def write_superposed_pdbs(self, output_pdb_folder, alignments: dict = None):
"""
Superposes PDBs according to alignment and writes transformed PDBs to files
(View with Pymol)
Parameters
----------
alignments
output_pdb_folder
"""
if alignments is None:
alignments = self.alignment
output_pdb_folder = Path(output_pdb_folder)
if not output_pdb_folder.exists():
output_pdb_folder.mkdir()
reference_name = self.structures[0].name
reference_pdb = pd.parsePDB(
str(self.output_folder / f"cleaned_pdb/{self.structures[0].name}.pdb")
)
core_indices = np.array(
[
i
for i in range(len(alignments[reference_name]))
if -1 not in [alignments[n][i] for n in alignments]
]
)
aln_ref = alignments[reference_name]
ref_coords_core = (
reference_pdb[helper.get_alpha_indices(reference_pdb)]
.getCoords()
.astype(np.float64)[np.array([aln_ref[c] for c in core_indices])]
)
ref_centroid = helper.nb_mean_axis_0(ref_coords_core)
ref_coords_core -= ref_centroid
transformation = pd.Transformation(np.eye(3), -ref_centroid)
reference_pdb = pd.applyTransformation(transformation, reference_pdb)
pd.writePDB(str(output_pdb_folder / f"{reference_name}.pdb"), reference_pdb)
for i in range(1, len(self.structures)):
name = self.structures[i].name
pdb = pd.parsePDB(
str(self.output_folder / f"cleaned_pdb/{self.structures[i].name}.pdb")
)
aln_name = alignments[name]
common_coords_2 = (
pdb[helper.get_alpha_indices(pdb)]
.getCoords()
.astype(np.float64)[np.array([aln_name[c] for c in core_indices])]
)
(
rotation_matrix,
translation_matrix,
) = superposition_functions.svd_superimpose(
ref_coords_core, common_coords_2
)
transformation = pd.Transformation(rotation_matrix.T, translation_matrix)
pdb = pd.applyTransformation(transformation, pdb)
pd.writePDB(str(output_pdb_folder / f"{name}.pdb"), pdb)
def getInitLig(lig, rec_init_cent, lig_init_cent): """ rec_init_cent, lig_init_cent should be numpy arraay lig: ligand structure data""" init_translation = rec_init_cent - lig_init_cent t = prody.Transformation( np.identity( 3 ), init_translation ) initlig = lig.copy() t.apply( initlig ) return initlig
def write_superposed_pdbs_reference(self, output_pdb_folder, alignments):
"""
Superposes PDBs according to reference structure and writes transformed PDBs to files
(View with Pymol)
Parameters
----------
alignments
output_pdb_folder
"""
reference_name = self.structures[self.reference_structure_index].name
reference_pdb = pd.parsePDB(
str(self.output_folder /
f"cleaned_pdb/{self.structures[self.reference_structure_index].name}.pdb"
))
aln_ref = alignments[reference_name]
reference_coords = (reference_pdb[helper.get_alpha_indices(
reference_pdb)].getCoords().astype(np.float64))
pd.writePDB(str(output_pdb_folder / f"{reference_name}.pdb"),
reference_pdb)
for i in range(1, len(self.structures)):
name = self.structures[i].name
pdb = pd.parsePDB(
str(self.output_folder /
f"cleaned_pdb/{self.structures[i].name}.pdb"))
aln_name = alignments[name]
common_coords_1, common_coords_2 = get_common_coordinates(
reference_coords,
pdb[helper.get_alpha_indices(pdb)].getCoords().astype(
np.float64),
aln_ref,
aln_name,
)
(
rotation_matrix,
translation_matrix,
) = superposition_functions.svd_superimpose(
common_coords_1, common_coords_2)
transformation = pd.Transformation(rotation_matrix.T,
translation_matrix)
pdb = pd.applyTransformation(transformation, pdb)
pd.writePDB(str(output_pdb_folder / f"{name}.pdb"), pdb)
rec_dict = initialize_res_score(rec)
lig_dict = initialize_res_score(lig)
for line in outFileLines[4:254]:
decoylig = lig.copy()
rotation = [float(x) for x in line.split('\t')[0:3]]
rotation = getRotationMatrix(rotation)
translation = [float(x) for x in line.split('\t')[3:6]]
translation = getTranslation(translation)
score = float(line.split('\t')[-1])
decoylig.setCoords(decoylig.getCoords() - lig_init_cent)
# apply rotation
t = prody.Transformation(rotation, np.zeros(3))
t.apply(decoylig)
decoylig.setCoords(decoylig.getCoords() + translation + rec_init_cent)
mobile = rec + decoylig
decoy_contacts_rec = prody.Contacts(rec)
decoy_contacts_rec = decoy_contacts_rec.select(4, decoylig)
decoy_contacts_lig = prody.Contacts(decoylig)
decoy_contacts_lig = decoy_contacts_lig.select(4, rec)
#lig_contact_atoms = prody.matchChains( lig, decoy_contacts_lig, overlap=0.01, subset='all' )[0][0]
interface_resnums += (list(set(decoy_contacts_rec.getResnums())))
l_interface_resnums += (list(set(decoy_contacts_lig.getResnums())))
interface_residue_pairs.append([