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Active and passive residue restraints
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@brianjimenez
brianjimenez committed Dec 17, 2018
1 parent dd94a97 commit c751702
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Showing 72 changed files with 9,870 additions and 536 deletions.
4 changes: 2 additions & 2 deletions bin/simulation/docking_mpi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,11 +69,11 @@ def set_scoring_function(parser, receptor, ligand, minion_id):

receptor_restraints = ligand_restraints = None
try:
receptor_restraints = parser.args.receptor_restraints
receptor_restraints = parser.args.receptor_restraints['active']
except:
pass
try:
ligand_restraints = parser.args.ligand_restraints
ligand_restraints = parser.args.ligand_restraints['active']
except:
pass
adapter = CurrentModelAdapter(receptor, ligand, receptor_restraints, ligand_restraints)
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6 changes: 3 additions & 3 deletions bin/simulation/docking_multiprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,13 +68,13 @@ def set_scoring_function(parser, receptor, ligand):
CurrentModelAdapter = getattr(module, "DefinedModelAdapter")
receptor_restraints = ligand_restraints = None
try:
receptor_restraints = parser.args.receptor_restraints
receptor_restraints = parser.args.receptor_restraints['active']
except:
pass
try:
ligand_restraints = parser.args.ligand_restraints
ligand_restraints = parser.args.ligand_restraints['active']
except:
pass
pass
adapter = CurrentModelAdapter(receptor, ligand, receptor_restraints, ligand_restraints)
scoring_function = CurrentScoringFunction(weight)
adapters.append(adapter)
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28 changes: 25 additions & 3 deletions bin/simulation/lightdock_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,11 +69,18 @@
if args.restraints:
log.info("Reading restraints from %s" % args.restraints)
restraints = parse_restraints_file(args.restraints)

# Calculate number of restraints in order to check them
num_rec_active = len(restraints['receptor']['active'])
num_rec_passive = len(restraints['receptor']['passive'])
num_lig_active = len(restraints['ligand']['active'])
num_lig_passive = len(restraints['ligand']['passive'])

# Check if restraints have been defined for the ligand, but not to the receptor
if len(restraints['ligand']) and not len(restraints['receptor']):
if not num_rec_active and not num_rec_passive and (num_lig_active or num_lig_passive):
raise LightDockError("Restraints defined for ligand, but not receptor. Try switching structures.")

if not len(restraints['receptor']) and not len(restraints['ligand']):
if not num_rec_active and not num_rec_passive and not num_lig_active and not num_lig_passive:
raise LightDockError("Restraints file specified, but not a single restraint found")

# Check if restraints correspond with real residues
Expand All @@ -82,11 +89,26 @@
ligand_restraints = get_restraints(ligand, restraints['ligand'])
args.ligand_restraints = restraints['ligand']

log.info("Number of receptor restraints is: %d (active), %d (passive)" % (num_rec_active, num_rec_passive))
log.info("Number of ligand restraints is: %d (active), %d (passive)" % (num_lig_active, num_lig_passive))

rec_restraints = None
try:
rec_restraints = receptor_restraints['active'] + receptor_restraints['passive']
except:
pass

lig_restraints = None
try:
lig_restraints = ligand_restraints['active'] + ligand_restraints['passive']
except:
pass

# Calculate surface points (swarm centers) over receptor structure
starting_points_files = calculate_starting_positions(receptor, ligand,
args.swarms, args.glowworms,
args.starting_points_seed,
receptor_restraints, ligand_restraints,
rec_restraints, lig_restraints,
rec_translation, lig_translation,
args.ftdock_file, args.use_anm, args.anm_seed,
args.anm_rec, args.anm_lig, args.membrane)
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50 changes: 25 additions & 25 deletions bin/test/golden_data/regression_fastdfire_restraints/init/initial_positions_0.dat
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Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
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22.304404370 -15.330496957 6.515641535 -0.525762235 0.041557584 -0.845489079 -0.083637653
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21.749849586 -27.249178039 -5.987001908 -0.302466905 0.610810364 -0.555807916 0.475922296
20.300312113 -22.112925280 0.223596093 -0.373520573 0.208313183 -0.428766625 -0.795768296
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21.815411226 -19.792858829 8.209034194 -0.235809453 0.215334879 -0.938641307 0.130296927
22.297782015 -20.681655343 -3.826485520 0.889813079 -0.311562613 0.020139766 0.332799960
18.585785764 -23.687230975 8.907203552 -0.869407148 0.022254922 0.434764128 0.233700840
15.711115193 -19.017264147 1.405134486 0.742795013 0.334868783 0.215401299 -0.538257139
23.046961680 -21.308803579 -1.414829345 0.397215932 0.449457984 -0.773311905 0.205415973
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17.365040226 -25.557520973 1.435725029 0.857253775 0.211870314 0.289470647 0.369369299
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