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Proposed .offxml format force fields for forcebalance refit experiments #3

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5344ae6
update plotting function
jmaat Oct 16, 2020
a3cc516
update plotting function
jmaat Oct 16, 2020
7e964cf
requirements
jmaat Oct 16, 2020
711dc0d
update script
jmaat Oct 16, 2020
dc36212
New FFs
jmaat Oct 16, 2020
922e9de
Add readme
jmaat Oct 17, 2020
eff6f56
initial guess .ppt with parameter outline
jmaat Oct 17, 2020
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120 changes: 93 additions & 27 deletions Analyze_WBO_Torsion.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 41,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -49,7 +49,7 @@
},
{
"cell_type": "code",
"execution_count": 42,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -113,7 +113,16 @@
" \n",
" # get dihedral indices and pass on to get_wbo function\n",
" dihedral_indices = list(tdr_object.dict()['keywords']['dihedrals'][0])\n",
" mol = chemi.smiles_to_oemol(smiles)\n",
" #mol = chemi.smiles_to_oemol(smiles)\n",
" \n",
" #debug\n",
" # create a new molecule\n",
" #mol = oechem.OEGraphMol()\n",
" mol = oechem.OEMol()\n",
" # convert the SMILES string into a molecule\n",
" oechem.OESmilesToMol(mol, smiles)\n",
" \n",
" \n",
" mol.SetData(\"TB\", max(torsion_barriers))\n",
" mol.SetData(\"TDindices\", dihedral_indices)\n",
" mol.SetData(\"TDid\", tdr_object.id)\n",
Expand Down Expand Up @@ -238,35 +247,63 @@
"\n",
" mols=[]\n",
" errors=[]\n",
" matched=0\n",
" for mol in molList:\n",
" any_match=0\n",
" charged = chemi.get_charges(mol)\n",
" for bond in charged.GetBonds():\n",
" #m1 = bond.GetBgn().GetMapIdx()\n",
" #m2 = bond.GetEnd().GetMapIdx()\n",
" m1=bond.GetBgnIdx()\n",
" m2=bond.GetEndIdx()\n",
" index=mol.GetData(\"TDindices\")\n",
" #print(m1)\n",
" #print(m2)\n",
" #print(index[1])\n",
" #print(index[2])\n",
" if m1 in [index[1], index[2]]:\n",
" if m2 in [index[1], index[2]]:\n",
" indices=[index[1], index[2]]\n",
" # DEBUGGING: ERROR IS HAPPENING HERE\n",
" # ISSUE WITH INDEX, ROWLEY DATASET IS NOT FINDING MATCH TO TORSION INDICES FOR ANY \n",
" if (m1 in indices and m2 in indices):\n",
" any_match+=1\n",
" matched+=1\n",
" #print(\"match\")\n",
" #if (m1 in map_idx or m2 in map_idx) and not bond.IsInRing():\n",
" try: \n",
" wbo = bond.GetData('WibergBondOrder')\n",
" #print(wbo)\n",
" mol.SetData(\"WBO\", wbo)\n",
" mols.append(mol)\n",
" except: \n",
" errors.append(mol)\n",
" pass\n",
" try: \n",
" wbo = bond.GetData('WibergBondOrder')\n",
" mol.SetData(\"WBO\", wbo)\n",
" mols.append(mol)\n",
" except Exception as e: \n",
" print(e)\n",
" errors.append(mol)\n",
" pass\n",
" if any_match==0:\n",
" print(\"no matches\")\n",
" oemol2mol2(mol, mol.GetData('cmiles'))\n",
" if any_match>0:\n",
" oemol2mol2(mol, \"match_\"+mol.GetData('cmiles'))\n",
" \n",
" \n",
" print(\"Out of \" +str(len(molList)) + \" molecules, \" + str(len(mols)) + \" were processed with WBO\")\n",
" print(matched)\n",
" return mols, errors\n",
" \n",
"\n",
"def oemol2mol2(mol, tag):\n",
" \"\"\"\n",
" Take mollist and create oeb file using the tag as the .oeb file name \n",
" \n",
" Parameters\n",
" ----------\n",
" molList : List of objects\n",
" List of oemols with datatags generated in genData function\n",
" tag : String\n",
" Title of the oeb file \n",
"\n",
" Returns\n",
" -------\n",
" \"\"\"\n",
" ofile = oechem.oemolostream(tag+'.mol2')\n",
" oechem.OEWriteConstMolecule(ofile, mol)\n",
" ofile.close()\n",
" return\n",
"\n",
" \n",
"\n",
"\n",
"def makeOEB(oemolList, tag):\n",
" \"\"\"\n",
Expand Down Expand Up @@ -471,17 +508,16 @@
},
{
"cell_type": "code",
"execution_count": 43,
"metadata": {
"scrolled": true
},
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Out of 43 molecules, 43 were processed with torsion data\n",
"Out of 43 molecules, 43 were processed with WBO\n"
"Out of 43 molecules, 43 were processed with WBO\n",
"43\n"
]
},
{
Expand Down Expand Up @@ -550,21 +586,49 @@
"source": [
"#An example of combining and comparing two datasets, let's try comparing with the phenyl dataset \n",
"genData(\"OpenFF Substituted Phenyl Set 1\", \"phenyl\")\n",
"\n",
"visualize_wbo_correlation_compare('phenyl.oeb', 'fragmentstability.oeb', \"fragmentStability_and_phenyl.pdf\")"
]
},
{
"cell_type": "code",
"execution_count": 47,
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Out of 86 molecules, 86 were processed with torsion data\n",
"Out of 86 molecules, 58 were processed with WBO\n"
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"no matches\n",
"Out of 86 molecules, 58 were processed with WBO\n",
"58\n"
]
},
{
Expand Down Expand Up @@ -598,6 +662,8 @@
],
"source": [
"#Let's also add the Rowley dataset and compare \n",
"#DEBUGGING ROWLEY DATASET\n",
"\n",
"genData(\"OpenFF Rowley Biaryl v1.0\", \"rowley\")\n",
"visualize_wbo_correlation_compare('phenyl.oeb', 'rowley.oeb', \"rowley_and_phenyl.pdf\")"
]
Expand Down
Binary file added ForceFields/InitalGuessWBO_Bayly.pptx
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10 changes: 10 additions & 0 deletions ForceFields/README.md
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@@ -0,0 +1,10 @@
# Force fields for proposed WBO interpolated torsion parameters

This repository contains the .offxml file format force fields for forcebalance refitting experiments.
These parameters were adapted from Chris Bayly's initial guess smarts for WBO interpolated parameters, round 0.

## Manifest
* `openff-1.2.1-biaryl.offxm` - Proposed parameters are TIG0 through TIG8
* `openff-1.2.1-phenyl.offxm` - Proposed parameters are T1i through t7i
* `openff-1.2.1-combined.offxm` - Contains both sets of parameters TIG0 through TIG8 and T1i through t7i.

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