QCflow 0.5

.github/workflows/docs_compile.yml

@@ -30,37 +30,24 @@ jobs:
         large-packages: true
         docker-images: true
         swap-storage: true
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+    - name: Setup micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Miniconda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        auto-update-conda: true
-        python-version: ${{ matrix.python-version }}
-        use-mamba: true
-
-    - name: Initialize conda
-      shell: bash -l {0}
-      run: conda init bash
+        environment-file: QCflow.yml
+        environment-name: QCflow
+        cache-environment: true
 
-    - name: Activate conda environment, install dependencies 
+    - name: Install dependencies 
       shell: bash -l {0}
       run: |
-        source ~/.bashrc
-        conda env create -f QCflow.yml
-        conda activate QCflow
-        conda install sphinx=8.2.3
+        micromamba install sphinx=8.2.3
         pip install sphinx_rtd_theme>=2.0.0
         pip install standard-imghdr
         pip install .
 
     - name: Run build
       shell: bash -l {0}
       run: |
-        source ~/.bashrc
-        conda activate QCflow
         cd docs/
         make html
 
@@ -69,4 +56,4 @@ jobs:
       with:
         publish_branch: docs
         github_token: ${{ secrets.qcflow2}}
-        publish_dir: ./docs/_build/html
+        publish_dir: ./docs/_build/html

.github/workflows/run_test.yml

@@ -11,29 +11,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          auto-activate-base: false
-      - name: Create and activate environment
+          environment-file: QCflow.yml
+          environment-name: QCflow
+          cache-environment: true
+      - name: Install dependencies
+        shell: bash -l {0}
         run: |
-          conda config --add channels defaults
-          conda config --add channels conda-forge
-          conda config --add channels anaconda
-          conda env create -f QCflow.yml
-          conda init bash
-          source ~/.bashrc
-          conda activate QCflow
           python -m pip install --upgrade pip
-          python -m pip install pytest  # Ensure pytest is installed
+          python -m pip install pytest
       - name: Debug Environment
+        shell: bash -l {0}
         run: |
-            source ~/.bashrc
-            conda activate QCflow
             python --version
             python -m pip show pytest
       - name: Run Tests
+        shell: bash -l {0}
         run: |
-          source ~/.bashrc
-          conda activate QCflow
           python -m pytest -v ./tests/test.py

