#!/usr/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Pipeline
========
Utility functions to help setting up Yank configurations.
"""
# =============================================================================================
# GLOBAL IMPORTS
# =============================================================================================
import os
import re
import sys
import copy
import inspect
import logging
import itertools
import collections
import mdtraj
import numpy as np
import openmmtools as mmtools
import openmoltools as moltools
from pdbfixer import PDBFixer
from simtk import openmm, unit
from simtk.openmm.app import PDBFile
from . import utils, mpi
logger = logging.getLogger(__name__)
# ==============================================================================
# Utility functions
# ==============================================================================
[docs]def compute_squared_distances(molecule1_positions, molecule2_positions):
"""Compute the squared distances between the atoms of two molecules.
All the positions must be expressed in the same unit of measure.
Parameters
----------
molecule1_positions : numpy.ndarray
An Nx3 array where, N is the number of atoms, containing the positions of
the atoms of molecule1.
molecule2_positions : numpy.ndarray
An Mx3 array where, M is the number of atoms, containing the positions of
the atoms of the molecule2.
Returns
-------
squared_distances : numpy.ndarray
An NxM array of squared distances. distances_squared[i][j] is the squared
distance between atom i of molecule1 and atom j of molecule 2.
"""
squared_distances = np.array([((molecule2_positions - atom_pos)**2).sum(1)
for atom_pos in molecule1_positions])
return squared_distances
[docs]def compute_min_dist(mol_positions, *args):
"""Compute the minimum distance between a molecule and a set of other molecules.
All the positions must be expressed in the same unit of measure.
Parameters
----------
mol_positions : numpy.ndarray
An Nx3 array where, N is the number of atoms, containing the positions of
the atoms of the molecule for which we want to compute the minimum distance
from the others
Other parameters
----------------
args
A series of numpy.ndarrays containing the positions of the atoms of the other
molecules
Returns
-------
min_dist : float
The minimum distance between ``mol_positions`` and the other set of positions
"""
for argmol_positions in args:
# Compute squared distances. Each row is an array of distances
# from a mol_positions atom to all argmol_positions atoms.
distances2 = compute_squared_distances(mol_positions, argmol_positions)
# Find closest atoms and their distance
min_idx = np.unravel_index(distances2.argmin(), distances2.shape)
try:
min_dist = min(min_dist, np.sqrt(distances2[min_idx]))
except UnboundLocalError:
min_dist = np.sqrt(distances2[min_idx])
return min_dist
[docs]def compute_min_max_dist(mol_positions, *args):
"""Compute minimum and maximum distances between a molecule and a set of
other molecules.
All the positions must be expressed in the same unit of measure.
Parameters
----------
mol_positions : numpy.ndarray
An Nx3 array where, N is the number of atoms, containing the positions of
the atoms of the molecule for which we want to compute the minimum distance
from the others
Other parameters
----------------
args
A series of numpy.ndarrays containing the positions of the atoms of the other
molecules
Returns
-------
min_dist : float
The minimum distance between mol_positions and the atoms of the other positions
max_dist : float
The maximum distance between mol_positions and the atoms of the other positions
Examples
--------
>>> mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], np.float)
>>> mol2_pos = np.array([[2, 2, 2], [2, 4, 5]], np.float) # determine min dist
>>> mol3_pos = np.array([[3, 3, 3], [3, 4, 5]], np.float) # determine max dist
>>> min_dist, max_dist = compute_min_max_dist(mol1_pos, mol2_pos, mol3_pos)
>>> min_dist == np.linalg.norm(mol1_pos[1] - mol2_pos[0])
True
>>> max_dist == np.linalg.norm(mol1_pos[1] - mol3_pos[1])
True
"""
min_dist = None
for argmol_positions in args:
# Compute squared distances of all atoms. Each row is an array of distances
# from an atom in argmol_positions to all the atoms in mol_positions.
distances2 = compute_squared_distances(argmol_positions, mol_positions)
# Find distances of each arg_pos atom to mol_positions
distances2 = np.amin(distances2, axis=1)
# Find closest and distant atom
if min_dist is None:
min_dist = np.sqrt(distances2.min())
max_dist = np.sqrt(distances2.max())
else:
min_dist = min(min_dist, np.sqrt(distances2.min()))
max_dist = max(max_dist, np.sqrt(distances2.max()))
return min_dist, max_dist
[docs]def compute_radius_of_gyration(positions):
"""
Compute the radius of gyration of the specified coordinate set.
Parameters
----------
positions : simtk.unit.Quantity with units compatible with angstrom
The coordinate set (natoms x 3) for which the radius of gyration is to be computed.
Returns
-------
radius_of_gyration : simtk.unit.Quantity with units compatible with angstrom
The radius of gyration
"""
unit = positions.unit
# Get dimensionless receptor positions.
x = positions / unit
# Get dimensionless restrained atom coordinate.
xref = x.mean(0)
xref = np.reshape(xref, (1,3)) # (1,3) array
# Compute distances from restrained atom.
natoms = x.shape[0]
# Distances[i] is the distance from the centroid to particle i
distances = np.sqrt(((x - np.tile(xref, (natoms, 1)))**2).sum(1))
# Compute std dev of distances from restrained atom.
radius_of_gyration = distances.std() * unit
return radius_of_gyration
[docs]def compute_net_charge(system, atom_indices):
"""Compute the total net charge of a subset of atoms in the system.
Parameters
----------
system : simtk.openmm.System
The system object containing the atoms of interest.
atom_indices : list of int
Indices of the atoms of interest.
Returns
-------
net_charge : int
Total net charge as the sum of the partial charges of the atoms.
"""
atom_indices = set(atom_indices) # convert to set to speed up searching
net_charge = 0.0 * unit.elementary_charge
for force_index in range(system.getNumForces()):
force = system.getForce(force_index)
if isinstance(force, openmm.NonbondedForce):
for particle_index in range(force.getNumParticles()):
if particle_index in atom_indices:
net_charge += force.getParticleParameters(particle_index)[0]
atom_indices.remove(particle_index)
assert len(atom_indices) == 0
net_charge = int(round(net_charge / unit.elementary_charge))
return net_charge
[docs]def find_alchemical_counterions(system, topography, region_name):
"""Return the atom indices of the ligand or solute counter ions.
In periodic systems, the solvation box needs to be neutral, and
if the decoupled molecule is charged, it will cause trouble. This
can be used to find a set of ions in the system that neutralize
the molecule, so that the solvation box will remain neutral all
the time.
Parameters
----------
system : simtk.openmm.System
The system object containing the atoms of interest.
topography : yank.Topography
The topography object holding the indices of the ions and the
ligand (for binding free energy) or solute (for transfer free
energy).
region_name : str
The region name in the topography (e.g. "ligand_atoms") for
which to find counter ions.
Returns
-------
counterions_indices : list of int
The list of atom indices in the system of the counter ions
neutralizing the region.
Raises
------
ValueError
If the topography region has no atoms, or if it impossible
to neutralize the region with the ions in the system.
"""
# Check whether we need to find counterions of ligand or solute.
atom_indices = getattr(topography, region_name)
if len(atom_indices) == 0:
raise ValueError("Cannot find counterions for region {}. "
"The region has no atoms.")
# If the net charge of alchemical atoms is 0, we don't need counterions.
mol_net_charge = compute_net_charge(system, atom_indices)
logger.debug('{} net charge: {}'.format(region_name, mol_net_charge))
if mol_net_charge == 0:
return []
# Find net charge of all ions in the system.
ions_net_charges = [(ion_id, compute_net_charge(system, [ion_id]))
for ion_id in topography.ions_atoms]
topology = topography.topology
ions_names_charges = [(topology.atom(ion_id).residue.name, ion_net_charge)
for ion_id, ion_net_charge in ions_net_charges]
logger.debug('Ions net charges: {}'.format(ions_names_charges))
# Find minimal subset of counterions whose charges sums to -mol_net_charge.
for n_ions in range(1, len(ions_net_charges) + 1):
for ion_subset in itertools.combinations(ions_net_charges, n_ions):
counterions_indices, counterions_charges = zip(*ion_subset)
if sum(counterions_charges) == -mol_net_charge:
return counterions_indices
# We couldn't find any subset of counterions neutralizing the region.
raise ValueError('Impossible to find a solution for region {}. '
'Net charge: {}, system ions: {}.'.format(
region_name, mol_net_charge, ions_names_charges))
# See Amber manual Table 4.1 http://ambermd.org/doc12/Amber15.pdf
_OPENMM_TO_TLEAP_PBRADII = {'HCT': 'mbondi', 'OBC1': 'mbondi2', 'OBC2': 'mbondi2',
'GBn': 'bondi', 'GBn2': 'mbondi3'}
[docs]def get_leap_recommended_pbradii(implicit_solvent):
"""Return the recommended PBradii setting for LeAP.
