text: """This module defines input and output functions for NMD format.
  
  .. _nmd-format:
  
  NMD Format
  -------------------------------------------------------------------------------
  
  Description
  ^^^^^^^^^^^
  
  NMD files (extension :file:`.nmd`) are plain text files that contain at
  least normal mode and system coordinate data.
  
  NMD files can be visualized using :ref:`nmwiz`.  ProDy functions
  :func:`.writeNMD` and :func:`.parseNMD` can be used to read and write NMD
  files.
  
  Data fields
  ^^^^^^^^^^^
  
  Data fields in bold face are required. All data arrays and lists must be in a
  single line and items must be separated by one or more space characters.
  
  **coordinates**: system coordinates as a list of decimal numbers
    Coordinate array is the most important line in an NMD file. All mode array
    lengths must match the length of the coordinate array. Also, number of atoms
    in the system is deduced from the length of the coordinate array.
  
  ::
  
    coordinates 27.552 4.354 23.629 24.179 4.807 21.907 ...
  
  **mode**: normal mode array as a list of decimal numbers
    Optionally, mode index and a scaling factor may be provided
    in the same line as a mode array. Both of these must precede the mode array.
    Providing a scaling factor enables relative scaling of the mode arrows and
    the amplitude of the fluctuations in animations. For NMA, scaling factors
    may be chosen to be the square-root of the inverse-eigenvalue associated
    with the mode. Analogously, for PCA data, scaling factor would be the
    square-root of the eigenvalue.
  
    If a mode line contains numbers preceding the mode array, they are evaluated
    based on their type. If an integer is encountered, it is considered the mode
    index. If a decimal number is encountered, it is considered the scaling
    factor. Scaling factor may be the square-root of the inverse eigenvalue
    if data is from an elastic network model, or the square-root of the
    eigenvalue if data is from an essential dynamics (or principal component)
    analysis.
  
    For example, all of the following lines are valid. The first line contains
    mode index and scaling factor. Second and third lines contain mode index or
    scaling factor. Last line contains only the mode array.
  
  ::
  
    mode 1 2.37    0.039 0.009 0.058 0.038 -0.011 0.052  ...
    mode 1    0.039 0.009 0.058 0.038 -0.011 0.052  ...
    mode 2.37    0.039 0.009 0.058 0.038 -0.011 0.052  ...
    mode 0.039 0.009 0.058 0.038 -0.011 0.052 0.043  ...
  
  *name*: name of the model
  
  The length of all following data fields must be equal to the number of atoms in
  the system. NMWiz uses such data when writing a temporary PDB files for
  loading coordinate data into VMD.
  
  *atomnames*: list of atom names
    If not provided, all atom names are set to "CA".
  
  *resnames*: list of residue names
    If not provided, all residue names are set to "GLY".
  
  *chainids*: list of chain identifiers
    If not provided, all chain identifiers are set to "A".
  
  *resids*: list of residue numbers
    If not provided, residue numbers are started from 1 and incremented by one
    for each atom.
  
  *bfactors*: list of experimental beta-factors
    If not provided, all beta-factors are set to zero.
    Beta-factors can be used to color the protein representation.
  
  NMD files may contain additional lines. Only lines that start with one of the
  above field names are evaluated by NMWiz.
  
  
  Autoload Trick
  ^^^^^^^^^^^^^^
  
  By adding a special line in an NMD file, file content can be automatically
  loaded into VMD at startup. The first line calls a NMWiz function to load the
  file itself (:file:`xyzeros.nmd`).
  
  ::
  
    nmwiz_load xyzeros.nmd
    coordinates 0 0 0 0 0 0  ...
    mode 0.039 0.009 0.058 0.038 -0.011 0.052 ...
    mode -0.045 -0.096 -0.009 -0.040 -0.076 -0.010 ...
    mode 0.007 -0.044 0.080 0.015 -0.037 0.062 ...
  
  
  In this case, VMD must be started from the command line by typing
  :program:`vmd -e xyzeros.nmd`."""
  
  
  __all__ = ['parseNMD', 'writeNMD', 'pathVMD', 'getVMDpath', 'setVMDpath',
             'viewNMDinVMD']
  
  import os
  from os.path import abspath, join, split, splitext
  
  import numpy as np
  
  from prody import LOGGER, SETTINGS, PY3K
  from prody.atomic import AtomGroup
  from prody.utilities import openFile, isExecutable, which, PLATFORM, addext
  
  from .nma import NMA
  from .anm import ANM
  from .gnm import GNM, ZERO
  from .pca import PCA
  from .mode import Vector, Mode
  from .modeset import ModeSet
  
  
  def pathVMD(*path):
      """Return VMD path, or set it to be a user specified *path*."""
  
      if not path:
          path = SETTINGS.get('vmd', None)
          if isExecutable(path):
              return path
          else:
              LOGGER.warning('VMD path is not set by user, looking for it.')
  
