Refactoring fragments screening protocol

FragmentsMerging.py

@@ -15,19 +15,19 @@ def alignment(ref, targ, output):
 
 def merging(r1, r2, core, output):
 
-    cmd = f"python /fccc/users/karanicolaslab/andriag/combichem/combichem/processing/Merging.py -ref_pose {r1} -target_pose {r2} -substructure {core} -output {output}"
+    cmd = f"python Merging.py -ref_pose {r1} -target_pose {r2} -substructure {core} -output {output}"
     os.system(cmd)
 
 def generate_params(sdf, output):
 
     cmd = f"convert.py {sdf} {output}.mol2"
     os.system(cmd)
-    cmd = f"python /fccc/users/karanicolaslab/andriag/combichem/combichem/external_apps/generic_potencial/mol2genparams.py -s {output}.mol2 --prefix={output}"
+    cmd = f"python external_apps/generic_potencial/mol2genparams.py -s {output}.mol2 --prefix={output}"
     os.system(cmd)
 
 def replace_charge(r_pdb, r_params, t_pdb, t_params, output):
 
-    cmd = f"python /fccc/users/karanicolaslab/andriag/combichem/combichem/processing/Params.py -ref_pdb {r_pdb} -ref_params {r_params} -target_pdb {t_pdb} -target_params {t_params} -out {output}"
+    cmd = f"python Params.py -ref_pdb {r_pdb} -ref_params {r_params} -target_pdb {t_pdb} -target_params {t_params} -out {output}"
     os.system(cmd)
 
 
@@ -39,7 +39,7 @@ def minimization(ligand, protein, params, hinge):
 
     mini_complexx = f"minimizations/mini_{complexx.split('/')[-1]}"
     mini_log = f"minimizations/mini_{complexx.split('/')[-1].split('.')[0]}.log"
-    cmd = f"python /fccc/users/karanicolaslab/andriag/combichem/combichem/processing/Screening.py -pdb {complexx} -params {params} -output {mini_complexx} -residues {hinge} > {mini_log}"
+    cmd = f"python Screening.py -pdb {complexx} -params {params} -output {mini_complexx} -residues {hinge} > {mini_log}"
 
     os.system(cmd)
 

FragmentsScreening.py

@@ -1,39 +1,55 @@
 import os, sys, glob
 
-if __name__ == "__main__":
+def make_dirs(prefix=""):
+
+    if prefix != "":
+        prefix += "_"
+
+    os.system(f"mkdir -p {prefix}mol2")
+    os.system(f"mkdir -p {prefix}pdb_params")
+    os.system(f"mkdir -p {prefix}replaced_params")
+    os.system(f"mkdir -p {prefix}complexes")
+    os.system(f"mkdir -p {prefix}minimization")
 
-	directory = sys.argv[1]
-	sdfs = glob.glob(f"{directory}/*.sdf")
-	done = [f"{directory}/" + f.split("/")[-1].split("__")[0].split("mini_")[-1] + ".sdf" for f in glob.glob(f"{directory}_minimization/*pdb")]
+    return f"{prefix}mol2", f"{prefix}pdb_params", f"{prefix}replaced_params",
+           f"{prefix}complexes", f"{prefix}minimization"
 
-	sdfs = set(sdfs).difference(set(done))
+def args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-sdf", required=True)
+    parser.add_argument("-prot", required=True)
+    parser.add_argument("-ref_charge_pdb", required=True)
+    parser.add_argument("-ref_charge_param", required=True)
+    parser.add_argument("-klifs-seq", nargs="+", required=True)
+    parser.add_argument("-out_prefix", default="")
+
+    args = parser.parse_args()
 
-	os.system(f"mkdir -p {directory}_mol2 {directory}_pdb_params {directory}_replaced_params {directory}_complexes {directory}_minimization")
+    return args
 
-	ref_pdb = "../mini_295_3BLQA_LG1_0001.pdb"
-	ref_params = "../mini_295_3BLQA_LG1.params"
 
-	ref_prot = "3BLQ_protein.pdb"
-	klifs = "23 24 25 26 27 28 29 30 31 32 33 34 35 45 46 47 48 49 50 62 63 64 65 66 67 68 69 70 71 72 73 74 76 77 78 79 80 81 82 83 84 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 165 166 167 168 169 170 171"
+if __name__ == "__main__":
+
+    args = args()
+    mol2_dir, pdb_params_dir, replaced_params_dir, complexes_dir, minimization_dir = make_dirs(args["out_prefix"])
 
-	for sdf in sdfs:
-		filename = sdf.split("/")[-1].split(".")[0]
+    filename = args["sdf"].split("/")[-1].split(".")[0]
 
-		mol2 = f"{directory}_mol2/{filename}.mol2"
-		pdb_params = f"{directory}_pdb_params/{filename}"
+    mol2 = f"{mol2_dir}/{filename}.mol2"
+    pdb_params = f"{pdb_params_dir}/{filename}"
 
-		am1bcc = f"assigncharges.py -method am1bcc -in {sdf} -out {mol2}"
-		genpot = f"python ~/combichem/combichem/external_apps/generic_potencial/mol2genparams.py -s {mol2} --prefix={pdb_params}"
+    am1bcc = f"assigncharges.py -method am1bcc -in {sdf} -out {mol2}"
+    genpot = f"python external_apps/generic_potencial/mol2genparams.py -s {mol2} --prefix={pdb_params}"
 
-		replaced_params = f"{directory}_replaced_params/{filename}.params"
-		replace = f"python ~/combichem/combichem/processing/Params.py -ref_pdb {ref_pdb} -ref_params {ref_params} -target_pdb {pdb_params}_0001.pdb -target_params {pdb_params}.params -out {replaced_params}"
+    replaced_params = f"{replaced_params_dir}/{filename}.params"
+    replace = f"python Params.py -ref_pdb {ref_pdb} -ref_params {ref_params} -target_pdb {pdb_params}_0001.pdb -target_params {pdb_params}.params -out {replaced_params}"
 
-		pdb_complex = f"{directory}_complexes/{filename}__{ref_prot}"
-		concat = f"cat {ref_prot} {pdb_params}_0001.pdb > {pdb_complex}"
+    pdb_complex = f"{complexes_dir}/{filename}__{ref_prot}"
+    concat = f"cat {ref_prot} {pdb_params}_0001.pdb > {pdb_complex}"
 
-		min_pdb_complex = f"{directory}_minimization/mini_{filename}__{ref_prot}"
-		min_log_complex = f"{directory}_minimization/mini_{filename}__{ref_prot}".replace(".pdb", ".log")
+    min_pdb_complex = f"{minimization_dir}/mini_{filename}__{ref_prot}"
+    min_log_complex = f"{minimization_dir}/mini_{filename}__{ref_prot}".replace(".pdb", ".log")
 
-		minimization = f"python ~/combichem/combichem/processing/Screening.py -pdb {pdb_complex} -params {replaced_params} -output {min_pdb_complex} -residues {klifs} -beta True > {min_log_complex}"
+    minimization = f"python Screening.py -pdb {pdb_complex} -params {replaced_params} -output {min_pdb_complex} -residues {klifs} -beta True > {min_log_complex}"
 
-		print("; ".join([am1bcc, genpot, replace, concat, minimization]))
+    print("; ".join([am1bcc, genpot, replace, concat, minimization]))