From 40cdadcf8b44d5f60e0817966efe9228733e72c6 Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Mon, 17 Apr 2023 16:09:23 +1000
Subject: [PATCH 1/9] re-jig BCCs to be more specific
---
.../generate_original_am1bcc.py | 312 ++
scripts/convert-am1-bcc/legacy/convert.py | 230 +
scripts/convert-am1-bcc/openeye-am1-bcc.json | 4155 +++++++++++++++++
3 files changed, 4697 insertions(+)
create mode 100644 scripts/convert-am1-bcc/generate_original_am1bcc.py
create mode 100644 scripts/convert-am1-bcc/legacy/convert.py
create mode 100644 scripts/convert-am1-bcc/openeye-am1-bcc.json
diff --git a/scripts/convert-am1-bcc/generate_original_am1bcc.py b/scripts/convert-am1-bcc/generate_original_am1bcc.py
new file mode 100644
index 0000000..70279c3
--- /dev/null
+++ b/scripts/convert-am1-bcc/generate_original_am1bcc.py
@@ -0,0 +1,312 @@
+"""This script converts the original AM1BCC values [1]_ into the data model expected by
+this framework.
+
+References
+----------
+[1] Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation of
+ high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
+ Journal of computational chemistry, 23(16), 1623–1641.
+"""
+import click
+import json
+import itertools
+import logging
+
+import numpy as np
+import pandas as pd
+from openeye import oechem
+
+from openff.recharge.charges.bcc import BCCParameter
+
+logging.basicConfig()
+logger = logging.getLogger(__name__)
+
+
+GENERAL_ATOM_CODES = {
+ # from more general to more specific
+ # patterns will get matched with more specific ones so order is important!
+
+ "X": {
+ # === HALOGENS ===
+ # F1 Fluorine
+ "71": [r"[#9:1]"],
+ # Cl1 Chlorine
+ "72": [r"[#17:1]"],
+ # Br1 Bromine
+ "73": [r"[#35:1]"],
+ # I1 Iodine
+ "74": [r"[#53:1]"],
+ # === OTHER ===
+ # Si4 Tetravalent silicon
+ "61": [r"[#14X4:1]"],
+ # H1 Hydrogen
+ "91": [r"[#1:1]"],
+ },
+
+ "S": {
+ # === SULFUR ===
+ # S1,2 Univalent or divalent sulfur
+ "51": [r"[#16X1:1]", "[#16X2:1]"],
+ # S3 Trivalent sulfur
+ "52": [r"[#16X3:1]"],
+ # S4 Tetravalent sulfur
+ "53": [r"[#16X4:1]"],
+ },
+
+
+ "P": {
+ # === PHOSPHORUS ===
+ # P2,3 Divalent or trivalent phosphorus
+ # "41": [r"[#15:1]", "[#15X2:1]", "[15X1:1]", "[#15X3:1]"],
+ "41": [r"[#15:1]"],
+
+ # P3,4 Trivalent or tetravalent double-bonded phosphorus
+ # "42": [r"[15X4:1]", "[#15X3;$(*=[*]):1]"],
+ "42": [r"[#15X4,#15X3$(*=[*]):1]"],
+ },
+
+ "O": {
+ # === OXYGEN ===
+ # O1,2 Univalent or divalent oxygen
+ # "31": [r"[#8:1]", "[#8X1:1]", "[#8X2:1]"],
+ "31": [r"[#8:1]"],
+ # O1ester,acid Double-bonded oxygen in an ester or acid
+ "32": [r"[#8X1$(*=[#6X3]-[#8X2]):1]"],
+ # O1lact Double-bonded oxygen in a lactone or lactam
+ "33": [r"[#8X1$(*=[#6r]@[#7r,#8r]):1]"],
+ },
+
+ "C": {
+ # === CARBON ===
+ # C4 Tetravalent carbon
+ "11": [r"[#6X4:1]"],
+ # C1,2 Univalent or divalent carbon
+ "15": [r"[#6X1:1]","[#6X2:1]"],
+ # C3=C Trivalent carbon, double bonded to carbon
+ "12": [r"[#6X3:1]"],
+ # Car Aromatic carbon
+ "16": [
+ r"[#6a:1]",
+ # or planar ring with two continuous single bonds and at least two double bonds
+ r"[#6X3R$([*](-,:[R]-,=,:[R])=,:[R]):1]"
+ ],
+ # Carlp Aromatic carbon bonded to an aromatic oxygen or nitrogen with a lone pair
+ "17": [
+ r"[#6aX3$(*~[#7aX2,#8aX2]):1]",
+ r"[#6X3R$(*~[#7aX2,#8aX2])&$([*](-,:[R]-,=,:[R])=,:[R]):1]"
+ ],
+ # C3=N,P Trivalent carbon, double bonded to nitrogen or phosphorus
+ "13": [r"[#6X3$(*=[#7,#15]):1]",],
+ # C3=O,S Trivalent carbon, double bonded to oxygen or sulfur
+ "14": [r"[#6X3$(*=[#8X1,#8X2+1,#16+0]):1]"],
+ "12b": [r"[#6X3A$(*=[#6]):1]"],
+ },
+
+ "N": {
+ # === NITROGEN ===
+ # N1,2 Univalent or cationic divalent nitrogen
+ "25": [r"[#7:1]", r"[#7X1,#7X2+1:1]"],
+ # N2 Neutral divalent nitrogen
+ "24": [r"[#7X2+0,#7X2-1ar5:1]"],
+ # N2,3,4 Amine nitrogen
+ "21": [r"[#7X4:1]", r"[#7X3:1]", r"[#7X2-1A:1]"],# "[#7X2$([*](-,:[*])-,:[*]):1]"],
+ # N3deloc Trivalent nitrogen with a delocalized lone pair
+ "22": [
+ r"[#7X2$(*(-,:[*])-,:[#6X3$(*=[#8,#16])]):1]", # N2-C(=O,S),
+ ],
+ "23": [
+ r"[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]):1]",
+ # "[#7X3R$([*](-[!#1&!])(-,:[R]=,:[R])-,:[R]=,:[R]):1]",
+ r"[#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]):1]",
+ r"[#7X3+1:1]",
+ r"[#7X3$([*](~[#8X1])~[#8X1]):1]",
+ # "[#7X3$([*]~[#7X2]=[#7X3]):1]",
+ r"[#7X3+0$(*-[#6X3$(*=[#7X3+1])]):1]",
+ ],
+ "22b": [
+ r"[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]", # amide
+ # "[#7X3+0$(*-[#6X3$(*(=[#8X2+1]-[#7X2-1])-[!#8&!#16])]):1]",
+ ],
+ "23b": [
+ r"[#7X3ar5:1]",
+ ]
+ }
+}
+
+SPECIFIC_PATTERNS = {
+ # P-O
+ r"[#8X1-1:1]~[#15&!$(*=*):2]": "310941",
+ r"[#8X2:1]-[#15X4+0,#15X3;!$(*=*):2]": "310141",
+
+ r"[#8X1:1]-,=[#15X4$([*](-[#8X1-1])-[#8X1-1,#8X2,#16X2]):2]": "310942",
+ r"[#8X1-1:1]-[#15X4$([*](=[#8X1])-[#8X1-1]):2]": "310942",
+ r"[#8X1-1:1]-,:[#15X4$([*](-[#8X1-1])(-[#8X1-1])=[#8]):2]": "310942",
+ r"[#8X1:1]=[#15X4$([*](-[#8X1-1])(-[#6])-[#6,#1]):2]": "310942",
+
+
+ # ...
