Merge pull request #130 from jvalegre/jv_branch

Update v1.4.5
jvalegre · Feb 25, 2023 · 82ed93c · 82ed93c
2 parents 13483c2 + 41f0c35
commit 82ed93c
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diff --git a/Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_RDKit_organics.ipynb b/Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_RDKit_organics.ipynb
@@ -128,50 +128,6 @@
     "qprep(destination=com_path,files=sdf_rdkit_files,program='gaussian',\n",
     "        qm_input='wb97xd/6-31+G* opt freq',mem='24GB',nprocs=8)"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 3: If you want to use the same functions using a YAML file that stores all the variables"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# to load the variables from a YAML file, use the varfile option\n",
-    "csearch(varfile='FILENAME.yaml')\n",
-    "\n",
-    "# for each option, specify it in the YAML file as follows:\n",
-    "# program='rdkit' --> program: 'rdkit'\n",
-    "# name='quinine' --> name: 'quinine'\n",
-    "# etc"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 4: If you want to use the same functions through command lines"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "csearch(destination=sdf_path,smi=smi,name='quinine',program='rdkit')\n",
-    "\n",
-    "# for each option, specify it in the command line as follows:\n",
-    "# program='rdkit' --> --program 'rdkit'\n",
-    "# name='quinine' --> --name quinine\n",
-    "# etc\n",
-    "# for example: python -m aqme --program rdkit --smi COC1=CC2=C(C=CN=C2C=C1)[C@H]([C@@H]3C[C@@H]4CCN3C[C@@H]4C=C)O --name quinine"
-   ]
   }
  ],
  "metadata": {

diff --git a/Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_RDKit_organometallic.ipynb b/Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_RDKit_organometallic.ipynb
@@ -35,11 +35,11 @@
     "# 2) Simple RDKit sampling (program='rdkit')\n",
     "# 3) SMILES string (smi=smi_metal)\n",
     "# 4) Name for the output SDF files (name='Pd_complex')\n",
-    "# 5) The metal is Pd (metal=['Pd'])\n",
-    "# 6) Oxidation number +2 (metal_oxi=[2])\n",
+    "# 5) Charge is -1 (charge=-1)\n",
+    "# 6) Multiplicity is 1 (mult=1)\n",
     "# 7) The complex is squareplanar (complex_type='squareplanar')\n",
     "csearch(destination=sdf_path,program='rdkit',smi=smi_metal,name='Pd_complex',\n",
-    "        metal_atoms=['Pd'],metal_oxi=[2],mult=1,complex_type='squareplanar')"
+    "        charge=-1,mult=1,complex_type='squareplanar')"
    ]
   },
   {
@@ -73,51 +73,6 @@
     "        bs_gen='def2svp',bs_nogen='6-31G*',gen_atoms=['Pd'],mem='24GB',nprocs=8)\n",
     " "
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 1: If you want to use the same functions using a YAML file that stores all the variables"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# to load the variables from a YAML file, use the varfile option\n",
-    "csearch(varfile='FILENAME.yaml')\n",
-    "\n",
-    "# for each option, specify it in the YAML file as follows:\n",
-    "# program='rdkit' --> program: 'rdkit'\n",
-    "# name='Pd_complex' --> name: 'Pd_complex'\n",
-    "# etc"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 2: If you want to use the same functions through command lines"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "csearch(w_dir_main=w_dir_main,destination=sdf_path,program='rdkit',smi=smi_metal,name='Pd_complex',\n",
-    "        metal=['Pd'],metal_oxi=[2],mult=1,complex_type='squareplanar')\n",
-    "\n",
-    "# for each option, specify it in the command line as follows:\n",
-    "# program='rdkit' --> --program 'rdkit'\n",
-    "# name='Pd_complex' --> --name Pd_complex\n",
-    "# etc\n",
-    "# for example: python -m aqme --program rdkit --smi I[Pd](Cl)([PH3+])[N+]1=CC=CC=C1 --name Pd_complex"
-   ]
   }
  ],
  "metadata": {

diff --git a/Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_fullmonte_organics.ipynb b/Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_fullmonte_organics.ipynb
@@ -67,51 +67,6 @@
     "        qm_input='wb97xd/6-31+G* opt freq',mem='24GB',nprocs=8)\n",
     " "
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 1: If you want to use the same functions using a YAML file that stores all the variables"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# to load the variables from a YAML file, use the varfile option\n",
-    "csearch(varfile='FILENAME.yaml')\n",
-    "\n",
-    "# for each option, specify it in the YAML file as follows:\n",
-    "# program='fullmonte' --> program: 'fullmonte'\n",
-    "# name='quinine' --> name: 'quinine'\n",
-    "# etc"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 2: If you want to use the same functions through command lines"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "csearch(destination=sdf_path,\n",
-    "        smi=smi,name='quinine',program='fullmonte')\n",
-    "\n",
-    "# for each option, specify it in the command line as follows:\n",
-    "# program='fullmonte' --> --program 'fullmonte'\n",
-    "# name='quinine' --> --name quinine\n",
-    "# etc\n",
-    "# for example: python -m aqme --program fullmonte --smi COC1=CC2=C(C=CN=C2C=C1)[C@H]([C@@H]3C[C@@H]4CCN3C[C@@H]4C=C)O --name quinine"
-   ]
   }
  ],
  "metadata": {

diff --git a/Example_workflows/QCORR_processing_QM_outputs/QCORR_Analysis_with_isomerization_check.ipynb b/Example_workflows/QCORR_processing_QM_outputs/QCORR_Analysis_with_isomerization_check.ipynb
@@ -36,20 +36,13 @@
     "qcorr(files=files,freq_conv='opt=(calcfc,maxstep=5)',\n",
     "      isom_type='com',isom_inputs=isom_inputs)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:svss-bm]",
+   "display_name": "base",
    "language": "python",
-   "name": "conda-env-svss-bm-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -61,7 +54,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.7"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "6c100345108a7047ea96fae483cb64f49bdc23a8b225db90a5987a96959e820b"
+   }
   }
  },
  "nbformat": 4,

diff --git a/...ple_workflows/QCORR_processing_QM_outputs/QCORR_Simple_analysis_for_json_generation.ipynb b/...ple_workflows/QCORR_processing_QM_outputs/QCORR_Simple_analysis_for_json_generation.ipynb
diff --git a/Example_workflows/QCORR_processing_QM_outputs/QCORR_Standard_Analysis_and_full_check.ipynb b/Example_workflows/QCORR_processing_QM_outputs/QCORR_Standard_Analysis_and_full_check.ipynb
@@ -31,28 +31,6 @@
     "# 2) Detect and fix calcs that converged during geometry optimization but didn't converge during frequency calcs (freq_conv='opt=(calcfc,maxstep=5)')\n",
     "qcorr(files=files,freq_conv='opt=(calcfc,maxstep=5)')\n"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "###### Bonus 1: If you want to use the same functions through command lines"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "qcorr_calcs = qcorr(files='*.log',freq_conv='opt=(calcfc,maxstep=5)')\n",
-    "\n",
-    "# for each option, specify it in the command line as follows:\n",
-    "# files='*.log' --> --files *.log\n",
-    "# freq_conv='opt=(calcfc,maxstep=5)' --> --freq_conv opt=(calcfc,maxstep=5)\n",
-    "# etc\n",
-    "# for example: python -m aqme --files *.log --freq_conv opt=(calcfc,maxstep=5)"
-   ]
   }
  ],
  "metadata": {

diff --git a/Installation instructions.txt b/Installation instructions.txt