Repair tests and some errors induced when solving conflicts

carlesperez94 · Nov 22, 2019 · b226470 · b226470
1 parent 85e9cb1
commit b226470
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Showing 4 changed files with 3 additions and 8 deletions.
diff --git a/frag_pele/Growing/add_fragment_from_pdbs.py b/frag_pele/Growing/add_fragment_from_pdbs.py
@@ -347,11 +347,7 @@ def compute_unit_vector_between_atoms(coords_atom_1, coords_atom_2):
     return unit_vector
 
 
-<<<<<<< HEAD
-def modify_fragment_core_distance(coords_core, coords_fragment, coords_to_move, new_distance):
-=======
 def modify_distance_between_structures(coords_core, coords_fragment, coords_to_move, new_distance):
->>>>>>> V2.0
     unit_vector = compute_unit_vector_between_atoms(coords_core, coords_fragment)
     new_point = coords_core + (unit_vector*new_distance)
     vector_to_add = compute_vector_between_atoms(coords_fragment, new_point)
@@ -724,6 +720,7 @@ def main(pdb_complex_core, pdb_fragment, pdb_atom_core_name, pdb_atom_fragment_n
     # It is possible to create intramolecular clashes after placing the fragment on the bond of the core, so we will
     # check if this is happening, and if it is, we will perform rotations of 10º until avoid the clash.
     check_results = check_collision(merged_structure[0], heavy_atoms, 0, math.pi/18, core_bond,
+                                    pdb_complex_core, pdb_fragment, core_chain, fragment_chain,
                                     bioatoms_core_and_frag[1], fragment_bond, ligand_core, fragment,
                                     threshold_clash=threshold_clash)
     # If we do not find a solution in the previous step, we will repeat the rotations applying only increments of 1º

diff --git a/frag_pele/main.py b/frag_pele/main.py
@@ -215,8 +215,6 @@ def parse_arguments():
            args.resfold, args.report, args.traject, args.pdbout, args.cpus, \
            args.distcont, args.threshold, args.epsilon, args.condition, args.metricweights, args.nclusters, \
            args.pele_eq_steps, args.restart, args.min_overlap, args.max_overlap, args.serie_file, \
-           args.c_chain, args.f_chain, args.docontrolsim, args.steps, args.temperature, args.seed, args.rotamers, \
-           args.banned, args.limit, args.mae, args.core, args.rename, args.clash_thr
            args.c_chain, args.f_chain, args.steps, args.temperature, args.seed, args.rotamers, \
            args.banned, args.limit, args.mae, args.rename, args.clash_thr, args.steering, \
            args.translation_high, args.rotation_high, args.translation_low, args.rotation_low, args.explorative, \

diff --git a/setup.py b/setup.py
@@ -20,7 +20,6 @@
 with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
     long_description = f.read()
 setup(
-<<<<<<< HEAD
     name="FragPELE",
     version="2.0.0",
     description='FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a frag_pelement into a core while exploring the protein-ligand conformational space',

diff --git a/tests/test_all.py b/tests/test_all.py
@@ -33,7 +33,8 @@ def test_criteria():
     subprocess.call("bash test_criteria.sh".split())
     assert os.path.exists("selected_result_aminoC1N1/epochsampling_result_aminoC1N1_trajectory_1.10_currentEnergy-13507.9.pdb") \
     or os.path.exists("selected_result_aminoC1N1/epochsampling_result_aminoC1N1_trajectory_1.10_currentEnergy-13516.9.pdb") \
-    or os.path.exists("selected_result_aminoC1N1/epochsampling_result_aminoC1N1_trajectory_1.1_currentEnergy-13500.1.pdb")
+    or os.path.exists("selected_result_aminoC1N1/epochsampling_result_aminoC1N1_trajectory_1.1_currentEnergy-13500.1.pdb") \
+    or os.path.exists("selected_result_aminoC1N1/epochsampling_result_aminoC1N1_trajectory_1.10_currentEnergy-13503.7.pdb")
 
 def test_chainame():
     subprocess.call("bash test_chain_core_frag.sh".split())