webmo 1.1.4__tar.gz → 1.2.0__tar.gz

{webmo-1.1.4/webmo.egg-info → webmo-1.2.0}/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.1
 Name: webmo
-Version: 1.1.4
+Version: 1.2.0
 Summary: A Python-based interface to WebMO
 Home-page: https://github.com/jrschmidt2/webmo-python
-Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.1.4.tar.gz
+Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.2.0.tar.gz
 Author: J.R. Schmidt
 Author-email: schmidt@webmo.net
 License: MIT
 Keywords: WEBMO,REST,API
+Provides-Extra: spectrum
 License-File: LICENSE

{webmo-1.1.4 → webmo-1.2.0}/setup.py

@@ -31,5 +31,8 @@ setup(
   install_requires=[
           'requests',
           'websockets',
-      ],
+  ],
+  extras_require={
+      "spectrum": ["numpy"]
+  }
 )

{webmo-1.1.4 → webmo-1.2.0}/webmo/__init__.py

@@ -1,2 +1,2 @@
 from .webmo_rest import WebMOREST
-__version__ = "1.1.4"
+__version__ = "1.2.0"

webmo-1.2.0/webmo/spectrum.py

@@ -0,0 +1,448 @@
+import numpy as np
+
+#
+# lineshape functions
+#
+
+def _faddeeva(z):
+    """
+    Calculates the scaled complex complementary function in the complex plane.
+    We use this to calculate voigt lineshapes.
+    """
+    if _faddeeva.run_yet == False:
+        _faddeeva.run_yet = True
+        _faddeeva.N = 1000
+        _faddeeva.L = np.sqrt(_faddeeva.N / np.sqrt(2))
+        # our basis set. 1000 elements hits a good blend of speed and accuracy.
+        l = [
+            5.11748989e-16,-1.44365777e-16,1.71205586e-16,1.43270169e-16,
+            2.40509424e-16,9.34400028e-17,3.33586468e-16,2.07038704e-16,
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+            3.91736558e-16,1.22245854e-16,5.72475581e-16,-2.79943119e-17,
+            5.39626522e-16,4.69224371e-16,1.79053135e-16,4.94826390e-16,
+            3.39932067e-16,8.38290822e-17,2.83931853e-16,5.55942954e-16,
+            4.19747676e-16,2.79124937e-16,2.03558902e-16,4.24519122e-16,
+            1.02658980e-16,1.89197331e-17,3.63112861e-16,1.41263763e-16,
+            -6.39833244e-17,2.94156130e-16,1.19279922e-16,2.62537867e-16,
+            9.23250107e-17,9.54340873e-17,2.02657914e-16,8.56837549e-17,
+            1.09912242e-16,3.25830034e-16,-6.06707638e-17,1.19561917e-16,
+            1.82940837e-18,-4.63814691e-17,-1.76004402e-16,-1.14268787e-16,
+            -1.99388849e-16,-2.34993921e-16,-2.91227483e-16,7.53550548e-18,
+            4.82690083e-18,-2.38575495e-16,-2.44652589e-16,-8.24120125e-17,
+            -1.33320590e-16,-2.00054414e-16,-1.43372915e-16,1.89338899e-16,
+            -3.10018714e-16,-1.46340691e-16,-1.07599704e-16,-1.64066751e-16,
+            -2.17562644e-16,-1.17636359e-16,-1.86483075e-16,5.34358570e-17,
+            -4.22094388e-17,1.49639967e-16,-9.19369910e-17,6.43735552e-17,
+            -4.95497319e-17,3.33550953e-16,-5.58797396e-18,1.08044533e-17,
+            -5.68782134e-17,-1.09699521e-16,2.02816822e-17,6.57529483e-18,
+            -5.62985774e-17,1.37422525e-16,3.68137873e-16,2.93855626e-16,
+            4.60911681e-16,2.79558527e-16,1.93645149e-16,4.29339673e-16,
+            3.94346119e-16,-9.11980916e-17,2.08587798e-16,4.60632308e-16,
+            2.46253693e-16,2.94939706e-16,2.89601071e-16,2.36630408e-16,
+            3.40090024e-16,2.08679525e-16,1.92263017e-16,9.71798469e-17,
+            2.75039790e-16,4.35625730e-16,3.44388483e-16,3.13739000e-16,
+            2.67825858e-16,5.23555689e-16,7.02254341e-17,1.24864649e-16,