+
+ # 'Delocalised' S-O
+ r"[#16X1,#16X2;$(*=[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]": "310951",
+ r"[#16X3$(*=[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]": "310952",
+ r"[#16X4$(*~[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]": "310953",
+
+
+ # 'Delocalised' S-S
+ r"[#16X1-1$([*]-S),#16X1+0$([*]=S):1]-,=[#16X4:2]": "510953",
+
+ # 'Delocalised' S-C
+ r"[#6a:1]-[#16X1-1:2]" : "160951",
+ r"[#6a$(*~[#7aX2,#8aX2]):1]-[#16X1-1:2]" : "170951",
+ r"[#6X3:1](~[#8X1,#16X1])(~[#16X1:2])": "140951",
+ r"[#6X3$(*=[#7,#15]):1]-[#16X1-1:2]": "130951",
+ r"[#6X3$(*=[#6]):1]-[#16X1-1:2]": "120951",
+ r"[#6X1,#6X2:1]-[#16X1-1:2]": "150951",
+ r"[#6X1,#6X2$([*]=[#8,#16]):1]=[#16:2]": "150951",
+ r"[#6X4:1]-[#16X1-1:2]": "110951",
+
+ # 'Delocalised' C-O
+ r"[#6a:1]-[#8X1-1:2]" : "160931",
+ r"[#6a$(*~[#7aX2,#8aX2]):1]-[#8X1-1:2]" : "170931",
+ r"[#6X3:1](~[#8X1,#16X1])(~[#8X1:2])": "140931",
+ r"[#6X3$(*=[#7,#15]):1]-[#8X1-1:2]" : "130931",
+ r"[#6X3$(*=[#6]):1]-[#8X1-1:2]": "120931",
+ r"[#6X1,#6X2:1]-[#8X1-1:2]" : "150931",
+ r"[#6X2$([*]=[#8,#16]):1]=[#8X1:2]" : "150931",
+ r"[#6X4:1]-[#8X1-1:2]" : "110931",
+
+ # 'Delocalised' N-O
+ r"[#7X2+0:1]-[#8X1-1:2]": "240631",
+ r"[#7X3+1:1]-[#8X1-1:2]": "230631",
+ r"[#7X4+1,#7X3+0$([*]-[#6X3]=,:[#7X2,#6X3]),#7X3+0$([*]-[#6X3]-,=,:[#7a,#6a]),#7X3+0$(*-[#6X4,#1]),#7X3+0$([*](-[#7X3])-[#7X3]),#7X3+0$([*](-[#8])-[#8]):1]-[#8X1-1:2]": "210631",
+ r"[#7X3+0$(*-[#6X3$(*=[#8,#16])]):1]-[#8X1-1:2]": "220631",
+ r"[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]),$([#7X3](-[#8X1])-[#8X1]):1]~[#8X1:2]": "230931",
+}
+
+GENERAL_BOND_CODES = {
+ "09": "~", # Single bond with charge or delocalized bond
+ "08": ":", # 'Double' aromatic Bond
+ "07": ":", # 'Single' aromatic Bond
+ "06": "-", # 'Single' Dative bond
+ "03": "#", # Triple bond
+ "02": "=", # Double bond
+ "01": "-", # Single bond
+}
+
+BCC_OVERRIDES = {
+ "110112": 0.0024,
+ "120114": -0.0172,
+}
+
+
+def build_bccs(
+ bcc_value_file: str = "am1bcc.csv",
+):
+ bcc_frame = pd.read_csv(bcc_value_file)
+ bcc_frame[r"Code"] = bcc_frame[r"Code"].astype(str)
+ bcc_frame[r"BCC"] = bcc_frame[r"BCC"].round(4)
+
+ BCC_VALUES = dict(zip(bcc_frame[r"Code"], bcc_frame[r"BCC"]))
+ BCC_VALUES.update(BCC_OVERRIDES)
+
+ flat_atom_codes = {}
+ for element_smirks in GENERAL_ATOM_CODES.values():
+ for atom_code, all_atom_smirks in element_smirks.items():
+ not_atom_map = [smirks[1:-3] for smirks in all_atom_smirks]
+ final_smirks = f"[{','.join(not_atom_map)}:1]"
+ flat_atom_codes[final_smirks] = atom_code[:2]
+
+ # create bcc patterns from less to more specific
+ bcc_patterns = []
+ for (
+ (atom_smirks1, atom_code1),
+ (atom_smirks2, atom_code2)
+ ) in itertools.combinations_with_replacement(flat_atom_codes.items(), 2):
+ for bond_code, bond_smirks in GENERAL_BOND_CODES.items():
+ smirks = atom_smirks1 + bond_smirks + atom_smirks2.replace(":1", ":2")
+ code = atom_code1 + bond_code + atom_code2
+ bcc_patterns.append((smirks, code))
+
+ if atom_smirks2 != atom_smirks1:
+ smirks2 = atom_smirks2 + bond_smirks + atom_smirks1.replace(":1", ":2")
+ code2 = atom_code2 + bond_code + atom_code1
+ bcc_patterns.append((smirks2, code2))
+
+ for smirks, code in SPECIFIC_PATTERNS.items():
+ bcc_patterns.append((smirks, code))
+
+ # create BCCs from more to less specific
+ bond_charge_corrections = []
+ unique_patterns = set()
+ for smirks, code in bcc_patterns[::-1]:
+ if smirks in unique_patterns:
+ continue
+ if code not in BCC_VALUES:
+ if code[:2] == code[-2:]:
+ value = 0
+ else:
+ continue
+ else:
+ value = BCC_VALUES[code]
+
+ # Validate the smirks
+ query = oechem.OEQMol()
+ assert oechem.OEParseSmarts(query, smirks)
+
+ bcc = BCCParameter(
+ smirks=smirks,
+ value=value,
+ provenance={"code": code}
+ )
+ bond_charge_corrections.append(bcc)
+ unique_patterns.add(smirks)
+
+ # TODO: reverse if we reverse the order of BCCs to go from less to more specific
+ return bond_charge_corrections[::-1]
+
+
+@click.command()
+@click.option(
+ "--bcc-value-file",
+ default="am1bcc.csv",
+ help="The name of the file containing the BCC values.",
+)
+@click.option(
+ "--output-file",
+ default="openeye-am1-bcc.json",
+ help="The name of the output file to write the BCCs to.",
+)
+def create_openeye_bccs(
+ bcc_value_file: str = "am1bcc.csv",
+ output_file: str = "openeye-am1-bcc.json",
+):
+ bcc_parameters = build_bccs(bcc_value_file=bcc_value_file)
+
+ # Remove duplicate parameters caused by the duplication of the aromatic
+ # bond type.
+ bcc_parameters_per_smirks = {}
+ unique_bcc_parameters = []
+
+ for bcc_parameter in bcc_parameters:
+ if bcc_parameter.smirks in bcc_parameters_per_smirks:
+ code = bcc_parameter.provenance[r"code"]
+ assert np.isclose(
+ bcc_parameter.value,
+ bcc_parameters_per_smirks[bcc_parameter.smirks].value,
+ ), (bcc_parameter, bcc_parameters_per_smirks[bcc_parameter.smirks])
+ is_aromatic = code[2:4] in [r"07", "08"]
+ is_self_to_self = code[:2] == code[-2:]
+ assert is_aromatic or is_self_to_self, bcc_parameter
+ continue
+ unique_bcc_parameters.append(bcc_parameter)
+ bcc_parameters_per_smirks[bcc_parameter.smirks] = bcc_parameter
+
+ with open(output_file, "w") as f:
+ json.dump(
+ # reverse for now while recharge still goes from more to less specific
+ {"parameters": [bcc.dict() for bcc in bcc_parameters][::-1]},
+ f, indent=4
+ )
+
+if __name__ == "__main__":
+ create_openeye_bccs()
\ No newline at end of file
diff --git a/scripts/convert-am1-bcc/legacy/convert.py b/scripts/convert-am1-bcc/legacy/convert.py
new file mode 100644
index 0000000..4a7daa7
--- /dev/null
+++ b/scripts/convert-am1-bcc/legacy/convert.py
@@ -0,0 +1,230 @@
+"""This script converts the original AM1BCC values [1]_ into the data model expected by
+this framework.
+
+References
+----------
+[1] Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation of
+ high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
+ Journal of computational chemistry, 23(16), 1623–1641.
+"""
+import json
+import logging
+from typing import Dict, List
+
+import numpy
+import pandas
+from openeye import oechem
+
+from openff.recharge.charges.bcc import BCCParameter
+
+logging.basicConfig()
+logger = logging.getLogger(__name__)
+
+
+def build_bond_charge_corrections(
+ atom_codes: Dict[str, str],
+ bond_codes: Dict[str, str],
+ bcc_overrides: Dict[str, float],
+ custom_bcc_smirks: Dict[str, str],
+) -> List[BCCParameter]:
+
+ # Convert the atom and bond codes into the six number codes used
+ # in the AM1BCC paper.
+ all_codes = [*custom_bcc_smirks]
+
+ for first_atom_code in atom_codes:
+ for bond_code in bond_codes:
+ for last_atom_code in atom_codes:
+
+ code = f"{first_atom_code}{bond_code}{last_atom_code}"
+
+ if code not in all_codes:
+ all_codes.append(code)
+
+ # Remove any BCCs defined for bond or atom codes which haven't yet been
+ # specified.
+ bcc_frame = pandas.read_csv("am1bcc.csv")
+
+ bcc_frame["BCC"] = bcc_frame["BCC"].round(4)
+ bcc_frame = bcc_frame.sort_values(by=["Index"])
+
+ unconverted_codes = bcc_frame[~bcc_frame["Code"].isin(all_codes)]
+
+ for unconverted_code in unconverted_codes["Code"].unique():
+ logger.warning(f"{unconverted_code} was not converted.")
+
+ bcc_frame = bcc_frame[bcc_frame["Code"].isin(all_codes)]
+
+ # Convert the data frame into a collection of correction objects.
