ratapi 0.0.0.dev16__cp315-cp315-win_amd64.whl

ratapi/examples/absorption/volume_thiol_bilayer.py

@@ -0,0 +1,144 @@
+"""Custom layer model file for the absorption example."""
+
+
+def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
+    """VolumeThiolBilayer  RAT Custom Layer Model File.
+
+    This file accepts 3 vectors containing the values for params, bulk in and bulk out.
+    The final parameter is an index of the contrast being calculated
+
+    The function should output a matrix of layer values, in the form...
+
+    Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1
+              ....
+              thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]
+
+    The "hydrate how" parameter decides if the layer is hydrated with Bulk out or Bulk in phases.
+    Set to 1 for Bulk out, zero for Bulk in.
+    Alternatively, leave out hydration and just return...
+
+    Output = [thick 1, SLD 1, Rough 1,
+              ....
+              thick n, SLD n, Rough n]
+
+    The second output parameter should be the substrate roughness.
+    """
+    # Note - The first contrast number is 1 (not 0) so be careful if you use
+    # this variable for array indexing.
+
+    subRough = params[0]
+    alloyThick = params[1]
+    alloySLDUp = params[2]
+    alloyISLDUp = params[3]
+    alloySLDDown = params[4]
+    alloyISLDDown = params[5]
+    alloyRough = params[6]
+    goldThick = params[7]
+    goldRough = params[8]
+    goldSLD = params[9]
+    goldISLD = params[10]
+    thiolAPM = params[11]
+    thiolHeadHydr = params[12]
+    thiolCoverage = params[13]
+    cwThick = params[14]
+    bilayerAPM = params[15]
+    bilHeadHydr = params[16]
+    bilayerRough = params[17]
+    bilayerCoverage = params[18]
+
+    # Make the metal layers
+    gold = [goldThick, goldSLD, goldISLD, goldRough]
+    alloyUp = [alloyThick, alloySLDUp, alloyISLDUp, alloyRough]
+    alloyDown = [alloyThick, alloySLDDown, alloyISLDDown, alloyRough]
+
+    # Neutron b's..
+    # define all the neutron b's.
+    bc = 0.6646e-4  # Carbon
+    bo = 0.5843e-4  # Oxygen
+    bh = -0.3739e-4  # Hydrogen
+    bp = 0.513e-4  # Phosphorus
+    bn = 0.936e-4  # Nitrogen
+
+    # Work out the total scattering length in each fragment
+    # Define scattering lengths
+    # Hydrogenated version
+    COO = (2 * bo) + (bc)
+    GLYC = (3 * bc) + (5 * bh)
+    CH3 = (1 * bc) + (3 * bh)
+    PO4 = (1 * bp) + (4 * bo)
+    CH2 = (1 * bc) + (2 * bh)
+    CH = (1 * bc) + (1 * bh)
+    CHOL = (5 * bc) + (12 * bh) + (1 * bn)
+
+    # And also volumes
+    vCH3 = 52.7  # CH3 volume in the paper appears to be for 2 * CH3's
+    vCH2 = 28.1
+    vCOO = 39.0
+    vGLYC = 68.8
+    vPO4 = 53.7
+    vCHOL = 120.4
+    vCHCH = 42.14
+
+    vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
+    vTail = (28 * vCH2) + (1 * vCHCH) + (2 * vCH3)  # Tail volume
+
+    # Calculate sum_b's for other fragments
+    sumbHead = CHOL + PO4 + GLYC + 2 * COO
+    sumbTail = (28 * CH2) + (2 * CH) + 2 * CH3
+
+    # Calculate SLDs and Thickness
+    sldHead = sumbHead / vHead
+    thickHead = vHead / thiolAPM
+
+    sldTail = sumbTail / vTail
+    thickTail = vTail / thiolAPM
+
+    # Correct head SLD based on hydration
+    thiolHeadHydr = thiolHeadHydr / 100
+    sldHead = sldHead * (1 - thiolHeadHydr) + (thiolHeadHydr * bulk_out[contrast - 1])
+
+    # Now correct both the SLDs for the coverage parameter
+    sldTail = (thiolCoverage * sldTail) + ((1 - thiolCoverage) * bulk_out[contrast - 1])
+    sldHead = (thiolCoverage * sldHead) + ((1 - thiolCoverage) * bulk_out[contrast - 1])
+
+    SAMTAILS = [thickTail, sldTail, 0, goldRough]
+    SAMHEAD = [thickHead, sldHead, 0, goldRough]
+
+    # Now do the same for the bilayer
+    vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
+    vTail = 28 * vCH2  # Tail volume
+    vMe = 2 * vCH3
+
+    sumbHead = CHOL + PO4 + GLYC + 2 * COO
+    sumbTail = 28 * CH2
+    sumbMe = 2 * CH3
+
+    sldHead = sumbHead / vHead
+    thickHead = vHead / bilayerAPM
+    bilHeadHydr = bilHeadHydr / 100
+    sldHead = sldHead * (1 - bilHeadHydr) + (bilHeadHydr * bulk_out[contrast - 1])
+
+    sldTail = sumbTail / vTail
+    thickTail = vTail / bilayerAPM
+
+    sldMe = sumbMe / vMe
+    thickMe = vMe / bilayerAPM
+
+    sldTail = (bilayerCoverage * sldTail) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
+    sldHead = (bilayerCoverage * sldHead) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
+    sldMe = (bilayerCoverage * sldMe) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
+
+    BILTAILS = [thickTail, sldTail, 0, bilayerRough]
+    BILHEAD = [thickHead, sldHead, 0, bilayerRough]
+    BILME = [thickMe, sldMe, 0, bilayerRough]
+
+    BILAYER = [BILHEAD, BILTAILS, BILME, BILME, BILTAILS, BILHEAD]
+
+    CW = [cwThick, bulk_out[contrast - 1], 0, bilayerRough]
+
+    if contrast == 2 or contrast == 4:
+        output = [alloyUp, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
+    elif contrast == 1 or contrast == 3:
+        output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
+
+    return output, subRough