+            3.20139668e-16,2.33491483e-16,2.19996198e-16,3.10765864e-16,
+            1.92283246e-16,4.58564011e-16,5.97928541e-16,1.65336064e-16,
+            1.97369721e-16,4.79474407e-16,4.74556351e-16,-2.72567462e-17,
+            4.84030144e-16,2.35944695e-16,-1.64178854e-16,2.08598406e-16,
+            4.78048738e-16,-1.07186669e-16,2.72374315e-16,1.30982162e-16,
+            6.19721697e-16,1.84166717e-16,2.19916975e-16,-8.38157837e-17,
+            3.10783706e-16,1.43651243e-16,8.32086938e-16,-8.60950101e-17,
+            1.12719684e-15,1.25055521e-15,1.59161573e-15,2.61479727e-15,
+            5.34328137e-15,8.24229573e-15,1.30739863e-14,2.09752216e-14,
+            3.33102435e-14,5.24096322e-14,8.29913915e-14,1.30512490e-13,
+            2.04465778e-13,3.19687388e-13,4.96527264e-13,7.69091457e-13,
+            1.18768639e-12,1.82723170e-12,2.80164159e-12,4.28093472e-12,
+            6.51965593e-12,9.89587079e-12,1.49690322e-11,2.25677468e-11,
+            3.39091173e-11,5.07809830e-11,7.57933947e-11,1.12751053e-10,
+            1.67175699e-10,2.47052924e-10,3.63894571e-10,5.34237415e-10,
+            7.81753258e-10,1.14021130e-09,1.65761999e-09,2.40199471e-09,
+            3.46936706e-09,4.99485579e-09,7.16792849e-09,1.02533485e-08,
+            1.46198336e-08,2.07791178e-08,2.94389945e-08,4.15750919e-08,
+            5.85276356e-08,8.21314254e-08,1.14889782e-07,1.60206498e-07,
+            2.22693985e-07,3.08581163e-07,4.26251360e-07,5.86949080e-07,
+            8.05705175e-07,1.10254346e-06,1.50404848e-06,2.04539498e-06,
+            2.77296513e-06,3.74771110e-06,5.04945887e-06,6.78239587e-06,
+            9.08204151e-06,1.21240672e-05,1.61354139e-05,2.14082509e-05,
+            2.83174350e-05,3.73422599e-05,4.90934463e-05,6.43464991e-05,
+            8.40827711e-05,1.09539808e-04,1.42272822e-04,1.84229443e-04,
+            2.37840239e-04,3.06127873e-04,3.92838172e-04,5.02596823e-04,
+            6.41095903e-04,8.15314926e-04,1.03378162e-03,1.30687819e-03,
+            1.64719925e-03,2.06996828e-03,2.59351969e-03,3.23985416e-03,
+            4.03527510e-03,5.01111418e-03,6.20455414e-03,7.65955651e-03,
+            9.42790170e-03,1.15703481e-02,1.41579155e-02,1.72732972e-02,
+            2.10124030e-02,2.54860316e-02,3.08216711e-02,3.71654197e-02,
+            4.46840156e-02,5.35669618e-02,6.40287248e-02,7.63109798e-02,
+            9.06848724e-02,1.07453255e-01,1.26952855e-01,1.49556315e-01,
+            1.75674058e-01,2.05755892e-01,2.40292299e-01,2.79815316e-01,
+            3.24898926e-01,3.76158879e-01,4.34251842e-01,4.99873794e-01,
+            5.73757579e-01,6.56669521e-01,7.49405043e-01,8.52783210e-01,
+            9.67640138e-01,1.09482124e00,1.23517231e00,1.38952936e00,
+            1.55870741e00,1.74348805e00,1.94460614e00,2.16273548e00,
+            2.39847384e00,2.65232736e00,2.92469468e00,3.21585089e00,
+            3.52593174e00,3.85491824e00,4.20262214e00,4.56867248e00,
+            4.95250359e00,5.35334499e00,5.77021329e00,6.20190671e00,
+            6.64700218e00,7.10385565e00,7.57060543e00,8.04517909e00,
+            8.52530380e00,9.00852024e00,9.49220006e00,9.97356678e00,
+            1.04497200e01,1.09176625e01,1.13743304e01,1.18166252e01,
+            1.22414481e01,1.26457352e01,1.30264942e01,1.33808408e01,
+            1.37060347e01,1.39995149e01,1.42589331e01,1.44821848e01,
+            1.46674378e01,1.48131571e01,1.49181262e01,1.49814637e01,