+ bond_charge_corrections = {}
+
+ for _, bcc_row in bcc_frame.iterrows():
+
+ code = str(bcc_row["Code"])[0:6]
+
+ first_atom_code = code[0:2]
+ bond_code = code[2:4]
+ last_atom_code = code[4:6]
+
+ smirks = (
+ f"{atom_codes[first_atom_code]}"
+ f"{bond_codes[bond_code]}"
+ f"{atom_codes[last_atom_code].replace(':1', ':2')}"
+ )
+
+ if code in custom_bcc_smirks:
+ smirks = custom_bcc_smirks.pop(code)
+
+ # Validate the smirks
+ query = oechem.OEQMol()
+ assert oechem.OEParseSmarts(query, smirks)
+
+ value = bcc_overrides.get(code, bcc_row["BCC"])
+
+ bond_charge_corrections[code] = BCCParameter(
+ smirks=smirks, value=value, provenance={"code": code}
+ )
+
+ assert len(custom_bcc_smirks) == 0
+
+ return [
+ bond_charge_corrections[code]
+ for code in all_codes
+ if code in bond_charge_corrections
+ ]
+
+
+def main():
+
+ atom_codes = {
+ # C4 Tetravalent carbon
+ "11": "[#6X4:1]",
+ # # C1,2 Univalent or divalent carbon
+ "15": "[#6X1,#6X2:1]",
+ # C3=C Trivalent carbon, double bonded to carbon
+ "12": "[#6X3$(*=[#6]):1]",
+ # C3=N,P Trivalent carbon, double bonded to nitrogen or phosphorus
+ "13": "[#6X3$(*=[#7,#15]):1]",
+ # C3=O,S Trivalent carbon, double bonded to oxygen or sulfur
+ "14": "[#6X3$(*=[#8,#16]):1]",
+ # Carlp Aromatic carbon bonded to an aromatic oxygen or nitrogen with a lone pair
+ "17": "[#6a$(*~[#7aX2,#8aX2]):1]",
+ # Car Aromatic carbon
+ "16": "[#6a:1]",
+ # N3hdeloc Trivalent nitrogen with a highly delocalized lone pair
+ "23": "[#7X3ar5,#7X3+1,#7X3+0$(*-[#6X3$(*=[#7X3+1])]),$([#7X3](-[#8X1-1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]):1]",
+ # N3deloc Trivalent nitrogen with a delocalized lone pair
+ "22": "[#7X2-1$(*-[#6X3$(*=[#8X1,#16X1])]),#7X3$(*-[#6X3$(*=[#8X1,#16X1])]):1]",
+ # N2,3,4 Amine nitrogen
+ "21": "[#7X4,#7X3,#7X2-1:1]",
+ # N1,2 Univalent or cationic divalent nitrogen
+ "25": "[#7X1,#7X2+1:1]",
+ # N2 Neutral divalent nitrogen
+ "24": "[#7X2+0,#7X2-1ar5:1]",
+ # O1lact Double-bonded oxygen in a lactone or lactam
+ "33": "[#8X1$(*=[#6r]@[#7r,#8r]):1]",
+ # O1ester,acid Double-bonded oxygen in an ester or acid
+ "32": "[#8X1$(*=[#6X3]-[#8X2]):1]",
+ # O1,2 Univalent or divalent oxygen
+ "31": "[#8X1,#8X2:1]",
+ # # P3,4 Trivalent or tetravalent double-bonded phosphorus 42
+ # "42": "[#15X3$(*=[*]),#15X4$(*=[*]):1]",
+ # # P2,3 Divalent or trivalent phosphorus
+ # "41": "[#15X2,#15X3:1]",
+ # # S4 Tetravalent sulfur
+ "53": "[#16X4:1]",
+ # # S3 Trivalent sulfur
+ "52": "[#16X3:1]",
+ # # S1,2 Univalent or divalent sulfur
+ "51": "[#16X1,#16X2:1]",
+ # Si4 Tetravalent silicon
+ "61": "[#14X4:1]",
+ # F1 Fluorine
+ "71": "[#9:1]",
+ # Cl1 Chlorine
+ "72": "[#17:1]",
+ # Br1 Bromine
+ "73": "[#35:1]",
+ # # # I1 Iodine
+ "74": "[#53:1]",
+ # H1 Hydrogen
+ "91": "[#1:1]",
+ }
+ bond_codes = {
+ "01": "-", # Single bond
+ "02": "=", # Double bond
+ "03": "#", # Triple bond
+ "06": "-", # 'Single' Dative bond
+ "07": ":", # 'Single' aromatic Bond
+ "08": ":", # 'Double' aromatic Bond
+ "09": "~", # Single bond with charge or delocalized bond
+ }
+
+ custom_bcc_smirks = {
+ # 'Delocalised' S-O
+ # "310951": "",
+ # "310952": "",
+ # "310953": "",
+ # 'Delocalised' S-S
+ # "510953": "",
+ # 'Delocalised' S-C
+ "110951": "[#6X4:1]-[#16X1-1:2]",
+ "150951": "[#6X1,#6X2:1]-[#16X1-1:2]",
+ "120951": "[#6X3$(*=[#6]):1]-[#16X1-1:2]",
+ "130951": "[#6X3$(*=[#7,#15]):1]-[#16X1-1:2]",
+ "140951": "[#6X3:1](~[#8X1,#16X1])(~[#16X1:2])",
+ "170951": "[#6a$(*~[#7aX2,#8aX2]):1]-[#16X1-1:2]",
+ "160951": "[#6a:1]-[#16X1-1:2]",
+ # 'Delocalised' N-O
+ "230931": "[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]):1]~[#8X1:2]",
+ # Dative N-O.
+ "230631": "[#7X3+1:1]-[#8X1-1:2]",
+ "220631": "[#7X3$(*-[#6X3$(*=[#8])]):1]-[#8X1-1:2]",
+ "210631": "[#7X4+1:1]-[#8X1-1:2]",
+ "250631": "[#7X1,#7X2+1:1]-[#8X1-1:2]",
+ "240631": "[#7X2+0:1]-[#8X1-1:2]",
+ # 'Delocalised' C-O.
+ "110931": "[#6X4:1]-[#8X1-1:2]",
+ "150931": "[#6X1,#6X2:1]-[#8X1-1:2]",
+ "120931": "[#6X3$(*=[#6]):1]-[#8X1-1:2]",
+ "130931": "[#6X3$(*=[#7,#15]):1]-[#8X1-1:2]",
+ "140931": "[#6X3:1](~[#8X1,#16X1])(~[#8X1:2])",
+ "170931": "[#6a$(*~[#7aX2,#8aX2]):1]-[#8X1-1:2]",
+ "160931": "[#6a:1]-[#8X1-1:2]",
+ }
+
+ bcc_overrides = {"110112": 0.0024, "120114": -0.0172}
+
+ bcc_parameters = build_bond_charge_corrections(
+ atom_codes, bond_codes, bcc_overrides, custom_bcc_smirks
+ )
+
+ # Remove duplicate parameters caused by the duplication of the aromatic
+ # bond type.
+ bcc_parameters_per_smirks = {}
+ unique_bcc_parameters = []
+
+ for bcc_parameter in bcc_parameters:
+
+ if bcc_parameter.smirks in bcc_parameters_per_smirks:
+
+ assert numpy.isclose(
+ bcc_parameter.value,
+ bcc_parameters_per_smirks[bcc_parameter.smirks].value,
+ )
+ assert bcc_parameter.provenance["code"][2:4] in ["07", "08"]
+
+ continue
+
+ unique_bcc_parameters.append(bcc_parameter)
+ bcc_parameters_per_smirks[bcc_parameter.smirks] = bcc_parameter
+
+ with open("original-am1-bcc.json", "w") as file:
+
+ json.dump(
+ [bcc_parameter.dict() for bcc_parameter in unique_bcc_parameters], file
+ )
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/convert-am1-bcc/openeye-am1-bcc.json b/scripts/convert-am1-bcc/openeye-am1-bcc.json
new file mode 100644
index 0000000..aae1d3d
--- /dev/null
+++ b/scripts/convert-am1-bcc/openeye-am1-bcc.json
@@ -0,0 +1,4155 @@
+{
+ "parameters": [
+ {
+ "smirks": "[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]),$([#7X3](-[#8X1])-[#8X1]):1]~[#8X1:2]",
+ "value": -0.15,
+ "provenance": {
+ "code": "230931"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*=[#8,#16])]):1]-[#8X1-1:2]",
+ "value": 0.0465,
+ "provenance": {
+ "code": "220631"
+ }
+ },
+ {
+ "smirks": "[#7X4+1,#7X3+0$([*]-[#6X3]=,:[#7X2,#6X3]),#7X3+0$([*]-[#6X3]-,=,:[#7a,#6a]),#7X3+0$(*-[#6X4,#1]),#7X3+0$([*](-[#7X3])-[#7X3]),#7X3+0$([*](-[#8])-[#8]):1]-[#8X1-1:2]",
+ "value": -0.1168,
+ "provenance": {
+ "code": "210631"
+ }
+ },
+ {
+ "smirks": "[#7X3+1:1]-[#8X1-1:2]",
+ "value": 0.1317,
+ "provenance": {
+ "code": "230631"
+ }
+ },
+ {
+ "smirks": "[#7X2+0:1]-[#8X1-1:2]",
+ "value": -0.0817,
+ "provenance": {
+ "code": "240631"
+ }
+ },
+ {
+ "smirks": "[#6X4:1]-[#8X1-1:2]",
+ "value": 0.1615,
+ "provenance": {
+ "code": "110931"
+ }
+ },
+ {
+ "smirks": "[#6X2$([*]=[#8,#16]):1]=[#8X1:2]",
+ "value": 0.2549,
+ "provenance": {
+ "code": "150931"
+ }
+ },
+ {
+ "smirks": "[#6X1,#6X2:1]-[#8X1-1:2]",
+ "value": 0.2549,
+ "provenance": {
+ "code": "150931"
+ }
+ },
+ {
+ "smirks": "[#6X3$(*=[#6]):1]-[#8X1-1:2]",
+ "value": 0.1844,
+ "provenance": {
+ "code": "120931"
+ }
+ },
+ {
+ "smirks": "[#6X3$(*=[#7,#15]):1]-[#8X1-1:2]",
+ "value": 0.3046,
+ "provenance": {
+ "code": "130931"
+ }
+ },
+ {
+ "smirks": "[#6X3:1](~[#8X1,#16X1])(~[#8X1:2])",
+ "value": 0.2653,
+ "provenance": {
+ "code": "140931"
+ }
+ },
+ {
+ "smirks": "[#6a$(*~[#7aX2,#8aX2]):1]-[#8X1-1:2]",
+ "value": 0.337,
+ "provenance": {
+ "code": "170931"
+ }
+ },
+ {
+ "smirks": "[#6a:1]-[#8X1-1:2]",
+ "value": 0.2797,
+ "provenance": {
+ "code": "160931"
+ }
+ },
+ {
+ "smirks": "[#6X4:1]-[#16X1-1:2]",
+ "value": 0.0833,
+ "provenance": {
+ "code": "110951"
+ }
+ },
+ {
+ "smirks": "[#6X1,#6X2$([*]=[#8,#16]):1]=[#16:2]",
+ "value": 0.3281,
+ "provenance": {
+ "code": "150951"
+ }
+ },
+ {
+ "smirks": "[#6X1,#6X2:1]-[#16X1-1:2]",
+ "value": 0.3281,
+ "provenance": {
+ "code": "150951"
+ }
+ },
+ {
+ "smirks": "[#6X3$(*=[#6]):1]-[#16X1-1:2]",
+ "value": 0.1879,
+ "provenance": {
+ "code": "120951"
+ }
+ },
+ {
+ "smirks": "[#6X3$(*=[#7,#15]):1]-[#16X1-1:2]",
+ "value": 0.1969,
+ "provenance": {
+ "code": "130951"
+ }
+ },
+ {
+ "smirks": "[#6X3:1](~[#8X1,#16X1])(~[#16X1:2])",
+ "value": 0.1713,
+ "provenance": {
+ "code": "140951"
+ }
+ },
+ {
+ "smirks": "[#6a$(*~[#7aX2,#8aX2]):1]-[#16X1-1:2]",
+ "value": 0.3476,
+ "provenance": {
+ "code": "170951"
+ }
+ },
+ {
+ "smirks": "[#6a:1]-[#16X1-1:2]",
+ "value": 0.2541,
+ "provenance": {
+ "code": "160951"
+ }
+ },
+ {
+ "smirks": "[#16X1-1$([*]-S),#16X1+0$([*]=S):1]-,=[#16X4:2]",
+ "value": 0.5218,
+ "provenance": {
+ "code": "510953"
+ }
+ },
+ {
+ "smirks": "[#16X4$(*~[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]",
+ "value": 0.3228,
+ "provenance": {
+ "code": "310953"
+ }
+ },
+ {
+ "smirks": "[#16X3$(*=[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]",
+ "value": 0.3916,
+ "provenance": {
+ "code": "310952"
+ }
+ },
+ {
+ "smirks": "[#16X1,#16X2;$(*=[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]",
+ "value": 0.153,
+ "provenance": {