Parameters
----------
implicit_solvent : str
The implicit solvent model.
Returns
-------
pbradii : str or object
The LeAP recommended PBradii for the model.
Raises
------
ValueError
If the implicit solvent model is not supported by OpenMM.
Examples
--------
>>> get_leap_recommended_pbradii('OBC2')
'mbondi2'
>>> from simtk.openmm.app import HCT
>>> get_leap_recommended_pbradii(HCT)
'mbondi'
"""
try:
return _OPENMM_TO_TLEAP_PBRADII[str(implicit_solvent)]
except KeyError:
raise ValueError('Implicit solvent {} is not supported.'.format(implicit_solvent))
_NONPERIODIC_NONBONDED_METHODS = [openmm.app.NoCutoff, openmm.app.CutoffNonPeriodic]
[docs]def create_system(parameters_file, box_vectors, create_system_args, system_options):
"""Create and return an OpenMM system.
Parameters
----------
parameters_file : simtk.openmm.app.AmberPrmtopFile or GromacsTopFile
The file used to create they system.
box_vectors : list of Vec3
The default box vectors of the system will be set to this value.
create_system_args : dict of str
The kwargs accepted by the ``createSystem()`` function of the ``parameters_file``.
system_options : dict
The kwargs to forward to ``createSystem()``.
Returns
-------
system : simtk.openmm.System
The system created.
"""
# Prepare createSystem() options
# OpenMM adopts camel case convention so we need to change the options format.
# Then we filter system options according to specific createSystem() args
system_options = {utils.underscore_to_camelcase(key): value
for key, value in system_options.items()}
system_options = {arg: system_options[arg] for arg in create_system_args
if arg in system_options}
# Determine if this will be an explicit or implicit solvent simulation.
if box_vectors is not None:
is_periodic = True
else:
is_periodic = False
# Adjust nonbondedMethod
# TODO: Ensure that selected method is appropriate.
if 'nonbondedMethod' not in system_options:
if is_periodic:
system_options['nonbondedMethod'] = openmm.app.CutoffPeriodic
else:
system_options['nonbondedMethod'] = openmm.app.NoCutoff
# Check for solvent configuration inconsistencies
# TODO: Check to make sure both files agree on explicit/implicit.
err_msg = ''
nonbonded_method = system_options['nonbondedMethod']
if is_periodic:
if 'implicitSolvent' in system_options and system_options['implicitSolvent'] is not None:
err_msg = 'Found periodic box in positions file and implicitSolvent specified.'
if nonbonded_method in _NONPERIODIC_NONBONDED_METHODS:
err_msg = ('Found periodic box in positions file but '
'nonbondedMethod is {}'.format(nonbonded_method))
else:
if nonbonded_method not in _NONPERIODIC_NONBONDED_METHODS:
err_msg = ('nonbondedMethod {} is periodic but could not '
'find periodic box in positions file.'.format(nonbonded_method))
if len(err_msg) != 0:
logger.error(err_msg)
raise RuntimeError(err_msg)
# Create system and update box vectors (if needed)
system = parameters_file.createSystem(removeCMMotion=False, **system_options)
if is_periodic:
system.setDefaultPeriodicBoxVectors(*box_vectors)
return system
[docs]def read_system_files(positions_file_path, parameters_file_path, system_options,
gromacs_include_dir=None):
"""Create a Yank arguments for a phase from system files.
Parameters
----------
positions_file_path : str
Path to system position file (e.g. 'complex.inpcrd/.gro/.pdb').
parameters_file_path : str
Path to system parameters file (e.g. 'complex.prmtop/.top/.xml').
system_options : dict
``system_options[phase]`` is a a dictionary containing options to
pass to ``createSystem()``. If the parameters file is an OpenMM
system in XML format, this will be ignored.
gromacs_include_dir : str, optional
Path to directory in which to look for other files included
from the gromacs top file.
Returns
-------
system : simtk.openmm.System
The OpenMM System built from the given files.
topology : openmm.app.Topology
The OpenMM Topology built from the given files.
sampler_state : openmmtools.states.SamplerState
The sampler state containing the positions of the atoms.
"""
# Load system files
parameters_file_extension = os.path.splitext(parameters_file_path)[1]
# Read OpenMM XML and PDB files.
if parameters_file_extension == '.xml':
logger.debug("xml: {}".format(parameters_file_path))
logger.debug("pdb: {}".format(positions_file_path))
positions_file = openmm.app.PDBFile(positions_file_path)
parameters_file = positions_file # Needed for topology.
with open(parameters_file_path, 'r') as f:
serialized_system = f.read()
system = openmm.XmlSerializer.deserialize(serialized_system)
box_vectors = positions_file.topology.getPeriodicBoxVectors()
if box_vectors is None:
box_vectors = system.getDefaultPeriodicBoxVectors()
# Read Amber prmtop and inpcrd files.
elif parameters_file_extension == '.prmtop':
logger.debug("prmtop: {}".format(parameters_file_path))
logger.debug("inpcrd: {}".format(positions_file_path))
parameters_file = openmm.app.AmberPrmtopFile(parameters_file_path)
positions_file = openmm.app.AmberInpcrdFile(positions_file_path)
box_vectors = positions_file.boxVectors
create_system_args = set(inspect.getargspec(openmm.app.AmberPrmtopFile.createSystem).args)
system = create_system(parameters_file, box_vectors, create_system_args, system_options)
# Read Gromacs top and gro files.
elif parameters_file_extension == '.top':
logger.debug("top: {}".format(parameters_file_path))
logger.debug("gro: {}".format(positions_file_path))
positions_file = openmm.app.GromacsGroFile(positions_file_path)
# gro files must contain box vectors, so we must determine whether system
# is non-periodic or not from provided nonbonded options
# WARNING: This uses the private API for GromacsGroFile, and may break.
if ('nonbonded_method' in system_options and
system_options['nonbonded_method'] in _NONPERIODIC_NONBONDED_METHODS):
logger.info('nonbonded_method = {}, so removing periodic box vectors '
'from gro file'.format(system_options['nonbonded_method']))
for frame, box_vectors in enumerate(positions_file._periodicBoxVectors):
positions_file._periodicBoxVectors[frame] = None
box_vectors = positions_file.getPeriodicBoxVectors()
parameters_file = openmm.app.GromacsTopFile(parameters_file_path,
periodicBoxVectors=box_vectors,
includeDir=gromacs_include_dir)
create_system_args = set(inspect.getargspec(openmm.app.GromacsTopFile.createSystem).args)
system = create_system(parameters_file, box_vectors, create_system_args, system_options)
# Unsupported file format.
else:
raise ValueError('Unsupported format for parameter file {}'.format(parameters_file_extension))
# Store numpy positions and create SamplerState.
positions = positions_file.getPositions(asNumpy=True)
sampler_state = mmtools.states.SamplerState(positions=positions, box_vectors=box_vectors)
# Check to make sure number of atoms match between prmtop and inpcrd.
n_atoms_system = system.getNumParticles()
n_atoms_positions = positions.shape[0]
if n_atoms_system != n_atoms_positions:
err_msg = "Atom number mismatch: {} has {} atoms; {} has {} atoms.".format(
parameters_file_path, n_atoms_system, positions_file_path, n_atoms_positions)
logger.error(err_msg)
raise RuntimeError(err_msg)
return system, parameters_file.topology, sampler_state
# =============================================================================
# SETUP PIPELINE UTILITY FUNCTIONS
# =============================================================================
# Map the OpenMM-style name for a solvent to the tleap
# name compatible with the solvateBox command.
_OPENMM_LEAP_SOLVENT_MODELS_MAP = {
'tip3p': 'TIP3PBOX',
'tip3pfb': 'TIP3PFBOX',
'tip4pew': 'TIP4PEWBOX',
'tip5p': 'TIP5PBOX',
'spce': 'SPCBOX',
}
# Map the OpenMM-style name for solvent to the tleap
# name for a list of files which would enable the
# solvent model to work. Servers as error checking,
# but is not foolproof
_OPENMM_LEAP_SOLVENT_FILES_MAP = {
'tip3p': 'leaprc.water.tip3p',
'tip3pfb': 'leaprc.water.tip3p',
'tip4pew': 'leaprc.water.tip4pew',
'tip5p': 'leaprc.water.tip4pew', # Enables the EP atom type
'spce': 'leaprc.water.spce',
}
[docs]def remove_overlap(mol_positions, *args, **kwargs):
"""Remove any eventual overlap between a molecule and a set of others.
The method both randomly shifts and rotates the molecule (when overlapping atoms
are detected) until it does not clash with any other given molecule anymore. All
the others are kept fixed.