Examples/FilteredSmilesFragments_props.csv

@@ -0,0 +1,111 @@
+smiles,valid,mw,n_rot,n_arom,psuedo_groups,fingerprint,subset
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+COC1=CC(O)=C2C(=C1)C=CC1=CC(O)=CC=C12,True,240.258,1,3,COc1cc(O)c2c(ccc3cc(O)ccc32)c1,[0. 0. 0. ... 0. 0. 0.],di
+COC1=C(O)C=C2OC3=CC=CC=C3C(=O)C2=C1O,True,258.229,1,3,COc1c(O)cc2oc3ccccc3c(=O)c2c1O,[0. 0. 0. ... 0. 0. 0.],di
+CC1=CC=CC(O)=C1O,True,124.13899999999998,0,1,Cc1cccc(O)c1O,[0. 0. 0. ... 0. 0. 0.],di
+O=C1OC2=CC(O)=C(O)C=C2C2=C1C1=CC=CC=C1O2,True,268.224,0,4,O=c1oc2cc(O)c(O)cc2c2oc3ccccc3c12,[0. 0. 0. ... 0. 0. 0.],di
+COC1=CC2=CC=C3C=C(O)C=CC3=C2C(O)=C1OC,True,270.284,2,3,COc1cc2ccc3cc(O)ccc3c2c(O)c1OC,[0. 0. 0. ... 0. 0. 0.],di
+NC1=NC=NC2=C1NC=N2,True,135.12999999999997,0,2,Nc1ncnc2nc[nH]c12,[0. 0. 0. ... 0. 0. 0.],di
+COC1=CC=C(C2=COC3=C(O)C(O)=CC=C3C2=O)C=C1,True,284.267,2,3,COc1ccc(-c2coc3c(O)c(O)ccc3c2=O)cc1,[0. 0. 0. ... 0. 0. 0.],di
+CC1=CC(=O)OC2=CC(O)=C(O)C=C12,True,192.17,0,2,Cc1cc(=O)oc2cc(O)c(O)cc12,[0. 0. 0. ... 0. 0. 0.],di
+CC1=C(O)C=C(C=CC2=CC=CC=C2)C=C1O,True,226.275,2,2,Cc1c(O)cc(C=Cc2ccccc2)cc1O,[0. 0. 0. ... 0. 0. 0.],di
+OC1=CC=C2C=CC=CC2=C1O,True,160.17199999999997,0,2,Oc1ccc2ccccc2c1O,[0. 0. 0. ... 0. 0. 0.],di
+OC1=CN=C2C(O)=CC=CC2=C1,True,161.15999999999997,0,2,Oc1cnc2c(O)cccc2c1,[0. 0. 0. ... 0. 0. 0.],di
+OC1=CC2=C(C=C1O)NC=C2,True,149.149,0,2,Cn1ccc2cc(O)c(O)cc21,[0. 0. 0. ... 0. 0. 0.],di
+O=C1C(C2=CC=CC=C2)=COC2=CC(O)=CC(O)=C12,True,254.24099999999996,1,3,O=c1c(-c2ccccc2)coc2cc(O)cc(O)c12,[0. 0. 0. ... 0. 0. 0.],di
+O=C1C=C(C2=CC=CC=C2)C2=CC=C(O)C(O)=C2O1,True,254.24099999999999,1,3,O=c1cc(-c2ccccc2)c2ccc(O)c(O)c2o1,[0. 0. 0. ... 0. 0. 0.],di
+CC1=C(O)C=CC2=C1C=CC1=CC(O)=CC(C=O)=C12,True,252.26899999999998,1,3,Cc1c(O)ccc2c1ccc1cc(O)cc(C=O)c12,[0. 0. 0. ... 0. 0. 0.],di
+COC1=C(O)C=CC2=C1OC(=O)C1=C2OC2=CC(O)=CC=C21,True,298.24999999999994,1,4,COc1c(O)ccc2c1oc(=O)c1c3ccc(O)cc3oc21,[0. 0. 0. ... 0. 0. 0.],di
+COC1=CC=C2C(=C1)OCC1=C2OC2=CC(O)=C(O)C=C12,True,284.267,1,3,COc1ccc2c(c1)OCc1c-2oc2cc(O)c(O)cc12,[0. 0. 0. ... 0. 0. 0.],di
+CC1=C(O)C=C(C2=CC3=CC=CC=C3O2)C=C1O,True,240.258,1,3,Cc1c(O)cc(-c2cc3ccccc3o2)cc1O,[0. 0. 0. ... 0. 0. 0.],di
+CC1=C(O)C(C=O)=C2OC(C3=CC=CC=C3)=CC(=O)C2=C1O,True,296.278,2,3,Cc1c(O)c(C=O)c2oc(-c3ccccc3)cc(=O)c2c1O,[0. 0. 0. ... 0. 0. 0.],di
+COC1=CC=C(O)C2=C1OC1=CC(C)=CC(O)=C1C2=O,True,272.25600000000003,1,3,COc1ccc(O)c2c(=O)c3c(O)cc(C)cc3oc12,[0. 0. 0. ... 0. 0. 0.],di
+COC1=C(C)C(O)=C2C(=O)C=C(C3=CC=CC=C3)OC2=C1O,True,298.29400000000004,2,3,COc1c(C)c(O)c2c(=O)cc(-c3ccccc3)oc2c1O,[0. 0. 0. ... 0. 0. 0.],di
+COC1=C(O)C=C2C(=O)OC3=CC(O)=CC4=CC=C1C2=C43,True,282.25100000000003,1,4,COc1c(O)cc2c(=O)oc3cc(O)cc4ccc1c2c43,[0. 0. 0. ... 0. 0. 0.],di
+CC1=CC2=C(C(=O)O1)C1=CC(O)=C(O)C=C1C(=O)O2,True,260.201,0,3,Cc1cc2oc(=O)c3cc(O)c(O)cc3c2c(=O)o1,[0. 0. 0. ... 0. 0. 0.],di
+OC1=CC=C2C(O)=CC=CC2=C1,True,160.172,0,2,Oc1ccc2c(O)cccc2c1,[0. 0. 0. ... 0. 0. 0.],di
+O=C1C=C(CCC2=CC=CC=C2)OC2=C(O)C=C(O)C=C12,True,282.295,3,3,O=c1cc(CCc2ccccc2)oc2c(O)cc(O)cc12,[0. 0. 0. ... 0. 0. 0.],di
+COC1=CC=C2C(=C1)OC1=C2C(=O)OC2=CC(O)=C(O)C=C21,True,298.25,1,4,COc1ccc2c(c1)oc1c3cc(O)c(O)cc3oc(=O)c21,[0. 0. 0. ... 0. 0. 0.],di
+NC1=NC=C2N=C(O)C=NC2=N1,True,163.14,0,2,Nc1ncc2nc(O)cnc2n1,[0. 0. 0. ... 0. 0. 0.],di
+COC1=C(O)C=CC2=C1C(=O)C1=CC(O)=CC=C1O2,True,258.229,1,3,COc1c(O)ccc2oc3ccc(O)cc3c(=O)c12,[0. 0. 0. ... 0. 0. 0.],di
+OC1=CC=C2C=C(O)C=CC2=C1,True,160.172,0,2,Oc1ccc2cc(O)ccc2c1,[0. 0. 0. ... 0. 0. 0.],di