+ "code": "310951"
+ }
+ },
+ {
+ "smirks": "[#8X1:1]=[#15X4$([*](-[#8X1-1])(-[#6])-[#6,#1]):2]",
+ "value": 0.3195,
+ "provenance": {
+ "code": "310942"
+ }
+ },
+ {
+ "smirks": "[#8X1-1:1]-,:[#15X4$([*](-[#8X1-1])(-[#8X1-1])=[#8]):2]",
+ "value": 0.3195,
+ "provenance": {
+ "code": "310942"
+ }
+ },
+ {
+ "smirks": "[#8X1-1:1]-[#15X4$([*](=[#8X1])-[#8X1-1]):2]",
+ "value": 0.3195,
+ "provenance": {
+ "code": "310942"
+ }
+ },
+ {
+ "smirks": "[#8X1:1]-,=[#15X4$([*](-[#8X1-1])-[#8X1-1,#8X2,#16X2]):2]",
+ "value": 0.3195,
+ "provenance": {
+ "code": "310942"
+ }
+ },
+ {
+ "smirks": "[#8X2:1]-[#15X4+0,#15X3;!$(*=*):2]",
+ "value": 0.2229,
+ "provenance": {
+ "code": "310141"
+ }
+ },
+ {
+ "smirks": "[#8X1-1:1]~[#15&!$(*=*):2]",
+ "value": 0.2354,
+ "provenance": {
+ "code": "310941"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]-[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "230123"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]=[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "230223"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]#[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "230323"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]:[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "230723"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]~[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "230923"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]-[#7X3ar5:2]",
+ "value": -0.0327,
+ "provenance": {
+ "code": "220123"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]-[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "220122"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]=[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "220222"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]#[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "220322"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]:[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "220722"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]~[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "220922"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]-[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):2]",
+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
+ "smirks": "[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):1]-[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "230123"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]=[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):2]",
+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
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+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
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+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
+ "smirks": "[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):1]#[#7X3ar5:2]",
+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
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+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
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+ }
+ },
+ {
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+ "value": 0.0,
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+ }
+ },
+ {
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+ "value": 0.0,
+ "provenance": {
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+ }
+ },
+ {
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+ "value": -0.0327,
+ "provenance": {
+ "code": "220123"
+ }
+ },
+ {
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+ "value": 0.0,
+ "provenance": {
+ "code": "230123"
+ }
+ },
+ {
+ "smirks": "[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):1]=[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):2]",
+ "value": 0.0,
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+ }
+ },
+ {
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+ "value": 0.0,
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+ }
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+ }
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+ {
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+ },
+ {
+ "smirks": "[#9:1]~[#9:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "710971"
+ }
+ }
+ ]
+}
\ No newline at end of file
From 350966fcd59896f84cc6ec13bdcab3cf43d12e4c Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Mon, 17 Apr 2023 16:12:19 +1000
Subject: [PATCH 2/9] add preliminary conversion to offxml
---
.../convert-am1-bcc/convert_bccs_to_offxml.py | 52 +++++++++++++++++++
1 file changed, 52 insertions(+)
create mode 100644 scripts/convert-am1-bcc/convert_bccs_to_offxml.py
diff --git a/scripts/convert-am1-bcc/convert_bccs_to_offxml.py b/scripts/convert-am1-bcc/convert_bccs_to_offxml.py
new file mode 100644
index 0000000..b553143
--- /dev/null
+++ b/scripts/convert-am1-bcc/convert_bccs_to_offxml.py
@@ -0,0 +1,52 @@
+import click
+
+from openff.toolkit import ForceField
+from openff.units import unit
+from openff.recharge.charges.bcc import BCCCollection
+
+@click.command()
+@click.option(
+ "--input-file",
+ default="openeye-am1-bcc.json",
+ type=click.Path(exists=True, dir_okay=False, file_okay=True),
+ help="Input BCC collection (JSON)"
+)
+@click.option(
+ "--output-file",
+ default="openeye-am1-bcc.offxml",
+ type=click.Path(exists=False, dir_okay=False, file_okay=True),
+ help="Output BCC force field (offxml)"
+)
+@click.option(
+ "--partial-charge-method",
+ default="AM1-Mulliken",
+ type=click.Choice(["zeros", "AM1-Mulliken"]),
+ help=(
+ "Charge method to use in combination with the BCCs. "
+ "Use 'zeros' for debugging, 'AM1-Mulliken' for production."
+ )
+)
+def convert_bccs_to_offxml(
+ input_file,
+ output_file,
+ partial_charge_method,
+):
+ collection = BCCCollection.parse_file(input_file)
+ ff = ForceField()
+
+ ff.get_parameter_handler("Electrostatics")
+ handler = ff.get_parameter_handler("ChargeIncrementModel")
+ handler.partial_charge_method = partial_charge_method
+
+ for parameter in collection.parameters[::-1]:
+ handler.add_parameter({
+ "smirks": parameter.smirks,
+ "charge_increment": [parameter.value * unit.elementary_charge],
+ "id": parameter.provenance["code"]
+ })
+
+ ff.to_file(output_file)
+
+
+if __name__ == "__main__":
+ convert_bccs_to_offxml()
From 0e52f3618a0412fed6c9e9d65bcb3cec557ca5f2 Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Mon, 17 Apr 2023 16:13:45 +1000
Subject: [PATCH 3/9] add original BCC file
---
scripts/convert-am1-bcc/legacy/convert.py | 1 +
scripts/convert-am1-bcc/legacy/original-am1-bcc.json | 1 +
2 files changed, 2 insertions(+)
create mode 100644 scripts/convert-am1-bcc/legacy/original-am1-bcc.json
diff --git a/scripts/convert-am1-bcc/legacy/convert.py b/scripts/convert-am1-bcc/legacy/convert.py
index 4a7daa7..1ec4e03 100644
--- a/scripts/convert-am1-bcc/legacy/convert.py
+++ b/scripts/convert-am1-bcc/legacy/convert.py
@@ -46,6 +46,7 @@ def build_bond_charge_corrections(
bcc_frame = pandas.read_csv("am1bcc.csv")
bcc_frame["BCC"] = bcc_frame["BCC"].round(4)
+ bcc_frame["Code"] = bcc_frame["Code"].astype(str)
bcc_frame = bcc_frame.sort_values(by=["Index"])
unconverted_codes = bcc_frame[~bcc_frame["Code"].isin(all_codes)]
diff --git a/scripts/convert-am1-bcc/legacy/original-am1-bcc.json b/scripts/convert-am1-bcc/legacy/original-am1-bcc.json
new file mode 100644
index 0000000..7b85542
--- /dev/null
+++ b/scripts/convert-am1-bcc/legacy/original-am1-bcc.json
@@ -0,0 +1 @@
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{"smirks": "[#16X1,#16X2:1]~[#16X4:2]", "value": 0.5218, "provenance": {"code": "510953"}}, {"smirks": "[#14X4:1]-[#17:2]", "value": -0.0555, "provenance": {"code": "610172"}}, {"smirks": "[#14X4:1]-[#1:2]", "value": -0.0258, "provenance": {"code": "610191"}}]
\ No newline at end of file
From 9292e4a729a5f919bffc46f8fabf3f9e892f9a3f Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Mon, 17 Apr 2023 16:45:21 +1000
Subject: [PATCH 4/9] replace original_am1bcc_corrections
---
openff/recharge/charges/bcc.py | 15 +-
openff/recharge/data/bcc/openeye-am1-bcc.json | 4155 +++++++++++++++++
2 files changed, 4160 insertions(+), 10 deletions(-)
create mode 100644 openff/recharge/data/bcc/openeye-am1-bcc.json
diff --git a/openff/recharge/charges/bcc.py b/openff/recharge/charges/bcc.py
index 4551b80..c794e98 100644
--- a/openff/recharge/charges/bcc.py
+++ b/openff/recharge/charges/bcc.py
@@ -454,19 +454,14 @@ def original_am1bcc_corrections() -> BCCCollection:
23(16), 1623–1641.
