'''High-level functionality for modelling module to build pipelines. Added in
the __init__.py file. To be used directly by passing a ModellingHandle instance
as argument.
'''
# internal
from promod3 import loop, sidechain, core
from _modelling import *
from _closegaps import *
from _ring_punches import *
# external
import ost
from ost import mol, conop
from ost.mol import mm
import os
###############################################################################
# helper functions
def _RemoveHydrogens(ent):
'''Hydrogen naming depends on the force field used.
To be on the safe side, we simply remove all of them.
Note that the pipeline ignores hydrogens when building the raw model and
when rebuilding sidechains.
'''
edi = ent.EditXCS(mol.BUFFERED_EDIT)
ha = ent.Select('ele=H')
for a in ha.atoms:
edi.DeleteAtom(a.handle)
edi.UpdateICS()
def _AddHeuristicHydrogens(ent, ff):
'''Add hydrogens with mm.HeuristicHydrogenConstructor.'''
for res in ent.residues:
if not res.IsPeptideLinking():
bb = ff.GetBuildingBlock(res.name)
edi = ent.EditXCS(mol.BUFFERED_EDIT)
h_constructor = mm.HeuristicHydrogenConstructor(bb)
h_constructor.ApplyOnResidue(res, edi)
edi.UpdateICS()
def _GetTopology(ent, settings, force_fields, add_heuristic_hydrogens=False):
'''Return topology or None if no topology could be created.
Note: if successful, this will update ent (adding hydrogens).
Set add_heuristic_hydrogens to True for ligands.
'''
# try all force fields in order
for i_ff, ff in enumerate(force_fields):
settings.forcefield = ff
try:
# check if we need to add hydrogens heuristically
if add_heuristic_hydrogens:
_AddHeuristicHydrogens(ent, ff)
# ok now we try...
topo = mm.TopologyCreator.Create(ent, settings)
except Exception as ex:
# report only for debugging
ost.LogVerbose("Could not create mm topology for ff %d. %s" \
% (i_ff, type(ex).__name__ + ": " + ex.message))
continue
else:
# all good
return topo
# if we got here, nothing worked
return None
def _AddLigands(ent, top, lig_ent, settings, force_fields):
'''Add ligands from lig_ent to topology top and update entity ent.'''
# connect them first
proc = conop.RuleBasedProcessor(conop.GetDefaultLib())
proc.Process(lig_ent)
cur_res = lig_ent.residues[0]
lig_num = 1
while cur_res.IsValid():
# setup connected components
cur_view = lig_ent.CreateEmptyView()
cur_view.AddResidue(cur_res, mol.INCLUDE_ATOMS)
cur_res = cur_res.next
while cur_res.IsValid() and mol.InSequence(cur_res.prev, cur_res):
cur_view.AddResidue(cur_res, mol.INCLUDE_ATOMS)
cur_res = cur_res.next
# try to add topology with special named chain
cur_ent = mol.CreateEntityFromView(cur_view, True)
edi = cur_ent.EditXCS()
edi.RenameChain(cur_ent.chains[0], '_' + str(lig_num))
lig_num += 1
cur_top = _GetTopology(cur_ent, settings, force_fields, True)
if cur_top is None:
view_res_str = str([str(r) for r in cur_view.residues])
ost.LogError("Failed to add ligands " + view_res_str + \
" for energy minimization! Skipping...")
else:
# merge into main topology
cur_top.SetFudgeLJ(top.GetFudgeLJ())
cur_top.SetFudgeQQ(top.GetFudgeQQ())
top.Merge(ent, cur_top, cur_ent)
def _SetupMmSimulation(model, force_fields):
'''Get mm simulation object for the model (incl. ligands in chain "_").
This tries to generate a topology for the protein and for each connected
component in the ligand chain separately by evaluating the force fields in
the same order as given. Ligands without force fields are skipped.
