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bump to v 0.0.3 - fixed pkg_resources deprecation with setuptools > 81; added pyproject.toml for installation; cleaned testing files and paths; added distribution/packaging files to .gitignore #40

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bump to v 0.0.3 - fixed pkg_resources deprecation with setuptools > 81; added pyproject.toml for installation; cleaned testing files and paths; added distribution/packaging files to .gitignore #40

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22 changes: 21 additions & 1 deletion .gitignore
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*~
__pychache__/
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
*.pyc
7 changes: 7 additions & 0 deletions MANIFEST.in
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include README.md
include LICENSE.txt
recursive-include espsim *.pt
recursive-include espsim/testfiles *.mol *.mol2 *.sdf
recursive-include benchmarks *.ipynb
recursive-include scripts *.py *.ipynb
recursive-include workshop *.ipynb *.md
49 changes: 25 additions & 24 deletions espsim/helpers.py
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Expand Up @@ -4,7 +4,7 @@
from argparse import Namespace
import os
import contextlib
import pkg_resources
from importlib.resources import files, as_file
import warnings
import logging

Expand Down Expand Up @@ -144,29 +144,30 @@ def mlCharges(mols):
#MUST use mols with hydrogens!
smiles = [Chem.MolToSmiles(mol) for mol in mols]

path = pkg_resources.resource_filename(__name__, 'QM_137k.pt')
args = Namespace(batch_size=50, checkpoint_dir=None, checkpoint_path=path, checkpoint_paths=[path], cuda=False, features_generator=None, features_path=None, gpu=None, max_data_size=None, no_features_scaling=False, preds_path=None, test_path=None, use_compound_names=False)

with open(os.devnull, 'w') as devnull:
with contextlib.redirect_stdout(devnull):
test_preds, test_smiles = make_predictions(args, smiles=smiles)
n_atoms, n_bonds = zip(*[num_atoms_bonds(x) for x in smiles])
partial_charge = test_preds[0]
partial_charge = np.split(partial_charge.flatten(), np.cumsum(np.array(n_atoms)))[:-1]

charges=[]
for i,mol in enumerate(mols):
try:
reorder_list = get_reorder_list(mol)
charges.append([partial_charge[i][reorder_list[x]] for x in range(mol.GetNumAtoms())])
except ValueError:
#Could not get prediction, default to Gasteiger
print("Warning: could not obtain prediction, defaulting to Gasteiger charges for one molecule")
AllChem.ComputeGasteigerCharges(mol)
charges.append([a.GetDoubleProp('_GasteigerCharge') for a in mol.GetAtoms()])


return charges
model_file = files('espsim').joinpath('QM_137k.pt')
with as_file(model_file) as path:
args = Namespace(batch_size=50, checkpoint_dir=None, checkpoint_path=str(path), checkpoint_paths=[str(path)], cuda=False, features_generator=None, features_path=None, gpu=None, max_data_size=None, no_features_scaling=False, preds_path=None, test_path=None, use_compound_names=False)

with open(os.devnull, 'w') as devnull:
with contextlib.redirect_stdout(devnull):
test_preds, test_smiles = make_predictions(args, smiles=smiles)
n_atoms, n_bonds = zip(*[num_atoms_bonds(x) for x in smiles])
partial_charge = test_preds[0]
partial_charge = np.split(partial_charge.flatten(), np.cumsum(np.array(n_atoms)))[:-1]

charges=[]
for i,mol in enumerate(mols):
try:
reorder_list = get_reorder_list(mol)
charges.append([partial_charge[i][reorder_list[x]] for x in range(mol.GetNumAtoms())])
except ValueError:
#Could not get prediction, default to Gasteiger
print("Warning: could not obtain prediction, defaulting to Gasteiger charges for one molecule")
AllChem.ComputeGasteigerCharges(mol)
charges.append([a.GetDoubleProp('_GasteigerCharge') for a in mol.GetAtoms()])


return charges

except ImportError:
def mlCharges(mols):
Expand Down
1 change: 1 addition & 0 deletions espsim/testfiles/__init__.py
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"""Test data files for espsim package."""
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0 scripts/prbmol1.mol2 → espsim/testfiles/prbmol1.mol2
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0 scripts/prbmol1.sdf → espsim/testfiles/prbmol1.sdf
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0 scripts/refmol1.mol → espsim/testfiles/refmol1.mol
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0 scripts/refmol1.mol2 → espsim/testfiles/refmol1.mol2
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0 scripts/refmol1.sdf → espsim/testfiles/refmol1.sdf
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65 changes: 65 additions & 0 deletions pyproject.toml
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[build-system]
requires = ["setuptools>=45", "wheel", "setuptools-scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"