"""
bcc_file_path = get_data_file_path(
- os.path.join("bcc", "original-am1-bcc.json"), "openff.recharge"
+ os.path.join("bcc", "openeye-am1-bcc.json"), "openff.recharge"
)
- with open(bcc_file_path) as file:
- bcc_dictionaries = json.load(file)
-
- bond_charge_corrections = [
- BCCParameter(**dictionary) for dictionary in bcc_dictionaries
- ]
-
- return BCCCollection(
- parameters=bond_charge_corrections, aromaticity_model=AromaticityModels.AM1BCC
+ collection = BCCCollection.parse_file(
+ bcc_file_path
)
+ collection.aromaticity_model = AromaticityModels.AM1BCC
+ return collection
def compare_openeye_parity(molecule: "Molecule") -> bool:
diff --git a/openff/recharge/data/bcc/openeye-am1-bcc.json b/openff/recharge/data/bcc/openeye-am1-bcc.json
new file mode 100644
index 0000000..aae1d3d
--- /dev/null
+++ b/openff/recharge/data/bcc/openeye-am1-bcc.json
@@ -0,0 +1,4155 @@
+{
+ "parameters": [
+ {
+ "smirks": "[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]),$([#7X3](-[#8X1])-[#8X1]):1]~[#8X1:2]",
+ "value": -0.15,
+ "provenance": {
+ "code": "230931"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*=[#8,#16])]):1]-[#8X1-1:2]",
+ "value": 0.0465,
+ "provenance": {
+ "code": "220631"
+ }
+ },
+ {
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+ "value": -0.1168,
+ "provenance": {
+ "code": "210631"
+ }
+ },
+ {
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+ "value": 0.1317,
+ "provenance": {
+ "code": "230631"
+ }
+ },
+ {
+ "smirks": "[#7X2+0:1]-[#8X1-1:2]",
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+ "provenance": {
+ "code": "240631"
+ }
+ },
+ {
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+ "value": 0.1615,
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+ "code": "110931"
+ }
+ },
+ {
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+ "value": 0.2549,
+ "provenance": {
+ "code": "150931"
+ }
+ },
+ {
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+ "value": 0.2549,
+ "provenance": {
+ "code": "150931"
+ }
+ },
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+ }
+ },
+ {
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+ }
+ },
+ {
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+ "value": 0.2653,
+ "provenance": {
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+ }
+ },
+ {
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+ "value": 0.337,
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+ }
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+ {
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+ }
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+ },
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+ "code": "150951"
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+ }
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+ "code": "420172"
+ }
+ },
+ {
+ "smirks": "[#15:1]-[#17:2]",
+ "value": -0.2065,
+ "provenance": {
+ "code": "410172"
+ }
+ },
+ {
+ "smirks": "[#16X4:1]-[#17:2]",
+ "value": -0.2761,
+ "provenance": {
+ "code": "530172"
+ }
+ },
+ {
+ "smirks": "[#16X3:1]-[#17:2]",
+ "value": -0.235,
+ "provenance": {
+ "code": "520172"
+ }
+ },
+ {
+ "smirks": "[#16X1,#16X2:1]-[#17:2]",
+ "value": -0.026,
+ "provenance": {
+ "code": "510172"
+ }
+ },
+ {
+ "smirks": "[#14X4:1]-[#17:2]",
+ "value": -0.0555,
+ "provenance": {
+ "code": "610172"
+ }
+ },
+ {
+ "smirks": "[#17:1]-[#17:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "720172"
+ }
+ },
+ {
+ "smirks": "[#17:1]=[#17:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "720272"
+ }
+ },
+ {
+ "smirks": "[#17:1]#[#17:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "720372"
+ }
+ },
+ {
+ "smirks": "[#17:1]:[#17:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "720772"
+ }
+ },
+ {
+ "smirks": "[#17:1]~[#17:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "720972"
+ }
+ },
+ {
+ "smirks": "[#7X3ar5:1]-[#9:2]",
+ "value": 0.0561,
+ "provenance": {
+ "code": "230171"
+ }
+ },
+ {
+ "smirks": "[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]-[#9:2]",
+ "value": -0.0155,
+ "provenance": {
+ "code": "220171"
+ }
+ },
+ {
+ "smirks": "[#7X3r5$([*](-,:[r5])(-,:[r5])-[!#1&!#6X4&!#6a]),#7X3r5$([*]1(-,:[r5]=,:[r5]-,:[r5]=,:[r5]:,-1)-[!#1&!#6a!#6X4]),#7X3+1,#7X3$([*](~[#8X1])~[#8X1]),#7X3+0$(*-[#6X3$(*=[#7X3+1])]):1]-[#9:2]",
+ "value": 0.0561,
+ "provenance": {
+ "code": "230171"
+ }
+ },
+ {
+ "smirks": "[#7X2$(*(-,:[*])-,:[#6X3$(*=[#8,#16])]):1]-[#9:2]",
+ "value": -0.0155,
+ "provenance": {
+ "code": "220171"
+ }
+ },
+ {
+ "smirks": "[#7X4,#7X3,#7X2-1A:1]-[#9:2]",
+ "value": -0.0204,
+ "provenance": {
+ "code": "210171"
+ }
+ },
+ {
+ "smirks": "[#7X2+0,#7X2-1ar5:1]-[#9:2]",
+ "value": -0.0554,
+ "provenance": {
+ "code": "240171"
+ }
+ },
+ {
+ "smirks": "[#6X3A$(*=[#6]):1]-[#9:2]",
+ "value": 0.0625,
+ "provenance": {
+ "code": "120171"
+ }
+ },
+ {
+ "smirks": "[#6X3$(*=[#8X1,#8X2+1,#16+0]):1]-[#9:2]",
+ "value": 0.1115,
+ "provenance": {
+ "code": "140171"
+ }
+ },
+ {
+ "smirks": "[#6X3$(*=[#7,#15]):1]-[#9:2]",
+ "value": 0.1055,
+ "provenance": {
+ "code": "130171"
+ }
+ },
+ {
+ "smirks": "[#6aX3$(*~[#7aX2,#8aX2]),#6X3R$(*~[#7aX2,#8aX2])&$([*](-,:[R]-,=,:[R])=,:[R]):1]-[#9:2]",
+ "value": 0.1402,
+ "provenance": {
+ "code": "170171"
+ }
+ },
+ {
+ "smirks": "[#6a,#6X3R$([*](-,:[R]-,=,:[R])=,:[R]):1]-[#9:2]",
+ "value": 0.0349,
+ "provenance": {
+ "code": "160171"
+ }
+ },
+ {
+ "smirks": "[#6X3:1]-[#9:2]",
+ "value": 0.0625,
+ "provenance": {
+ "code": "120171"
+ }
+ },
+ {
+ "smirks": "[#6X1,#6X2:1]-[#9:2]",
+ "value": 0.0021,
+ "provenance": {
+ "code": "150171"
+ }
+ },
+ {
+ "smirks": "[#6X4:1]-[#9:2]",
+ "value": 0.0713,
+ "provenance": {
+ "code": "110171"
+ }
+ },
+ {
+ "smirks": "[#8:1]-[#9:2]",
+ "value": 0.0375,
+ "provenance": {
+ "code": "310171"
+ }
+ },
+ {
+ "smirks": "[#15X4,#15X3$(*=[*]):1]-[#9:2]",
+ "value": -0.1976,
+ "provenance": {
+ "code": "420171"
+ }
+ },
+ {
+ "smirks": "[#15:1]-[#9:2]",
+ "value": -0.2769,
+ "provenance": {
+ "code": "410171"
+ }
+ },
+ {
+ "smirks": "[#16X4:1]-[#9:2]",
+ "value": -0.2041,
+ "provenance": {
+ "code": "530171"
+ }
+ },
+ {
+ "smirks": "[#16X1,#16X2:1]-[#9:2]",
+ "value": -0.0547,
+ "provenance": {
+ "code": "510171"
+ }
+ },
+ {
+ "smirks": "[#9:1]-[#9:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "710171"
+ }
+ },
+ {
+ "smirks": "[#9:1]=[#9:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "710271"
+ }
+ },
+ {
+ "smirks": "[#9:1]#[#9:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "710371"
+ }
+ },
+ {
+ "smirks": "[#9:1]:[#9:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "710771"
+ }
+ },
+ {
+ "smirks": "[#9:1]~[#9:2]",
+ "value": 0.0,
+ "provenance": {
+ "code": "710971"
+ }
+ }
+ ]
+}
\ No newline at end of file
From 3026580637a05a953abab17c416bde7abfc5a168 Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Tue, 18 Apr 2023 06:09:19 +1000
Subject: [PATCH 5/9] update with ff
---
.../convert-am1-bcc/openeye-am1-bcc.offxml | 599 ++++++++++++++++++
1 file changed, 599 insertions(+)
