Source code for moldesign.interfaces.pdbfixer_interface

# Copyright 2016 Autodesk Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

import imp

import numpy as np

import moldesign as mdt
from moldesign import units as u
from moldesign import compute

from . import openmm as opm

except (ImportError, OSError) as exc:
    print 'PDBFixer could not be imported; using remote docker container'
    force_remote = True
    force_remote = False

[docs]def add_hydrogen(mol, pH=7.4): fixer = _get_fixer(mol) fixer.addMissingHydrogens(pH) return _get_mol(fixer)
[docs]def mutate(mol, mutationmap): fixer = _get_fixer(mol) chain_mutations = {} for res in mutationmap: chain_mutations.setdefault(res.chain.pdbname, {})[res] = mutationmap[res] for chainid, mutations in chain_mutations.iteritems(): mutstrings = ['%s-%d-%s' % (res.resname, res.pdbindex, newname) for res,newname in mutations.iteritems()] print 'Applying mutations to chain %s: %s' % (chainid, ', '.join(mutstrings)) fixer.applyMutations(mutations, chainid) return _get_mol(fixer)
[docs]def add_water(mol, min_box_size=None, padding=None, ion_concentration=None, neutralize=True, positive_ion='Na+', negative_ion='Cl-'): """ Solvate a molecule in a water box with optional ions Args: mol (moldesign.Molecule): solute molecule min_box_size (u.Scalar[length] or u.Vector[length]): size of the water box - either a vector of x,y,z dimensions, or just a uniform cube length. Either this or ``padding`` (or both) must be passed padding (u.Scalar[length]): distance to edge of water box from the solute in each dimension neutralize (bool): add ions to neutralize solute charge (in addition to specified ion concentration) positive_ion (str): type of positive ions to add, if needed. Allowed values (from OpenMM modeller) are Cs, K, Li, Na (the default) and Rb negative_ion (str): type of negative ions to add, if needed. Allowed values (from OpenMM modeller) are Cl (the default), Br, F, and I ion_concentration (float or u.Scalar[molarity]): ionic concentration in addition to whatever is needed to neutralize the solute. (if float is passed, we assume the number is Molar) Returns: moldesign.Molecule: new Molecule object containing both solvent and solute """ import pdbfixer if padding is None and min_box_size is None: raise ValueError('Solvate arguments: must pass padding or min_box_size or both.') # add +s and -s to ion names if not already present if positive_ion[-1] != '+': assert positive_ion[-1] != '-' positive_ion += '+' if negative_ion[-1] != '-': assert negative_ion[-1] != '+' negative_ion += '-' if ion_concentration is not None: ion_concentration = u.MdtQuantity(ion_concentration) if ion_concentration.dimensionless: ion_concentration *= u.molar # calculate box size - in each dimension, use the largest of min_box_size or # the calculated padding boxsize = np.zeros(3) * u.angstrom if min_box_size: boxsize[:] = min_box_size if padding: ranges = mol.positions.max(axis=0) - mol.positions.min(axis=0) for idim, r in enumerate(ranges): boxsize[idim] = max(boxsize[idim], r+padding) assert (boxsize >= 0.0).all() modeller = opm.mol_to_modeller(mol) # TODO: this is like 10 bad things at once. Should probably submit a # PR to PDBFixer to make this a public staticmethod instead of a private instancemethod # Alternatively, PR to create Fixers directly from Topology objs ff = pdbfixer.PDBFixer.__dict__['_createForceField'](None, modeller.getTopology(), True) modeller.addSolvent(ff, boxSize=opm.pint2simtk(boxsize), positiveIon=positive_ion, negativeIon=negative_ion, ionicStrength=opm.pint2simtk(ion_concentration), neutralize=neutralize) return opm.topology_to_mol(modeller.getTopology(), positions=modeller.getPositions(), name='%s with water box' %
def _get_fixer(mol): import pdbfixer mol.write('/tmp/tmp.pdb', format='pdb') fixer = pdbfixer.PDBFixer('/tmp/tmp.pdb') return fixer def _get_mol(f): return opm.topology_to_mol(f.topology, positions=f.positions)