Separated lattice scaling from RDMol population

polymerist/rdutils/rdcoords/tiling.py

@@ -5,30 +5,38 @@
 from rdkit import Chem
 from rdkit.Chem import rdGeometry, rdMolTransforms
 
+from ...genutils.typetools.numpytypes import Shape, N
 from ..rdtypes import RDMol
 from ...maths.linearalg import affine
+from ...maths.lattices.coordinates import Coordinates
 
 
-def tile_lattice_with_rdmol(rdmol : RDMol, unit_lattice : np.ndarray, rotate_randomly : bool=True) -> RDMol:
+def rdmol_effective_radius(rdmol : Chem.Mol, conf_id : int=0) -> float:
+    '''Determine an effective radius of influence of a molecule such that all atoms are within this radius'''
+    conformer = rdmol.GetConformer(conf_id)
+    positions = Coordinates(conformer.GetPositions())
+    dists_to_centroid = positions.dists_to_centroid()
+
+    # polymerist-agnostic implementation
+    # centroid  = rdMolTransforms.ComputeCentroid(conformer, ignoreHs=True) # = positions.mean(axis=0) # TOSELF : mean positiona dn centroid give slightly different result, but don't affect validity of tiling
+    # dists_to_centroid = np.linalg.norm(positions - centroid, axis=1)
+
+    return dists_to_centroid.max()
+
+def tile_lattice_with_rdmol(rdmol : RDMol, lattice_points : np.ndarray[Shape[N, 3], float], rotate_randomly : bool=True, conf_id : int=0) -> RDMol:
     '''
     Generate a tiled topology of copies of an RDKit molecule, transformed to occupy the same relative positions as points on the given lattice with unit dimensions
     if "random_rotations" is True, each occurrence of the molecule will also have a random rotation applied to it. RDMol is NOT modified at any point in the procedure
     '''
     if rdmol.GetNumConformers() < 1:
         raise ValueError('Molecule must have at least one conformer to be tiled')
 
-    conformer = rdmol.GetConformer(0)
-    positions = conformer.GetPositions()
-    centroid  = rdMolTransforms.ComputeCentroid(conformer) # = positions.mean(axis=0) # TOSELF : mean positiona dn centroid give slightly different result, but don't affect validity of tiling
-    centering = rdMolTransforms.ComputeCanonicalTransform(conformer, centroid) # translation which centers the given conformer
-
-    dists_to_centroid = np.linalg.norm(positions - centroid, axis=1)
-    r_eff = dists_to_centroid.max() # effective radius of the molecule; ensures adjacent tiled copied don't intersect
-    scaled_lattice = 2 * r_eff * unit_lattice # generate scaled lattice with non-unit radius
+    conformer = rdmol.GetConformer(conf_id)
+    centering = rdMolTransforms.ComputeCanonicalTransform(conformer, ignoreHs=True) # translation which centers the given conformer
 
     tiled_topology = None
-    for point in scaled_lattice:
-        translation = affine.xyzTrans(*point) # translation to the current point on the scaled lattice
+    for point in lattice_points:
+        translation = affine.xyzTrans(*point) # translation to the current point on the lattice
         rotation    = affine.randRot(about_x=rotate_randomly, about_y=rotate_randomly, about_z=rotate_randomly) # rotation about either all axes or the identity matrix
         transform = translation @ rotation @ centering # NOTE : (right-to-left) order matters here!! Must first move to origin, then rotate, and then translate to latice point