+        ]
+        a = np.array(l)
+        a = np.flip(a)
+        _faddeeva.vals = a
+        _faddeeva.poly = np.polynomial.polynomial.Polynomial(a)
+
+    Z = (_faddeeva.L + 1j * z) / (_faddeeva.L - 1j * z)
+    p = _faddeeva.poly(Z)
+    w = 2 * p / (_faddeeva.L - 1j * z)**2 + (1 / np.sqrt(np.pi)) / (_faddeeva.L - 1j * z)
+
+    return(w)
+
+_faddeeva.run_yet = False
+_faddeeva.vals = None
+_faddeeva.L = None
+_faddeeva.N = None
+_faddeeva.poly = None
+
+def _arb_voigt(center, intensity, ratio, peak_width):
+    """
+    Use the Faddeeva function to calculate a voigt line shape. See
+    https://en.wikipedia.org/wiki/Voigt_profile#The_uncentered_Voigt_profile
+    """
+
+    def _voigt_decoder(q, k):
+        """
+        Takes the FWHM (k) and a ratio (q) and determines the values of gamma and sigma.
+
+        Accurate to within around 1.2%.
+        """
+        f_l = (-k*(q**2) + (-1 + q)**2 * np.sqrt(((k**2)*(q**2) * (4 - 8 * q + 5 * (q**2)))/(-1 + q)**4))/(2 * (-1 + q)**2)
+        f_g = (k * (q**2) - (-1 + q)**2 * np.sqrt(((k**2) * (q**2) * (4 - 8 * q + 5 * (q**2)))/(-1 + q)**4))/(2 * (-1 + q) * q)
+
+
+        gamma = f_l/2 # because gamma = FWHM/2
+        sigma = f_g / (2 * np.sqrt(2*np.log(2)))
+
+        return(gamma,sigma)
+
+    from math import sqrt, pi
+
+    gamma, sigma = _voigt_decoder(ratio, peak_width)
+    denom = sigma * sqrt(2 * pi) # denomonator
+    z = lambda x: _faddeeva((x - center + gamma*1j)/(sqrt(2) * sigma)) # Define z(x) as numerator, more or less
+    l = lambda x: intensity * ((z(x).real)/denom) # define the actual voigt function
+
+    return l
+
+def voigt_line(center, intensity, width=10, q=0.5, start=0, stop=4000, step=1):
+    """Calculate a voigt lineshape
+
+    This function returns a pair of numpy arrays that define a voigt line.
+
+    Arguments:
+    	center(float): the center point of the line
+    	intensity(float): the area under the line (NOT the height!)
+    	width(float,optional): the full width half max of the desired line
+    	q(float,optional): the ratio of gaussian to lorentzian, from 0 < q < 1.
+    	start(float,optional): the starting point of the returned array
+    	stop(float,optional): the ending point of the returned array
+    	step(float,optional): the space between points of the returned array
+
+    Returns:
+    	(x,y): a tuple of the x and y numpy arrays of the specified line
+    """
+    if (not 0 < q < 1):
+        q = 0.5
+
+    x = np.arange(start=start, stop=stop, step=step)
+    vfunc = np.vectorize(_arb_voigt(center, intensity, q, width))
+    return((x,vfunc(x)))
+
+def _arb_gaussian(center, intensity, width=10):
+    """
+    Return a gaussian with an arbitrary height and intensity, with sigma being determined by calculating
+    it from our FWHM peak width.
+    """
+    from math import sqrt, pi, exp, log
+
+    sigma = (width / (2 * sqrt(2 * log(2))))
+    l = lambda x: intensity * (1/sigma*sqrt(2*pi)) * exp(-((x-center)**2/(2*sigma**2)))
+
+    return l
+
+def gauss_line(center, intensity, width=10, start=0, stop=4000, step=1):
+    """Calculate a gaussian lineshape
+
+    This function returns a pair of numpy arrays that define a gaussian with
+    given parameters.
+
+    Arguments:
+    	center(float): the center point of the line
+    	intensity(float): the area under the line (NOT the height!)
+    	width(float,optional): the full width half max of the desired line