[project]
name = "espsim"
version = "0.0.2"
description = "Scoring of shape and ESP similarity with RDKit"
readme = "README.md"
license = {text = "MIT"}
authors = [
{name = "Esther Heid", email = "eheid@mit.edu"}
]
classifiers = [
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent"
]
keywords = [
"chemistry",
"electrostatic potential",
"shape",
"similarity",
"RDKit"
]
requires-python = ">=3.9"
dependencies = [
"rdkit>=2023.03",
"torch>=2.0",
"numpy<2",
"scikit-learn>=1.0",
"scipy>=1.8",
"matplotlib>=3.5",
"joblib>=1.2",
"tqdm>=4.6",
"py3dmol>=0.8",
]

[project.optional-dependencies]
dev = [
"jupyter>=1.0",
"pytest>=7.0",
"black>=23.0",
"flake8>=4.0",
"mypy>=1.0",
]
chemprop = [
"chemprop-atom-bond @ git+https://github.com/hesther/chemprop-atom-bond.git",
]
psi4 = [
"psi4>=1.5",
"resp>=1.0",
]

[project.urls]
Homepage = "https://github.com/hesther/espsim"
Repository = "https://github.com/hesther/espsim"
Issues = "https://github.com/hesther/espsim/issues"

[tool.setuptools]
packages = ["espsim", "espsim.testfiles"]
include-package-data = true
34 changes: 22 additions & 12 deletions scripts/test_esp_function.py
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from espsim import GetEspSim, readMolFile, readMol2File, readSdfFile
from importlib.resources import files, as_file

# Get paths to test files from package data
testfiles = files('espsim.testfiles')

#The following block of code reads in prealigned molecules in mol format and calculates their ESP similarity:
mol1=readMolFile("scripts/prbmol1.mol")
mol2=readMolFile("scripts/refmol1.mol")
sim_esp=GetEspSim(mol1,mol2)
print("%15s %5.2f" % ("ESP similarity (mols read from mol file):",sim_esp))
with as_file(testfiles.joinpath('prbmol1.mol')) as prbmol_path, \
as_file(testfiles.joinpath('refmol1.mol')) as refmol_path:
mol1=readMolFile(str(prbmol_path))
mol2=readMolFile(str(refmol_path))
sim_esp=GetEspSim(mol1,mol2)
print("%15s %5.2f" % ("ESP similarity (mols read from mol file):",sim_esp))


#The following block of code reads in prealigned molecules in mol2 format with custom charges and calculates their ESP similarity:
mol1,charge1=readMol2File("scripts/prbmol1.mol2")
mol2,charge2=readMol2File("scripts/refmol1.mol2")
sim_esp=GetEspSim(mol1,mol2,prbCharge=charge1,refCharge=charge2)
print("%15s %5.2f" % ("ESP similarity (mols read from mol2 file):",sim_esp))
with as_file(testfiles.joinpath('prbmol1.mol2')) as prbmol_path, \
as_file(testfiles.joinpath('refmol1.mol2')) as refmol_path:
mol1,charge1=readMol2File(str(prbmol_path))
mol2,charge2=readMol2File(str(refmol_path))
sim_esp=GetEspSim(mol1,mol2,prbCharge=charge1,refCharge=charge2)
print("%15s %5.2f" % ("ESP similarity (mols read from mol2 file):",sim_esp))


#The following block of code reads in prealigned molecules in sdf format with custom charges as a comma-separated list
#in the SDF file and calculates their ESP similarity:
mol1,charge1=readSdfFile("scripts/prbmol1.sdf")
mol2,charge2=readSdfFile("scripts/refmol1.sdf")
sim_esp=GetEspSim(mol1,mol2,prbCharge=charge1,refCharge=charge2)
print("%15s %5.2f" % ("ESP similarity (mols read from sdf file):",sim_esp))
with as_file(testfiles.joinpath('prbmol1.sdf')) as prbmol_path, \
as_file(testfiles.joinpath('refmol1.sdf')) as refmol_path:
mol1,charge1=readSdfFile(str(prbmol_path))
mol2,charge2=readSdfFile(str(refmol_path))
sim_esp=GetEspSim(mol1,mol2,prbCharge=charge1,refCharge=charge2)
print("%15s %5.2f" % ("ESP similarity (mols read from sdf file):",sim_esp))
31 changes: 0 additions & 31 deletions setup.py
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31 changes: 31 additions & 0 deletions testfiles/prbmol1.mol
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RDKit 3D

