import bpy
from bpy import context
import mathutils
from mathutils import Vector,Quaternion,Matrix
import math

#obj = bpy.data.objects["Cube"]  # particular object by name
obj = bpy.context.scene.objects.active # active object

# setup whatever matrix
mx = Matrix([[0, 1, 0, 0],
    [0, 0, 1, 0],
    [1, 0, 0, 0],
    [2.94099, -0.32091, 0.92944, 1]])
mx.transpose()

bpy.ops.ed.undo_push()

mesh = obj.data
for vert in mesh.vertices:
    vert.co = mx * vert.co