create mode 100644 scripts/convert-am1-bcc/openeye-am1-bcc.offxml
diff --git a/scripts/convert-am1-bcc/openeye-am1-bcc.offxml b/scripts/convert-am1-bcc/openeye-am1-bcc.offxml
new file mode 100644
index 0000000..a7e0048
--- /dev/null
+++ b/scripts/convert-am1-bcc/openeye-am1-bcc.offxml
@@ -0,0 +1,599 @@
+
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\ No newline at end of file
From 0a70678903f4a14d71b2cf14263bd5819c2363bc Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Wed, 24 May 2023 07:44:17 +1000
Subject: [PATCH 6/9] add force field
---
.../recharge/data/bcc/openeye-am1-bcc.offxml | 599 ++++++++++++++++++
1 file changed, 599 insertions(+)
create mode 100644 openff/recharge/data/bcc/openeye-am1-bcc.offxml
diff --git a/openff/recharge/data/bcc/openeye-am1-bcc.offxml b/openff/recharge/data/bcc/openeye-am1-bcc.offxml
new file mode 100644
index 0000000..a7e0048
--- /dev/null
+++ b/openff/recharge/data/bcc/openeye-am1-bcc.offxml
@@ -0,0 +1,599 @@
+
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\ No newline at end of file
From ddf5f07a53ed26d375a0533a778d5ebe4824564f Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Wed, 24 May 2023 07:44:40 +1000
Subject: [PATCH 7/9] remove old convert script
---
scripts/convert-am1-bcc/convert.py | 230 ----------------------
scripts/convert-am1-bcc/legacy/convert.py | 3 +-
2 files changed, 1 insertion(+), 232 deletions(-)
delete mode 100644 scripts/convert-am1-bcc/convert.py
diff --git a/scripts/convert-am1-bcc/convert.py b/scripts/convert-am1-bcc/convert.py
deleted file mode 100644
index 1ca0c83..0000000
--- a/scripts/convert-am1-bcc/convert.py
+++ /dev/null
@@ -1,230 +0,0 @@
-"""This script converts the original AM1BCC values [1]_ into the data model expected by
-this framework.
-
-References
-----------
-[1] Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation of
- high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
- Journal of computational chemistry, 23(16), 1623–1641.
-"""
-import json
-import logging
-from typing import Dict, List
-
-import numpy
-import pandas
-from openeye import oechem
-
-from openff.recharge.charges.bcc import BCCParameter
-
-logging.basicConfig()
-logger = logging.getLogger(__name__)
-
-
-def build_bond_charge_corrections(
- atom_codes: Dict[str, str],
- bond_codes: Dict[str, str],
- bcc_overrides: Dict[str, float],
- custom_bcc_smirks: Dict[str, str],
-) -> List[BCCParameter]:
-
- # Convert the atom and bond codes into the six number codes used
- # in the AM1BCC paper.
- all_codes = [*custom_bcc_smirks]
-
- for first_atom_code in atom_codes:
- for bond_code in bond_codes:
- for last_atom_code in atom_codes:
-
- code = f"{first_atom_code}{bond_code}{last_atom_code}"
-
- if code not in all_codes:
- all_codes.append(code)
-
- # Remove any BCCs defined for bond or atom codes which haven't yet been
- # specified.
- bcc_frame = pandas.read_csv("am1bcc.csv")
-
- bcc_frame["BCC"] = bcc_frame["BCC"].round(4)
- bcc_frame = bcc_frame.sort_values(by=["Index"])
-
- unconverted_codes = bcc_frame[~bcc_frame["Code"].isin(all_codes)]
-
- for unconverted_code in unconverted_codes["Code"].unique():
- logger.warning(f"{unconverted_code} was not converted.")
-
- bcc_frame = bcc_frame[bcc_frame["Code"].isin(all_codes)]
-
- # Convert the data frame into a collection of correction objects.
- bond_charge_corrections = {}
-
- for _, bcc_row in bcc_frame.iterrows():
-
- code = str(bcc_row["Code"])[0:6]
-
- first_atom_code = code[0:2]
- bond_code = code[2:4]
- last_atom_code = code[4:6]
-
- smirks = (
- f"{atom_codes[first_atom_code]}"
- f"{bond_codes[bond_code]}"
- f"{atom_codes[last_atom_code].replace(':1', ':2')}"
- )
-
- if code in custom_bcc_smirks:
- smirks = custom_bcc_smirks.pop(code)
-
- # Validate the smirks
- query = oechem.OEQMol()
- assert oechem.OEParseSmarts(query, smirks)
-
- value = bcc_overrides.get(code, bcc_row["BCC"])
-
- bond_charge_corrections[code] = BCCParameter(
- smirks=smirks, value=value, provenance={"code": code}
- )
-
- assert len(custom_bcc_smirks) == 0
-
- return [
- bond_charge_corrections[code]
- for code in all_codes
- if code in bond_charge_corrections
- ]
-
-
-def main():
-
- atom_codes = {
- # C4 Tetravalent carbon
- "11": "[#6X4:1]",
- # # C1,2 Univalent or divalent carbon
- "15": "[#6X1,#6X2:1]",
- # C3=C Trivalent carbon, double bonded to carbon
- "12": "[#6X3$(*=[#6]):1]",
- # C3=N,P Trivalent carbon, double bonded to nitrogen or phosphorus
- "13": "[#6X3$(*=[#7,#15]):1]",
- # C3=O,S Trivalent carbon, double bonded to oxygen or sulfur
- "14": "[#6X3$(*=[#8,#16]):1]",
- # Carlp Aromatic carbon bonded to an aromatic oxygen or nitrogen with a lone pair
- "17": "[#6a$(*~[#7aX2,#8aX2]):1]",
- # Car Aromatic carbon
- "16": "[#6a:1]",
- # N3hdeloc Trivalent nitrogen with a highly delocalized lone pair
- "23": "[#7X3ar5,#7X3+1,#7X3+0$(*-[#6X3$(*=[#7X3+1])]),$([#7X3](-[#8X1-1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]):1]", # noqa
- # N3deloc Trivalent nitrogen with a delocalized lone pair
- "22": "[#7X2-1$(*-[#6X3$(*=[#8X1,#16X1])]),#7X3$(*-[#6X3$(*=[#8X1,#16X1])]):1]",
- # N2,3,4 Amine nitrogen
- "21": "[#7X4,#7X3,#7X2-1:1]",
- # N1,2 Univalent or cationic divalent nitrogen
- "25": "[#7X1,#7X2+1:1]",
- # N2 Neutral divalent nitrogen
- "24": "[#7X2+0,#7X2-1ar5:1]",
- # O1lact Double-bonded oxygen in a lactone or lactam
- "33": "[#8X1$(*=[#6r]@[#7r,#8r]):1]",
- # O1ester,acid Double-bonded oxygen in an ester or acid
- "32": "[#8X1$(*=[#6X3]-[#8X2]):1]",
- # O1,2 Univalent or divalent oxygen
- "31": "[#8X1,#8X2:1]",
- # # P3,4 Trivalent or tetravalent double-bonded phosphorus 42
- # "42": "[#15X3$(*=[*]),#15X4$(*=[*]):1]",
- # # P2,3 Divalent or trivalent phosphorus
- # "41": "[#15X2,#15X3:1]",
- # # S4 Tetravalent sulfur
- "53": "[#16X4:1]",
- # # S3 Trivalent sulfur
- "52": "[#16X3:1]",
- # # S1,2 Univalent or divalent sulfur
- "51": "[#16X1,#16X2:1]",
- # Si4 Tetravalent silicon
- "61": "[#14X4:1]",
- # F1 Fluorine
- "71": "[#9:1]",
- # Cl1 Chlorine
- "72": "[#17:1]",
- # Br1 Bromine
- "73": "[#35:1]",
- # # # I1 Iodine
- "74": "[#53:1]",
- # H1 Hydrogen
- "91": "[#1:1]",
- }
- bond_codes = {
- "01": "-", # Single bond
- "02": "=", # Double bond
- "03": "#", # Triple bond
- "06": "-", # 'Single' Dative bond
- "07": ":", # 'Single' aromatic Bond
- "08": ":", # 'Double' aromatic Bond
- "09": "~", # Single bond with charge or delocalized bond
- }
-
- custom_bcc_smirks = {
- # 'Delocalised' S-O
- # "310951": "",
- # "310952": "",
- # "310953": "",
- # 'Delocalised' S-S
- # "510953": "",
- # 'Delocalised' S-C
- "110951": "[#6X4:1]-[#16X1-1:2]",
- "150951": "[#6X1,#6X2:1]-[#16X1-1:2]",
- "120951": "[#6X3$(*=[#6]):1]-[#16X1-1:2]",
- "130951": "[#6X3$(*=[#7,#15]):1]-[#16X1-1:2]",
- "140951": "[#6X3:1](~[#8X1,#16X1])(~[#16X1:2])",
- "170951": "[#6a$(*~[#7aX2,#8aX2]):1]-[#16X1-1:2]",
- "160951": "[#6a:1]-[#16X1-1:2]",
- # 'Delocalised' N-O
- "230931": "[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]):1]~[#8X1:2]",
- # Dative N-O.