              vmdbin = None
              vmddir = None
              if PLATFORM == 'Windows':
                  if PY3K:
                      import winreg
                  else:
                      import _winreg as winreg  # PY3K: OK
                  for vmdversion in ('1.8.7', '1.9', '1.9.1'):
                      try:
                          key = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE,
                                  'Software\\University of Illinois\\VMD\\' +
                                  vmdversion)
                          vmddir = winreg.QueryValueEx(key, 'VMDDIR')[0]
                          vmdbin = join(vmddir, 'vmd.exe')
                      except:
                          pass
                      try:
                          key = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE,
                      'Software\\WOW6432node\\University of Illinois\\VMD\\' +
                      vmdversion)
                          vmddir = winreg.QueryValueEx(key, 'VMDDIR')[0]
                          vmdbin = join(vmddir, 'vmd.exe')
                      except:
                          pass
              else:
                  vmdbin = which('vmd')
                  if False:
                      pipe = os.popen('which vmd')
                      vmdbin = pipe.next().strip()
                      vmdfile = open(vmdbin)
                      for line in vmdfile:
                          if line.startswith('defaultvmddir='):
                              vmddir = line.split('=')[1].replace('"', '')
                              break
                      vmdfile.close()
              if isExecutable(vmdbin):
                  setVMDpath(vmdbin)
                  return vmdbin
      elif len(path) == 1:
          path = path[0]
          if isExecutable(path):
              SETTINGS['vmd'] = path
              SETTINGS.save()
              LOGGER.info("VMD path is set to '{0}'.".format(path))
          else:
              raise OSError('{0} is not executable.'.format(str(path)))
      else:
          raise ValueError('specify a single path string')
  
  
  def getVMDpath():
      """Deprecated for removal in v1.5, use :func:`pathVMD` instead."""
  
      return pathVMD()
  
  
  def setVMDpath(path):
      """Deprecated for removal in v1.5, use :func:`pathVMD` instead."""
  
      return pathVMD(path)
  
  
  NMD_LABEL_MAP = {
      'atomnames': 'name',
      'resnames': 'resname',
      'resnums': 'resnum',
      'resids': 'resnum',
      'chainids': 'chain',
      'bfactors': 'beta',
      'segnames': 'segment',
      'segments': 'segment',
  }
  
  
  def parseNMD(filename, type=None):
      """Return :class:`.NMA` and :class:`.AtomGroup` instances storing data
      parsed from *filename* in :file:`.nmd` format.  Type of :class:`.NMA`
      instance, e.g. :class:`.PCA`, :class:`.ANM`, or :class:`.GNM` will
      be determined based on mode data."""
  
      assert not isinstance(type, NMA), 'type must be NMA, ANM, GNM, or PCA'
  
      atomic = {}
      atomic.update([(label, None) for label in NMD_LABEL_MAP])
      atomic['coordinates'] = None
      atomic['name'] = None
      modes = []
  
      with open(filename) as nmd:
          for i, line in enumerate(nmd):
              try:
                  label, data = line.split(None, 1)
              except ValueError:
                  pass
  
              if label == 'mode':
                  modes.append((i + 1, data))
              elif label in atomic:
                  if atomic[label] is None:
                      atomic[label] = (i + 1, data)
                  else:
                      LOGGER.warn('Data label {0} is found more than once in '
                                  '{1}.'.format(repr(label), repr(filename)))
  
      name = atomic.pop('name', '')[1].strip() or splitext(split(filename)[1])[0]
      ag = AtomGroup(name)
      dof = None
      n_atoms = None
  
      line, coords = atomic.pop('coordinates', None)
      if coords is not None:
          coords = np.fromstring(coords, dtype=float, sep=' ')
          dof = coords.shape[0]
          if dof % 3 != 0:
              LOGGER.warn('Coordinate data in {0} at line {1} is corrupt '
                          'and will be omitted.'.format(repr(filename), line))
          else:
              n_atoms = dof / 3
              coords = coords.reshape((n_atoms, 3))
              ag.setCoords(coords)
  
      from prody.atomic import ATOMIC_FIELDS
  
      for label, data in atomic.items():  # PY3K: OK
          if data is None:
              continue
          line, data = data
          data = data.split()
          if n_atoms is None:
              n_atoms = len(data)
              dof = n_atoms * 3
          elif len(data) != n_atoms:
              LOGGER.warn('Data with label {0} in {1} at line {2} is '
                          'corrupt, expected {2} values, parsed {3}.'.format(
                          repr(label), repr(filename), line, n_atoms, len(data)))
              continue
          label = NMD_LABEL_MAP[label]
          data = np.array(data, dtype=ATOMIC_FIELDS[label].dtype)
          ag.setData(label, data)
  
      if not modes:
          return None, ag
  
      length = len(modes[0][1].split())
      is3d = length > n_atoms + 2
      if dof is None:
          dof = length - (length % 3)
      elif not is3d:  # GNM
          dof = n_atoms
  
