breaks)-1):
-        residues = N.take(backbone, helix_indices[breaks[i]:breaks[i+1]])
+        residues = numpy.take(backbone, helix_indices[breaks[i]:breaks[i+1]])
         helices.append(Collection(list(residues)))
 helices = [h for h in helices if len(h) > 4]
 
@@ -41,7 +42,7 @@ for helix in helices:
     cms, inertia = helix.centerAndMomentOfInertia()
     moments, axes = inertia.diagonalization()
     axes = [a.asVector() for a in axes]
-    helix_axis = axes[N.argmax([abs(end_to_end*v) for v in axes])]
+    helix_axis = axes[numpy.argmax([abs(end_to_end*v) for v in axes])]
     hmv = ParticleVector(universe)
     helix_motion_vectors.append(hmv)
     for residue in helix:

Examples/NormalModes/subset_modes.py

@@ -9,8 +9,6 @@ from MMTK.Subspace import Subspace
 from MMTK.Minimization import ConjugateGradientMinimizer
 from MMTK.Trajectory import StandardLogOutput
 
-from Scientific import N
-
 # Construct system
 universe = InfiniteUniverse(Amber94ForceField())
 universe.protein1 = Protein('bala1')

Examples/Proteins/rotamers.py

 # Modify sidechain dihedral angles
 #
 
+import numpy
+
 from MMTK import *
 from MMTK.Proteins import Protein
 from MMTK.Trajectory import Trajectory, SnapshotGenerator, TrajectoryOutput
-from Scientific import N
 
 # Construct system: lysozyme in vaccuum
 universe = InfiniteUniverse()
@@ -27,7 +28,7 @@ snapshot()
 for residue in residues:
     print residue
     chi = residue.chiAngle()
-    for angle in N.arange(-N.pi, N.pi, N.pi/10.):
+    for angle in numpy.arange(-numpy.pi, numpy.pi, numpy.pi/10.):
         chi.setValue(angle)
         print angle
         snapshot()

Examples/Trajectories/calpha_trajectory.py

@@ -9,10 +9,11 @@
 #       "full_trajectory.nc" below.
 #
 
+import numpy
+
 from MMTK import *
 from MMTK.Trajectory import Trajectory, TrajectoryOutput, SnapshotGenerator
 from MMTK.Proteins import Protein, PeptideChain
-from Scientific import N
 
 # Open the input trajectory.
 trajectory = Trajectory(None, 'full_trajectory.nc')
@@ -62,7 +63,7 @@ first = 1
 for step in trajectory:
     conf = universe.contiguousObjectConfiguration(proteins,
                                                   step['configuration'])
-    conf_calpha = Configuration(universe_calpha, N.take(conf.array, map),
+    conf_calpha = Configuration(universe_calpha, numpy.take(conf.array, map),
                                 None)
     universe_calpha.setConfiguration(conf_calpha)
     if first:

Examples/Visualization/additional_objects.py

 # Generate a protein backbone representation plus an indication
 # of the principal axes of inertia by arrows.
 #
+
+import numpy
+
 from MMTK import *
 from MMTK.Proteins import Protein
-from Scientific import N, LA
+from Scientific import LA
 
 # Import the graphics module. Substitute any other graphics
 # module name to make the example use that module.
@@ -16,7 +19,7 @@ center, inertia = protein.centerAndMomentOfInertia()
 # Diagonalize the inertia tensor and scale the axes to a suitable length.
 mass = protein.mass()
 diagonal, directions = LA.eigenvectors(inertia.array)
-diagonal = N.sqrt(diagonal/mass)
+diagonal = numpy.sqrt(diagonal/mass)
 
 # Generate the backbone graphics objects.
 graphics = protein.graphicsObjects(graphics_module = module,

Include/MMTK/numeric.pxi

@@ -24,7 +24,7 @@ cdef extern from "MMTK/arrayobject.h":
         PyArray_Descr *descr 
         int flags
 
-    ctypedef class Scientific.N.ArrayType [object PyArrayObject]: 
+    ctypedef class numpy.ndarray [object PyArrayObject]: 
         cdef char *data 
         cdef int nd 
         cdef int *dimensions, *strides 

MMTK/Database/Atoms/ch

@@ -7,9 +7,9 @@ color = 'black'
 
 vdW_radius = 0.17
 
-from Scientific import N
+import numpy
 b_coherent = (6.648 + (-3.741))*fm
-b_incoherent = N.sqrt(0.285**2 + 25.217**2)*fm
+b_incoherent = numpy.sqrt(0.285**2 + 25.217**2)*fm
 b_coherent_deut = (6.648 + (6.674))*fm
-b_incoherent_deut = N.sqrt(0.285**2 + 4.022**2)*fm
-del N
+b_incoherent_deut = numpy.sqrt(0.285**2 + 4.022**2)*fm
+del numpy

MMTK/Database/Atoms/ch2

@@ -7,9 +7,9 @@ color = 'black'
 
 vdW_radius = 0.17
 
-from Scientific import N
+import numpy
 b_coherent = (6.648 + 2*(-3.741))*fm
-b_incoherent = N.sqrt(0.285**2 + 2*25.217**2)*fm
+b_incoherent = numpy.sqrt(0.285**2 + 2*25.217**2)*fm
 b_coherent_deut = (6.648 + 2*6.674)*fm
-b_incoherent_deut = N.sqrt(0.285**2 + 2*4.022**2)*fm
-del N
+b_incoherent_deut = numpy.sqrt(0.285**2 + 2*4.022**2)*fm
+del numpy

MMTK/Database/Atoms/ch3

@@ -7,9 +7,9 @@ color = 'black'
 
 vdW_radius = 0.17
 
-from Scientific import N
+import numpy
 b_coherent = (6.648 + 3*(-3.741))*fm
-b_incoherent = N.sqrt(0.285**2 + 3*25.217**2)*fm
+b_incoherent = numpy.sqrt(0.285**2 + 3*25.217**2)*fm
 b_coherent_deut = (6.648 + 3*6.674)*fm
-b_incoherent_deut = N.sqrt(0.285**2 + 3*4.022**2)*fm
-del N
+b_incoherent_deut = numpy.sqrt(0.285**2 + 3*4.022**2)*fm
+del numpy

MMTK/Database/Atoms/deut.py

+import numpy
+
 from MMTK import *
 from MMTK.ChemicalObjects import Group
-from Scientific.N import sqrt
 
 residues = ['alanine', 'arginine', 'asparagine', 'aspartic_acid',
             'cysteine', 'cystine_ss', 'glutamic_acid', 'glutamine',
@@ -23,7 +24,7 @@ for r in residues:
         bcoh_deut_sq = bcoh_deut_sq + (a.b_coherent_deut/Units.fm)**2
         mass = mass + a.mass()
     print r
-    print "b_coherent = %f*fm" % sqrt(bcoh_sq)
+    print "b_coherent = %f*fm" % numpy.sqrt(bcoh_sq)
     print "b_incoherent = %f*fm" % binc
-    print "b_coherent_deut = %f*fm" % sqrt(bcoh_deut_sq)
+    print "b_coherent_deut = %f*fm" % numpy.sqrt(bcoh_deut_sq)
     print "b_incoherent_deut = %f*fm" % binc_deut

MMTK/Database/Atoms/nh

@@ -4,9 +4,9 @@ mass = 15.014699
 color = 'blue'
 vdW_radius = 0.155000
 
-from Scientific import N
+import numpy
 b_coherent = (9.300 + 1*(-3.741))*fm
-b_incoherent = N.sqrt(2.241**2 + 1*25.217**2)*fm
+b_incoherent = numpy.sqrt(2.241**2 + 1*25.217**2)*fm
 b_coherent_deut = (9.300 + 1*6.674)*fm
-b_incoherent_deut = N.sqrt(2.241**2 + 1*4.022**2)*fm
-del N
+b_incoherent_deut = numpy.sqrt(2.241**2 + 1*4.022**2)*fm
+del numpy

MMTK/Database/Atoms/nh2

@@ -4,9 +4,9 @@ mass = 16.022675
 color = 'blue'
 vdW_radius = 0.155000
 
-from Scientific import N
+import numpy
 b_coherent = (9.300 + 2*(-3.741))*fm
-b_incoherent = N.sqrt(2.241**2 + 2*25.217**2)*fm
+b_incoherent = numpy.sqrt(2.241**2 + 2*25.217**2)*fm
 b_coherent_deut = (9.300 + 2*6.674)*fm
-b_incoherent_deut = N.sqrt(2.241**2 + 2*4.022**2)*fm
-del N
+b_incoherent_deut = numpy.sqrt(2.241**2 + 2*4.022**2)*fm
+del numpy