All the positions must be expressed in the same unit of measure.
Parameters
----------
mol_positions : numpy.ndarray
An Nx3 array where, N is the number of atoms, containing the positions of
the atoms of the molecule that we want to not clash with the others.
min_distance : float
The minimum distance accepted to consider the molecule not clashing with
the others. Must be in the same unit of measure of the positions.
sigma : float
The maximum displacement for a single step. Must be in the same unit of
measure of the positions.
Other parameters
----------------
args
A series of numpy.ndarrays containing the positions of the atoms of the
molecules that are kept fixed.
Returns
-------
x : numpy.ndarray
Positions of the atoms of the given molecules that do not clash.
"""
x = np.copy(mol_positions)
sigma = kwargs.get('sigma', 1.0)
min_distance = kwargs.get('min_distance', 1.0)
# Try until we have a non-overlapping conformation w.r.t. all fixed molecules
while compute_min_dist(x, *args) <= min_distance:
# Compute center of geometry
x0 = x.mean(0)
# Randomize orientation of ligand.
Rq = mmtools.mcmc.MCRotationMove.generate_random_rotation_matrix()
x = ((Rq * np.matrix(x - x0).T).T + x0).A
# Choose a random displacement vector and translate
x += sigma * np.random.randn(3)
return x
[docs]def pull_close(fixed_mol_pos, translated_mol_pos, min_bound, max_bound):
"""Heuristic algorithm to quickly translate the ligand close to the receptor.
The distance of the ligand from the receptor here is defined as the shortest
Euclidean distance between an atom of the ligand and one of the receptor.
The molecules positions will not be modified if the ligand is already at a
distance in the interval [min_bound, max_bound].
Parameters
----------
fixed_mol_pos : numpy.array
The positions of the molecule to keep fixed as a Nx3 array.
translated_mol_pos : numpy.array
The positions of the molecule to translate as a Nx3 array.
min_bound : float
Minimum distance from the receptor to the ligand. This should be high
enough for the ligand to not overlap the receptor atoms at the beginning
of the simulation.
max_bound : float
Maximum distance from the receptor to the ligand. This should be short
enough to make the ligand and the receptor interact since the beginning
of the simulation.
Returns
-------
translation : numpy.array
A 1x3 array containing the translation vector to apply to translated_mol_pos
to move the molecule at a distance between min_bound and max_bound from
fixed_mol_pos.
"""
goal_distance = (min_bound + max_bound) / 2
trans_pos = copy.deepcopy(translated_mol_pos) # positions that we can modify
# Find translation
final_translation = np.zeros(3)
while True:
# Compute squared distances between all atoms
# Each row is an array of distances from a translated atom to all fixed atoms
# We don't need to apply square root to everything
distances2 = np.array([((fixed_mol_pos - pos)**2).sum(1) for pos in trans_pos])
# Find closest atoms and their distance
min_idx = np.unravel_index(distances2.argmin(), distances2.shape)
min_dist = np.sqrt(distances2[min_idx])
# If closest atom is between boundaries translate ligand
if min_bound <= min_dist <= max_bound:
break
# Compute unit vector that connects receptor and ligand atom
if min_dist != 0:
direction = fixed_mol_pos[min_idx[1]] - trans_pos[min_idx[0]]
else: # any deterministic direction
direction = np.array([1, 1, 1])
direction = direction / np.sqrt((direction**2).sum()) # normalize
if max_bound < min_dist: # the atom is far away
translation = (min_dist - goal_distance) * direction
trans_pos += translation
final_translation += translation
elif min_dist < min_bound: # the two molecules overlap
max_dist = np.sqrt(distances2.max())
translation = (max_dist + goal_distance) * direction
trans_pos += translation
final_translation += translation
return final_translation
[docs]def strip_protons(input_file_path, output_file_path):
"""
Remove all hydrogens from PDB file and save the result.
Input and output file cannot be the same file
Parameters
----------
input_file_path : str
Full file path to the file to read, including extensions
output_file_path : str
Full file path to the file to save, including extensions
"""
output_file = open(output_file_path, 'w')
with open(input_file_path, 'r') as input_file:
for line in input_file:
if not (line[:6] == 'ATOM ' and (line[12] == 'H' or line[13] == 'H')):
output_file.write(line)
output_file.close()
# For mutate_protein
_three_letter_code = {
'A': 'ALA',
'C': 'CYS',
'D': 'ASP',
'E': 'GLU',
'F': 'PHE',
'G': 'GLY',
'H': 'HIS',
'I': 'ILE',
'K': 'LYS',
'L': 'LEU',
'M': 'MET',
'N': 'ASN',
'P': 'PRO',
'Q': 'GLN',
'R': 'ARG',
'S': 'SER',
'T': 'THR',
'V': 'VAL',
'W': 'TRP',
'Y': 'TYR'
}
_one_letter_code = dict()
for one_letter in _three_letter_code.keys():
three_letter = _three_letter_code[one_letter]
_one_letter_code[three_letter] = one_letter
def decompose_mutation(mutation):
match = re.match('(\D)(\d+)(\D)', mutation)
try:
original_residue_name = _three_letter_code[match.group(1)]
residue_index = int(match.group(2))
mutated_residue_name = _three_letter_code[match.group(3)]
except AttributeError:
error_string = 'Mutation "{}" could not be parsed! '.format(mutation)
error_string += 'Should be of form {single letter}{integer}{another single letter}'
raise ValueError(error_string)
return original_residue_name, residue_index, mutated_residue_name
def generate_pdbfixer_mutation_code(original_residue_name, residue_index, mutated_residue_name):
return '{0:s}-{1:d}-{2:s}'.format(original_residue_name, residue_index, mutated_residue_name)
[docs]def apply_pdbfixer(input_file_path, output_file_path, directives):
"""
Apply PDBFixer to make changes to the specified molecule.
Single mutants are supported in the form "T315I"
Double mutants are supported in the form "L858R/T790M"
The string "WT" still pushes the molecule through PDBFixer, but makes no mutations.
This is useful for testing.
Original PDB file numbering scheme is used.
Currently, only PDB files are supported.
pdbfixer is used to make the mutations
Parameters
----------
input_file_path : str
Full file path to the file to read, including extensions
output_file_path : str
Full file path to the file to save, including extensions
directives : dict
Dict containing directives for PDBFixer.
"""
DEFAULT_PH = 7.4 # default pH
# Make a copy since we will delete from the dictionary to validate
directives = copy.deepcopy(directives)
# Create a PDBFixer object
fixer = PDBFixer(input_file_path)
fixer.missingResidues = {}
# Dispatch functions
# These won't be documented individually because they are so short
def dispatch_pH(value):
pH = DEFAULT_PH
try:
pH = float(value)
logger.info('pdbfixer: Will use user-specified pH {}'.format(pH))
except:
raise ValueError("'ph' must be a floating-point number: found '{}'".format(value))
return pH
pH = process_tool_directive(directives, 'ph', dispatch_pH, None, yields_value=True)
def add_missing_residues(value):
if value == 'yes':
fixer.findMissingResidues()
logger.info('pdbfixer: Will add missing residues specified in SEQRES')
def apply_mutations(value):
# Extract chain id
chain_id = None
if 'chain_id' in value:
chain_id = value['chain_id']
if chain_id == 'none':
chain_id = None
# Extract mutations
mutations = value['mutations']
# Convert mutations to PDBFixer format
if mutations != 'WT':
pdbfixer_mutations = [generate_pdbfixer_mutation_code(*decompose_mutation(mutation))
for mutation in mutations.split('/')]
logger.info('pdbfixer: Will make mutations {} to chain_id {}.'.format(pdbfixer_mutations, chain_id))
fixer.applyMutations(pdbfixer_mutations, chain_id)
else:
logger.info('pdbfixer: No mutations will be applied since "WT" specified.')
def replace_nonstandard_residues(value):
if value == 'yes':
logger.info('pdbfixer: Will replace nonstandard residues.')
