# Visualizing Torsional Angle Distribution new¶

## Problem¶

You want to generate an interactive image (in svg file format) that visualizes the distribution of dihedral angles of rotatable bond in a multi-conformer molecule. See example in Figure 1.

hover over any rotatable bond in the molecule (marked with a circle)

Figure 1. Example of visualizing torsional information

## Ingredients¶

 OEChem TK - cheminformatics toolkit (including OEBio TK) OEDepict TK - molecule depiction toolkit Grapheme TK - molecule and property visualization toolkit

## Difficulty level¶

dihedral2img.py

## Solution¶

The first step of generating the image is to identify the rotatable bonds in the input molecule using the IsRotatableOrMacroCycleBond bond predicate. The get_dihedrals function iterates over rotatable bonds and identifies their dihedral atoms. These dihedral atoms are stored on the molecule in a OEGroupBase object for further process.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 class IsRotatableOrMacroCycleBond(oechem.OEUnaryBondPred): """ Identifies rotatable bonds and single bonds in macro-cycles. """ def __call__(self, bond): """ :type mol: oechem.OEBondBase :rtype: boolean """ if bond.GetOrder() != 1: return False if bond.IsAromatic(): return False isrotor = oechem.OEIsRotor() if isrotor(bond): return True if oechem.OEBondGetSmallestRingSize(bond) >= 10: return True return False 
  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 def get_dihedrals(mol, itag): """ Iterates over rotatable bonds and identifies their dihedral atoms. These atoms are added to the molecule in a group using the given tag. :type mol: oechem.OEMol :type itag: int :return: Number of dihedral angles identified :rtype: int """ nrdihedrals = 0 for bond in mol.GetBonds(IsRotatableOrMacroCycleBond()): atomB = bond.GetBgn() atomE = bond.GetEnd() neighB = None neighE = None for atom in atomB.GetAtoms(oechem.OEIsHeavy()): if atom != atomE: neighB = atom break for atom in atomE.GetAtoms(oechem.OEIsHeavy()): if atom != atomB: neighE = atom break if neighB is None or neighE is None: continue atoms = oechem.OEAtomVector() atoms.append(neighB) atoms.append(atomB) atoms.append(atomE) atoms.append(neighE) bonds = oechem.OEBondVector() bonds.append(mol.GetBond(neighB, atomB)) bonds.append(bond) bonds.append(mol.GetBond(neighE, atomE)) nrdihedrals += 1 mol.NewGroup(itag, atoms, bonds) return nrdihedrals 

After the dihedral atoms are identified, the set_dihedral_histograms function is used to iterate over the conformation of the molecule and calculate torsion angles using the OEGetTorsion function . These angles are binned to

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 def set_dihedral_histograms(mol, itag, angleinc, nrbins): """ Iterates over the dihedral groups and bins the torsional angles for each conformation. :type mol: oechem.OEMol :type itag: int :type angleinc: float :type nrbins: int """ for group in mol.GetGroups(oechem.OEHasGroupType(itag)): atoms = oechem.OEAtomVector() for atom in group.GetAtoms(): atoms.append(atom) histogram = oechem.OEUIntVector(nrbins) for conf in mol.GetConfs(): rad = oechem.OEGetTorsion(conf, atoms[0], atoms[1], atoms[2], atoms[3]) deg = math.degrees(rad) deg = (deg + 360.0) % 360.0 binidx = int(math.floor((deg / angleinc))) histogram[binidx] += 1 group.SetData(itag, histogram) 

The last step is to highlight the dihedral atoms when hovered over and depict the corresponding dihedral angle histogram. In order to achieve the hover effect in the generated SVG image, SVG groups are utilized (OESVGGroup) in the depict_dihedrals function. For each dihedral two groups are created. These groups are associated by calling the OEAddSVGHover function: while hovering the mouse over objects drawn inside the torsion_area_<id> the objects drawn in the torsion_data_<id> will be displayed. The group id must be unique amongst all the ids in the SVG image. Everything that is rendered between the OEImageBase.PushGroup and the corresponding OEImageBase.PopGroup methods is considered “inside” the group.

It is important that the molecule is rendered into the image after the dihedral angles are highlighted (after the second loop). As a result the highlight will appear underneath the molecule rather than on top of.

In the last loop of the depict_dihedrals function transparent circles are drawn (using OESVGAreaPen) in the middle of the the dihedral angle representing the hover areas in the interactive SVG image.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 def depict_dihedrals(image, dimage, mol, opts, itag, angleinc, nrbins): """ Highlights the dihedral atoms and the depicts the corresponding dihedral angle histogram in hover :type image: oedepict.OEImageBase :type dimage: oedepict.OEImageBase :type mol: oechem.OEMol :type opts: oedepict.OE2DMolDisplayOptions :type itag: int :type angleinc: float :type nrbins: int """ nrconfs = mol.NumConfs() center = oedepict.OEGetCenter(dimage) radius = min(dimage.GetWidth(), dimage.GetHeight()) * 0.40 draw_dihedral_circle(dimage, center, radius, angleinc, nrbins, nrconfs) oegrapheme.OEPrepareDepictionFrom3D(mol, True) disp = oedepict.OE2DMolDisplay(mol, opts) dihedrals = [] centers = [] agroups = [] dgroups = [] nrdihedrals = 0 for group in mol.GetGroups(oechem.OEHasGroupType(itag)): uniqueid = uuid.uuid4().hex agroup = image.NewSVGGroup("torsion_area_" + uniqueid) dgroup = image.NewSVGGroup("torsion_data_" + uniqueid) oedepict.OEAddSVGHover(agroup, dgroup) dihedrals.append(group) centers.append(get_center(disp, group)) agroups.append(agroup) dgroups.append(dgroup) nrdihedrals += 1 for didx in range(0, nrdihedrals): image.PushGroup(dgroups[didx]) dihedral = dihedrals[didx] abset = oechem.OEAtomBondSet(dihedral.GetAtoms(), dihedral.GetBonds()) draw_highlight(image, disp, abset) draw_dihedral_histogram(dimage, dihedral.GetData(itag), center, radius, angleinc, nrbins, nrconfs) image.PopGroup(dgroups[didx]) clearbackground = True oedepict.OERenderMolecule(image, disp, not clearbackground) markpen = oedepict.OEPen(oechem.OEBlack, oechem.OEWhite, oedepict.OEFill_On, 1.0) for didx in range(0, nrdihedrals): image.PushGroup(agroups[didx]) markradius = disp.GetScale() / 10.0 image.DrawCircle(centers[didx], markradius, markpen) radius = disp.GetScale() / 4.0 image.DrawCircle(centers[didx], radius, oedepict.OESVGAreaPen) image.PopGroup(agroups[didx]) 

## Usage¶

dihedral2img.py script and acyclovi.sdf multi-conformer molecule file

Usage

prompt > python3 dihedral2img.py -in acyclovi.sdf  -out acyclovi.svg


## Discussion¶

OpenEye’s Omega TK toolkit can be used to generate diverse sets of low-energy conformations.

omega.py

Usage

prompt > echo "c1nc2c(=O)[nH]c(nc2n1COCCO)N acyclovi" > acyclovi.ism
prompt > omega.py acyclovi.ism acyclovi.sdf