- "230631": "[#7X3+1:1]-[#8X1-1:2]",
- "220631": "[#7X3$(*-[#6X3$(*=[#8])]):1]-[#8X1-1:2]",
- "210631": "[#7X4+1:1]-[#8X1-1:2]",
- "250631": "[#7X1,#7X2+1:1]-[#8X1-1:2]",
- "240631": "[#7X2+0:1]-[#8X1-1:2]",
- # 'Delocalised' C-O.
- "110931": "[#6X4:1]-[#8X1-1:2]",
- "150931": "[#6X1,#6X2:1]-[#8X1-1:2]",
- "120931": "[#6X3$(*=[#6]):1]-[#8X1-1:2]",
- "130931": "[#6X3$(*=[#7,#15]):1]-[#8X1-1:2]",
- "140931": "[#6X3:1](~[#8X1,#16X1])(~[#8X1:2])",
- "170931": "[#6a$(*~[#7aX2,#8aX2]):1]-[#8X1-1:2]",
- "160931": "[#6a:1]-[#8X1-1:2]",
- }
-
- bcc_overrides = {"110112": 0.0024, "120114": -0.0172}
-
- bcc_parameters = build_bond_charge_corrections(
- atom_codes, bond_codes, bcc_overrides, custom_bcc_smirks
- )
-
- # Remove duplicate parameters caused by the duplication of the aromatic
- # bond type.
- bcc_parameters_per_smirks = {}
- unique_bcc_parameters = []
-
- for bcc_parameter in bcc_parameters:
-
- if bcc_parameter.smirks in bcc_parameters_per_smirks:
-
- assert numpy.isclose(
- bcc_parameter.value,
- bcc_parameters_per_smirks[bcc_parameter.smirks].value,
- )
- assert bcc_parameter.provenance["code"][2:4] in ["07", "08"]
-
- continue
-
- unique_bcc_parameters.append(bcc_parameter)
- bcc_parameters_per_smirks[bcc_parameter.smirks] = bcc_parameter
-
- with open("original-am1-bcc.json", "w") as file:
-
- json.dump(
- [bcc_parameter.dict() for bcc_parameter in unique_bcc_parameters], file
- )
-
-
-if __name__ == "__main__":
- main()
diff --git a/scripts/convert-am1-bcc/legacy/convert.py b/scripts/convert-am1-bcc/legacy/convert.py
index 1ec4e03..1ca0c83 100644
--- a/scripts/convert-am1-bcc/legacy/convert.py
+++ b/scripts/convert-am1-bcc/legacy/convert.py
@@ -46,7 +46,6 @@ def build_bond_charge_corrections(
bcc_frame = pandas.read_csv("am1bcc.csv")
bcc_frame["BCC"] = bcc_frame["BCC"].round(4)
- bcc_frame["Code"] = bcc_frame["Code"].astype(str)
bcc_frame = bcc_frame.sort_values(by=["Index"])
unconverted_codes = bcc_frame[~bcc_frame["Code"].isin(all_codes)]
@@ -113,7 +112,7 @@ def main():
# Car Aromatic carbon
"16": "[#6a:1]",
# N3hdeloc Trivalent nitrogen with a highly delocalized lone pair
- "23": "[#7X3ar5,#7X3+1,#7X3+0$(*-[#6X3$(*=[#7X3+1])]),$([#7X3](-[#8X1-1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]):1]",
+ "23": "[#7X3ar5,#7X3+1,#7X3+0$(*-[#6X3$(*=[#7X3+1])]),$([#7X3](-[#8X1-1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]):1]", # noqa
# N3deloc Trivalent nitrogen with a delocalized lone pair
"22": "[#7X2-1$(*-[#6X3$(*=[#8X1,#16X1])]),#7X3$(*-[#6X3$(*=[#8X1,#16X1])]):1]",
# N2,3,4 Amine nitrogen
From 49853a66f48dad7cd75223f07e7842c054d2a1a8 Mon Sep 17 00:00:00 2001
From: Lily Wang
Date: Fri, 30 Jun 2023 15:09:28 +1000
Subject: [PATCH 8/9] fix formatting
---
openff/recharge/charges/bcc.py | 1 -
.../convert-am1-bcc/convert_bccs_to_offxml.py | 1 +
.../generate_original_am1bcc.py | 79 ++++++++-----------
3 files changed, 34 insertions(+), 47 deletions(-)
diff --git a/openff/recharge/charges/bcc.py b/openff/recharge/charges/bcc.py
index c794e98..65ac33b 100644
--- a/openff/recharge/charges/bcc.py
+++ b/openff/recharge/charges/bcc.py
@@ -1,5 +1,4 @@
"""Generate bond charge corrections for molecules from a collection of BCC parameters."""
-import json
import os
from typing import TYPE_CHECKING, Any, Dict, List, Optional
diff --git a/scripts/convert-am1-bcc/convert_bccs_to_offxml.py b/scripts/convert-am1-bcc/convert_bccs_to_offxml.py
index b553143..f48104d 100644
--- a/scripts/convert-am1-bcc/convert_bccs_to_offxml.py
+++ b/scripts/convert-am1-bcc/convert_bccs_to_offxml.py
@@ -4,6 +4,7 @@
from openff.units import unit
from openff.recharge.charges.bcc import BCCCollection
+
@click.command()
@click.option(
"--input-file",
diff --git a/scripts/convert-am1-bcc/generate_original_am1bcc.py b/scripts/convert-am1-bcc/generate_original_am1bcc.py
index 70279c3..1f9f2dc 100644
--- a/scripts/convert-am1-bcc/generate_original_am1bcc.py
+++ b/scripts/convert-am1-bcc/generate_original_am1bcc.py
@@ -25,7 +25,6 @@
GENERAL_ATOM_CODES = {
# from more general to more specific
# patterns will get matched with more specific ones so order is important!
-
"X": {
# === HALOGENS ===
# F1 Fluorine
@@ -42,9 +41,8 @@
# H1 Hydrogen
"91": [r"[#1:1]"],
},
-
"S": {
- # === SULFUR ===
+ # === SULFUR ===
# S1,2 Univalent or divalent sulfur
"51": [r"[#16X1:1]", "[#16X2:1]"],
# S3 Trivalent sulfur
@@ -52,19 +50,15 @@
# S4 Tetravalent sulfur
"53": [r"[#16X4:1]"],
},
-
-
"P": {
# === PHOSPHORUS ===
# P2,3 Divalent or trivalent phosphorus
# "41": [r"[#15:1]", "[#15X2:1]", "[15X1:1]", "[#15X3:1]"],
"41": [r"[#15:1]"],
-
# P3,4 Trivalent or tetravalent double-bonded phosphorus
# "42": [r"[15X4:1]", "[#15X3;$(*=[*]):1]"],
"42": [r"[#15X4,#15X3$(*=[*]):1]"],
},
-
"O": {
# === OXYGEN ===
# O1,2 Univalent or divalent oxygen
@@ -75,33 +69,33 @@
# O1lact Double-bonded oxygen in a lactone or lactam
"33": [r"[#8X1$(*=[#6r]@[#7r,#8r]):1]"],
},
-
"C": {
# === CARBON ===
# C4 Tetravalent carbon
"11": [r"[#6X4:1]"],
# C1,2 Univalent or divalent carbon
- "15": [r"[#6X1:1]","[#6X2:1]"],
+ "15": [r"[#6X1:1]", "[#6X2:1]"],
# C3=C Trivalent carbon, double bonded to carbon
"12": [r"[#6X3:1]"],
# Car Aromatic carbon
"16": [
r"[#6a:1]",
# or planar ring with two continuous single bonds and at least two double bonds
- r"[#6X3R$([*](-,:[R]-,=,:[R])=,:[R]):1]"
+ r"[#6X3R$([*](-,:[R]-,=,:[R])=,:[R]):1]",
],
# Carlp Aromatic carbon bonded to an aromatic oxygen or nitrogen with a lone pair
"17": [
r"[#6aX3$(*~[#7aX2,#8aX2]):1]",
- r"[#6X3R$(*~[#7aX2,#8aX2])&$([*](-,:[R]-,=,:[R])=,:[R]):1]"
+ r"[#6X3R$(*~[#7aX2,#8aX2])&$([*](-,:[R]-,=,:[R])=,:[R]):1]",
],
# C3=N,P Trivalent carbon, double bonded to nitrogen or phosphorus
- "13": [r"[#6X3$(*=[#7,#15]):1]",],
+ "13": [
+ r"[#6X3$(*=[#7,#15]):1]",
+ ],
# C3=O,S Trivalent carbon, double bonded to oxygen or sulfur
"14": [r"[#6X3$(*=[#8X1,#8X2+1,#16+0]):1]"],
"12b": [r"[#6X3A$(*=[#6]):1]"],
},
-
"N": {
# === NITROGEN ===
# N1,2 Univalent or cationic divalent nitrogen
@@ -109,7 +103,11 @@
# N2 Neutral divalent nitrogen
"24": [r"[#7X2+0,#7X2-1ar5:1]"],
# N2,3,4 Amine nitrogen
- "21": [r"[#7X4:1]", r"[#7X3:1]", r"[#7X2-1A:1]"],# "[#7X2$([*](-,:[*])-,:[*]):1]"],
+ "21": [
+ r"[#7X4:1]",
+ r"[#7X3:1]",
+ r"[#7X2-1A:1]",
+ ], # "[#7X2$([*](-,:[*])-,:[*]):1]"],
# N3deloc Trivalent nitrogen with a delocalized lone pair
"22": [
r"[#7X2$(*(-,:[*])-,:[#6X3$(*=[#8,#16])]):1]", # N2-C(=O,S),
@@ -124,57 +122,48 @@
r"[#7X3+0$(*-[#6X3$(*=[#7X3+1])]):1]",
],
"22b": [
- r"[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]", # amide
+ r"[#7X3+0$(*-[#6X3$(*(=,:[#8,#16])-[!#8&!#16])]):1]", # amide
# "[#7X3+0$(*-[#6X3$(*(=[#8X2+1]-[#7X2-1])-[!#8&!#16])]):1]",
],
"23b": [
r"[#7X3ar5:1]",
- ]