'''
prof = core.StaticRuntimeProfiler.StartScoped('pipeline::_SetupMmSimulation')
# get general settings
settings = mm.Settings()
settings.integrator = mm.LangevinIntegrator(310, 1, 0.002)
settings.init_temperature = 0
settings.nonbonded_method = mm.NonbondedMethod.CutoffNonPeriodic
settings.keep_ff_specific_naming = False
# prepare entity with protein
_RemoveHydrogens(model)
ent = mol.CreateEntityFromView(model.Select("cname!='_'"), True)
top = _GetTopology(ent, settings, force_fields)
if top is None:
raise RuntimeError("Failed to setup protein for energy minimization!")
# prepare ligands: we reprocess them to ensure connectivity
lig_ent = mol.CreateEntityFromView(model.Select("cname='_'"), True)
if lig_ent.residue_count > 0:
_AddLigands(ent, top, lig_ent, settings, force_fields)
# finally set up the simulation
try:
# use fast CPU platform by default
# NOTE: settings.platform only relevant for mm.Simulation!
settings.platform = mm.Platform.CPU
num_cpu_threads = os.getenv('PM3_OPENMM_CPU_THREADS')
if num_cpu_threads is None:
settings.cpu_properties["CpuThreads"] = "1"
else:
settings.cpu_properties["CpuThreads"] = num_cpu_threads
sim = mm.Simulation(top, ent, settings)
except RuntimeError as ex:
ost.LogWarning("OpenMM failed to initialize with error: %s" % str(ex))
# switch to "mm.Platform.Reference" as fallback
settings.platform = mm.Platform.Reference
sim = mm.Simulation(top, ent, settings)
ost.LogWarning("Switched to slower reference platform of OpenMM!")
return sim
def _GetSimEntity(sim):
'''Get Entity from mm sim and reverse ligand chain naming.'''
ent = sim.GetEntity().Copy()
# merge ligand chains into _
ent_ed = ent.EditXCS(mol.BUFFERED_EDIT)
chain_names = [ch.name for ch in ent.chains]
for chain_name in chain_names:
# all separate ligand chains start with _
if chain_name[0] == '_':
# add to chain _
if not ent.FindChain('_').IsValid():
ent_ed.InsertChain('_')
lig_ch = ent.FindChain('_')
cur_ch = ent.FindChain(chain_name)
for res in cur_ch.residues:
ent_ed.AppendResidue(lig_ch, res, deep=True)
# remove old chain
ent_ed.DeleteChain(cur_ch)
ent_ed.UpdateICS()
return ent
###############################################################################
def BuildSidechains(mhandle, merge_distance=4, scorer=None, fragment_db=None,
structure_db=None, torsion_sampler=None):
'''Build sidechains for model.
This is a wrapper for :func:`promod3.sidechain.Reconstruct`, followed
by a check for ring punches. If ring punches are found it introduces gaps
for the residues with punched rings and tries to fill them with
:func:`FillLoopsByDatabase` with *ring_punch_detection=2*.
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
:param merge_distance: Used as parameter for :func:`MergeGapsByDistance`
if ring punches are found.
:type merge_distance: :class:`int`
:param scorer: Used as parameter for :func:`FillLoopsByDatabase`
if ring punches are found. A default one is created
if None.
:type scorer: :class:`~promod3.loop.BackboneLoopScorer`
:param fragment_db: Used as parameter for :func:`FillLoopsByDatabase`
if ring punches are found. A default one is loaded
if None.
:type fragment_db: :class:`~promod3.loop.FragDB`
:param structure_db: Used as parameter for :func:`FillLoopsByDatabase`
if ring punches are found. A default one is loaded
if None.
:type structure_db: :class:`~promod3.loop.StructureDB`
:param torsion_sampler: Used as parameter for :func:`FillLoopsByDatabase`
if ring punches are found. A default one is loaded
if None.