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
def remove_heterogens(value):
if value == 'water':
logger.info('pdbfixer: Will remove heterogens, retaining water.')
fixer.removeHeterogens(keepWater=True)
elif value == 'all':
logger.info('pdbfixer: Will remove heterogens, discarding water.')
fixer.removeHeterogens(keepWater=False)
def add_missing_atoms(value):
fixer.findMissingAtoms()
if value not in ('all', 'heavy'):
fixer.missingAtoms = {}
fixer.missingTerminals = {}
logger.info('pdbfixer: Will add missing atoms: {}.'.format(value))
fixer.addMissingAtoms()
if value in ('all', 'hydrogens'):
logger.info('pdbfixer: Will add hydrogens in default protonation state for pH {}.'.format(pH))
fixer.addMissingHydrogens(pH)
# Set default atom addition method
if 'add_missing_atoms' not in directives:
directives['add_missing_atoms'] = 'heavy'
# Dispatch directives
process_tool_directive(directives, 'add_missing_residues', add_missing_residues, [True, False])
process_tool_directive(directives, 'apply_mutations', apply_mutations, None)
process_tool_directive(directives, 'replace_nonstandard_residues', replace_nonstandard_residues, [True, False])
process_tool_directive(directives, 'remove_heterogens', remove_heterogens, ['all', 'water', 'none'])
process_tool_directive(directives, 'add_missing_atoms', add_missing_atoms, ['all', 'heavy', 'hydrogens', 'none'])
# Check that there were no extra options
if len(directives) > 0:
raise ValueError("The 'pdbfixer:' block contained some nodes that it didn't know how to process: {}".format(directives))
# Write the final structure
PDBFile.writeFile(fixer.topology, fixer.positions, open(output_file_path, 'w'))
[docs]def apply_modeller(input_file_path, output_file_path, directives):
"""
Apply Salilab Modeller to make changes to the specified molecule.
Single mutants are supported in the form "T315I"
Double mutants are not currently supported.
The string "WT" makes no mutations.
Original PDB file numbering scheme is used.
Currently, only PDB files are supported.
modeller is used to make the mutations. You must have a license file installed for this to work
Parameters
----------
input_file_path : str
Full file path to the file to read, including extensions
output_file_path : str
Full file path to the file to save, including extensions
directives : dict
Dict containing directives for modeller.
"""
if not utils.is_modeller_installed():
raise ImportError('Modeller and license must be installed to use this feature.')
import modeller
directives = copy.deepcopy(directives)
# Silence unnecessary output to the log files
modeller.log.none()
# Create modeller environment and point it to the PDB file
env = modeller.environ()
atom_files_directory = os.path.dirname(input_file_path)
atom_file_name = os.path.basename(input_file_path)
# Read in topology and parameter files
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
env.io.atom_files_directory = [atom_files_directory]
alignment = modeller.alignment(env)
model = modeller.model(env, file=atom_file_name)
model_original_numbering = modeller.model(env, file=atom_file_name)
alignment.append_model(model, atom_files=atom_file_name, align_codes=atom_file_name)
def apply_mutations_modeller(value):
# Extract chain id
chain_id = None
if 'chain_id' in value:
chain_id = value['chain_id']
if chain_id == 'none':
chain_id = 0
# Extract mutations
mutations = value['mutations']
# Convert mutations to PDBFixer format
if mutations != 'WT':
modeller_mutations = [generate_pdbfixer_mutation_code(*decompose_mutation(mutation))
for mutation in mutations.split('/')]
if len(modeller_mutations) > 1:
raise ValueError('{} is a double mutant and not supported by Modeller currently.'.format(mutations))
else:
logger.info('modeller: Will make mutations {} to chain_id {}.'.format(modeller_mutations, chain_id))
sel = modeller.selection(model.chains[chain_id].residues[modeller_mutations[0].split('-')[1]])
sel.mutate(residue_type=modeller_mutations[0].split('-')[2])
alignment.append_model(model, align_codes=modeller_mutations[0])
model.clear_topology()
model.generate_topology(alignment[modeller_mutations[0]])
model.transfer_xyz(alignment)
model.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
else:
logger.info('modeller: No mutations will be applied since "WT" specified.')
alignment.append_model(model, align_codes='WT')
process_tool_directive(directives, 'apply_mutations', apply_mutations_modeller, None)
# Check that there were no extra options
if len(directives) > 0:
raise ValueError("The 'modeller:' block contained some nodes that it didn't know how to process: {}".format(directives))
# Write the final model
model.res_num_from(model_original_numbering, alignment)
model.write(file=output_file_path)
[docs]def read_csv_lines(file_path, lines):
"""Return a list of CSV records.
The function takes care of ignoring comments and blank lines.
Parameters
----------
file_path : str
The path to the CSV file.
lines : 'all' or int
The index of the line to read or 'all' to return
the list of all lines.
Returns
-------
records : str or list of str
The CSV record if lines is an integer, or a list of CSV
records if it is 'all'.
"""
# Read all lines ignoring blank lines and comments.
with open(file_path, 'r') as f:
all_records = [line for line in f
if bool(line) and not line.strip().startswith('#')]
if lines == 'all':
return all_records
return all_records[lines]
# ==============================================================================
# SETUP DATABASE
# ==============================================================================
[docs]class SetupDatabase:
"""Provide utility functions to set up systems and molecules.
The object allows to access molecules, systems and solvents by 'id' and takes
care of parametrizing molecules and creating the AMBER prmtop and inpcrd files
describing systems.
Parameters
----------
setup_dir : str
Path to the main setup directory. Changing this means changing the database.
molecules : dict, Optional. Default: None
YAML description of the molecules.
Dictionary should be of form {molecule_id : molecule YAML description}
solvents : dict, Optional. Default: None
YAML description of the solvents.
Dictionary should be of form {solvent_id : solvent YAML description}
systems : dict, Optional. Default: None
YAML description of the systems.
Dictionary should be of form {system_id : system YAML description}
"""
SYSTEMS_DIR = 'systems' #: Stock system's sub-directory name
MOLECULES_DIR = 'molecules' #: Stock Molecules sub-directory name
CLASH_THRESHOLD = 1.5 #: distance in Angstroms to consider two atoms clashing
def __init__(self, setup_dir, molecules=None, solvents=None, systems=None):
"""Initialize the database."""
self.setup_dir = setup_dir
self.molecules = molecules
self.solvents = solvents
self.systems = systems
# Private attributes
self._pos_cache = {} # cache positions of molecules
self._processed_mols = set() # keep track of parametrized molecules
[docs] def get_molecule_dir(self, molecule_id):
"""Return the directory where the parameter files are stored.
Parameters
----------
molecule_id : str
The ID of the molecule.
Returns
-------
str
The path to the molecule directory.
"""
return os.path.join(self.setup_dir, self.MOLECULES_DIR, molecule_id)
[docs] def get_system_files_paths(self, system_id):
"""Return the paths to the systems files.
Parameters
----------
system_id : str
The ID of the system.
Returns
-------
system_files_paths : list of namedtuple
Elements of the list contain the paths to the system files for
each phase. Each namedtuple contains the fields position_path (e.g.
inpcrd, gro, or pdb) and parameters_path (e.g. prmtop, top, or xml).
"""
Paths = collections.namedtuple('Paths', ['position_path', 'parameters_path'])
system_dir = os.path.join(self.setup_dir, self.SYSTEMS_DIR, system_id)
if 'receptor' in self.systems[system_id]:
system_files_paths = [
Paths(position_path=os.path.join(system_dir, 'complex.inpcrd'),
parameters_path=os.path.join(system_dir, 'complex.prmtop')),
Paths(position_path=os.path.join(system_dir, 'solvent.inpcrd'),
parameters_path=os.path.join(system_dir, 'solvent.prmtop'))
]
elif 'solute' in self.systems[system_id]:
system_files_paths = [
Paths(position_path=os.path.join(system_dir, 'solvent1.inpcrd'),
parameters_path=os.path.join(system_dir, 'solvent1.prmtop')),
Paths(position_path=os.path.join(system_dir, 'solvent2.inpcrd'),
parameters_path=os.path.join(system_dir, 'solvent2.prmtop'))
]
else:
parameter_file_extensions = {'prmtop', 'top', 'xml'}
system_files_paths = []
for phase_path_name in ['phase1_path', 'phase2_path']:
file_paths = self.systems[system_id][phase_path_name]
assert len(file_paths) == 2
# Make sure that the position file is first.
first_file_extension = os.path.splitext(file_paths[0])[1][1:]
if first_file_extension in parameter_file_extensions:
file_paths = list(reversed(file_paths))
# Append Paths object.
system_files_paths.append(Paths(position_path=file_paths[0],
parameters_path=file_paths[1]))
return system_files_paths
[docs] def is_molecule_setup(self, molecule_id):
"""Check whether the molecule has been processed previously.
The molecule must be set up if it needs to be parametrize by antechamber
(and the gaff.mol2 and frcmod files do not exist), if the molecule must be
generated by OpenEye, or if it needs to be extracted by a multi-molecule file.
An example to clarify the difference between the two return values: a protein
in a single-frame pdb does not have to be processed (since it does not go through
antechamber) thus the function will return ``is_setup=True`` and ``is_processed=False``.
Parameters
----------
molecule_id : str
The id of the molecule.
Returns
-------
is_setup : bool
True if the molecule's parameter files have been specified by the user
or if they have been generated by SetupDatabase.
is_processed : bool
True if parameter files have been generated previously by SetupDatabase
(i.e. if the parameter files were not manually specified by the user).
