Ligandfit update (#329)

* Add scaling_id param to ligandfit

* Make pipeline_final directory

* Update conda requirements

Author: rowanwalker96

requirements.conda.txt

@@ -4,9 +4,11 @@ ispyb>=11.0.3
 junit-xml>=1.9
 marshmallow-sqlalchemy
 minio>=7.1.0
+molviewspec
 msgpack-python
 networkx
 nxmx
+openbabel
 pandas
 pika
 pint
@@ -19,7 +21,6 @@ python-jose
 python-relion
 pyyaml
 pyzmq
-rdkit
 seaborn
 sqlalchemy>=2.0.39,<3
 stomp.py>=7,<9

src/dlstbx/services/trigger.py

@@ -2699,6 +2699,7 @@ def trigger_ligand_fit(
             "smiles": parameters.smiles,
             "pipeline": parameters.pipeline,
             "acronym": acronym,
+            "scaling_id": scaling_id,
         }
 
         jp = self.ispyb.mx_processing.get_job_params()

src/dlstbx/wrapper/ligand_fit.py

@@ -8,10 +8,10 @@
 import subprocess
 from shutil import ignore_patterns
 
-# import molviewspec as mvs
 from iotbx import pdb
-from rdkit import Chem
-from rdkit.Chem import Draw
+
+# import molviewspec as mvs
+from openbabel import pybel
 
 import dlstbx.util.symlink
 from dlstbx.wrapper import Wrapper
@@ -34,7 +34,7 @@ def pull_CC_from_log(self, pipeline_directory):
         CC = float(match.group(1))
         return CC
 
-    def send_attachments_to_ispyb(self, pipeline_directory):
+    def send_attachments_to_ispyb(self, pipeline_directory, final_directory):
         for f in pipeline_directory.iterdir():
             if f.stem.endswith("final"):
                 file_type = "Result"
@@ -54,6 +54,7 @@ def send_attachments_to_ispyb(self, pipeline_directory):
             else:
                 continue
             try:
+                shutil.copy(pipeline_directory / f.name, final_directory)
                 result_dict = {
                     "file_path": str(pipeline_directory),
                     "file_name": f.name,
@@ -62,6 +63,7 @@ def send_attachments_to_ispyb(self, pipeline_directory):
                 }
                 self.record_result_individual_file(result_dict)
                 self.log.info(f"Uploaded {f.name} as an attachment")
+
             except Exception:
                 self.log.warning(f"Could not attach {f.name} to ISPyB", exc_info=True)
 
@@ -102,6 +104,15 @@ def run(self):
         working_directory.mkdir(parents=True, exist_ok=True)
         results_directory = pathlib.Path(params["results_directory"])
         results_directory.mkdir(parents=True, exist_ok=True)
+
+        if pipeline_final_params := params.get("pipeline-final", []):
+            final_directory = pathlib.Path(pipeline_final_params["path"])
+            final_directory.mkdir(parents=True, exist_ok=True)
+            if params.get("create_symlink"):
+                dlstbx.util.symlink.create_parent_symlink(
+                    final_directory, params.get("create_symlink")
+                )
+
         with open(working_directory / "LIG.smi", "w") as smi_file:
             smi_file.write(smiles)
 
@@ -110,7 +121,7 @@ def run(self):
         # if pipeline == "phenix":
         #     phenix_command = f"phenix.ligandfit data={mtz}  model={pdb} ligand=LIG.smi min_ligand_cc_keep={min_cc_keep} nproc=8"  # ligand={ligand_code}
         if pipeline == "phenix_pipeline":
-            phenix_command = f"phenix.ligand_pipeline {pdb} {mtz} LIG.smi min_ligand_cc_keep={min_cc_keep} nproc=8"
+            phenix_command = f"phenix.ligand_pipeline {pdb} {mtz} LIG.smi min_ligand_cc_keep={min_cc_keep} nproc=8"  # build=False
 
         try:
             result = subprocess.run(
@@ -145,7 +156,7 @@ def run(self):
             acr = params.get("acronym", "Protein")
 
             os.system(
-                f"module load molviewspec; gen_html.py --pdb_file {out_pdb} --map_file {out_map} --cc {CC} --outdir {pipeline_directory} --smiles '{smiles}' --acr {acr}"
+                f"module load molviewspec; gen_html_ligandfit.py --pdb_file {out_pdb} --map_file {out_map} --cc {CC} --outdir {pipeline_directory} --smiles '{smiles}' --acr {acr}"
             )
 
         self.generate_smiles_png(smiles, pipeline_directory)
@@ -175,7 +186,7 @@ def run(self):
             )
 
         self.log.info("Sending results to ISPyB")
-        self.send_attachments_to_ispyb(pipeline_directory)
+        self.send_attachments_to_ispyb(pipeline_directory, final_directory)
 
         if CC >= min_cc_keep:
             self.log.info("Ligand_fitting pipeline finished successfully")
@@ -187,9 +198,9 @@ def run(self):
             return False
 
     def generate_smiles_png(self, smiles, outdir):
-        mol = Chem.MolFromSmiles(smiles)
-        img = Draw.MolToImage(mol, size=(450, 450))
-        img.save(f"{outdir}/SMILES.png")
+        mol = pybel.readstring("smi", smiles)
+        mol.make2D()
+        mol.draw(show=False, filename=(f"{outdir}/SMILES.png"))
 
 
 # def generate_html_visualisation(pdb_file, map_file, outdir, acr, smiles, cc):