:type torsion_sampler: :class:`~promod3.loop.TorsionSampler`
'''
prof = core.StaticRuntimeProfiler.StartScoped('pipeline::BuildSidechains')
ost.LogInfo("Rebuilding sidechains.")
sidechain.Reconstruct(mhandle.model, keep_sidechains=True)
# check for ring punches
rings = GetRings(mhandle.model)
ring_punches = GetRingPunches(rings, mhandle.model)
# try to fix them
if len(ring_punches) > 0:
ost.LogInfo("Trying to fix %d ring punch(es)." % len(ring_punches))
# backup old gaps
old_gaps = [g.Copy() for g in mhandle.gaps]
# new gaps for mhandle
# NOTE: we currently do not delete the punched residues here
# BUT they could be deleted when merging gaps below...
mhandle.gaps = StructuralGapList()
for res in ring_punches:
mygap = StructuralGap(res.prev, res.next, res.one_letter_code)
mhandle.gaps.append(mygap)
# load stuff if needed
if scorer is None:
scorer = SetupBackboneScorer(mhandle)
if fragment_db is None:
fragment_db = loop.LoadFragDB()
if structure_db is None:
structure_db = loop.LoadStructureDB()
if torsion_sampler is None:
torsion_sampler = loop.LoadTorsionSamplerCoil()
# fix it
MergeGapsByDistance(mhandle, merge_distance)
FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
torsion_sampler, ring_punch_detection=2)
# re-build sidechains
sidechain.Reconstruct(mhandle.model, keep_sidechains=True)
# restore gaps
mhandle.gaps = StructuralGapList()
for g in old_gaps:
mhandle.gaps.append(g)
def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
max_iter_lbfgs=10, use_amber_ff=False,
extra_force_fields=list()):
'''Minimize energy of final model using molecular mechanics.
Uses :mod:`ost.mol.mm` to perform energy minimization.
It will iteratively (at most *max_iterations* times):
- run up to *max_iter_sd* minimization iter. of a steepest descend method
- run up to *max_iter_lbfgs* minimization iter. of a Limited-memory
Broyden-Fletcher-Goldfarb-Shanno method
- abort if no stereochemical problems found
The idea is that we don't want to minimize "too much". So, we iteratively
minimize until there are no stereochemical problems and not more.
To speed things up, this can run on multiple CPU threads by setting the
env. variable ``PM3_OPENMM_CPU_THREADS`` to the number of desired threads.
If the variable is not set, 1 thread will be used by default.
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
:param max_iterations: Max. number of iterations for SD+LBFGS
:type max_iterations: :class:`int`
:param max_iter_sd: Max. number of iterations within SD method
:type max_iter_sd: :class:`int`
:param max_iter_lbfgs: Max. number of iterations within LBFGS method
:type max_iter_lbfgs: :class:`int`
:param use_amber_ff: if True, use the AMBER force field instead of the def.
CHARMM one (see :meth:`BuildFromRawModel`).
:type use_amber_ff: :class:`bool`
:param extra_force_fields: Additional list of force fields to use (see
:meth:`BuildFromRawModel`).
:type extra_force_fields: :class:`list` of :class:`ost.mol.mm.Forcefield`
:return: The model including all oxygens as used in the minimizer.
:rtype: :class:`Entity <ost.mol.EntityHandle>`
'''
prof = core.StaticRuntimeProfiler.StartScoped('pipeline::MinimizeModelEnergy')
ost.LogInfo("Minimize energy.")