Examples/example_psi4_opt_submission.py

@@ -0,0 +1,21 @@
+import rdkit
+from rdkit import Chem
+from rdkit.Chem import Draw
+from rdkit.Chem import AllChem
+import numpy as np
+import pandas as pd
+import QCflow
+from QCflow.load_gaussian import *
+from QCflow.torsion_parser import *
+from QCflow.find_torsion import *
+from QCflow.write_psi4 import *
+from QCflow.run_psi4 import *
+from QCflow.energy_calculations import *
+import os
+
+df = pd.read_csv('FilteredSmilesFragments_props.csv')
+
+smiles_dict = {str(i): row['smiles'] for i, row in df.iterrows()}
+
+for k, v in smiles_dict.items():
+    run_psi4('opt', k, v, 12, 10, 'b3lyp', '3-21G')

Examples/example_torsional_scan_script.py

@@ -0,0 +1,43 @@
+import rdkit
+from rdkit import Chem
+from rdkit.Chem import Draw
+from rdkit.Chem import AllChem
+import numpy as np
+import pandas as pd
+from QCflow.load_gaussian import *
+from QCflow.torsion_parser import *
+from QCflow.find_torsion import *
+from QCflow.write_psi4 import *
+from QCflow.run_psi4 import *
+from QCflow.energy_calculations import *
+import os
+
+# This is an example for one molecule
+# This can easily be converted into a loop for multiple molecules
+# The getTorsion assumes single bonded but can be altered if required
+# If you have more than 1 torsion or tiple, double etc bond link
+# Refer to this --> https://github.com/matta-research-group/QCflow/blob/qcflow-0.5/QCflow/torsion_parser.py
+# torsion_parser.py also has the scripts to extract the data you may want
+# The docs  --> https://matta-research-group.github.io/QCflow/
+
+smiles_example = 'CC(=O)Oc1c(OC(C)=O)c(-c2c(OC(C)=O)c(OC(C)=O)cc3cc[nH]c23)c2cc[nH]c2c1'
+
+mol = Chem.MolFromSmiles(smiles_example)
+
+#adds H's and 3D coordinates
+mol = embed_molecule(mol)
+
+#finds the rotatable bond in the molecule
+bond = getBond(mol)
+
+#Gets the whole torsion
+mol_torsions = getTorsion(mol, bond[0])
+
+#writes the Gaussian input file for the torsion scan
+write_gaussian('tor', 'example_mol', smiles_example, functional='B3LYP', basis_set='6-31G*', mol=mol, 
+                                                                                       torsion=mol_torsions)
+#writes the SLURM script to run the Gaussian job
+write_slurm('tor', 'example_mol', cpus=10)
+
+#submits the SLURM job, with retries in case of failure
+submit_slurm_job('tor', 'example_mol', max_retries=5, wait_seconds=30)

QCflow.yml

@@ -1,9 +1,7 @@
 name: QCflow
 channels:
   - conda-forge
-  - lich
-  - defaults
-  - anaconda
+  # - lich causing issues in instal
 dependencies:
   - brotli
   - brotli-bin
@@ -103,7 +101,6 @@ dependencies:
   - seaborn-base
   - six
   - statsmodels
-  - syba
   - tk
   - tornado
   - typing-extensions

QCflow/__init__.py

@@ -10,3 +10,5 @@
 from . import write_psi4
 from . import run_psi4
 from . import sa_score
+from . import write_xTB
+from . import run_xTB