ratapi/examples/convert_rascal_project/Model_IIb.py

@@ -0,0 +1,90 @@
+"""A custom model file for a monolayer volume model."""
+
+from math import cos, radians
+
+
+def Model_IIb(params, bulk_in, bulk_out, contrast):
+    """Calculate layer parameters for a monolayer volume model at two deuterations."""
+    # Note - The first contrast number is 1 (not 0) so be careful if you use
+    # this variable for array indexing. Same applies to the domain number.
+
+    # converted from matlab file Model_IIb.m
+
+    Roughness, APM, thickHead, theta = params
+
+    # Make a flag to say which deuteration this is calculating
+    # [subs head tail]
+    deut = [[0, 0, 1], [1, 0, 1], [0, 1, 0], [1, 1, 0], [0, 1, 1], [1, 1, 1], [1, 0, 0]]
+
+    bc = 0.6646e-4  # Carbon
+    bo = 0.5843e-4  # Oxygen
+    bh = -0.3739e-4  # Hydrogen
+    bp = 0.513e-4  # Phosphorus
+    bn = 0.936e-4  # Nitrogen
+    bd = 0.6671e-4  # Deuterium
+
+    # Work out the total scattering length in each fragment
+    # for hydrogenated:
+    COO = (4 * bo) + (2 * bc)
+    GLYC = (3 * bc) + (5 * bh)
+    CH3 = (2 * bc) + (6 * bh)
+    PO4 = (1 * bp) + (4 * bo)
+    CH2 = (1 * bc) + (2 * bh)
+    CHOL = (5 * bc) + (12 * bh) + (1 * bn)
+    H2O = (2 * bh) + (1 * bo)
+
+    # for deuterated:
+    dCH3 = (2 * bc) + (6 * bd)
+    dCH2 = (1 * bc) + (2 * bd)
+    dCHOL = (5 * bc) + (12 * bd) + (1 * bn)
+    D2O = (2 * bd) + (1 * bo)
+
+    # for volumes:
+    vCH3 = 52.7
+    vCH2 = 28.1
+    vCOO = 39.0
+    vGLYC = 68.8
+    vPO4 = 53.7
+    vCHOL = 120.4
+    vWAT = 30.4
+
+    vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
+    vTail = 2 * (16 * vCH2) + 2 * (vCH3)
+
+    # make SLDs
+    thisMask = deut[contrast - 1]
+
+    if thisMask[0] == 0:
+        thisWater = (H2O * 0.9249) + (D2O * 0.0871)
+    else:
+        thisWater = D2O
+
+    # Calculate mole fraction of D2O from the bulk SLD
+    d2o_molfr = (1 / D2O - H2O) * ((bulk_out[contrast - 1] / 0.036182336306) - H2O)
+    thisWater = (d2o_molfr * D2O) + ((1 - d2o_molfr) * H2O)
+
+    if thisMask[1] == 0:
+        thisHead = CHOL + PO4 + GLYC + COO
+    else:
+        thisHead = dCHOL + PO4 + GLYC + COO
+
+    if thisMask[2] == 0:
+        thisTail = (32 * CH2) + CH3
+    else:
+        thisTail = (32 * dCH2) + dCH3
+
+    noWat = ((thickHead * APM) - vHead) / vWAT
+    thisHead = thisHead + noWat * thisWater
+    vHead = vHead + noWat * vWAT
+
+    sldHead = thisHead / vHead
+
+    sldTail = thisTail / vTail
+
+    thickTail = (1.5 + 16 * 1.265) * cos(radians(theta))
+
+    output = [[thickTail, sldTail, Roughness], [thickHead, sldHead, Roughness]]
+
+    sub_rough = Roughness
+
+    return output, sub_rough

