def main(argv):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <receptor>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-1>
for constraint in oedocking.OEReceptorGetProteinConstraints(receptor):
print("Atom %i has a constraint" % constraint.GetAtom().GetIdx())
# @ </SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-1>
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-2>
for constraint in oedocking.OEReceptorGetProteinConstraints(receptor):
print("Protein constraint on atom %d" % constraint.GetAtom().GetIdx())
print(" Type : %s" % oedocking.OEProteinConstraintTypeGetName(constraint.GetType()))
print(" Name : %s" % constraint.GetName())
# @ </SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-2>
for heavyAtom in receptor.GetAtoms(oechem.OENotAtom(oechem.OEIsHydrogen())):
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-3>
proteinConstraint = oedocking.OEProteinConstraint()
proteinConstraint.SetAtom(heavyAtom)
proteinConstraint.SetType(oedocking.OEProteinConstraintType_Contact)
proteinConstraint.SetName("Example constraint")
oedocking.OEReceptorSetProteinConstraint(receptor, proteinConstraint)
# @ </SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-3>
break
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-4>
oedocking.OEReceptorClearProteinConstraints(receptor)
def GetFragmentScore(mol):
score = 0.0
score += 2.0 * oechem.OECount(mol, oechem.OEAtomIsInRing())
score += 1.0 * oechem.OECount(mol, oechem.OENotAtom(oechem.OEAtomIsInRing()))
return score
def AddRelevantRingAtoms(mol, torsion, torsionSet):
atom1or2 = oechem.OEOrAtom(oechem.OEHasMapIdx(1),
oechem.OEHasMapIdx(2))
ringNbrs = []
for atom in mol.GetAtoms(
oechem.OEAndAtom(oechem.OEAtomIsInRing(), atom1or2)):
for nbr in atom.GetAtoms(
oechem.OEAndAtom(oechem.OENotAtom(atom1or2),
oechem.OENotAtom(
oechem.OEAtomIsInRing()))):
if nbr.IsHydrogen():
ringNbrs.append(nbr)
continue
if nbr.IsOxygen() and mol.GetBond(atom, nbr).GetOrder() == 2:
ringNbrs.append(nbr)
continue
if TorsionGenerator.IsOrtho(nbr, torsion):
ringNbrs.append(nbr)
for nbr in ringNbrs:
if not torsionSet.HasAtom(nbr):
nbr.SetMapIdx(2)
torsionSet.AddAtom(nbr)
def has_undesirable_elements(mol):
'''
returns True if molecule contains any element other than
H, C, N, O, F, S, Cl, or P
@param mol:
@type mol: OEGraphMol
@return: bool
'''
atomsHC = oechem.OEOrAtom(oechem.OEIsHydrogen(), oechem.OEIsCarbon())
atomsNO = oechem.OEOrAtom(oechem.OEIsNitrogen(), oechem.OEIsOxygen())
atomsFS = oechem.OEOrAtom(oechem.OEHasAtomicNum(9), oechem.OEIsSulfur())
atomsHCNO = oechem.OEOrAtom(atomsHC, atomsNO)
atomsHCNOFS = oechem.OEOrAtom(atomsHCNO, atomsFS)
atomsHCNOFSCl = oechem.OEOrAtom(atomsHCNOFS, oechem.OEHasAtomicNum(17))
atomsHCNOFSClP = oechem.OEOrAtom(atomsHCNOFSCl, oechem.OEIsPhosphorus())
undesirable_atom = mol.GetAtom(oechem.OENotAtom(atomsHCNOFSClP))
if undesirable_atom is not None:
return True
return False
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cnc(O)cc1CCCBr")
print("Number of chain atoms =", end=" ")
print(oechem.OECount(mol, oechem.OENotAtom(oechem.OEAtomIsInRing())))
print("Number of aromatic nitrogens =", end=" ")
print(
oechem.OECount(
mol, oechem.OEAndAtom(oechem.OEIsNitrogen(),
oechem.OEIsAromaticAtom())))
print("Number of non-carbons =", end=" ")
print(
oechem.OECount(mol,
oechem.OENotAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_C))))
print("Number of nitrogen and oxygen atoms =", end=" ")
print(
oechem.OECount(
def _oe_render_fragment(
parent: Molecule,
fragment: Molecule,
bond_indices: BondTuple,
image_width: int = 283,
image_height: int = 169,
) -> str:
from openeye import oechem, oedepict
# Map the OpenFF molecules into OE ones, making sure to explicitly set the atom
# map on the OE object as this is not handled by the OpenFF toolkit.
oe_parent = parent.to_openeye()
for atom in oe_parent.GetAtoms():
atom.SetMapIdx(get_map_index(parent, atom.GetIdx(), False))
oedepict.OEPrepareDepiction(oe_parent)
oe_fragment = fragment.to_openeye()
for atom in oe_fragment.GetAtoms():
atom.SetMapIdx(get_map_index(fragment, atom.GetIdx(), False))
oe_parent_bond = oe_parent.GetBond(
oe_parent.GetAtom(oechem.OEHasMapIdx(bond_indices[0])),
oe_parent.GetAtom(oechem.OEHasMapIdx(bond_indices[1])),
)
# Set-up common display options.
image = oedepict.OEImage(image_width, image_height)
display_options = oedepict.OE2DMolDisplayOptions(
image_width, image_height, oedepict.OEScale_AutoScale)
display_options.SetTitleLocation(oedepict.OETitleLocation_Hidden)
display_options.SetAtomColorStyle(
oedepict.OEAtomColorStyle_WhiteMonochrome)
display_options.SetAtomLabelFontScale(1.2)
# display_options.SetBondPropertyFunctor(_oe_wbo_label_display({bond_indices}))
display = oedepict.OE2DMolDisplay(oe_parent, display_options)
fragment_atom_predicate, fragment_bond_predicate = _oe_fragment_predicates(
{atom.GetMapIdx()
for atom in oe_fragment.GetAtoms()})
not_fragment_atoms = oechem.OENotAtom(fragment_atom_predicate)
not_fragment_bonds = oechem.OENotBond(fragment_bond_predicate)
oedepict.OEAddHighlighting(
display,
oedepict.OEHighlightByColor(oechem.OEGrey, 0.75),
not_fragment_atoms,
not_fragment_bonds,
)
rotatable_bond = oechem.OEAtomBondSet()
rotatable_bond.AddBond(oe_parent_bond)
rotatable_bond.AddAtom(oe_parent_bond.GetBgn())
rotatable_bond.AddAtom(oe_parent_bond.GetEnd())
oedepict.OEAddHighlighting(
display,
oechem.OEColor(oechem.OELimeGreen),
oedepict.OEHighlightStyle_BallAndStick,
rotatable_bond,
)
oedepict.OERenderMolecule(image, display)
svg_contents = oedepict.OEWriteImageToString("svg", image)
return svg_contents.decode()
def DepictMoleculeWithFragmentCombinations(report, mol, frags, opts): #fragcombs, opts):
""" This function was taken from https://docs.eyesopen.com/toolkits/cookbook/python/depiction/enumfrags.html with some modification
"""
stag = "fragment idx"
itag = oechem.OEGetTag(stag)
for fidx, frag in enumerate(frags):
for bond in frags[frag].GetBonds():
bond.SetData(itag, fidx)
# setup depiction styles
nrfrags = len(frags)
colors = [c for c in oechem.OEGetLightColors()]
if len(colors) < nrfrags:
colors = [c for c in oechem.OEGetColors(oechem.OEYellowTint, oechem.OEDarkOrange, nrfrags)]
bondglyph = ColorBondByFragmentIndex(colors, itag)
lineWidthScale = 0.75
fadehighlight = oedepict.OEHighlightByColor(oechem.OEGrey, lineWidthScale)
# depict each fragment combinations
for frag in frags:
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, opts)
fragatoms = oechem.OEIsAtomMember(frags[frag].GetAtoms())
fragbonds = oechem.OEIsBondMember(frags[frag].GetBonds())
notfragatoms = oechem.OENotAtom(fragatoms)
notfragbonds = oechem.OENotBond(fragbonds)
oedepict.OEAddHighlighting(disp, fadehighlight, notfragatoms, notfragbonds)
bond = mol.GetBond(oechem.OEHasBondIdx(frag))
atomBondSet = oechem.OEAtomBondSet()
atomBondSet.AddBond(bond)
atomBondSet.AddAtom(bond.GetBgn())
atomBondSet.AddAtom(bond.GetEnd())
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet)
#oegrapheme.OEAddGlyph(disp, bondglyph, fragbonds)
oedepict.OERenderMolecule(cell, disp)
# depict original fragmentation in each header
cellwidth, cellheight = report.GetHeaderWidth(), report.GetHeaderHeight()
opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
bondlabel = LabelBondOrder()
opts.SetBondPropertyFunctor(bondlabel)
disp = oedepict.OE2DMolDisplay(mol, opts)
