Allow Geometry objects as arguments for Calculation command, move con…

…formers/CREST options, and add solvate command (#50) * Add support for passing Geometry objects as arguments for Calculation, and add a solvate() calculation type * Use deepcopy on empty_cjson * Tidy up conformers user options and move crest configuration to general config * Don't put empty layer array in CJSON template as not valid for Avogadro * Use config value for GFN-xTB method version * Add solvate command to plugin * Read cluster geom from file * Keep solute bonding information when solvating * Extract version numbers using regex * Warn when using broken versions of CREST or incompatible CREST/xtb combos
matterhorn103 · Dec 4, 2024 · 97a42d7 · 97a42d7
1 parent f5fd831
commit 97a42d7
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Showing 11 changed files with 664 additions and 167 deletions.
diff --git a/avo_xtb/about.py b/avo_xtb/about.py
@@ -4,6 +4,7 @@
 import argparse
 import json
 import logging
+import re
 import subprocess
 import sys
 
@@ -13,6 +14,30 @@
 logger = logging.getLogger(__name__)
 
 
+# Get xtb and crest versions
+# Regex to match version numbers (e.g., 6.7.1, 2.12, 6.4.0)
+pattern = r"\bversion\s+(\d+\.\d+\.\d+|\d+\.\d+)\b"
+
+if easyxtb.XTB_BIN:
+    xtb_version_info = subprocess.run(
+        [str(easyxtb.XTB_BIN), "--version"],
+        encoding="utf-8",
+        capture_output=True,
+    ).stdout
+    XTB_VERSION = re.findall(pattern, xtb_version_info, re.IGNORECASE)[0]
+else:
+    XTB_VERSION = None
+if easyxtb.CREST_BIN:
+    crest_version_info = subprocess.run(
+        [str(easyxtb.CREST_BIN), "--version"],
+        encoding="utf-8",
+        capture_output=True,
+    ).stdout
+    CREST_VERSION = re.findall(pattern, crest_version_info, re.IGNORECASE)[0]
+else:
+    CREST_VERSION = None
+
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument("--debug", action="store_true")
@@ -37,30 +62,22 @@
         avo_input = json.loads(sys.stdin.read())
         output = avo_input.copy()
 
-        if easyxtb.XTB_BIN:
-            xtb_version = subprocess.run(
-                [str(easyxtb.XTB_BIN), "--version"],
-                encoding="utf-8",
-                capture_output=True,
-            ).stdout.splitlines()[-2].strip()
+        if XTB_VERSION:
+            xtb_version_msg = XTB_VERSION
         else:
-            xtb_version = "No xtb binary found"
-        if easyxtb.CREST_BIN:
-            crest_version = subprocess.run(
-                [str(easyxtb.CREST_BIN), "--version"],
-                encoding="utf-8",
-                capture_output=True,
-            ).stdout.splitlines()[-4].strip()
+            xtb_version_msg = "No xtb binary found"
+        if CREST_VERSION:
+            crest_version_msg = CREST_VERSION
         else:
-            crest_version = "No CREST binary found"
+            crest_version_msg = "No CREST binary found"
 
         # Do nothing to data other than add message with version and path info
         output["message"] = (
             "avo_xtb plugin\n"
             + f"easyxtb version: {easyxtb.configuration.easyxtb_VERSION}\n"
-            + f"xtb version: {xtb_version}\n"
+            + f"xtb version: {xtb_version_msg}\n"
             + f"xtb path: {easyxtb.XTB_BIN}\n"
-            + f"CREST version: {crest_version}\n"
+            + f"CREST version: {crest_version_msg}\n"
             + f"CREST path: {easyxtb.CREST_BIN}"
         )
 