ratapi/examples/convert_rascal_project/__init__.py

@@ -0,0 +1 @@
+"""An example of converting between RAT and RasCAL-1."""

ratapi/examples/convert_rascal_project/convert_rascal.py

@@ -0,0 +1,49 @@
+"""An example of how to convert a RasCAL-1 project to RAT."""
+
+import pathlib
+from pprint import pp
+
+import ratapi as RAT
+
+
+# convert R1 project to Project class
+def convert_rascal(mat_filename="lipid_bilayer.mat"):
+    """Convert a project from RasCAL-1 and a project to RasCAL-1.
+
+    We convert a RasCAL-1 monolayer volume model to RAT, and the DSPC Standard Layers
+    example to RasCAL-1.
+
+    Parameters
+    ----------
+    mat_filename : str
+        The filename of the output of the RAT project converted to RasCAL-2.
+
+    Returns
+    -------
+    project, struct
+        A RasCAL-1 monolayer volume model converted to a RAT project, and the
+        struct of the DSPC standard layers example converted to a RasCAL-1 struct.
+
+    """
+    project_path = pathlib.Path(__file__).parent / "R1monolayerVolumeModel.mat"
+    project = RAT.utils.convert.r1_to_project(project_path)
+
+    # change values if you like, including ones not supported by R1
+    project.parameters["Head Thickness"].prior_type = "gaussian"
+    project.parameters["Theta"].mu = 2.0
+    project.parameters["Area per molecule"].sigma = 50.0
+
+    # convert DSPC standard layers example to a struct and save as file
+    lipid_bilayer_project = RAT.examples.DSPC_standard_layers()[0]
+    RAT.utils.convert.project_to_r1(lipid_bilayer_project, filename=mat_filename)
+
+    # convert and return as a Python dictionary
+    struct = RAT.utils.convert.project_to_r1(lipid_bilayer_project, return_struct=True)
+
+    return project, struct
+
+
+if __name__ == "__main__":
+    project, struct = convert_rascal()
+    print(project)
+    pp(struct)

ratapi/examples/data/D2O_spin_down.dat

@@ -0,0 +1,100 @@
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ratapi/examples/data/D2O_spin_up.dat

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ratapi/examples/data/DSPC_D2O.dat

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ratapi/examples/data/DSPC_SMW.dat

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