Merge pull request #5 from cheminfo-py/dev_MM

dev MM

docker-compose.yml

@@ -9,8 +9,8 @@ services:
       - CACHEDIR=/xpscache
       - WORKERS=${WORKERS}
       - OMP_NUM_THREADS=${OMP_NUM_THREADS}
-      - MAX_ATOMS_XTB=100
-      - MAX_ATOMS_FF=100
+      - MAX_ATOMS_XTB=200
+      - MAX_ATOMS_FF=200
       - TIMEOUT=${TIMEOUT}
       - LOG_LEVEL=DEBUG
     ports:

run_docker.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
 echo "connect to http://localhost:8091"
-docker run -d -p 8091:8091 -e PORT=8091 -e WORKERS=1 -e OMP_NUM_THREADS=1 -e TIMEOUT=200 --rm --name=xps-serviceinstance --security-opt=seccomp:unconfined  xps-service
+docker run -d -p 8091:8091 -e PORT=8091 -e WORKERS=1 -e OMP_NUM_THREADS=1 -e TIMEOUT=500 --rm --name=xps-serviceinstance --security-opt=seccomp:unconfined  xps-service

xpsservice/models.py

@@ -6,7 +6,7 @@
 from ase import Atoms
 from pydantic import BaseModel, Field, validator
 from rdkit import Chem
-from .settings import ALLOWED_FMAX, ALLOWED_ELEMENTS, ALLOWED_FF, ALLOWED_METHODS, transition_map
+from .settings import ALLOWED_FMAX, ALLOWED_ELEMENTS, ALLOWED_FF, ALLOWED_METHODS, ALLOWED_ENERGY_REFERENCE, transition_map
 
 
 class TransitionValidator(BaseModel):
@@ -33,9 +33,13 @@ class XPSRequest(BaseModel):
         description="Method for geometry optimization and XPS binding energies calculation. Allowed values: `GFNFF`, `GFN2xTB`, `GFN1xTB`.",
     )
     fmax: Optional[float] = Field(
-        0.01,
+        0.001,
         description="Maximum force admissible during geometry optimization. Typically ranging from 0.1 to 0.0001."
     )
+    energyReference: Optional[str] = Field(
+        "solid",
+        description="Energy referencing performed through polynomial regression, for gaz phase, solid state or none (raw data)"
+    )
 
     @validator("smiles")
     def validate_smiles(cls, v):
@@ -70,6 +74,12 @@ def validate_fmax(cls, v):
         if not (ALLOWED_FMAX[0] <= v <= ALLOWED_FMAX[1]):
             raise ValueError(f"fmax must be within the range {ALLOWED_FMAX}")
         return v
+
+    @validator("energyReference")
+    def validate_energy_reference(cls, v):
+        if v not in ALLOWED_ENERGY_REFERENCE:
+            raise ValueError(f"Method must be in {ALLOWED_ENERGY_REFERENCE}")
+        return v
 
 
 class Position(BaseModel):

xpsservice/settings.py

@@ -7,36 +7,44 @@
 
 #Conformer generation method
 ALLOWED_FF = ("uff", "mmff94", "mmff94s")
-MAX_ATOMS_FF = int(os.getenv("MAX_ATOMS_FF", 100))
+MAX_ATOMS_FF = int(os.getenv("MAX_ATOMS_FF", 200))
 
 
 #XTB optimization method
 ALLOWED_METHODS = ("GFNFF", "GFN2xTB", "GFN1xTB")
-MAX_ATOMS_XTB = int(os.getenv("MAX_ATOMS_XTB", 100))
+MAX_ATOMS_XTB = int(os.getenv("MAX_ATOMS_XTB", 200))
 ALLOWED_FMAX = (0.000001, 0.1)
+ALLOWED_ENERGY_REFERENCE = ("none", "solid")
 
 
 #timeout for the overall calculation
-TIMEOUT = int(os.getenv("TIMEOUT", 100))
+TIMEOUT = int(os.getenv("TIMEOUT", 500))
 
 
 # Define transition_map dictionary(list of orbitals for which a photoelectron emission is calculated)
 # Several maps possible. Adjust which one to load in xpsservice
+# The regression coefficient are for polynomial a + bx + cx^2 + ..., given in an array [a,b,c,...]
 transition_map = {
     "C1s": {
         "element": "C",
         "orbital": "1s",
         "soap_config_filepath": os.path.abspath("SOAP_configs/soap_config_C1s.pkl"),
-        "model_filepath": os.path.abspath("ML_models/XPS_GPR_C1s_xtb.pkl")
+        "model_filepath": os.path.abspath("ML_models/XPS_GPR_C1s_xtb.pkl"),
+        "regression_coefficients": [-2501.002792622873, 18.12807741, -0.02938832]
     },
     "O1s": {
         "element": "O",
         "orbital": "1s",
         "soap_config_filepath": os.path.abspath("SOAP_configs/soap_config_O1s.pkl"),
-        "model_filepath": os.path.abspath("ML_models/XPS_GPR_O1s_xtb.pkl")
+        "model_filepath": os.path.abspath("ML_models/XPS_GPR_O1s_xtb.pkl"),
+        "regression_coefficients": [-14914.578039681715, 5.67166123e+01, -5.20506217e-02]
     }
 }
 
+# Derive allowed elements from transition_map
+def derive_allowed_elements(transition_map: dict) -> Set[str]:
+    allowed_elements = {info["element"] for info in transition_map .values()}
+    return allowed_elements
 
 # Derive allowed elements from transition_map
 def derive_allowed_elements(transition_map: dict) -> Set[str]: