Nanoengineer-1 dependencies

* PyQt4
aptitude install python-qt4

* Numpy
aptitude install python-numpy

* Numeric

PROBLEM:

File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/VQT.py", line 23, in <module>
    import Numeric 
ImportError: No module named Numeric


http://qwone.com/~jason/python/numeric/

>2/1/06 UPDATE A new, master module, named NumPy  has been released that is touted as a replacement for Numeric and Numarray.

SOLUTION:

#import Numeric 
import numpy.oldnumeric as Numeric

PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/model/atomtypes.py", line 97, in __init__
    if (bondvectors):
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

SOLUTION:

if (bondvectors != None):
            # number of distinct bonds to different other atoms (a
            # double bond is counted as 1)
            self.numbonds = len(bondvectors)

            s = bondvectors[0]
            self.base = s
            for v in bondvectors[1:]:
                self.quats += [Q(s,v)]
        else:
            self.numbonds = 0
 
        if (bondvectors != None):
           self.bondvectors = bondvectors
        else:
           self.bondvectors = []
					 
PROBLEM:

File "/home/user/Desktop/kanzure-nanoengineer/cad/src/model/chunk.py", line 74, in <module>
    import Numeric # for sqrt
ImportError: No module named Numeric

SOLUTION:

#import Numeric 
import numpy.oldnumeric as Numeric

PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/model/chunk.py", line 90, in <module>
    from OpenGL.GL import glPushMatrix
ImportError: No module named OpenGL.GL

SOLUTION:

sudo aptitude install python-opengl

PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawers.py", line 28, in <module>
    import Numeric
ImportError: No module named Numeric

SOLUTION:

Replaced Numeric with numpy.oldnumeric
in
chunk.py
Line.py
Plane.py
jigs_motors.py
pi_bond_sp_chain.py
NamedView.py
PAM_Atom_methods.py
jigs_planes.py
bonds.py
chem.py
jigs_measurements.py
./cad/src/files/dpb_trajectory/moviefile.py:20:from Numeric import array, Int8
./cad/src/protein/model/Residue.py:375:    from Numeric import dot
./cad/src/protein/commands/InsertPeptide/PeptideGenerator.py:34:from Numeric import zeros, sqrt, pi, sin, cos, Float
./cad/src/foundation/state_utils.py:1139:    from Numeric import array, PyObject
./cad/src/foundation/state_utils.py:2324:    from Numeric import array
./cad/src/temporary_commands/ZoomInOutMode.py:11:from Numeric import exp
./cad/src/temporary_commands/ZoomToAreaMode.py:14:from Numeric import dot
./cad/src/temporary_commands/RotateAboutPoint_Command.py:16:from Numeric import dot
./cad/src/cnt/model/NanotubeParameters.py:19:from Numeric import dot, argmax, argmin, sqrt
./cad/src/cnt/commands/EditNanotube/EditNanotube_GraphicsMode.py:21:from Numeric import dot

.... ~80 more files

PROBLEM:

./cad/src/atombasehelp.c:8:#include "Numeric/arrayobject.h"
./cad/src/samevalshelp.c:12:#include "Numeric/arrayobject.h"

???SOLUTION

PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/foundation/undo_archive.py", line 1405, in <module>
    from idlelib.Delegator import Delegator
ImportError: No module named idlelib.Delegator

SOLUTION:

sudo aptitude install idle

PROBLEM:

 File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/geometryUtilities.py", line 26, in <module>
    from LinearAlgebra import solve_linear_equations, eigenvectors
ImportError: No module named LinearAlgebra


SOLUTION:

#from LinearAlgebra import solve_linear_equations, eigenvectors
from numpy.linalg import solve as solve_linear_equations
from numpy.linalg import eig as eigenvectors

PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/VQT.py", line 619, in cat
    if not a:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

SOLUTION:

  if not a.any():
        if (_DEBUG_QUATS or debug_flags.atom_debug):
            print "_DEBUG_QUATS: cat(a, b) with false a -- is it right?", a
        return b
    if not b.any():
        if (_DEBUG_QUATS or debug_flags.atom_debug):
            print "_DEBUG_QUATS: cat(a, b) with false b -- is it right?", b
        return a
				
PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/widgets/GLPane_event_methods.py", line 20, in <module>
    from PyQt4.QtOpenGL import QGLWidget
ImportError: No module named QtOpenGL

SOLUTION:

aptitude install python-qt4-gl

PROBLEM:

File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/VQT.py", line 383, in __eq__
    return not (self.vec != other.vec) # assumes all quats have .vec; true except for bugs
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

SOLUTION:

def __eq__(self, other): #bruce 070227 revised this
        try:
            if self.__class__ is not other.__class__:
                return False
        except AttributeError:
            # some objects have no __class__ (e.g. Numeric arrays)
            return False
        return not (self.vec.any() != other.vec.any()) # assumes all quats have .vec; true except for bugs
            #bruce 070227 fixed "Numeric array == bug" encountered by this line (when it said "self.vec == other.vec"),
            # which made Q(1, 0, 0, 0) == Q(0.877583, 0.287655, 0.38354, 0) (since they're equal in at least one component)!!
            # Apparently it was my own bug, since it says above that I wrote this method on 060209.
        pass
				
PROBLEM:

 File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawcompass.py", line 78, in __init__
    _draw_compass_geometry()
  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawcompass.py", line 193, in _draw_compass_geometry
    [r1,r2,r3,r4,0,0])
  File "/usr/lib/pymodules/python2.7/OpenGL/latebind.py", line 45, in __call__
    return self._finalCall( *args, **named )
  File "/usr/lib/pymodules/python2.7/OpenGL/wrapper.py", line 573, in wrapperCall
    result = self.wrappedOperation( *cArguments )
  File "/usr/lib/pymodules/python2.7/OpenGL/platform/baseplatform.py", line 340, in __call__
    self.__name__, self.__name__,
OpenGL.error.NullFunctionError: Attempt to call an undefined function glePolyCone, check for bool(glePolyCone) before calling

SOLUTION:

sudo aptitude install libgle3

PROBLEM:

  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/widgets/GLPane_rendering_methods.py", line 122, in _init_GLPane_rendering_methods
    self.compass = Compass(self) #bruce 081015 refactored this
  File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawcompass.py", line 77, in __init__
    glNewList(self._compass_dl, GL_COMPILE)
  File "/usr/lib/pymodules/python2.7/OpenGL/error.py", line 208, in glCheckError
    baseOperation = baseOperation,
OpenGL.error.GLError: GLError(
	err = 1282,
	description = 'invalid operation',
	baseOperation = glNewList,
	cArguments = (17L, GL_COMPILE)
)

???SOLUTION