diff --git a/avo_xtb/config.py b/avo_xtb/config.py
@@ -33,25 +33,31 @@
                     "default": str(easyxtb.XTB_BIN),
                     "order": 1.0,
                 },
+                "crest_bin": {
+                    "type": "string",
+                    "label": "Location of the CREST binary",
+                    "default": str(easyxtb.CREST_BIN),
+                    "order": 2.0,
+                },
                 "user_dir": {
                     "type": "string",
                     "label": "Run calculations (in subfolder) in",
                     "default": str(easyxtb.CALC_DIR),
-                    "order": 2.0,
+                    "order": 3.0,
                 },
                 "n_proc": {
                     "type": "integer",
                     "label": "Parallel processes to run",
                     "minimum": 1,
                     "default": 1,
-                    "order": 3.0
+                    "order": 4.0
                     },
                 "energy_units": {
                     "type": "stringList",
                     "label": "Preferred energy units",
                     "values": ["kJ/mol", "kcal/mol"],
                     "default": 0,
-                    "order": 4.0,
+                    "order": 5.0,
                 },
                 "solvent": {
                     "type": "stringList",
@@ -84,14 +90,14 @@
                         "water",
                     ],
                     "default": 0,
-                    "order": 5.0,
+                    "order": 6.0,
                 },
                 "method": {
                     "type": "stringList",
-                    "label": "Method (xtb only)",
+                    "label": "Method",
                     "values": methods,
                     "default": methods[-1],
-                    "order": 6.0,
+                    "order": 7.0,
                 },
                 "opt_lvl": {
                     "type": "stringList",
@@ -107,7 +113,7 @@
                         "extreme",
                     ],
                     "default": 4,
-                    "order": 7.0,
+                    "order": 8.0,
                 },
                 "warning": {
                     "type": "text",
@@ -146,24 +152,30 @@
             easyxtb.config["calc_dir"] = str(easyxtb.CALC_DIR)
 
         # Save change to xtb_bin if there has been one
-        if avo_input["xtb_bin"] != str(easyxtb.XTB_BIN):
+        if avo_input["xtb_bin"] in ["none", ""]:
+            pass
+        elif avo_input["xtb_bin"] != str(easyxtb.XTB_BIN):
             easyxtb.XTB_BIN = Path(avo_input["xtb_bin"])
             easyxtb.config["xtb_bin"] = str(easyxtb.XTB_BIN)
+
+        # Save change to crest_bin if there has been one
+        if avo_input["crest_bin"] in ["none", ""]:
+            pass
+        elif Path(avo_input["crest_bin"]) != easyxtb.CREST_BIN:
+            easyxtb.CREST_BIN = Path(avo_input["crest_bin"])
+            easyxtb.config["crest_bin"] = str(easyxtb.CREST_BIN)
 
         # Update number of threads
         easyxtb.config["n_proc"] = avo_input["n_proc"]
 
         # Update energy units
         easyxtb.config["energy_units"] = avo_input["energy_units"]
 
-        # Convert "none" string to Python None
+        # Update solvent
         if avo_input["solvent"] == "none":
-            solvent_selected = None
+            easyxtb.config["solvent"] = None
         else:
-            solvent_selected = avo_input["solvent"]
-
-        # Update solvent
-        easyxtb.config["solvent"] = solvent_selected
+            easyxtb.config["solvent"] = avo_input["solvent"]
 
         # Update method
         easyxtb.config["method"] = methods.index(avo_input["method"])

diff --git a/avo_xtb/conformers.py b/avo_xtb/conformers.py
@@ -31,74 +31,7 @@
 
     if args.print_options:
         options = {
-            "inputMoleculeFormat": "xyz",
             "userOptions": {
-                "crest_bin": {
-                    "type": "string",
-                    "label": "Location of the CREST binary",
-                    "default": str(easyxtb.CREST_BIN),
-                    "order": 1.0,
-                },
-                "save_dir": {
-                    "type": "string",
-                    "label": "Save results in",
-                    "default": str(easyxtb.CALC_DIR),
-                    "order": 2.0,
-                },
-                # "Number of threads": {
-                #    "type": "integer",
-                #    #"label": "Number of cores",
-                #    "minimum": 1,
-                #    "default": 1,
-                #    "order": 3.0
-                #    },
-                # "Memory per core": {
-                #    "type": "integer",
-                #    #"label" "Memory per core",
-                #    "minimum": 1,
-                #    "default": 1,
-                #    "suffix": " GB",
-                #    "order": 4.0
-                #    },
-                "help": {
-                    "type": "text",
-                    "label": "For help see",
-                    "default": "https://crest-lab.github.io/crest-docs/",
-                    "order": 9.0,
-                },
-                "solvent": {
-                    "type": "stringList",
-                    "label": "Solvation",
-                    "values": [
-                        "none",
-                        "acetone",
-                        "acetonitrile",
-                        "aniline",
-                        "benzaldehyde",
-                        "benzene",
-                        "ch2cl2",
-                        "chcl3",
-                        "cs2",
-                        "dioxane",
-                        "dmf",
-                        "dmso",
-                        "ether",
-                        "ethylacetate",
-                        "furane",
-                        "hexandecane",
-                        "hexane",
-                        "methanol",
-                        "nitromethane",
-                        "octanol",
-                        "woctanol",
-                        "phenol",
-                        "toluene",
-                        "thf",
-                        "water",
-                    ],
-                    "default": 0,
-                    "order": 6.0,
-                },
                 "ewin": {
                     "type": "integer",
                     "label": "Keep all conformers within",
@@ -114,15 +47,18 @@
                     "default": False,
                     "order": 8.0,
                 },
+                "help": {
+                    "type": "text",
+                    "label": "For help see",
+                    "default": "https://crest-lab.github.io/crest-docs/",
+                    "order": 9.0,
+                },
             },
         }
         # Display energy in kcal if user has insisted on it
         if easyxtb.config["energy_units"] == "kcal/mol":
             options["userOptions"]["ewin"]["default"] = 6
             options["userOptions"]["ewin"]["suffix"] = " kcal/mol"
-        # Make solvation default if found in user config
-        if easyxtb.config["solvent"] is not None:
-            options["userOptions"]["solvent"]["default"] = easyxtb.config["solvent"]
         print(json.dumps(options))
     if args.display_name:
         print("Conformers…")
@@ -135,30 +71,17 @@
         # Extract the coords
         geom = easyxtb.Geometry.from_cjson(avo_input["cjson"])
 
