def show_docked(df):
oechem = import_("openeye.oechem")
if not oechem.OEChemIsLicensed(): raise(ImportError("Need License for OEChem!"))
# def show_docked(df):
mol2_blocks_docked = list(df['mol2_blocks_docked'])
smiles_template = list(df['smiles'])
names = list(df['names'])
v = PyMol.MolViewer()
v.DeleteAll()
for count,molblock in enumerate(mol2_blocks_docked):
molout = mol2_string_IO_san(molblock)
mol = Chem.MolFromPDBBlock(molout)
template = Chem.MolFromSmiles(smiles_template[count])
new_mol = AllChem.AssignBondOrdersFromTemplate(template, mol)
# mol2_blocks_template = Chem.MolFromMol2Block(molblock)
print(type(new_mol))
molid = names[count]
print(molid)
mol.SetProp('_Name', molid)
probe = Chem.Mol(new_mol.ToBinary())
v.ShowMol(probe, name=molid, showOnly=False)
def mols_to_pymol(df):
v = PyMol.MolViewer()
v.DeleteAll()
mols = [Chem.MolFromMol2Block(m, removeHs=False) for m in df['mol_block_am1bcc']]
names = list(df['names'])
for count,m in enumerate(mols):
molid = names[count]
m.SetProp('_Name', molid)
probe = Chem.Mol(m.ToBinary())
v.ShowMol(probe, name=molid, showOnly=False)
def mols_to_pymol(mols, names):
v = PyMol.MolViewer()
v.DeleteAll()
mols_3d = [dm.conformers.generate(m, n_confs=1) for m in mols]
# names = list(df['names'])
for count,m in enumerate(mols_3d):
molid = names[count]
m.SetProp('_Name', molid)
probe = Chem.Mol(m.ToBinary())
v.ShowMol(probe, name=molid, showOnly=False)
def main():
smiles = [EPINEPHRINE, CLONIPIDINE]
mols = [Chem.MolFromSmiles(m) for m in smiles]
mols = [Chem.AddHs(m) for m in mols]
i = 0
for m in mols:
print(m)
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m, maxIters=200)
Chem.MolToMolFile(m, '{0}.mol'.format(i))
Draw.MolToFile(m, 'm{0}.png'.format(i))
i += 1
refMol1 = AllChem.MMFFGetMoleculeProperties(mols[0])
refMol2 = AllChem.MMFFGetMoleculeProperties(mols[1])
# somehow this shit is the key
pyO3A = AllChem.GetO3A(mols[0], mols[1], refMol1, refMol2)
print('align')
print(pyO3A.Align())
print(pyO3A.Matches())
Chem.MolToMolFile(mols[0], '0_.mol')
Chem.MolToMolFile(mols[1], '1_.mol')
ff = AllChem.UFFGetMoleculeForceField(mols[0])
ff.Initialize()
ff.Minimize(maxIts=200)
rmsd = ChemAlign.AlignMol(mols[0], mols[1], atomMap=pyO3A.Matches())
print('rmsd')
print(rmsd)
print('energy')
print(ff.CalcEnergy())
# launch pymol in server mode: `./pymol -R`
# it resides in ~/anaconda/bin
v = PyMol.MolViewer()
v.ShowMol(mols[0])
v.GetPNG(h=200)
def show_axes(mol, confId, mol_coms, conf_axes):
"""
Show the principal moments of inertia on a single conformation.
"""
# show the principle axes on one conformer
try:
v = PyMol.MolViewer()
except ConnectionRefusedError:
print("run 'pymol -R' to visualise structures")
print('visualisation will be skipped')
v.server.do('reinitialize')
v.server.do('delete all')
# v.DeleteAll()
v.ShowMol(mol, confId=confId, name='Conf-0', showOnly=False)
# com
v.server.sphere(
list([float(i) for i in mol_coms[confId]]),
0.2,
(2, 1, 0),
'COM'
)
# principal axes
v.server.sphere(
list([float(i) for i in conf_axes[confId][0, :]]),
0.2,
(2, 0, 0),
'AX1'
)
v.server.sphere(
list([float(i) for i in conf_axes[confId][1, :]]),
0.2,
(1, 0, 1),
'AX2'
)
v.server.sphere(
list([float(i) for i in conf_axes[confId][2, :]]),
0.2,
(0, 1, 0),
'AX3'
)
v.GetPNG()
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolAlign
from rdkit.Chem import rdShapeHelpers
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import PyMol
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
import pyarrow as pa
from pyarrow import csv
import pandas as pd
import pyarrow.feather as feather
import copy
from rich import print
import numpy as np
import pandas as pd
v = PyMol.MolViewer()
mols_ref = Chem.SDMolSupplier(
'/Users/tom/code_test_repository/arrow_testing/cdk2.sdf', removeHs=False)
cdk2mol_ref = [m for m in mols_ref]
cdk2mol_reference = cdk2mol_ref[0]
cdk2mol_reference
df = feather.read_feather(
'/Users/tom/code_test_repository/arrow_testing/test2.feather')
df = df.sort_values(by=['fps'], ascending=False)
df = df.reset_index(drop=True)
df[['name', 'conf', 'number']] = df.name.str.split('_', expand=True)
d2f = df.drop_duplicates(subset="name", keep="first")
# lis2 = df['fps']
d2f = d2f.reset_index(drop=True)
lis = d2f['mol_blocks']
def get_ellip_diameters(
mol,
cids,
vdwScale=1.0,
boxMargin=2.0,
spacing=0.2,
show=False,
plot=False,
do_step_plot=False
):
"""
Fit an ellipsoid to the points within the VDW cloud of a all
conformers.
Keywords:
mol (RDKIT Molecule) - RDKIT molecule object to calculate
ellipsoid for
cids (list) - list of RDKIT conformer IDs of mol
vdwScale (float) - Scaling factor for the radius of the atoms
to
determine the base radius used in the encoding
- grid points inside this sphere carry the maximum
occupancy
default = 1.0 Angstrom
boxMargin (float) - added margin to grid surrounding molecule
default=4.0 Angstrom
spacing (float) - grid spacing - default = 1.0 Angstrom
show (bool) - show VDW cloud using PYMOL? - default = False
plot (bool) - show ellipsoid around VDW? - default = False
Returns:
conf_diameters (list) - 3 principal diameters of ellipsoids
for all
conformers
conf_axes (list) - 3 principal axes of mol for all conformers
conf_axes (list) - 3 principal moments of mol for all
conformers
"""
# over conformers
conf_diameters = []
conf_axes = []
conf_moments = []
for confId in cids:
conf = mol.GetConformer(confId)
box, sideLen, shape = get_molec_shape(
mol, conf, confId,
vdwScale=vdwScale,
boxMargin=boxMargin,
spacing=spacing
)
if show:
try:
v = PyMol.MolViewer()
except ConnectionRefusedError:
print("run 'pymol -R' to visualise structures")
print('visualisation will be skipped')
show_shape(v, mol, confId, shape)
v.server.do('set transparency=0.5')
# get ellipsoid fitting all points with value > 2
# - i.e. within vdw shape
hit_points = []
for idx in range(shape.GetSize()):
pt = shape.GetGridPointLoc(idx)
value = shape.GetVal(idx)
if value > 2:
point = np.array([pt.x, pt.y, pt.z])
hit_points.append(point)
hit_points = np.asarray(hit_points)
# get inertial properties of conformer
axes, moments = Chem.ComputePrincipalAxesAndMoments(
conf,
ignoreHs=False
)
conf_axes.append(axes)
conf_moments.append(moments)
# find the ellipsoid that envelopes all hit points
ET = ellipsoid.EllipsoidTool()
(center, radii, rotation) = ET.getMinVolEllipse(
P=hit_points,
tolerance=0.01,
do_step_plot=do_step_plot
)
conf_diameters.append(sorted(np.asarray(radii)*2))
# only do plot for the first conformer
if confId == 0 and plot is True:
hit_point_plot(
hit_points,
ET,
center,
radii,
rotation
)
return conf_diameters, conf_axes, conf_moments
def get_vdw_diameters(
mol,
cids,
mol_coms,
vdwScale=1.0,
boxMargin=2.0,
spacing=0.2,
vec_spacing=0.05,
show=False,
plot=False
):
"""Get the extent of the VDW size of each conformer along its
principle axes.
"""
# over conformers
conf_diameters = []
conf_axes = []
conf_moments = []
for confId in cids:
conf = mol.GetConformer(confId)
print(confId)
# try:
# Chem.CanonicalizeConformer(conf)
# except RuntimeError:
# pass
box, sideLen, shape = get_molec_shape(mol, conf, confId,
vdwScale=vdwScale,
boxMargin=boxMargin,
spacing=spacing)
if show is True:
try:
v = PyMol.MolViewer()
except ConnectionRefusedError:
print("run 'pymol -R' to visualise structures")
print('visualisation will be skipped')
show_shape(v, mol, confId, shape)
v.server.do('set transparency=0.5')
# get extent of shape along principle axes
axes, moments = Chem.ComputePrincipalAxesAndMoments(
conf,
ignoreHs=False
)
conf_axes.append(axes)
conf_moments.append(moments)
sml_PMI, mid_PMI, lge_PMI = moments
COM = mol_coms[confId]
com_pt = def_point(*COM)
# define vector from COM along each principal axis
max_side_len = max([i*2 for i in sideLen])
diameters = []
vectors = []
vals = []
for AX in [0, 1, 2]:
axis = axes[AX, :]
vector = define_vector(axis, max_side_len, vec_spacing)
vectors.append(vector)
values, distances = get_dist_and_values(
vector,
com_pt,
shape
)
vals.append(values)
ind_1, ind_2 = get_boundary_idx(values)
print(ind_1, ind_2)
if ind_1 is not None or ind_2 is not None:
diameter = distances[ind_1] + distances[ind_2]
diameters.append(diameter)
else:
try:
v = PyMol.MolViewer()
except ConnectionRefusedError:
print("run 'pymol -R' to visualise structures")
print('visualisation will be skipped')
show_shape(v, mol, confId, shape)
print(max_side_len)
print(com_pt)
print(axis)
v.server.do('set transparency=0.5')
v.server.sphere(
list([
float(i) for i in com_pt
]), 0.2, (2, 1, 0), 'COM'
)
# principal axes
v.server.sphere(
list([
float(i) for i in axis
]), 0.2, (2, 0, 0), 'AX'
)
import sys
sys.exit()
if len(diameters) == 3:
conf_diameters.append(diameters)
# only do plot for the first conformer
if confId == 0 and plot is True:
try:
v = PyMol.MolViewer()
except ConnectionRefusedError:
pass
show_shape(v, mol, confId, shape)
v.server.do('set transparency=0.5')
v.server.sphere(
list(
[float(i) for i in mol_coms[confId]]
), 0.2, (2, 1, 0), 'COM'
)
# principal axes
v.server.sphere(
list(
[float(i) for i in conf_axes[confId][0, :]]
), 0.2, (2, 0, 0), 'AX1'
)
v.server.sphere(
list(
[float(i) for i in conf_axes[confId][1, :]]
), 0.2, (1, 0, 1), 'AX2'
)
v.server.sphere(
list(
[float(i) for i in conf_axes[confId][2, :]]
), 0.2, (0, 1, 0), 'AX3'
)
for ax in [0, 1, 2]:
for i, vec in enumerate(vectors[ax]):
if vals[ax][i] <= 2:
C = (1, 1, 1)
else:
C = (1, 0, 0)
v.server.sphere(
list([float(i) for i in vec]), 0.05, C, 'pt'
)
return conf_diameters, conf_axes, conf_moments