"""
# The only way to check if we processed the molecule in the current run is
# through self._processed_mols as 'parameters' will be changed after setup
if molecule_id in self._processed_mols:
return True, True
# Some convenience variables
molecule_descr = self.molecules[molecule_id]
molecule_dir = self.get_molecule_dir(molecule_id)
molecule_id_path = os.path.join(molecule_dir, molecule_id)
try:
extension = os.path.splitext(molecule_descr['filepath'])[1]
except KeyError:
extension = None
# The following checks must be performed in reverse order w.r.t. how they
# are executed in _setup_molecules()
files_to_check = {}
# If the molecule must go through antechamber we search for its output
if 'antechamber' in molecule_descr:
files_to_check = [('filepath', molecule_id_path + '.gaff.mol2'),
(['leap', 'parameters'], molecule_id_path + '.frcmod')]
# If the molecule must be generated by OpenEye, a mol2 should have been created
elif extension is None or extension == '.smiles' or extension == '.csv':
files_to_check = [('filepath', molecule_id_path + '.mol2')]
# If we have to strip the protons off a PDB, a new PDB should have been created
elif 'strip_protons' in molecule_descr and molecule_descr['strip_protons']:
files_to_check = [('filepath', molecule_id_path + '.pdb')]
# If we have to make mutations, a new PDB should be created
elif 'pdbfixer' in molecule_descr:
files_to_check = [('filepath', molecule_id_path + '.pdb')]
# If we have to make mutations using modeller, a new PDB should be created
elif 'modeller' in molecule_descr:
files_to_check = [('filepath', molecule_id_path + '.pdb')]
# If a single structure must be extracted we search for output
elif 'select' in molecule_descr:
files_to_check = [('filepath', molecule_id_path + extension)]
# Check if this needed to be processed at all
if not files_to_check:
return True, False
# Check if all output files exist
all_file_exist = True
for descr_key, file_path in files_to_check:
all_file_exist &= os.path.isfile(file_path) and os.path.getsize(file_path) > 0
if all_file_exist: # Make sure internal description is correct
try:
molecule_descr[descr_key] = file_path
except TypeError: # nested key, list are unhashable
molecule_descr[descr_key[0]][descr_key[1]].append(file_path)
# Compute and update small molecule net charge
if all_file_exist:
extension = os.path.splitext(molecule_descr['filepath'])[1]
# TODO what if this is a peptide? This should be computed in get_system()
if extension == '.mol2':
molecule_descr['net_charge'] = utils.Mol2File(molecule_descr['filepath']).net_charge
return all_file_exist, all_file_exist
[docs] def is_system_setup(self, system_id):
"""Check whether the system has been already processed.
Parameters
----------
system_id : str
The ID of the system.
Returns
-------
is_setup : bool
True if the system is ready to be used for an experiment. Either because
the system has directly provided the system files, or because it already
went through the setup pipeline.
is_processed : bool
True if the system has already gone through the setup pipeline.
"""
if 'ligand' in self.systems[system_id] or 'solute' in self.systems[system_id]:
system_files_paths = self.get_system_files_paths(system_id)
is_setup = (os.path.exists(system_files_paths[0].position_path) and
os.path.exists(system_files_paths[0].parameters_path) and
os.path.exists(system_files_paths[1].position_path) and
os.path.exists(system_files_paths[1].parameters_path))
return is_setup, is_setup
else:
return True, False
[docs] def get_system(self, system_id):
"""Make sure that the system files are set up and return the system folder.
If necessary, create the prmtop and inpcrd files from the given components.
The system files are generated with tleap. If no molecule specifies a general
force field, leaprc.ff14SB is loaded.
Parameters
----------
system_id : str
The ID of the system.
Returns
-------
system_files_paths : list of namedtuple
Elements of the list contain the paths to the system files for
each phase. Each namedtuple contains the fields position_path (e.g.
inpcrd, gro, or pdb) and parameters_path (e.g. prmtop, top, or xml).
"""
# Check if system has been already processed
system_files_paths = self.get_system_files_paths(system_id)
if self.is_system_setup(system_id)[0]:
return system_files_paths
system_descr = self.systems[system_id]
log_message = 'Setting up the systems for {} and {} using solvent {}'
if 'receptor' in system_descr: # binding free energy calculation
receptor_id = system_descr['receptor']
ligand_id = system_descr['ligand']
solvent_id = system_descr['solvent']
system_parameters = system_descr['leap']['parameters']
logger.info(log_message.format(receptor_id, ligand_id, solvent_id))
# solvent phase
logger.debug('Setting up solvent phase')
self._setup_system(system_files_paths[1].position_path, False,
0, system_parameters, solvent_id, ligand_id)
try:
alchemical_charge = int(round(self.molecules[ligand_id]['net_charge']))
except KeyError:
alchemical_charge = 0
# complex phase
logger.debug('Setting up complex phase')
self._setup_system(system_files_paths[0].position_path,
system_descr['pack'], alchemical_charge,
system_parameters, solvent_id, receptor_id,
ligand_id)
else: # partition/solvation free energy calculation
solute_id = system_descr['solute']
solvent1_id = system_descr['solvent1']
solvent2_id = system_descr['solvent2']
system_parameters = system_descr['leap']['parameters']
logger.info(log_message.format(solute_id, solvent1_id, solvent2_id))
# solvent1 phase
logger.debug('Setting up solvent1 phase')
self._setup_system(system_files_paths[0].position_path, False,
0, system_parameters, solvent1_id, solute_id)
# solvent2 phase
logger.debug('Setting up solvent2 phase')
self._setup_system(system_files_paths[1].position_path, False,
0, system_parameters, solvent2_id, solute_id)
return system_files_paths
[docs] def setup_all_systems(self):
"""Setup all molecules and systems in the database.
The method supports parallelization through MPI.
"""
# Find all molecules that need to be set up.
molecules_to_setup = []
for molecule_id in self.molecules:
if not self.is_molecule_setup(molecule_id)[0]:
molecules_to_setup.append(molecule_id)
molecules_to_setup.sort()
# Parallelize generation of all molecules among nodes.
mpi.distribute(self._setup_molecules,
distributed_args=molecules_to_setup,
send_results_to=None, group_size=1, sync_nodes=True)
# Find all systems that need to be set up.
systems_to_setup = []
for system_id in self.systems:
if not self.is_system_setup(system_id)[0]:
systems_to_setup.append(system_id)
systems_to_setup.sort()
# Parallelize generation of all systems among nodes.
mpi.distribute(self.get_system,
distributed_args=systems_to_setup,
send_results_to=None, group_size=1, sync_nodes=True)
def _generate_molecule(self, molecule_id):
"""Generate molecule using the OpenEye toolkit from name or smiles.
The molecule is charged with OpenEye's recommended AM1BCC charge
selection scheme and it is saved into the OpenEye molecules cache.
Parameters
----------
molecule_id : str
The id of the molecule as given in the YAML script
Returns
-------
molecule : OEMol
The generated molecule.
"""
mol_descr = self.molecules[molecule_id] # molecule description
try:
if 'name' in mol_descr:
molecule = moltools.openeye.iupac_to_oemol(mol_descr['name'])
elif 'smiles' in mol_descr:
molecule = moltools.openeye.smiles_to_oemol(mol_descr['smiles'])
molecule = moltools.openeye.get_charges(molecule, keep_confs=1)
except ImportError as e:
error_msg = ('requested molecule generation from name or smiles but '
'could not find OpenEye toolkit: ' + str(e))
logger.error(error_msg)
raise RuntimeError(error_msg)
return molecule
def _generate_residue_name(self, molecule_id):
"""Generates a residue name for a molecule.
The function guarantees to not generate twice the same residue name.
Purely numeric residue names mess up the pipeline, so we generate
residue names of the form YXX, where Y is a letter and X are digits
(e.g. A01, A02, ..., Z99).
The order of the generated residue name is not guaranteed.
WARNING: The algorithm may fail when new molecules are added to
self.molecules after construction. This is not the case right now,
but it's good to keep in mind.
Parameters
----------
molecule_id : str
The molecule identifier.
Returns
-------
residue_name : str
A three-character residue name.
"""
# We need to associate a unique number to this molecule, and do
# so in such a way that distributing molecule setups over multiple
# MPI process still ends up in unique residue names for each molecule.
molecule_ids = sorted(self.molecules.keys())
n_molecule = molecule_ids.index(molecule_id)
assert n_molecule < 2600
# Build 3-character identifier.
character = chr(n_molecule // 100 + 65)
digits = str(n_molecule % 100)
residue_name = character + digits.zfill(2)
return residue_name
def _setup_molecules(self, *args):
"""Set up the files needed to generate the system for all the molecules.
