class MatrixHandler(object):
def __init__(self, statistics_folder=None):
"""
Class constructor.
@param statistics_folder: Path to the folder that will contain the statistics summary. If None,
no statistics will be saved.
"""
self.distance_matrix = None
self.statistics_folder = statistics_folder
def getMatrix(self):
"""
@return: The inner condensed matrix.
"""
return self.distance_matrix
def createMatrix(self, pdb_coordsets, calculator="QCP_OMP_CALCULATOR"):
"""
Generates a condensed matrix given a set of coordinates (usually representing a trajectory) and
a calculator definition.
@param pdb_coordsets: Input coordinates in Prody format.
@param calculator: One of the possible available calculator types.
@return: A consensed matrix with the pairwise RMSD matrix.
"""
print "Calculating matrix..."
rmsd = pyRMSD.RMSDCalculator.RMSDCalculator(
pdb_coordsets, calculator).pairwiseRMSDMatrix()
self.distance_matrix = CondensedMatrix(rmsd)
self.distance_matrix.recalculateStatistics()
self.__save_statistics()
print " Done\n"
return self.distance_matrix
def saveMatrix(self, matrix_file_without_extension):
"""
Saves the internal matrix to a file. It adds the extension '.bin' to that name.
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
"""
print "Writing matrix data (in " + matrix_file_without_extension + ".bin) ..."
MatrixHandler.save_matrix(matrix_file_without_extension,
self.distance_matrix)
print " Done\n"
def loadMatrix(self, matrix_file_without_extension):
"""
Loads a condensed matrix from disk.
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
"""
print "Loading matrix data from " + matrix_file_without_extension + ".bin ..."
self.distance_matrix = MatrixHandler.load_matrix(
matrix_file_without_extension)
self.distance_matrix.recalculateStatistics()
MatrixHandler.save_statistics(self.statistics_folder,
self.distance_matrix)
print " Done\n"
@classmethod
def save_matrix(cls, matrix_file_without_extension, distance_matrix):
"""
Saves the internal matrix to a file. It adds the extension '.bin' to that name.
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
@param distance_matrix: The matrix to be saved.
"""
numpy.save(matrix_file_without_extension, distance_matrix.get_data())
@classmethod
def load_matrix(cls, matrix_file_without_extension):
"""
Loads a condensed matrix from disk. <ATT> Without the cast to list, the matrix
is not loaded properly.</ATT>
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
@return: The loaded condensed matrix.
"""
return CondensedMatrix(
list(numpy.load(matrix_file_without_extension + ".npy")))
@classmethod
def save_statistics(cls, statistics_folder, distance_matrix):
"""
Saves a file with some statistics of the internal matrix.
@param statistics_folder: Folder where the file 'statistics.json' will be stored.
@param distance_matrix: The distance matrix from which the statistics are calculated.
"""
if statistics_folder is not None:
stats_dic = {}
stats_dic["Minimum"] = distance_matrix.calculateMin()
stats_dic["Maximum"] = distance_matrix.calculateMax()
stats_dic["Mean"] = distance_matrix.calculateMean()
stats_dic["Std. Dev."] = distance_matrix.calculateVariance()
stats_dic["Skewness"] = distance_matrix.calculateSkewness()
stats_dic["Kurtosis"] = distance_matrix.calculateKurtosis()
open(os.path.join(statistics_folder, "statistics.json"),
"w").write(
json.dumps(stats_dic, indent=4, separators=(',', ': ')))
return os.path.join(statistics_folder, "statistics.json")
return None
class MatrixHandler(object):
def __init__(self, statistics_folder=None):
"""
Class constructor.
@param statistics_folder: Path to the folder that will contain the statistics summary. If None,
no statistics will be saved.
"""
self.distance_matrix = None
self.statistics_folder = statistics_folder
def getMatrix(self):
"""
@return: The inner condensed matrix.
"""
return self.distance_matrix
def createMatrix(self, pdb_coordsets, calculator = "QCP_OMP_CALCULATOR"):
"""
Generates a condensed matrix given a set of coordinates (usually representing a trajectory) and
a calculator definition.
@param pdb_coordsets: Input coordinates in Prody format.
@param calculator: One of the possible available calculator types.
@return: A consensed matrix with the pairwise RMSD matrix.
"""
print "Calculating matrix..."
rmsd = pyRMSD.RMSDCalculator.RMSDCalculator(pdb_coordsets, calculator).pairwiseRMSDMatrix()
self.distance_matrix = CondensedMatrix(rmsd)
self.distance_matrix.recalculateStatistics()
self.__save_statistics()
print " Done\n"
return self.distance_matrix
def saveMatrix(self, matrix_file_without_extension):
"""
Saves the internal matrix to a file. It adds the extension '.bin' to that name.
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
"""
print "Writing matrix data (in "+matrix_file_without_extension+".bin) ..."
MatrixHandler.save_matrix(matrix_file_without_extension, self.distance_matrix)
print " Done\n"
def loadMatrix(self, matrix_file_without_extension):
"""
Loads a condensed matrix from disk.
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
"""
print "Loading matrix data from "+matrix_file_without_extension+".bin ..."
self.distance_matrix = MatrixHandler.load_matrix(matrix_file_without_extension)
self.distance_matrix.recalculateStatistics()
MatrixHandler.save_statistics(self.statistics_folder, self.distance_matrix)
print " Done\n"
@classmethod
def save_matrix(cls, matrix_file_without_extension, distance_matrix):
"""
Saves the internal matrix to a file. It adds the extension '.bin' to that name.
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
@param distance_matrix: The matrix to be saved.
"""
numpy.save(matrix_file_without_extension,distance_matrix.get_data())
@classmethod
def load_matrix(cls, matrix_file_without_extension):
"""
Loads a condensed matrix from disk. <ATT> Without the cast to list, the matrix
is not loaded properly.</ATT>
@param matrix_file_without_extension: Is the matrix file name without any
extension ('.bin' will be added).
@return: The loaded condensed matrix.
"""
return CondensedMatrix(list(numpy.load(matrix_file_without_extension+".npy")))
@classmethod
def save_statistics(cls, statistics_folder, distance_matrix):
"""
Saves a file with some statistics of the internal matrix.
@param statistics_folder: Folder where the file 'statistics.json' will be stored.
@param distance_matrix: The distance matrix from which the statistics are calculated.
"""
if statistics_folder is not None:
stats_dic = {}
stats_dic["Minimum"] = distance_matrix.calculateMin()
stats_dic["Maximum"] = distance_matrix.calculateMax()
stats_dic["Mean"] = distance_matrix.calculateMean()
stats_dic["Std. Dev."] =distance_matrix.calculateVariance()
stats_dic["Skewness"] = distance_matrix.calculateSkewness()
stats_dic["Kurtosis"] = distance_matrix.calculateKurtosis()
open( os.path.join(statistics_folder,"statistics.json"),"w").write(json.dumps(stats_dic,indent=4, separators=(',', ': ')))
return os.path.join(statistics_folder,"statistics.json")
return None