# ignore LogInfo in stereochemical problems if output up to info done
ignore_stereo_log = (ost.GetVerbosityLevel() == 3)
# setup force fields
if use_amber_ff:
force_fields = [mm.LoadAMBERForcefield()]
else:
force_fields = [mm.LoadCHARMMForcefield()]
force_fields.extend(extra_force_fields)
# setup mm simulation
sim = _SetupMmSimulation(mhandle.model, force_fields)
# settings to check for stereochemical problems
clashing_distances = mol.alg.DefaultClashingDistances()
bond_stereo_chemical_param = mol.alg.DefaultBondStereoChemicalParams()
angle_stereo_chemical_param = mol.alg.DefaultAngleStereoChemicalParams()
for i in range(max_iterations):
# update atoms
ost.LogInfo("Perform energy minimization "
"(iteration %d, energy: %g)" % (i+1, sim.GetEnergy()))
sim.ApplySD(tolerance = 1.0, max_iterations = max_iter_sd)
sim.ApplyLBFGS(tolerance = 1.0, max_iterations = max_iter_lbfgs)
sim.UpdatePositions()
# check for stereochemical problems
if ignore_stereo_log:
ost.PushVerbosityLevel(2)
temp_ent = sim.GetEntity()
temp_ent = temp_ent.Select("aname!=OXT")
temp_ent_clash_filtered = mol.alg.FilterClashes(\
temp_ent, clashing_distances)[0]
# note: 10,10 parameters below are hard coded bond-/angle-tolerances
temp_ent_stereo_checked = mol.alg.CheckStereoChemistry(\
temp_ent_clash_filtered,
bond_stereo_chemical_param,
angle_stereo_chemical_param,
10, 10)[0]
if ignore_stereo_log:
ost.PopVerbosityLevel()
# checks above would remove bad atoms
if len(temp_ent_stereo_checked.Select("ele!=H").atoms) \
== len(temp_ent.Select("ele!=H").atoms):
ost.LogInfo("No more stereo-chemical problems "
"-> final energy: %g" % (sim.GetEnergy()))
break
# update model
simulation_ent = _GetSimEntity(sim)
mhandle.model = mol.CreateEntityFromView(simulation_ent.Select("ele!=H"),
True)
# return model with hydrogens
return simulation_ent
def CheckFinalModel(mhandle):
'''Performs samity checks on final models and reports problems.
:param mhandle: Modelling handle for which to perform checks.
:type mhandle: :class:`ModellingHandle`
'''
prof_name = 'pipeline::CheckFinalModel'
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
# report incomplete models
for chain in mhandle.model.chains:
if chain.residue_count < 3:
ost.LogWarning("Chain %s of returned model contains only %d "\
"residues! This typically indicates that the "\
"template is mostly a Calpha trace or contains "\
"too many D-peptides."\
% (chain.name, chain.residue_count))
if len(mhandle.gaps) > 0:
ost.LogWarning("Failed to close %d gap(s). Returning incomplete model!"\
% len(mhandle.gaps))
else:
# check sequences
for chain, seq in zip(mhandle.model.chains, mhandle.seqres):
a = chain.residues[0].GetNumber().GetNum()
b = chain.residues[-1].GetNumber().GetNum()
expected_seq = seq[a-1:b]
actual_seq = ''.join([r.one_letter_code for r in chain.residues])
if expected_seq != actual_seq:
ost.LogWarning("Sequence mismatch in chain %s!"\
" Expected '%s'. Got '%s'" \
% (chain.name, expected_seq, actual_seq))
# report ring punchings
rings = GetRings(mhandle.model)
ring_punches = GetRingPunches(rings, mhandle.model)
for res in ring_punches:
ost.LogWarning("Ring of " + str(res) + " has been punched!")
