How to use the chempy.cpv.cross_product function in chempy

To help you get started, we’ve selected a few chempy examples, based on popular ways it is used in public projects.

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Pymol-Scripts / Pymol-script-repo / plane.py View on Github

def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
    v1 = cpv.sub(p1, p2)
    v2 = cpv.sub(p3, p2)
    normal = cpv.cross_product(v1, v2)

    if 'translate' in settings:
        vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
        p1_t = cpv.sub(p1, vtran)
        p2_t = cpv.sub(p2, vtran)
        p3_t = cpv.sub(p3, vtran)
        print("New coordinates are:")
        print_info("New", p1_t, p2_t, p3_t)
        print("New coordinates are for normalized plane:")
        v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
        v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
        normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
        v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
        p1_t2 = cpv.add(v1_t, p2_t)
        p3_t2 = cpv.add(v2_t, p2_t)
        print_info("Newnormal", p1_t2, p2_t, p3_t2)

    if vm1!=None:
        v1 = cpv.scale(cpv.normalize(v1), vm1)
    if vm2!=None:
        v2 = cpv.scale(cpv.normalize(v2), vm2)

    centrum = p2
    if center:
        corner1 = cpv.add(cpv.add(centrum, v1), v2)
        corner2 = cpv.sub(cpv.add(centrum, v1), v2)
        corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
        corner4 = cpv.add(cpv.sub(centrum, v1), v2)

edraizen / molmimic / molmimic / visualize / pymol.py View on Github

def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
    v1 = cpv.sub(p1, p2)
    v2 = cpv.sub(p3, p2)
    normal = cpv.cross_product(v1, v2)

    if 'translate' in settings:
        vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
        p1_t = cpv.sub(p1, vtran)
        p2_t = cpv.sub(p2, vtran)
        p3_t = cpv.sub(p3, vtran)
        print("New coordinates are:")
        print_info("New", p1_t, p2_t, p3_t)
        print("New coordinates are for normalized plane:")
        v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
        v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
        normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
        v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
        p1_t2 = cpv.add(v1_t, p2_t)
        p3_t2 = cpv.add(v2_t, p2_t)
        print_info("Newnormal", p1_t2, p2_t, p3_t2)

    if vm1!=None:
        v1 = cpv.scale(cpv.normalize(v1), vm1)
    if vm2!=None:
        v2 = cpv.scale(cpv.normalize(v2), vm2)

    centrum = p2
    if center:
        corner1 = cpv.add(cpv.add(centrum, v1), v2)
        corner2 = cpv.sub(cpv.add(centrum, v1), v2)
        corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
        corner4 = cpv.add(cpv.sub(centrum, v1), v2)

Pymol-Scripts / Pymol-script-repo / plane.py View on Github

v1 = cpv.sub(p1, p2)
    v2 = cpv.sub(p3, p2)
    normal = cpv.cross_product(v1, v2)

    if 'translate' in settings:
        vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
        p1_t = cpv.sub(p1, vtran)
        p2_t = cpv.sub(p2, vtran)
        p3_t = cpv.sub(p3, vtran)
        print("New coordinates are:")
        print_info("New", p1_t, p2_t, p3_t)
        print("New coordinates are for normalized plane:")
        v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
        v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
        normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
        v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
        p1_t2 = cpv.add(v1_t, p2_t)
        p3_t2 = cpv.add(v2_t, p2_t)
        print_info("Newnormal", p1_t2, p2_t, p3_t2)

    if vm1!=None:
        v1 = cpv.scale(cpv.normalize(v1), vm1)
    if vm2!=None:
        v2 = cpv.scale(cpv.normalize(v2), vm2)

    centrum = p2
    if center:
        corner1 = cpv.add(cpv.add(centrum, v1), v2)
        corner2 = cpv.sub(cpv.add(centrum, v1), v2)
        corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
        corner4 = cpv.add(cpv.sub(centrum, v1), v2)
    else:

edraizen / molmimic / molmimic / visualize / pymol.py View on Github

def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
    v1 = cpv.sub(p1, p2)
    v2 = cpv.sub(p3, p2)
    normal = cpv.cross_product(v1, v2)

    if 'translate' in settings:
        vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
        p1_t = cpv.sub(p1, vtran)
        p2_t = cpv.sub(p2, vtran)
        p3_t = cpv.sub(p3, vtran)
        print("New coordinates are:")
        print_info("New", p1_t, p2_t, p3_t)
        print("New coordinates are for normalized plane:")
        v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
        v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
        normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
        v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
        p1_t2 = cpv.add(v1_t, p2_t)
        p3_t2 = cpv.add(v2_t, p2_t)
        print_info("Newnormal", p1_t2, p2_t, p3_t2)

Pymol-Scripts / Pymol-script-repo / plane.py View on Github

def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
    v1 = cpv.sub(p1, p2)
    v2 = cpv.sub(p3, p2)
    normal = cpv.cross_product(v1, v2)

    if 'translate' in settings:
        vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
        p1_t = cpv.sub(p1, vtran)
        p2_t = cpv.sub(p2, vtran)
        p3_t = cpv.sub(p3, vtran)
        print("New coordinates are:")
        print_info("New", p1_t, p2_t, p3_t)
        print("New coordinates are for normalized plane:")
        v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
        v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
        normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
        v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
        p1_t2 = cpv.add(v1_t, p2_t)
        p3_t2 = cpv.add(v2_t, p2_t)
        print_info("Newnormal", p1_t2, p2_t, p3_t2)

Pymol-Scripts / Pymol-script-repo / bbPlane.py View on Github

# populate the position array
        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]

        # if the data are incomplete for any residues, ignore
        if None in pos:
            if not quiet:
                print(' bbPlane: peptide bond %s -&gt; %s incomplete' % (curIdx, nextIdx))
            continue

        if cpv.distance(pos[0], pos[3]) &gt; 4.0:
            if not quiet:
                print(' bbPlane: %s and %s not adjacent' % (curIdx, nextIdx))
            continue

        normal = cpv.normalize(cpv.cross_product(
            cpv.sub(pos[1], pos[0]),
            cpv.sub(pos[2], pos[0])))

        obj.append(cgo.NORMAL)
        obj.extend(normal)

        # need to order vertices to generate correct triangles for plane
        if cpv.dot_product(cpv.sub(pos[0], pos[1]), cpv.sub(pos[2], pos[3])) &lt; 0:
            vorder = [0, 1, 2, 2, 3, 0]
        else:
            vorder = [0, 1, 2, 3, 2, 1]

        # fill in the vertex data for the triangles;
        for i in vorder:
            obj.append(VERTEX)
            obj.extend(pos[i])

How to use the chempy.cpv.cross_product function in chempy

To help you get started, we’ve selected a few chempy examples, based on popular ways it is used in public projects.

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