-        # If provided crest path different to that stored, use it and save it
-        if Path(avo_input["crest_bin"]) != easyxtb.CREST_BIN:
-            crest_bin = Path(avo_input["crest_bin"])
-            easyxtb.config["crest_bin"] = str(crest_bin)
-            with open(easyxtb.config_file, "w", encoding="utf-8") as config_path:
-                json.dump(easyxtb.config, config_path)
-
         # crest takes energies in kcal so convert if provided in kJ (default)
         if easyxtb.config["energy_units"] == "kJ/mol":
             ewin_kcal = avo_input["ewin"] / 4.184
         else:
             ewin_kcal = avo_input["ewin"]
-
-        # Convert "none" string to Python None
-        if avo_input["solvent"] == "none":
-            solvation = None
-        else:
-            solvation = avo_input["solvent"]
 
         # Run calculation; returns set of conformers as well as Calculation object
         conformers, calc = easyxtb.calculate.conformers(
             geom,
-            solvation=solvation,
-            method=2,
+            solvation=easyxtb.config["solvent"],
+            method=easyxtb.config["method"],
             ewin=ewin_kcal,
             hess=avo_input["hess"],
             return_calc=True,
@@ -190,13 +113,6 @@
         with open(easyxtb.TEMP_DIR / "result.cjson", "w", encoding="utf-8") as save_file:
             json.dump(output["cjson"], save_file, indent=2)
 
-        # If user specified a save location, copy calculation directory to there
-        if not (
-            avo_input["save_dir"] in ["", None]
-            or Path(avo_input["save_dir"]) == easyxtb.TEMP_DIR
-        ):
-            copytree(easyxtb.TEMP_DIR, Path(avo_input["save_dir"]), dirs_exist_ok=True)
-
         # Pass back to Avogadro
         print(json.dumps(output))
         logger.debug(f"The following dictionary was passed back to Avogadro: {output}")
diff --git a/avo_xtb/deprotonate.py b/avo_xtb/deprotonate.py
@@ -45,7 +45,7 @@
         tautomers, calc = easyxtb.calculate.deprotonate(
             geom,
             solvation=easyxtb.config["solvent"],
-            method=2,
+            method=easyxtb.config["method"],
             return_calc=True,
         )
 

diff --git a/avo_xtb/protonate.py b/avo_xtb/protonate.py
@@ -5,6 +5,7 @@
 import json
 import logging
 import sys
+from copy import deepcopy
 
 from support import easyxtb
 
@@ -19,7 +20,7 @@ def cleanup_after_taut(cjson: dict) -> dict:
     Essentially gives an empty cjson, with only the total charge and spin retained.
     """
 
-    output = easyxtb.convert.empty_cjson.copy()
+    output = deepcopy(easyxtb.convert.empty_cjson)
     output["properties"]["totalCharge"] = cjson["properties"]["totalCharge"]
     output["properties"]["totalSpinMultiplicity"] = cjson["properties"]["totalSpinMultiplicity"]
 

diff --git a/avo_xtb/run_xtb.py b/avo_xtb/run_xtb.py
@@ -7,6 +7,7 @@
 import json
 import logging
 import sys
+from copy import deepcopy
 from pathlib import Path
 from shutil import copytree
 
@@ -120,7 +121,7 @@
         # Start by passing back an empty cjson, then add changes
         output = {
             "moleculeFormat": "cjson",
-            "cjson": easyxtb.convert.empty_cjson.copy(),
+            "cjson": deepcopy(easyxtb.convert.empty_cjson),
         }
 
         # TODO Catch errors in xtb execution