Merge pull request #51 from carlesperez94/devel

FragPELE 2.2
carlesperez94 · Jul 1, 2020 · cbdbc58 · cbdbc58
2 parents 1790525 + 849f5a7
commit cbdbc58
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Showing 9 changed files with 285 additions and 35 deletions.
diff --git a/conda_recipe/meta.yaml b/conda_recipe/meta.yaml
@@ -1,7 +1,7 @@
 # must do: conda-build -c conda-forge -c nostrumbiodiscovery -c rdkit -c carlesperez94 . 
 package:
   name: frag_pele
-  version: "2.1.3"
+  version: "2.2.0"
 
 about:
   home: https://github.com/carlesperez94/frag_pele

diff --git a/frag_pele/Growing/AddingFragHelpers/atom_constants.py b/frag_pele/Growing/AddingFragHelpers/atom_constants.py
@@ -20,14 +20,17 @@
     ("C", "F", "single"): 1.35,
     ("C", "CL", "single"): 1.77,
     ("C", "BR", "single"): 1.94,
-    ("C", "I", "single"): 2.14,
+    ("C", "I", "single"): 2.18,
     ("N", "C", "single"): 1.47,
     ("O", "C", "single"): 1.43,
     ("S", "C", "single"): 1.82,
     ("F", "C", "single"): 1.35,
     ("CL", "C", "single"): 1.77,
     ("BR", "C", "single"): 1.94,
-    ("I", "C", "single"): 2.14,
+    ("I", "C", "single"): 2.18,
+    # Other single bonds
+    ("N", "S", "single"): 1.77,
+    ("S", "N", "single"): 1.77,
     # Bonding with H
     ("H", "C", "single"): 1.08,
     ("H", "N", "single"): 1.01,
@@ -54,8 +57,10 @@
     ("O", "S", "double"): 1.48,
     ("C", "N", "double"): 1.28,
     ("N", "C", "double"): 1.28,
+    ("S", "C", "double"): 1.66,
+    ("C", "S", "double"): 1.66,
     # Triple bonds
     ("N", "N", "triple"): 1.1,
     ("C", "N", "triple"): 1.14,
-    ("N", "C", "triple"): 1.14,
+    ("N", "C", "triple"): 1.14
 }
diff --git a/frag_pele/Growing/AddingFragHelpers/pdb_joiner.py b/frag_pele/Growing/AddingFragHelpers/pdb_joiner.py
@@ -60,7 +60,8 @@ def get_H_bonded_to_grow(PDB_atom_name, prody_complex, PDB_atom_to_replace=None,
     # Select the hydrogens bonded to the heavy atom 'PDB_atom_name'
 
     # When non specific atom is selected we search hydrogens automatically
-    selected_atom = prody_complex.select("chain {} and hydrogen within 1.70 of name {}".format(chain, PDB_atom_name))  # Replace for 1.53 :)
+    selected_atom = prody_complex.select("chain {} and hydrogen within 1.74 of name {}".format(chain, 
+                                                                                             PDB_atom_name))
     # If it is selected, we have to differentiate between hydrogens or heavy atoms
     if PDB_atom_to_replace:
         print("ATOM TO REPLACE: {}".format(PDB_atom_to_replace))

diff --git a/frag_pele/Growing/simulations_linker.py b/frag_pele/Growing/simulations_linker.py
@@ -93,7 +93,7 @@ def simulation_runner(path_to_pele, control_in, cpus=4):
             logger.critical("Sorry, to run mpi PELE you need at least 2 CPUs!")
         else:
             logger.info("Starting PELE simulation. You will run mpi PELE with {} cores.".format(cpus))
-            cmd = "mpirun -np {} {} {}".format(cpus, path_to_pele, control_in)
+            cmd = "srun -n {} {} {}".format(cpus, path_to_pele, control_in)
             print(cmd)
             logger.info("Running {}".format(cmd))
             subprocess.call(cmd.split())

diff --git a/frag_pele/Growing/template_fragmenter.py b/frag_pele/Growing/template_fragmenter.py
diff --git a/frag_pele/constants.py b/frag_pele/constants.py
@@ -15,9 +15,9 @@
 # Paths definitions (IMPORTANT!)
 if "bsc.mn" in machine:
     # PELE parameters
-    PATH_TO_PELE = "/gpfs/projects/bsc72/PELE++/mniv/rev12536/bin/Pele_mpi"
-    PATH_TO_PELE_DATA = "/gpfs/projects/bsc72/PELE++/data/rev12360/Data"
-    PATH_TO_PELE_DOCUMENTS = "/gpfs/projects/bsc72/PELE++/Documents/rev12360"
+    PATH_TO_PELE = "/gpfs/projects/bsc72/PELE++/mniv/V1.6.1/bin/PELE-1.6.1_mpi"
+    PATH_TO_PELE_DATA = "/gpfs/projects/bsc72/PELE++/mniv/V1.6.1/Data"
+    PATH_TO_PELE_DOCUMENTS = "/gpfs/projects/bsc72/PELE++/mniv/V1.6.1/Documents"
     PATH_TO_LICENSE = "/gpfs/projects/bsc72/PELE++/license"
     # PlopRotTemp parameters
     SCHRODINGER_PY_PATH = "/gpfs/projects/bsc72/SCHRODINGER_ACADEMIC/utilities/python"

diff --git a/tests/data/original/control_folder/0_test.conf b/tests/data/original/control_folder/0_test.conf
@@ -1,5 +1,5 @@
 {
-  "licenseDirectoryPath" : "/scratch/PELE-repo/licenses",
+  "licenseDirectoryPath" : "/gpfs/projects/bsc72/PELE++/license",
 
   "Initialization" : {
      "allowMissingTerminals": true,

diff --git a/tests/data/original/control_folder/1_test.conf b/tests/data/original/control_folder/1_test.conf
@@ -1,5 +1,5 @@
 {
-  "licenseDirectoryPath" : "/scratch/PELE-repo/licenses",
+  "licenseDirectoryPath" : "/gpfs/projects/bsc72/PELE++/license",
 
   "Initialization" : {
      "allowMissingTerminals": true,

diff --git a/tests/data/original/control_folder/test.conf b/tests/data/original/control_folder/test.conf
@@ -1,5 +1,5 @@
 {
-  "licenseDirectoryPath" : "/scratch/PELE-repo/licenses",
+  "licenseDirectoryPath" : "/gpfs/projects/bsc72/PELE++/license",
 
   "Initialization" : {
      "allowMissingTerminals": true,