# report stereo-chemical problems
ost.PushVerbosityLevel(0)
clashing_distances = mol.alg.DefaultClashingDistances()
bond_stereo_chemical_param = mol.alg.DefaultBondStereoChemicalParams()
angle_stereo_chemical_param = mol.alg.DefaultAngleStereoChemicalParams()
# extract problems
model_src = mhandle.model.Select("aname!=OXT")
clash_info = mol.alg.FilterClashes(model_src, clashing_distances)[1]
# note: 10,10 parameters below are hard coded bond-/angle-tolerances
stereo_info = mol.alg.CheckStereoChemistry(model_src,
bond_stereo_chemical_param,
angle_stereo_chemical_param,
10, 10)[1]
ost.PopVerbosityLevel()
# set bool props in model-residues
atoms = [e.GetFirstAtom() for e in clash_info.GetClashList()]\
+ [e.GetFirstAtom() for e in stereo_info.GetBondViolationList()]\
+ [e.GetSecondAtom() for e in stereo_info.GetAngleViolationList()]
for atomui in atoms:
res = model_src.FindResidue(atomui.GetChainName(), atomui.GetResNum())
res.SetBoolProp("stereo_chemical_problem", True)
if atomui.GetAtomName() in ["CA", "N", "O", "C"]:
res.SetBoolProp("stereo_chemical_problem_backbone", True)
# report bad residues
for res in model_src.residues:
if res.HasProp("stereo_chemical_problem_backbone") and\
res.GetBoolProp("stereo_chemical_problem_backbone"):
ost.LogInfo("Stereo-chemical problem in backbone " + \
"of residue " + str(res))
elif res.HasProp("stereo_chemical_problem") and\
res.GetBoolProp("stereo_chemical_problem"):
ost.LogInfo("Stereo-chemical problem in sidechain " + \
"of residue " + str(res))
def BuildFromRawModel(mhandle, scorer = None, use_amber_ff=False, extra_force_fields=list()):
'''Build a model starting with a raw model (see :func:`BuildRawModel`).
This function implements a recommended pipeline to generate complete models
from a raw model. The steps are shown in detail in the code example
:ref:`above <modelling_steps_example>`. If you wish to use your own
pipeline, you can use that code as a starting point for your own custom
modelling pipeline. For reproducibility, we recommend that you keep copies
of custom pipelines.
If the function fails to close all gaps, it will produce a warning and
return an incomplete model.
:param mhandle: The prepared template coordinates loaded with the input
alignment.
:type mhandle: :class:`ModellingHandle`
:param use_amber_ff: if True, use the AMBER force field instead of the def.
CHARMM one (see :meth:`ost.mol.mm.LoadAMBERForcefield`
and :meth:`ost.mol.mm.LoadCHARMMForcefield`).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in `extra_force_fields`.
:type use_amber_ff: :class:`bool`
:param extra_force_fields: Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
existing parametrization are skipped.
:type extra_force_fields: :class:`list` of :class:`ost.mol.mm.Forcefield`
:return: Delivers the model as an |ost_s| entity.
:rtype: :class:`Entity <ost.mol.EntityHandle>`
'''
prof_name = 'pipeline::BuildFromRawModel'
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
# ignore empty models
if mhandle.model.residue_count == 0:
ost.LogError("Cannot perform modelling with an empty raw model.")
return mhandle.model
else:
ost.LogInfo("Starting modelling based on a raw model.")
# a bit of setup
fragment_db = loop.LoadFragDB()
structure_db = loop.LoadStructureDB()
torsion_sampler = loop.LoadTorsionSamplerCoil()
merge_distance = 4
if scorer == None:
scorer = SetupBackboneScorer(mhandle)
# remove terminal gaps and close small deletions
RemoveTerminalGaps(mhandle)
CloseSmallDeletions(mhandle, scorer)
# iteratively merge gaps of distance i and fill loops by database
for distance in range(merge_distance):
MergeGapsByDistance(mhandle, distance)
FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
torsion_sampler, min_loops_required=-1,
max_res_extension=6)
FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
torsion_sampler, min_loops_required=-1)
FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
torsion_sampler)
# close remaining gaps by Monte Carlo
FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler)
CloseLargeDeletions(mhandle, scorer, structure_db)
# build sidechains
BuildSidechains(mhandle, merge_distance, scorer, fragment_db,
structure_db, torsion_sampler)
# minimize energy of final model using molecular mechanics
MinimizeModelEnergy(mhandle, use_amber_ff=use_amber_ff,
extra_force_fields=extra_force_fields)
# sanity checks
CheckFinalModel(mhandle)
# done
return mhandle.model
# these methods will be exported into module
__all__ = ('BuildFromRawModel', 'BuildSidechains', 'MinimizeModelEnergy',
'CheckFinalModel')