- }
+ ],
+ },
}
SPECIFIC_PATTERNS = {
# P-O
r"[#8X1-1:1]~[#15&!$(*=*):2]": "310941",
r"[#8X2:1]-[#15X4+0,#15X3;!$(*=*):2]": "310141",
-
r"[#8X1:1]-,=[#15X4$([*](-[#8X1-1])-[#8X1-1,#8X2,#16X2]):2]": "310942",
r"[#8X1-1:1]-[#15X4$([*](=[#8X1])-[#8X1-1]):2]": "310942",
r"[#8X1-1:1]-,:[#15X4$([*](-[#8X1-1])(-[#8X1-1])=[#8]):2]": "310942",
r"[#8X1:1]=[#15X4$([*](-[#8X1-1])(-[#6])-[#6,#1]):2]": "310942",
-
-
# ...
-
# 'Delocalised' S-O
r"[#16X1,#16X2;$(*=[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]": "310951",
r"[#16X3$(*=[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]": "310952",
r"[#16X4$(*~[#8X1]);$(*-[#8X1-1]):2]~[#8X1:1]": "310953",
-
-
# 'Delocalised' S-S
r"[#16X1-1$([*]-S),#16X1+0$([*]=S):1]-,=[#16X4:2]": "510953",
-
# 'Delocalised' S-C
- r"[#6a:1]-[#16X1-1:2]" : "160951",
- r"[#6a$(*~[#7aX2,#8aX2]):1]-[#16X1-1:2]" : "170951",
+ r"[#6a:1]-[#16X1-1:2]": "160951",
+ r"[#6a$(*~[#7aX2,#8aX2]):1]-[#16X1-1:2]": "170951",
r"[#6X3:1](~[#8X1,#16X1])(~[#16X1:2])": "140951",
r"[#6X3$(*=[#7,#15]):1]-[#16X1-1:2]": "130951",
r"[#6X3$(*=[#6]):1]-[#16X1-1:2]": "120951",
r"[#6X1,#6X2:1]-[#16X1-1:2]": "150951",
r"[#6X1,#6X2$([*]=[#8,#16]):1]=[#16:2]": "150951",
r"[#6X4:1]-[#16X1-1:2]": "110951",
-
# 'Delocalised' C-O
- r"[#6a:1]-[#8X1-1:2]" : "160931",
- r"[#6a$(*~[#7aX2,#8aX2]):1]-[#8X1-1:2]" : "170931",
+ r"[#6a:1]-[#8X1-1:2]": "160931",
+ r"[#6a$(*~[#7aX2,#8aX2]):1]-[#8X1-1:2]": "170931",
r"[#6X3:1](~[#8X1,#16X1])(~[#8X1:2])": "140931",
- r"[#6X3$(*=[#7,#15]):1]-[#8X1-1:2]" : "130931",
+ r"[#6X3$(*=[#7,#15]):1]-[#8X1-1:2]": "130931",
r"[#6X3$(*=[#6]):1]-[#8X1-1:2]": "120931",
- r"[#6X1,#6X2:1]-[#8X1-1:2]" : "150931",
- r"[#6X2$([*]=[#8,#16]):1]=[#8X1:2]" : "150931",
- r"[#6X4:1]-[#8X1-1:2]" : "110931",
-
+ r"[#6X1,#6X2:1]-[#8X1-1:2]": "150931",
+ r"[#6X2$([*]=[#8,#16]):1]=[#8X1:2]": "150931",
+ r"[#6X4:1]-[#8X1-1:2]": "110931",
# 'Delocalised' N-O
r"[#7X2+0:1]-[#8X1-1:2]": "240631",
r"[#7X3+1:1]-[#8X1-1:2]": "230631",
@@ -215,13 +204,13 @@ def build_bccs(
not_atom_map = [smirks[1:-3] for smirks in all_atom_smirks]
final_smirks = f"[{','.join(not_atom_map)}:1]"
flat_atom_codes[final_smirks] = atom_code[:2]
-
+
# create bcc patterns from less to more specific
bcc_patterns = []
- for (
- (atom_smirks1, atom_code1),
- (atom_smirks2, atom_code2)
- ) in itertools.combinations_with_replacement(flat_atom_codes.items(), 2):
+ for (atom_smirks1, atom_code1), (
+ atom_smirks2,
+ atom_code2,
+ ) in itertools.combinations_with_replacement(flat_atom_codes.items(), 2):
for bond_code, bond_smirks in GENERAL_BOND_CODES.items():
smirks = atom_smirks1 + bond_smirks + atom_smirks2.replace(":1", ":2")
code = atom_code1 + bond_code + atom_code2
@@ -253,11 +242,7 @@ def build_bccs(
query = oechem.OEQMol()
assert oechem.OEParseSmarts(query, smirks)
- bcc = BCCParameter(
- smirks=smirks,
- value=value,
- provenance={"code": code}
- )
+ bcc = BCCParameter(smirks=smirks, value=value, provenance={"code": code})
bond_charge_corrections.append(bcc)
unique_patterns.add(smirks)
@@ -305,8 +290,10 @@ def create_openeye_bccs(
json.dump(
# reverse for now while recharge still goes from more to less specific
{"parameters": [bcc.dict() for bcc in bcc_parameters][::-1]},
- f, indent=4
+ f,
+ indent=4,
)
+
if __name__ == "__main__":
- create_openeye_bccs()
\ No newline at end of file
+ create_openeye_bccs()
From f1c0957ac3ae1cf5b691c72819e18d0702ba0306 Mon Sep 17 00:00:00 2001
From: Lily Wang
Date: Fri, 30 Jun 2023 15:15:59 +1000
Subject: [PATCH 9/9] newline smirks
---
scripts/convert-am1-bcc/generate_original_am1bcc.py | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/scripts/convert-am1-bcc/generate_original_am1bcc.py b/scripts/convert-am1-bcc/generate_original_am1bcc.py
index 1f9f2dc..b700558 100644
--- a/scripts/convert-am1-bcc/generate_original_am1bcc.py
+++ b/scripts/convert-am1-bcc/generate_original_am1bcc.py
@@ -167,9 +167,16 @@
# 'Delocalised' N-O
r"[#7X2+0:1]-[#8X1-1:2]": "240631",
r"[#7X3+1:1]-[#8X1-1:2]": "230631",
- r"[#7X4+1,#7X3+0$([*]-[#6X3]=,:[#7X2,#6X3]),#7X3+0$([*]-[#6X3]-,=,:[#7a,#6a]),#7X3+0$(*-[#6X4,#1]),#7X3+0$([*](-[#7X3])-[#7X3]),#7X3+0$([*](-[#8])-[#8]):1]-[#8X1-1:2]": "210631",
+ (
+ r"[#7X4+1,#7X3+0$([*]-[#6X3]=,:[#7X2,#6X3]),#7X3+0$([*]-[#6X3]-,=,:[#7a,#6a]),"
+ r"#7X3+0$(*-[#6X4,#1]),#7X3+0$([*](-[#7X3])-[#7X3]),"
+ r"#7X3+0$([*](-[#8])-[#8]):1]-[#8X1-1:2]"
+ ): "210631",
r"[#7X3+0$(*-[#6X3$(*=[#8,#16])]):1]-[#8X1-1:2]": "220631",
- r"[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]),$([#7X3](-[#8X1])-[#8X1]):1]~[#8X1:2]": "230931",
+ (
+ r"[$([#7X3](-[#8X1])=[#8X1]),$([#7X3](=[#8X1])=[#8X1]),"
+ r"$([#7X3](-[#8X1])-[#8X1]):1]~[#8X1:2]"
+ ): "230931",
}
GENERAL_BOND_CODES = {