from __future__ import absolute_import, division, print_function import os, sys import time from six.moves import cStringIO as StringIO from mmtbx import conformation_dependent_library as cdl from mmtbx.conformation_dependent_library import cdl_utils from mmtbx.conformation_dependent_library.omega_database import omega_database from mmtbx.conformation_dependent_library import omega from mmtbx.conformation_dependent_library.tst_cdl import \ output_filenames, filenames, get_managers ''' A 2 VAL:33.01:-99.29:113.00:Favored:Isoleucine or valine A 3 PHE:43.27:-73.90:147.34:Favored:General A 4 GLY:50.95:-77.18:161.87:Favored:Glycine ''' filenames["cdl_test_1.pdb"][1] = [(-100, 110), (-70, 150), (-80, 160), ] filenames["cdl_test_1.pdb"][2] = [['B', 56, 179.87, 5.62], ['B', 293, 174.28, 7.05], ['B', 25, 176.89, 5.69], ] ''' A 239 AGLU:0.00:167.75:-41.93:OUTLIER:General A 239 BGLU:0.00:167.75:-41.93:OUTLIER:General A 249 TYR:12.65:-106.45:163.70:Favored:General ''' filenames["cdl_test_2.pdb"][1] = [( 170, -40), (-110, 160), ( 170, -40), (-110, 160), ] filenames["cdl_test_2.pdb"][2] = [['I', 20342, 178.94, 6.38], ['B', 165, 173.56, 7.52], ['I', 20342, 178.94, 6.38], ['B', 165, 173.56, 7.52], ] filenames["cdl_test_3.pdb"][1] = [(0, -130, 20, -120), (-120, 90, -50), (-50, 130, 90), (90, 0, -80), ] filenames["cdl_test_3.pdb"][2] = [['I', 20342, 178.94, 6.38], ['I', 928, 180.09, 6.71], ['I', 1214, 178.49, 6.3], ['I', 2599, 180.43, 5.63], ] filenames["cdl_test_4.pdb"][1] = [(50, -150, 150, -70), (-70, 140, -60), (50, -150, 150, -70), (-70, 140, -60), ] filenames["cdl_test_4.pdb"][2] = [['I', 177, 180.02, 5.36], ['I', 1214, 178.49, 6.3], ['I', 177, 180.02, 5.36], ['I', 1214, 178.49, 6.3], ] filenames["cdl_test_5.pdb"][1] = [(80, 170, 70, -30), (-30, 160, -30), (-30, 160, -180), (-180, -160, 100), ] filenames["cdl_test_5.pdb"][2] = [['I', 100, 183.21, 5.51], ['I', 29, 178.55, 6.54], ['I', 1214, 178.49, 6.3], ['I', 2599, 180.43, 5.63], ] filenames["cdl_test_7.pdb"][1] = [(-10, -110, 100, -60), (-60, -30, -60), (-60, -30, -130), (-10, -110, 100, -50), (-50, -40, -70), (-70, -20, -110), ] filenames["cdl_test_7.pdb"][2] = [['I', 20342, 178.94, 6.38], ['I', 20342, 178.94, 6.38], ['I', 20342, 178.94, 6.38], ['B', 3, 179.78, 7.53], ['I', 20342, 178.94, 6.38], ['I', 20342, 178.94, 6.38], ] filenames["cdl_test_7.pdb"][3] = [(10, 11, 27, 28)] filenames["cdl_test_8.pdb"] = [ [ "NonPGIV_xpro", ], [ (30, -70, 130, -80), ], [ ['I', 928, 180.09, 6.71], ], [ True, ], ] def test_phi_psi_key(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, #restraints_manager=restraints_manager geometry=restraints_manager.geometry, cdl_class=True, ) ): key = threes.get_cdl_key(force_plus_one=True) print(key, filenames[filename][1]) assert key == filenames[filename][1][i] def test_cdl_lookup(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, #restraints_manager=restraints_manager geometry=restraints_manager.geometry, cdl_class=True, ) ): res_type_group = cdl_utils.get_res_type_group( threes[1].resname, threes[2].resname, ) key = threes.get_cdl_key(force_plus_one=True) key = key[-2:] print('res_type_group',res_type_group,key) restraint_values = omega_database[res_type_group][key] print(i, key, restraint_values[:4], filenames[filename][2]) del threes.registry.n threes.registry.n = {} assert restraint_values[:4] == filenames[filename][2][i] def test_average(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, geometry=restraints_manager.geometry, cdl_class=True, ) ): if threes.registry.n: atoms = hierarchy.atoms() for key in threes.registry.n: print(key) for atom in key: print(atoms[atom].quote()) #assert threes.registry.n.keys() == filenames[filename][3] assert filenames[filename][3][0] in threes.registry.n def run_apply(filename, testing=False, verbose=False): processed_pdb_file, restraints_manager = get_managers(filename) if testing: #test_res_type(processed_pdb_file.all_chain_proxies.pdb_hierarchy, # filename, # restraints_manager, # ) test_phi_psi_key(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) test_cdl_lookup(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) #test_cis_trans_peptide(processed_pdb_file.all_chain_proxies.pdb_hierarchy, # filename, # restraints_manager, # ) print("OK") sites_cart = processed_pdb_file.all_chain_proxies.sites_cart_exact() if True: lines = StringIO() restraints_manager.geometry.show_sorted(sites_cart=sites_cart, f=lines) f=open("%s_pre.geo" % os.path.basename(filename)[:-4], "w") f.write(lines.getvalue()) f.close() t0=time.time() cdl_proxies = omega.setup_restraints(restraints_manager.geometry, verbose=verbose, ) omega.update_restraints(processed_pdb_file.all_chain_proxies.pdb_hierarchy, geometry=restraints_manager.geometry, cdl_proxies=cdl_proxies, verbose=verbose, ) if testing: test_average(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) print('OK') print('Time to update restraints %0.5fs' % (time.time()-t0)) if True: lines = StringIO() restraints_manager.geometry.show_sorted(sites_cart=sites_cart, f=lines) f=open("%s_post.geo" % os.path.basename(filename)[:-4], "w") f.write(lines.getvalue()) f.close() def run(filename=None): if filename: print('run oCDL on',filename) run_apply(filename, #verbose=True, ) else: print('Running tests') for filename in sorted(output_filenames): print(filename) f=open(filename, "w") f.write(output_filenames[filename]) f.close() for i, filename in enumerate(sorted(filenames)): #if filename.find("_7")==-1: continue print(('%s ' % filename)*5) run_apply(filename, testing=True) if i: break if __name__=="__main__": args = sys.argv[1:] del sys.argv[1:] run(*tuple(args))