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Reduce overhead for ligtype assignment.
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@mgt16-LANL
mgt16-LANL committed May 2, 2024
1 parent 0a323ec commit 7a6f6f5
Showing 1 changed file with 50 additions and 41 deletions.
91 changes: 50 additions & 41 deletions architector/io_process_input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,45 +102,47 @@ def assign_ligType_default(core_geo_class, ligsmiles, ligcoords, metal,
else:
tcore_geo_class = copy.deepcopy(core_geo_class)
tcore_geo_class.get_lig_ref_inds_dict(metal,
tolerance=30)
tolerance=20)
lig_denticity = len(ligcoords)
possible_Ligtypes = tcore_geo_class.cn_ligType_dict[lig_denticity]
rot_vals = []
possible_saves = []
conformers = []
for ligtype in possible_Ligtypes:
rot_vals.append(None)
possible_saves.append(False)
conformers.append(False)
best_dict = tcore_geo_class.best_liglist_geos.get(ligtype, False)
if isinstance(best_dict, dict):
corecoordList = best_dict.get('corecoordList', None)
core_cons = best_dict.get('coreInds', None)
tmp_ligList = []
for i in range(len(ligcoords)):
tmp_ligList.append([ligcoords[i], core_cons[i]])
# Test mapping on just single ligand conformation.
# Minval represents the loss
conf_list, val_list, _, _, _, _, _ = io_lig.find_conformers(
ligsmiles,
tmp_ligList,
corecoordList,
metal,
ligtype=ligtype,
covrad_metal=covrad_metal,
vdwrad_metal=vdwrad_metal
)
if len(conf_list) > 0:
minind = np.argmin(val_list)
rot_vals[-1] = val_list[minind]
possible_saves[-1] = True
conf = conf_list[minind]
conf = conf + Atoms(symbols=[metal], positions=[(0, 0, 0)])
conformers[-1] = conf
save_inds = [i for i, x in enumerate(possible_saves) if x]
conformers = [x for i, x in enumerate(conformers) if (i in save_inds)]
possible_Ligtypes = [x for i, x in enumerate(
possible_Ligtypes) if (i in save_inds)]
exitloop=False
while not exitloop:
rot_vals = []
possible_saves = []
conformers = []
count = 0
for ligtype in possible_Ligtypes:
if debug:
print('Ligtype testing: ', count, ligtype)
count += 1
rot_vals.append(None)
possible_saves.append(False)
conformers.append(False)
best_dict = tcore_geo_class.best_liglist_geos.get(ligtype, False)
if isinstance(best_dict, dict):
corecoordList = best_dict.get('corecoordList', None)
core_cons = best_dict.get('coreInds', None)
tmp_ligList = []
for i in range(len(ligcoords)):
tmp_ligList.append([ligcoords[i], core_cons[i]])
# Test mapping on just single ligand conformation.
# Minval represents the loss
conf, minval, sane, _, _, _, _ = io_lig.get_aligned_conformer(
ligsmiles, tmp_ligList, corecoordList, metal=tmetal,
covrad_metal=covrad_metal, vdwrad_metal=vdwrad_metal,
ligtype=ligtype)
if sane:
rot_vals[-1] = minval
possible_saves[-1] = True
conf = conf + Atoms(symbols=[metal], positions=[(0, 0, 0)])
conformers[-1] = conf
save_inds = [i for i, x in enumerate(possible_saves) if x]
conformers = [x for i, x in enumerate(conformers) if (i in save_inds)]
tpossible_Ligtypes = [x for i, x in enumerate(
possible_Ligtypes) if (i in save_inds)]
if len(tpossible_Ligtypes) > 0:
possible_Ligtypes = tpossible_Ligtypes
exitloop=True
out_types = []
confidences = []
min_losses = []
Expand All @@ -155,6 +157,7 @@ def assign_ligType_default(core_geo_class, ligsmiles, ligcoords, metal,
out_types.append(ltype)
min_losses.append(minloss)
confidences.append(confidence)
out_types = np.unique(all_out_types).tolist()
if debug:
print('Out Types:', all_out_types, possible_Ligtypes)
print('OUt Losses', all_losses)
Expand Down Expand Up @@ -576,8 +579,11 @@ def inparse(inputDict):
raise ValueError('Need a inputDict["ligands"] list passed')
newliglist = []

tdebug = newinpDict.get('parameters',{}).get('debug',False)
if tdebug:
print('Starting Ligand Assignment')

if isinstance(ligList, list):
tdebug = newinpDict.get('parameters',{}).get('debug',False)
for ligDict in ligList:
newdict = dict()
if isinstance(ligDict, dict):
Expand All @@ -586,9 +592,7 @@ def inparse(inputDict):
if (ligDict['smiles'] == '[H-]')or (ligDict['smiles'] == '[O-2]'): # Handle hydrides
newinpDict['parameters']['relax'] = False
# newinpDict['parameters']['metal_spin'] = 0 # Set to low_spin
if (ligDict['ligType'] in core_geo_class.liglist_geo_map_dict.keys()) or (ligDict['ligType'] == 'mono'):
newdict.update({'ligType':ligDict['ligType']})
elif isinstance(ligDict['ligType'],list):
if isinstance(ligDict['ligType'], list):
good_list = []
for lt in ligDict['ligType']:
if (lt in core_geo_class.liglist_geo_map_dict.keys()) or (lt == 'mono') or ('edge' in lt):
Expand All @@ -598,6 +602,8 @@ def inparse(inputDict):
if len(good_list) > min_n_conformers:
min_n_conformers = len(good_list)
newdict.update({'ligType': good_list})
elif (ligDict['ligType'] in core_geo_class.liglist_geo_map_dict.keys()) or (ligDict['ligType'] == 'mono'):
newdict.update({'ligType':ligDict['ligType']})
elif ('edge' in ligDict['ligType']):
lt = assign_ligType_default(core_geo_class, ligDict['smiles'], ligDict['coordList'], metal,
covrad_metal=covrad_metal, vdwrad_metal=vdwrad_metal,
Expand Down Expand Up @@ -816,6 +822,9 @@ def inparse(inputDict):

newinpDict['ligands'] = newliglist

if tdebug:
print('Finished Ligand Assignment')

coreTypes_run = []
for coreType in coreTypes:
good = True
Expand Down

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