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Update v1.4.5 #130

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merged 7 commits into from
Feb 25, 2023
Merged

Update v1.4.5 #130

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e230688
1. Suffix and prefix to csearch, cmin and qprep
jvalegre Feb 14, 2023
7ec6235
added auto metal detection
Feb 21, 2023
73fdb7a
1. Migrating Readme to ReadtheDocs
jvalegre Feb 24, 2023
3bbb692
Merge pull request #129 from turkiAlturaifi/jv_branch
jvalegre Feb 24, 2023
7cd36e8
1. Adapting auto_metal_atoms option
jvalegre Feb 24, 2023
8f1d0ac
1. Adding #p in qprep-gaussian
jvalegre Feb 25, 2023
41f0c35
1. Change storing out file from csearch-crest
jvalegre Feb 25, 2023
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44 changes: 0 additions & 44 deletions Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_RDKit_organics.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down
51 changes: 3 additions & 48 deletions Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_RDKit_organometallic.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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')"
]
},
{
Expand Down Expand Up @@ -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": {
Expand Down
45 changes: 0 additions & 45 deletions Example_workflows/CSEARCH_CMIN_conformer_generation/CSEARCH_fullmonte_organics.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down
18 changes: 8 additions & 10 deletions Example_workflows/QCORR_processing_QM_outputs/QCORR_Analysis_with_isomerization_check.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -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,
Expand Down
64 changes: 0 additions & 64 deletions ...ple_workflows/QCORR_processing_QM_outputs/QCORR_Simple_analysis_for_json_generation.ipynb
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22 changes: 0 additions & 22 deletions Example_workflows/QCORR_processing_QM_outputs/QCORR_Standard_Analysis_and_full_check.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down
12 changes: 0 additions & 12 deletions Installation instructions.txt
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