Source code for schrodinger.application.desmond.depictor

from schrodinger.infra import canvas2d

from .image_generator import SchrodImageGenerator


[docs]def singleton(cls):
    instances = {}

    def getinstance():
        if cls not in instances:
            instances[cls] = cls()
        return instances[cls]

    return getinstance


[docs]@singleton
class Depictor(SchrodImageGenerator):

    def __init__(self):
        SchrodImageGenerator.__init__(self)
        self._model.setShowHydrogenPreference(-1)
        self._model.setFontSize(18)


[docs]def ct2chmmol(st):
    """
    convert mmct to chmmol object
    """
    adaptor = canvas2d.ChmMmctAdaptor()
    stereo = canvas2d.ChmMmctAdaptor.StereoFromGeometry_Safe
    mol = adaptor.create(st.handle, stereo)
    return mol


[docs]def get_aligned_chmmol_from_ct(ct0, ct1, ma0, ma1, attached_atom0,
                               attached_atom1):
    """
    generated aligned chmmol pair from ct and SMARTS
    :type ct0: Structure
    :param ct0: reference structure
    :type ct1: Structure
    :param ct1: structure to be aligned
    :type smarts0: string
    :param smarts0: SMARTS pattern for ct0
    :type smarts1: string
    :param smarts1: SMARTS pattern for ct1
    :return two ChmMol instances as a tuple
    """
    # convert to 0-base index
    ma0 = [i - 1 for i in ma0]
    ma1 = [i - 1 for i in ma1]

    # convert ct to chmmol
    chmmol0 = ct2chmmol(ct0)
    chmmol1 = ct2chmmol(ct1)
    return align_chmmol(chmmol0, chmmol1, ma0, ma1, attached_atom0,
                        attached_atom1)


[docs]def show_attached_hydrogen(chmmol, attached_atom):
    for atom in attached_atom:
        chmmol.getAtom(atom).setHydrogensHidden(False)


[docs]def align_chmmol(chmmol0, chmmol1, ma0, ma1, attached_atom0, attached_atom1):
    """
    generated aligned chmmol pair from ct and SMARTS
    :type chmmol0: ChmMol
    :param chmmol0: reference structure
    :type chmmol1: ChmMol
    :param chmmol0: structure to be aligned
    :type smarts0: string
    :param smarts0: SMARTS pattern for ct0
    :type smarts1: string
    :param smarts1: SMARTS pattern for ct1
    :return two ChmMol instances as a tuple
    """
    HYDROGEN = canvas2d.ChmAtomOption.H_Never
    RESCALE = canvas2d.ChmCoordGenOption.Physical

    # we try to minimize the number of hydrogen to be rendered, in order to
    # avoid the accidental flipping that can cause stereo center to be
    # shown incorrectly
    chmmol0.markHydrogens(canvas2d.ChmAtomOption.H_Never)
    chmmol1.markHydrogens(canvas2d.ChmAtomOption.H_Never)

    # we show the selected hydrogens
    show_attached_hydrogen(chmmol0, attached_atom0)
    show_attached_hydrogen(chmmol1, attached_atom1)

    for i in range(0, len(ma0)):
        atom0 = chmmol0.getAtom(ma0[i])
        atom1 = chmmol1.getAtom(ma1[i])
        # show hydrogen atoms in stereo center
        if atom0.isHydrogen():
            atom0.setHidden(False)
        if atom1.isHydrogen():
            atom1.setHidden(False)

    # generate 2D coordinates
    canvas2d.Chm2DCoordGen.generateAndApply(chmmol0, HYDROGEN, RESCALE)
    canvas2d.Chm2DCoordGen.generateAndApply(chmmol1, HYDROGEN, RESCALE)

    # allow adjustment of 2D coordinates after alignment
    FIXUP = False
    BYPASSCOORDGEN = False
    CopyOverOriginalTemplateCoords = False
    # align 2D coordinates
    canvas2d.Chm2DCoordGen.generateFromTemplateAndApply(
        chmmol1, chmmol0, ma1, ma0, HYDROGEN, RESCALE, FIXUP, BYPASSCOORDGEN,
        CopyOverOriginalTemplateCoords)

    return chmmol0, chmmol1