13 12 0 0 0 0 0 0 0 0999 V2000
-1.0829 -0.6637 -0.5103 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2977 0.2486 0.4436 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1617 -0.0925 0.4114 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6689 -0.7861 1.3333 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9501 0.3238 -0.6576 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.4657 1.5946 0.0836 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6651 -0.4911 -1.8389 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.9239 -1.7249 -0.2214 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1739 -0.4579 -0.4169 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6777 0.0902 1.4808 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9334 0.0857 -0.7021 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3815 1.8546 0.3656 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1122 0.3289 -2.1752 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 2 0
3 5 1 0
2 6 1 0
1 7 1 0
1 8 1 0
1 9 1 0
2 10 1 0
5 11 1 0
6 12 1 0
7 13 1 0
M END

33 changes: 33 additions & 0 deletions testfiles/prbmol1.mol2
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@<TRIPOS>MOLECULE
*****
13 12 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
1 C -1.0829 -0.6637 -0.5103 C.3 1 UNL1 0.079954117054076082
2 C -0.2977 0.2486 0.4436 C.3 1 UNL1 0.17402774992656297
3 C 1.1617 -0.0925 0.4114 C.2 1 UNL1 0.33445172084859559
4 O 1.6689 -0.7861 1.3333 O.2 1 UNL1 -0.24924322634924762
5 O 1.9501 0.3238 -0.6576 O.3 1 UNL1 -0.47926124554573318
6 O -0.4657 1.5946 0.0836 O.3 1 UNL1 -0.37926397069925832
7 O -0.6651 -0.4911 -1.8389 O.3 1 UNL1 -0.3930474388646486
8 H -0.9239 -1.7249 -0.2214 H 1 UNL1 0.059756578060591724
9 H -2.1739 -0.4579 -0.4169 H 1 UNL1 0.059756578060591724
10 H -0.6777 0.0902 1.4808 H 1 UNL1 0.074910619371653109
11 H 2.9334 0.0857 -0.7021 H 1 UNL1 0.2963731884212602
12 H -1.3815 1.8546 0.3656 H 1 UNL1 0.21139157568550943
13 H -1.1122 0.3289 -2.1752 H 1 UNL1 0.21019375403004686
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 2
4 3 5 1
5 2 6 1
6 1 7 1
7 1 8 1
8 1 9 1
9 2 10 1
10 5 11 1
11 6 12 1
12 7 13 1
34 changes: 34 additions & 0 deletions testfiles/prbmol1.sdf
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RDKit 3D

13 12 0 0 0 0 0 0 0 0999 V2000
-1.0829 -0.6637 -0.5103 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2977 0.2486 0.4436 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1617 -0.0925 0.4114 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6689 -0.7861 1.3333 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9501 0.3238 -0.6576 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.4657 1.5946 0.0836 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6651 -0.4911 -1.8389 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.9239 -1.7249 -0.2214 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1739 -0.4579 -0.4169 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6777 0.0902 1.4808 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9334 0.0857 -0.7021 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3815 1.8546 0.3656 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1122 0.3289 -2.1752 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 2 0
3 5 1 0
2 6 1 0
1 7 1 0
1 8 1 0
1 9 1 0
2 10 1 0
5 11 1 0
6 12 1 0
7 13 1 0
M END
> <CHARGES> (1)
0.079954117054076082,0.17402774992656297,0.33445172084859559,-0.24924322634924762,-0.47926124554573318,-0.37926397069925832,-0.3930474388646486,0.059756578060591724,0.059756578060591724,0.074910619371653109,0.2963731884212602,0.21139157568550943,0.21019375403004686

$$$$
44 changes: 44 additions & 0 deletions testfiles/refmol1.mol
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RDKit 3D

19 19 0 0 0 0 0 0 0 0999 V2000
-2.4221 -2.3715 -2.2672 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4433 -2.6197 -0.8925 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7629 -1.7692 -0.0154 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0616 -0.6544 -0.5079 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0351 -0.4210 -1.8957 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7170 -1.2744 -2.7684 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3019 0.2449 0.4424 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1570 -0.0966 0.4089 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6657 -0.7876 1.3321 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9461 0.3212 -0.6592 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.4675 1.5927 0.0857 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.9484 -3.0317 -2.9445 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9847 -3.4736 -0.5061 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.7826 -1.9811 1.0464 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4859 0.4195 -2.3011 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6959 -1.0869 -3.8342 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6753 0.0966 1.4839 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9304 0.0858 -0.7021 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3844 1.8525 0.3644 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
4 7 1 0
7 8 1 0
8 9 2 0
8 10 1 0
7 11 1 0
6 1 1 0
1 12 1 0
2 13 1 0
3 14 1 0
5 15 1 0
6 16 1 0
7 17 1 0
10 18 1 0
11 19 1 0
M END

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