If OpenEye tools are installed, this generate the molecules when the source is
not a file. If two (or more) molecules generated by OpenEye have overlapping
atoms, the molecules are randomly shifted and rotated until the clash is resolved.
With the OpenEye toolkit installed, we also perform a sanity check to verify that
the molecules from files do not have overlapping atoms. An Exception is raised if
this is not the case.
If the Schrodinger's suite is install, this can enumerate tautomeric and protonation
states with epik when requested.
This also parametrize the molecule with antechamber when requested.
Other parameters
----------------
args
All the molecules ids that compose the system. These molecules are the only
ones considered when trying to resolve the overlapping atoms.
"""
for mol_id in args:
net_charge = None # used by antechamber
mol_descr = self.molecules[mol_id]
# Have we already processed this molecule? Do we have to do it at all?
# We don't want to create the output folder if we don't need to
if self.is_molecule_setup(mol_id)[0]:
continue
# Create output directory if it doesn't exist
mol_dir = self.get_molecule_dir(mol_id)
if not os.path.exists(mol_dir):
os.makedirs(mol_dir)
try:
extension = os.path.splitext(mol_descr['filepath'])[1]
except KeyError:
extension = None
# Extract single model if this is a multi-model file
if 'select' in mol_descr:
model_idx = mol_descr['select']
single_file_path = os.path.join(mol_dir, mol_id + extension)
if extension == '.pdb':
# Create single-model PDB file
pdb_file = PDBFile(mol_descr['filepath'])
with open(single_file_path, 'w') as f:
PDBFile.writeHeader(pdb_file.topology, file=f)
PDBFile.writeModel(pdb_file.topology, pdb_file.getPositions(frame=model_idx), file=f)
# We might as well already cache the positions
self._pos_cache[mol_id] = pdb_file.getPositions(asNumpy=True, frame=model_idx) / unit.angstrom
elif extension == '.smiles' or extension == '.csv':
# Extract the correct line and save it in a new file.
smiles_line = read_csv_lines(mol_descr['filepath'], lines=model_idx)
with open(single_file_path, 'w') as f:
f.write(smiles_line)
elif extension == '.mol2' or extension == '.sdf':
if not utils.is_openeye_installed(oetools=('oechem',)):
raise RuntimeError('Cannot support {} files selection without OpenEye'.format(
extension[1:]))
oe_molecule = utils.load_oe_molecules(mol_descr['filepath'], molecule_idx=model_idx)
if extension == '.mol2':
mol_names = list(utils.Mol2File(mol_descr['filepath']).resnames)
utils.write_oe_molecule(oe_molecule, single_file_path, mol2_resname=mol_names[model_idx])
else:
utils.write_oe_molecule(oe_molecule, single_file_path)
else:
raise RuntimeError('Model selection is not supported for {} files'.format(extension[1:]))
# Save new file path
mol_descr['filepath'] = single_file_path
# Strip off protons if required
if 'strip_protons' in mol_descr and mol_descr['strip_protons']:
if extension != '.pdb':
raise RuntimeError('Cannot strip protons from {} files.'.format(extension[1:]))
output_file_path = os.path.join(mol_dir, mol_id + '.pdb')
strip_protons(mol_descr['filepath'], output_file_path)
mol_descr['filepath'] = output_file_path
# Apply PDBFixer if requested
if 'pdbfixer' in mol_descr:
if extension not in ['.pdb', '.PDB']:
raise RuntimeError('Cannot apply PDBFixer to {} files; a .pdb file is required.'.format(extension[1:]))
output_file_path = os.path.join(mol_dir, mol_id + '.pdb')
apply_pdbfixer(mol_descr['filepath'], output_file_path, mol_descr['pdbfixer'])
mol_descr['filepath'] = output_file_path
# Apply modeller if requested
if 'modeller' in mol_descr:
if extension not in ['.pdb', '.PDB']:
raise RuntimeError('Cannot apply modeller to {} files; a .pdb file is required.'.format(extension[1:]))
output_file_path = os.path.join(mol_dir, mol_id + '.pdb')
apply_modeller(mol_descr['filepath'], output_file_path, mol_descr['modeller'])
mol_descr['filepath'] = output_file_path
# Generate missing molecules with OpenEye. At the end of parametrization
# we update the 'filepath' key also for OpenEye-generated molecules so
# we don't need to keep track of the molecules we have already generated
if extension is None or extension == '.smiles' or extension == '.csv':
if not utils.is_openeye_installed(oetools=('oechem', 'oeiupac', 'oequacpac', 'oeomega')):
if extension is None:
raise RuntimeError('Cannot generate molecule {} without OpenEye licensed with '
'OEChem, OEIUPAC, OEOmega, and OEQuacPack.'.format(mol_id))
else:
raise RuntimeError('Cannot support {} files without OpenEye licensed with '
'OEChem, OEIUPAC, OEOmega, and OEQuacPack.'.format(extension[1:]))
# Retrieve the first SMILES string (eventually extracted
# while handling of the 'select' keyword above)
if extension is not None:
# Get first record in CSV file.
first_line = read_csv_lines(mol_descr['filepath'], lines=0)
# Automatically detect if delimiter is comma or semicolon
for delimiter in ',;':
logger.debug("Attempt to parse smiles file with delimiter '{}'".format(delimiter))
line_fields = first_line.split(delimiter)
# If there is only one column, take that, otherwise take second
if len(line_fields) > 1:
smiles_str = line_fields[1].strip()
else:
smiles_str = line_fields[0].strip()
# try to generate the smiles and try new delimiter if it fails
mol_descr['smiles'] = smiles_str
try:
oe_molecule = self._generate_molecule(mol_id)
break
except (ValueError, RuntimeError):
oe_molecule = None
# Raise an error if no delimiter worked
if oe_molecule is None:
raise RuntimeError('Cannot detect SMILES file format.')
else:
# Generate molecule from mol_descr['smiles']
oe_molecule = self._generate_molecule(mol_id)
# Cache atom positions
self._pos_cache[mol_id] = utils.get_oe_mol_positions(oe_molecule)
# Write OpenEye generated molecules in mol2 files
# We update the 'filepath' key in the molecule description
mol_descr['filepath'] = os.path.join(mol_dir, mol_id + '.mol2')
# Generate a residue name for the SMILES molecule.
residue_name = self._generate_residue_name(mol_id)
moltools.openeye.molecule_to_mol2(oe_molecule, mol_descr['filepath'],
residue_name=residue_name)
# Enumerate protonation states with epik
if 'epik' in mol_descr:
epik_base_path = os.path.join(mol_dir, mol_id + '-epik.')
epik_mae_file = epik_base_path + 'mae'
epik_mol2_file = epik_base_path + 'mol2'
epik_sdf_file = epik_base_path + 'sdf'
# Run epik and convert from maestro to both mol2 and sdf
# to not lose neither the penalties nor the residue name
epik_kwargs = mol_descr['epik']
moltools.schrodinger.run_epik(mol_descr['filepath'], epik_mae_file, **epik_kwargs)
moltools.schrodinger.run_structconvert(epik_mae_file, epik_sdf_file)
moltools.schrodinger.run_structconvert(epik_mae_file, epik_mol2_file)
# Save new net charge from the i_epik_Tot_Q property
net_charge = int(moltools.schrodinger.run_proplister(epik_sdf_file)[0]['i_epik_Tot_Q'])
# Keep filepath consistent
mol_descr['filepath'] = epik_mol2_file
# Antechamber does not support sdf files so we need to convert them
extension = os.path.splitext(mol_descr['filepath'])[1]
if extension == '.sdf':
if not utils.is_openeye_installed(oetools=('oechem',)):
raise RuntimeError('Cannot support sdf files without OpenEye OEChem')
mol2_file_path = os.path.join(mol_dir, mol_id + '.mol2')
oe_molecule = utils.load_oe_molecules(mol_descr['filepath'], molecule_idx=0)
# Generate a residue name for the sdf molecule.
residue_name = self._generate_residue_name(mol_id)
moltools.openeye.molecule_to_mol2(oe_molecule, mol2_file_path,
residue_name=residue_name)
# Update filepath information
mol_descr['filepath'] = mol2_file_path
# Parametrize the molecule with antechamber
if 'antechamber' in mol_descr:
# Generate charges with OpenEye if requested
if 'openeye' in mol_descr:
if not utils.is_openeye_installed(oetools=('oechem', 'oequacpac', 'oeomega')):
err_msg = ('Cannot find OpenEye toolkit with OEChem and OEQuacPac to compute charges '
'for molecule {}').format(mol_id)
logger.error(err_msg)
raise RuntimeError(err_msg)
mol2_file_path = os.path.join(mol_dir, mol_id + '.mol2')
oe_molecule = utils.load_oe_molecules(mol_descr['filepath'], molecule_idx=0)
# Setting keep_confs = None keeps the original conformation
oe_molecule = moltools.openeye.get_charges(oe_molecule, keep_confs=None)
residue_name = utils.Mol2File(mol_descr['filepath']).resname
moltools.openeye.molecule_to_mol2(oe_molecule, mol2_file_path,
residue_name=residue_name)