#oegrapheme.OEAddGlyph(disp, bondglyph, oechem.IsTrueBond())
headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_Off, 2.0)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, headerpen)
def process(self, record, port):
try:
opt = dict(self.opt)
if not record.has_value(Fields.md_components):
raise ValueError("Missing the MD Components Field")
md_components = record.get_value(Fields.md_components)
solute, map_comp = md_components.create_flask
if not record.has_value(Fields.title):
self.log.warn("Missing Title field")
solute_title = solute.GetTitle()[0:12]
else:
solute_title = record.get_value(Fields.title)
self.log.info("[{}] solvating flask {}".format(
self.title, solute_title))
# Update cube simulation parameters
for field in record.get_fields(include_meta=True):
field_name = field.get_name()
if field_name in ['molar_fractions', 'density', 'solvents']:
rec_value = record.get_value(field)
if field_name == 'molar_fractions':
opt[field_name] = str(rec_value)
else:
opt[field_name] = rec_value
opt['Logger'].info(
"{} Updating parameters for molecule: {} {} = {}".
format(self.title, solute.GetTitle(), field_name,
rec_value))
# Set the flag to return the solvent molecule components
opt['return_components'] = True
# Solvate the system
sol_system, solvent, salt, counter_ions = packmol.oesolvate(
solute, **opt)
# Separate the Water from the solvent
pred_water = oechem.OEIsWater(checkHydrogens=True)
water = oechem.OEMol()
oechem.OESubsetMol(water, solvent, pred_water)
if water.NumAtoms():
if md_components.has_water:
water_comp = md_components.get_water
if not oechem.OEAddMols(water_comp, water):
raise ValueError(
"Cannot add the MD Component Water and the Packmol Water"
)
md_components.set_water(water_comp)
else:
md_components.set_water(water)
pred_not_water = oechem.OENotAtom(
oechem.OEIsWater(checkHydrogens=True))
solvent_not_water = oechem.OEMol()
oechem.OESubsetMol(solvent_not_water, solvent, pred_not_water)
if solvent_not_water.NumAtoms():
solvent = solvent_not_water
else:
solvent = oechem.OEMol()
self.log.info(
"[{}] Solvated simulation flask {} yielding {} atoms overall".
format(self.title, solute_title, sol_system.NumAtoms()))
sol_system.SetTitle(solute.GetTitle())
if salt is not None and counter_ions is not None:
if not oechem.OEAddMols(counter_ions, salt):
raise ValueError(
"Cannot add the salt component and the counter ion component"
)
elif salt is not None:
counter_ions = salt
else:
pass
if md_components.has_solvent:
solvent_comp = md_components.get_solvent
if not oechem.OEAddMols(solvent_comp, solvent):
raise ValueError(
"Cannot add the MD Component solvent and the Packmol Solvent"
)
else:
solvent_comp = solvent
if solvent_comp.NumAtoms():
md_components.set_solvent(solvent_comp)
if counter_ions is not None:
if md_components.has_counter_ions:
counter_ions_comp = md_components.get_counter_ions
if not oechem.OEAddMols(counter_ions_comp, counter_ions):
raise ValueError(
"Cannot add the MD Component counter ions and the Packmol counter ions"
)
else:
counter_ions_comp = counter_ions
md_components.set_counter_ions(counter_ions_comp)
# Set Box Vectors
vec_data = pack_utils.getData(sol_system, tag='box_vectors')
box_vec = pack_utils.decodePyObj(vec_data)
md_components.set_box_vectors(box_vec)
flask, map_comp = md_components.create_flask
record.set_value(Fields.md_components, md_components)
record.set_value(Fields.flask, flask)
record.set_value(Fields.title, solute_title)
self.success.emit(record)
except Exception as e:
print("Failed to complete", str(e), flush=True)
self.opt['Logger'].info('Exception {} {}'.format(
str(e), self.title))
self.log.error(traceback.format_exc())
self.failure.emit(record)
return