+    	start(float,optional): the starting point of the returned array
+    	stop(float,optional): the ending point of the returned array
+    	step(float,optional): the space between points of the returned array
+
+    Returns:
+    	(x,y): a tuple of the x and y numpy arrays of the specified line
+    """
+    x = np.arange(start=start, stop=stop, step=step)
+    vfunc = np.vectorize(_arb_gaussian(center, intensity, width))
+    return((x,vfunc(x)))
+
+def _arb_lorentz(center, intensity, width=10):
+    """
+    Return a lorentzian with an arbitrary height and intensity, with gamma being calculated from our
+    FWHM peak width.
+    """
+    from math import pi
+
+    gamma = (width / 2)
+    l = lambda x: (intensity/pi) * (gamma/((x-(center))**2 + gamma**2))
+
+    return l
+
+def lorentz_line(center, intensity, width=10, start=0, stop=4000, step=1):
+    """Calculate a lorentzian lineshape
+
+    This function returns a pair of numpy arrays that define a lorentzian line
+    given a set of parameters.
+
+    Arguments:
+    	center(float): the center point of the line
+    	intensity(float): the area under the line (NOT the height!)
+    	width(float,optional): the full width half max of the desired line
+    	start(float,optional): the starting point of the returned array
+    	stop(float,optional): the ending point of the returned array
+    	step(float,optional): the space between points of the returned array
+
+    Returns:
+    	(x,y): a tuple of the x and y numpy arrays of the specified line
+    """
+    x = np.arange(start=start, stop=stop, step=step)
+    vfunc = np.vectorize(_arb_lorentz(center, intensity, width))
+    return((x,vfunc(x)))
+
+def construct_spectrum(points, intensities, lineshape="gauss", width=10, start=0, stop=4000, step=1):
+    """Construct an entire spectrum plot of data
+
+    This function returns a pair of numpy arrays that make a spectrum; an x axis
+    and a y axis of the spectrum at each point on the x axis. This can then be
+    plotted or analyzed.
+
+    Arguments:
+    	points([float]): a list of peak positions
+    	intensities([float]): a list of corresponding peak intensities - the order must
+    			      match `points`
+    	lineshape(string,optional): the desired lineshape. The options are "gauss", "lorentz", and "voigt"
+    	width(float,optional): the full width half max of each peak
+    	start(float,optional): the starting point of the returned array
+    	stop(float,optional): the ending point of the returned array
+    	step(float,optional): the space between points of the returned array
+
+    Returns:
+    	(x,y): a tuple of the x and y numpy arrays for the constructed spectrum
+    """
+    l = []
+
+    linefuncs = {
+        "gauss": gauss_line,
+        "lorentz": lorentz_line,
+        "voigt": voigt_line
+    }
+    if (lineshape not in linefuncs.keys()):
+        linefunc = gauss_line
+    else:
+        linefunc = linefuncs[lineshape]
+
+    if (len(points) == 0 or len(intensities) == 0):
+        raise AssertionError("points or intensities are empty")
+
+    if (len(points) != len(intensities)):
+        raise AssertionError("peaks and intensities do not match size")
+
+    for (x,y) in zip(points, intensities):
+        axis, tmp = linefunc(x,y,width=width,start=start,stop=stop,step=step)
+        l.append(tmp)
+
+    return((axis,np.array(l).sum(axis=0)))