utils.Mol2File(mol2_file_path).round_charge() # normalize charges
# We don't need Epik's or input net charge as antechamber will
# infer the net charge from the sum of the OpenEye charges.
net_charge = None
mol_descr['filepath'] = mol2_file_path
# Check if use specified a net_charge, but don't overwrite Epik's protonation state.
elif net_charge is not None:
net_charge = mol_descr['antechamber'].get('net_charge', None)
# Generate parameters
charge_method = mol_descr['antechamber']['charge_method']
input_mol_path = os.path.abspath(mol_descr['filepath'])
# Use Gaff in parameters, otherwise default to gaff2
gaff = 'gaff2' if 'leaprc.gaff2' in mol_descr['leap']['parameters'] else 'gaff'
with moltools.utils.temporary_cd(mol_dir):
moltools.amber.run_antechamber(mol_id, input_mol_path,
charge_method=charge_method,
net_charge=net_charge,
gaff_version=gaff)
# Save new parameters paths
mol_descr['filepath'] = os.path.join(mol_dir, mol_id + '.gaff.mol2')
mol_descr['leap']['parameters'].append(os.path.join(mol_dir, mol_id + '.frcmod'))
# Normalize charges if not done before
if 'openeye' not in mol_descr:
utils.Mol2File(mol_descr['filepath']).round_charge()
# Determine small molecule net charge
extension = os.path.splitext(mol_descr['filepath'])[1]
if extension == '.mol2':
# TODO what if this is a peptide? this should be computed in get_system()
mol_descr['net_charge'] = utils.Mol2File(mol_descr['filepath']).net_charge
# Keep track of processed molecule
self._processed_mols.add(mol_id)
def _setup_system(self, system_file_path, pack, alchemical_charge,
system_parameters, solvent_id, *molecule_ids, **kwargs):
"""Setup a system and create its prmtop/inpcrd files.
IMPORTANT: This function does not check if it's about to overwrite
files. Use get_system() for safe setup.
Parameters
----------
system_file_path : str
The path to either the prmtop or inpcrd output file. The other one
will be saved in the same folder with the same base name.
pack : bool
True to automatically solve atom clashes and reduce box dimension.
alchemical_charge : int
Number of counterions to alchemically modify during the simulation.
system_parameters : list of str
Contain the parameters file that must be loaded in tleap for the
system in addition to the molecule-specific ones.
solvent_id : str
The ID of the solvent.
ignore_ionic_strength : bool, optional
If True, no ions will be added to reach the ionic strength (default
is False).
save_amber_files : bool, optional
If False, prmtop and inpcrd files are not saved (default is True).
Other Parameters
----------------
*molecule_ids : list-like of str
List the IDs of the molecules to pack together in the system.
"""
# Get kwargs
ignore_ionic_strength = kwargs.pop('ignore_ionic_strength', False)
save_amber_files = kwargs.pop('save_amber_files', True)
assert len(kwargs) == 0
# Make sure molecules are set up
self._setup_molecules(*molecule_ids)
solvent = self.solvents[solvent_id]
# Start error tracking variables
# Water
known_solvent_files = [file for file in _OPENMM_LEAP_SOLVENT_FILES_MAP.values()]
loaded_water_files = [] # Detected loaded water files
def extend_list_of_waters(leap_parameters):
"""Extend the loaded_water_files list given the leap_parameters"""
loaded_water_files.extend([water for water
in leap_parameters
if water in known_solvent_files])
# Create tleap script
tleap = utils.TLeap()
# Load all parameters
# --------------------
tleap.new_section('Load parameters')
for mol_id in molecule_ids:
molecule_parameters = self.molecules[mol_id]['leap']['parameters']
# Track loaded water models
extend_list_of_waters(molecule_parameters)
tleap.load_parameters(*molecule_parameters)
extend_list_of_waters(system_parameters)
tleap.load_parameters(*system_parameters)
solvent_leap = solvent['leap']['parameters']
extend_list_of_waters(solvent_leap)
tleap.load_parameters(*solvent_leap)
# Load molecules and create complexes
# ------------------------------------
tleap.new_section('Load molecules')
for mol_id in molecule_ids:
tleap.load_unit(unit_name=mol_id, file_path=self.molecules[mol_id]['filepath'])
if len(molecule_ids) > 1:
# Check that molecules don't have clashing atoms. Also, if the ligand
# is too far away from the molecule we want to pull it closer
# TODO this check should be available even without OpenEye
if pack and utils.is_openeye_installed(oetools=('oechem',)):
# Load atom positions of all molecules
positions = [0 for _ in molecule_ids]
for i, mol_id in enumerate(molecule_ids):
if mol_id not in self._pos_cache:
self._pos_cache[mol_id] = utils.get_oe_mol_positions(
utils.load_oe_molecules(self.molecules[mol_id]['filepath'], molecule_idx=0))
positions[i] = self._pos_cache[mol_id]
# Find and apply the transformation to fix clashing
# TODO this doesn't work with more than 2 molecule_ids
try:
max_dist = solvent['clearance'].value_in_unit(unit.angstrom) / 1.5
except KeyError:
max_dist = 10.0
transformation = pack_transformation(positions[0], positions[1],
self.CLASH_THRESHOLD, max_dist)
if (transformation != np.identity(4)).any():
logger.warning('Changing starting positions for {}.'.format(molecule_ids[1]))
tleap.new_section('Fix clashing atoms')
tleap.transform(molecule_ids[1], transformation)
# Create complex
tleap.new_section('Create complex')
tleap.combine('complex', *molecule_ids)
unit_to_solvate = 'complex'
else:
unit_to_solvate = molecule_ids[0]
# Configure solvent
# ------------------
if solvent['nonbonded_method'] == openmm.app.NoCutoff:
try:
implicit_solvent = solvent['implicit_solvent']
except KeyError: # vacuum
pass
else: # implicit solvent
tleap.new_section('Set GB radii to recommended values for OBC')
tleap.add_commands('set default PBRadii {}'.format(
get_leap_recommended_pbradii(implicit_solvent)))
else: # explicit solvent
tleap.new_section('Solvate systems')
# Solvate unit. Solvent models different than tip3p need parameter modifications.
solvent_model = solvent['solvent_model']
# Check that solvent model has loaded the appropriate leap parameters.
# This does guarantee a failure, but is a good sign of it.
if _OPENMM_LEAP_SOLVENT_FILES_MAP[solvent_model] not in loaded_water_files:
solvent_warning = ("WARNING: The solvent_model {} may not work for loaded "
"leaprc.water.X files.\n We expected {} to make your "
"solvent model work, but did not find it.\n "
"This is okay for tip4pew leaprc file with tip3p solvent_model, "
"but not the other way around.\nThis does "
"not mean the system will not build, but it may throw "
"an error.".format(solvent_model,
_OPENMM_LEAP_SOLVENT_FILES_MAP[solvent_model]))
logger.warning(solvent_warning)
leap_solvent_model = _OPENMM_LEAP_SOLVENT_MODELS_MAP[solvent_model]
clearance = float(solvent['clearance'].value_in_unit(unit.angstroms))
tleap.solvate(unit_name=unit_to_solvate, solvent_model=leap_solvent_model, clearance=clearance)
# First, determine how many ions we need to add for the ionic strength.
if not ignore_ionic_strength and solvent['ionic_strength'] != 0.0*unit.molar:
# Currently we support only monovalent ions.
for ion_name in [solvent['positive_ion'], solvent['negative_ion']]:
assert '2' not in ion_name and '3' not in ion_name
logger.debug('Estimating number of water molecules in the box.')
n_waters = self._get_number_box_waters(pack, alchemical_charge, system_parameters,
solvent_id, *molecule_ids)
logger.debug('Estimated number of water molecules: {}'.format(n_waters))
# Water molarity at room temperature: 998.23g/L / 18.01528g/mol ~= 55.41M
n_ions_ionic_strength = int(np.round(n_waters * solvent['ionic_strength'] / (55.41*unit.molar)))
logging.debug('Adding {} ions in {} water molecules to reach ionic strength '
'of {}'.format(n_ions_ionic_strength, n_waters, solvent['ionic_strength']))
else:
n_ions_ionic_strength = 0
# Add alchemically modified ions that we don't already add for ionic strength.
if abs(alchemical_charge) > n_ions_ionic_strength:
n_alchemical_ions = abs(alchemical_charge) - n_ions_ionic_strength
try:
if alchemical_charge > 0:
ion = solvent['negative_ion']
else:
ion = solvent['positive_ion']
except KeyError:
err_msg = ('Found charged ligand but no indications for ions in '
'solvent {}').format(solvent_id)
logger.error(err_msg)
raise RuntimeError(err_msg)
tleap.add_ions(unit_name=unit_to_solvate, ion=ion,
num_ions=n_alchemical_ions, replace_solvent=True)
logging.debug('Adding {} {} ion to neutralize ligand charge of {}'
''.format(n_alchemical_ions, ion, alchemical_charge))
# Neutralizing solvation box
if 'positive_ion' in solvent:
tleap.add_ions(unit_name=unit_to_solvate, ion=solvent['positive_ion'],
replace_solvent=True)
if 'negative_ion' in solvent:
tleap.add_ions(unit_name=unit_to_solvate, ion=solvent['negative_ion'],
replace_solvent=True)
# Ions for the ionic strength must be added AFTER neutralization.
if n_ions_ionic_strength != 0:
tleap.add_ions(unit_name=unit_to_solvate, ion=solvent['positive_ion'],
num_ions=n_ions_ionic_strength, replace_solvent=True)
tleap.add_ions(unit_name=unit_to_solvate, ion=solvent['negative_ion'],
num_ions=n_ions_ionic_strength, replace_solvent=True)
# Check charge
tleap.new_section('Check charge')
tleap.add_commands('check ' + unit_to_solvate)
# Save output files
# ------------------
system_dir = os.path.dirname(system_file_path)
base_file_path = os.path.basename(system_file_path).split('.')[0]
base_file_path = os.path.join(system_dir, base_file_path)
# Create output directory
if not os.path.exists(system_dir):
os.makedirs(system_dir)
# Save prmtop, inpcrd and reference pdb files
tleap.new_section('Save prmtop and inpcrd files')
if save_amber_files:
tleap.save_unit(unit_to_solvate, system_file_path)
tleap.save_unit(unit_to_solvate, base_file_path + '.pdb')
# Save tleap script for reference
tleap.export_script(base_file_path + '.leap.in')
# Run tleap and log warnings
# Handle common errors we know of
try:
warnings = tleap.run()
except RuntimeError as e:
error = RuntimeError('Solvent {}: {}'.format(solvent_id, str(e)))
error.with_traceback(sys.exc_info()[2])
raise error
for warning in warnings:
logger.warning('TLeap: ' + warning)
def _get_number_box_waters(self, *args):
"""Build a system in a temporary directory and count the number of waters."""
with mmtools.utils.temporary_directory() as tmp_dir:
system_file_path = os.path.join(tmp_dir, 'temp_system.prmtop')
self._setup_system(system_file_path, *args, ignore_ionic_strength=True,
save_amber_files=False)
# Count number of waters of created system.
system_file_path = os.path.join(tmp_dir, 'temp_system.pdb')
system_traj = mdtraj.load(system_file_path)
n_waters = sum([1 for res in system_traj.topology.residues if res.is_water])
return n_waters
# ==============================================================================
# FUNCTIONS FOR ALCHEMICAL PATH OPTIMIZATION
# ==============================================================================
[docs]def trailblaze_alchemical_protocol(thermodynamic_state, sampler_state, mcmc_move, state_parameters,
std_energy_threshold=0.5, threshold_tolerance=0.05,
n_samples_per_state=100):
"""
Find an alchemical path by placing alchemical states at a fixed distance.
The distance between two states is estimated by collecting ``n_samples_per_state``
configurations through the MCMCMove in one of the two alchemical states,
and computing the standard deviation of the difference of potential energies
between the two states at those configurations.
Two states are chosen for the protocol if their standard deviation is
within ``std_energy_threshold +- threshold_tolerance``.
Parameters
----------
thermodynamic_state : openmmtools.states.CompoundThermodynamicState
The state of the alchemically modified system.
sampler_state : openmmtools.states.SamplerState
The sampler states including initial positions and box vectors.
mcmc_move : openmmtools.mcmc.MCMCMove
The MCMCMove to use for propagation.
state_parameters : list of tuples (str, [float, float])
Each element of this list is a tuple containing first the name
of the parameter to be modified (e.g. ``lambda_electrostatics``,
``lambda_sterics``) and a list specifying the initial and final
values for the path.
std_energy_threshold : float
The threshold that determines how to separate the states between
each others.
threshold_tolerance : float
The tolerance on the found standard deviation.
n_samples_per_state : int
How many samples to collect to estimate the overlap between two
states.
Returns
-------
optimal_protocol : dict {str, list of floats}
The estimated protocol. Each dictionary key is one of the
parameters in ``state_parameters``, and its values is the
list of values that it takes in each state of the path.
"""
# Make sure that the state parameters to optimize have a clear order.
assert(isinstance(state_parameters, list) or isinstance(state_parameters, tuple))
# Make sure that thermodynamic_state is in correct state
# and initialize protocol with starting value.
optimal_protocol = {}
for parameter, values in state_parameters:
setattr(thermodynamic_state, parameter, values[0])
optimal_protocol[parameter] = [values[0]]
# We change only one parameter at a time.
for state_parameter, values in state_parameters:
logger.debug('Determining alchemical path for parameter {}'.format(state_parameter))
# Is this a search from 0 to 1 or from 1 to 0?
search_direction = np.sign(values[1] - values[0])
# If the parameter doesn't change, continue to the next one.
if search_direction == 0:
continue
# Gather data until we get to the last value.
while optimal_protocol[state_parameter][-1] != values[-1]:
# Simulate current thermodynamic state to obtain energies.
sampler_states = []
simulated_energies = np.zeros(n_samples_per_state)
for i in range(n_samples_per_state):
mcmc_move.apply(thermodynamic_state, sampler_state)
context, _ = mmtools.cache.global_context_cache.get_context(thermodynamic_state)
sampler_state.apply_to_context(context, ignore_velocities=True)
simulated_energies[i] = thermodynamic_state.reduced_potential(context)
sampler_states.append(copy.deepcopy(sampler_state))
# Find first state that doesn't overlap with simulated one
# with std(du) within std_energy_threshold +- threshold_tolerance.
# We stop anyway if we reach the last value of the protocol.
std_energy = 0.0
current_parameter_value = optimal_protocol[state_parameter][-1]
while (abs(std_energy - std_energy_threshold) > threshold_tolerance and
not (current_parameter_value == values[1] and std_energy < std_energy_threshold)):
# Determine next parameter value to compute.
if np.isclose(std_energy, 0.0):
# This is the first iteration or the two state overlap significantly
# (e.g. small molecule in vacuum). Just advance by a +- 0.05 step.
old_parameter_value = current_parameter_value
current_parameter_value += (values[1] - values[0]) / 20.0
else:
# Assume std_energy(parameter_value) is linear to determine next value to try.
derivative_std_energy = ((std_energy - old_std_energy) /
(current_parameter_value - old_parameter_value))
old_parameter_value = current_parameter_value
current_parameter_value += (std_energy_threshold - std_energy) / derivative_std_energy
# Keep current_parameter_value inside bound interval.
if search_direction * current_parameter_value > values[1]:
current_parameter_value = values[1]
assert search_direction * (optimal_protocol[state_parameter][-1] - current_parameter_value) < 0
# Get context in new thermodynamic state.
setattr(thermodynamic_state, state_parameter, current_parameter_value)
context, integrator = mmtools.cache.global_context_cache.get_context(thermodynamic_state)
# Compute the energies at the sampled positions.
reweighted_energies = np.zeros(n_samples_per_state)
for i, sampler_state in enumerate(sampler_states):
sampler_state.apply_to_context(context, ignore_velocities=True)
reweighted_energies[i] = thermodynamic_state.reduced_potential(context)
# Compute standard deviation of the difference.
old_std_energy = std_energy
denergies = reweighted_energies - simulated_energies
std_energy = np.std(denergies)
logger.debug('trailblazing: state_parameter {}, simulated_value {}, current_parameter_value {}, '
'std_du {}'.format(state_parameter, optimal_protocol[state_parameter][-1],
current_parameter_value, std_energy))
# Update the optimal protocol with the new value of this parameter.
# The other parameters remain fixed.
for par_name in optimal_protocol:
# Make sure we append to a Python float to the list.
# Lists of numpy types sometimes give problems.
if par_name == state_parameter:
protocol_value = float(current_parameter_value)
else:
protocol_value = float(optimal_protocol[par_name][-1])
optimal_protocol[par_name].append(protocol_value)
logger.debug('Alchemical path found: {}'.format(optimal_protocol))
return optimal_protocol
if __name__ == '__main__':
import doctest
doctest.testmod()