      array = np.zeros((dof, len(modes)))
      less = 0
      eigvals = []
      count = 0
      for i, (line, mode) in enumerate(modes):
          mode = np.fromstring(mode, dtype=float, sep=' ')
          diff = len(mode) - dof
          if diff < 0 or diff > 2:
              LOGGER.warn('Mode data in {0} at line {1} is corrupt.'
                          .format(repr(filename), line))
              continue
          array[:, i - less] = mode[diff:]
          count += 1
          eigvals.append(mode[:diff])
  
      if count == 0:
          return None, ag
  
      try:
          eigvals = np.array(eigvals, dtype=float)
      except TypeError:
          LOGGER.warn('Failed to parse eigenvalues from {0}.'
                      .format(repr(filename)))
  
      if eigvals.shape[1] > 2:
          LOGGER.warn('Failed to parse eigenvalues from {0}.'
                      .format(repr(filename)))
          eigvals = None
      elif eigvals.shape[1] == 1:
          if np.all(eigvals % 1 == 0):
              LOGGER.warn('Failed to parse eigenvalues from {0}.'
                          .format(repr(filename)))
              eigvals = None
          else:
              eigvals = eigvals.flatten() ** 2
      else:
          eigvals = eigvals[:, 1] ** 2
  
      if is3d:
          if eigvals is not None and np.all(eigvals[:-1] >= eigvals[1:]):
              nma = PCA(name)
          else:
              nma = ANM(name)
      else:
          nma = GNM(name)
      if count != array.shape[1]:
          array = array[:, :count].copy()
  
      nma.setEigens(array, eigvals)
      return nma, ag
  
  
  def writeNMD(filename, modes, atoms):
      """Return *filename* that contains *modes* and *atoms* data in NMD format
      described in :ref:`nmd-format`.  :file:`.nmd` extension is appended to
      filename, if it does not have an extension.
  
      .. note::
         #. This function skips modes with zero eigenvalues.
         #. If a :class:`.Vector` instance is given, it will be normalized
            before it is written. It's length before normalization will be
            written as the scaling factor of the vector."""
  
      if not isinstance(modes, (NMA, ModeSet, Mode, Vector)):
          raise TypeError('modes must be NMA, ModeSet, Mode, or Vector, '
                          'not {0}'.format(type(modes)))
      if modes.numAtoms() != atoms.numAtoms():
          raise Exception('number of atoms do not match')
      out = openFile(addext(filename, '.nmd'), 'w')
  
      #out.write('#!{0} -e\n'.format(VMDPATH))
      out.write('nmwiz_load {0}\n'.format(abspath(filename)))
      name = modes.getTitle()
      name = name.replace(' ', '_').replace('.', '_')
      if not name.replace('_', '').isalnum() or len(name) > 30:
          name = str(atoms)
          name = name.replace(' ', '_').replace('.', '_')
      if not name.replace('_', '').isalnum() or len(name) > 30:
          name = splitext(split(filename)[1])[0]
      out.write('name {0}\n'.format(name))
      try:
          coords = atoms.getCoords()
      except:
          raise ValueError('coordinates could not be retrieved from atoms')
      if coords is None:
          raise ValueError('atom coordinates are not set')
  
      try:
          data = atoms.getNames()
          if data is not None:
              out.write('atomnames {0}\n'.format(' '.join(data)))
      except:
          pass
      try:
          data = atoms.getResnames()
          if data is not None:
              out.write('resnames {0}\n'.format(' '.join(data)))
      except:
          pass
      try:
          data = atoms.getResnums()
          if data is not None:
              out.write('resids ')
              data.tofile(out, ' ')
              out.write('\n')
      except:
          pass
      try:
          data = atoms.getChids()
          if data is not None:
              out.write('chainids {0}\n'.format(' '.join(data)))
      except:
          pass
      try:
          data = atoms.getSegnames()
          if data is not None:
              out.write('segnames {0}\n'.format(' '.join(data)))
      except:
          pass
  
      try:
          data = atoms.getBetas()
          if data is not None:
              out.write('bfactors ')
              data.tofile(out, ' ', '%.2f')
              out.write('\n')
      except:
          pass
  
      format = '{0:.3f}'.format
      out.write('coordinates ')
      coords.tofile(out, ' ', '%.3f')
      out.write('\n')
      count = 0
      if isinstance(modes, Vector):
          out.write('mode 1 {0:.2f} '.format(abs(modes)))
          modes.getNormed()._getArray().tofile(out, ' ', '%.3f')
          out.write('\n')
          count += 1
      else:
          if isinstance(modes, Mode):
              modes = [modes]
          for mode in modes:
              if mode.getEigval() < ZERO:
                  continue
              out.write('mode {0} {1:.2f} '.format(
                         mode.getIndex()+1, mode.getVariance()**0.5))
              arr = mode._getArray().tofile(out, ' ', '%.3f')
              out.write('\n')
              count += 1
      if count == 0:
          LOGGER.warning('No normal mode data was written. '
                         'Given modes might have 0 eigenvalues.')
      out.close()
      return filename
  
  
  def viewNMDinVMD(filename):
      """Start VMD in the current Python session and load NMD data."""
  
      vmd = pathVMD()
      if vmd:
          os.system('{0} -e {1}'.format(vmd, abspath(filename)))
  