{webmo-1.1.4 → webmo-1.2.0}/webmo/webmo_rest.py

@@ -316,7 +316,7 @@ class WebMOREST:
         return r.json()["jobNumber"]
         
     async def display_job_property(self, job_number, property_name, property_index=1, peak_width=0.0, tms_shift=0.0, proton_coupling=0.0, nmr_field=400.0, x_range=None, y_range=None, width=400, height=400, background_color=(255,255,255), transparent_background=False, rotate=(0.,0.,0.)):
-        """Uses Javascript and IPython to display and image of the specified molecule and property,
+        """Uses Javascript and IPython to display an image of the specified molecule and property,
         calculated from a previous WebMO job.
         
         This call outputs (via IPython) a PNG-formatted image of the molecule and property into the
@@ -706,45 +706,45 @@ class WebMOREST:
 
         return EmbeddedImage(data=decoded_image_data)
 
+if has_ipython:
+    class EmbeddedImage(Image):
+        """The EmbeddedImage class is a IPython-displayable image object with additional functionality.
 
-class EmbeddedImage(Image):
-    """The EmbeddedImage class is a IPython-displayable image object with additional functionality.
+    The EmbeddedImage class is a Jupyter-renderable image object, derived from IPython.display.image.   
+        However, the EmbeddedImage also adds additional utility conversion methods.
+        """
+        def __init__(self, data):
+            super().__init__(data)
 
-    The EmbeddedImage class is a Jupyter-renderable image object, derived from IPython.display.image.
-    However, the EmbeddedImage also adds additional utility conversion methods.
-    """
-    def __init__(self, data):
-        super().__init__(data)
+        def save(self, filename):
+            """Saves the EmbeddedImage to disk as a PNG-formatted image.
 
-    def save(self, filename):
-        """Saves the EmbeddedImage to disk as a PNG-formatted image.
+            This call saves the EmbeddedImage object to disk as PNG-formatted image.
 
-        This call saves the EmbeddedImage object to disk as PNG-formatted image.
+            Arguments:
+                filename(str): The path to the target PNG file. A "png" extension is added, if not provided.
 
-        Arguments:
-            filename(str): The path to the target PNG file. A "png" extension is added, if not provided.
+            Returns:
+                None
+            """
+            if not filename.endswith(".png"):
+                filename += ".png"
+            with open(filename, 'wb') as fp:
+                fp.write(self.data)
 
-        Returns:
-            None
-        """
-        if not filename.endswith(".png"):
-            filename += ".png"
-        with open(filename, 'wb') as fp:
-            fp.write(self.data)
+        def to_pil_image(self):
+            """Returns an equivalent Pillow (PIL) Image object.
 
-    def to_pil_image(self):
-        """Returns an equivalent Pillow (PIL) Image object.
+            This call converts and returns and equivalent Pillow (PIL) Image representation of the
+            current EmbeddedImage object, for further manipulation.
 
-        This call converts and returns and equivalent Pillow (PIL) Image representation of the
-        current EmbeddedImage object, for further manipulation.
+            Arguments:
+                None
 
-        Arguments:
-            None
-
-        Returns:
-            A Pillow PIL.Image.Image object.
-        """
-        from PIL import Image
-        from io import BytesIO
+            Returns:
+                A Pillow PIL.Image.Image object.
+            """
+            from PIL import Image
+            from io import BytesIO
 
-        return Image.open(BytesIO(self.data))
+            return Image.open(BytesIO(self.data))

{webmo-1.1.4 → webmo-1.2.0/webmo.egg-info}/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.1
 Name: webmo
-Version: 1.1.4
+Version: 1.2.0
 Summary: A Python-based interface to WebMO
 Home-page: https://github.com/jrschmidt2/webmo-python
-Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.1.4.tar.gz
+Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.2.0.tar.gz
 Author: J.R. Schmidt
 Author-email: schmidt@webmo.net
 License: MIT
 Keywords: WEBMO,REST,API
+Provides-Extra: spectrum
 License-File: LICENSE

{webmo-1.1.4 → webmo-1.2.0}/webmo.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ README.md
 setup.cfg
 setup.py
 webmo/__init__.py
+webmo/spectrum.py
 webmo/webmo_rest.py
 webmo.egg-info/PKG-INFO
 webmo.egg-info/SOURCES.txt

{webmo-1.1.4 → webmo-1.2.0}/webmo.egg-info/requires.txt

@@ -1,2 +1,5 @@
 requests
 websockets
+
+[spectrum]
+numpy