Cleaning version

Author: Rodrigo Ochoa

config.txt

@@ -1,4 +1,4 @@
-folder: granzymeH_200_2
+folder: granzymeH
 mode: start
 pdbID: granzymeH
 peptide: PRO-THR-SER-TYR-ALA-GLY-ASP-ASP-SER 
@@ -8,7 +8,7 @@ scoring: consensus
 score_list: vina,dligand2,rosetta,nnscore,internal,cyscore
 threshold: 4
 teffective: 4
-num_mutations: 200
+num_mutations: 100
 residues_mod: 2,4,6,8
 source: ./input
-rosetta_version: /home/ochoadeo/Downloads/rosetta.binary.linux.release-296
+rosetta_version: ~/rosetta.binary.linux.release-296

config_categories.txt

@@ -1,4 +1,4 @@
-folder: granzymeH_cat_2
+folder: granzymeH_cat
 mode: start
 pdbID: granzymeH
 peptide: PRO-THR-SER-TYR-ALA-GLY-ASP-ASP-SER 
@@ -11,5 +11,5 @@ teffective: 4
 num_mutations: 100
 residues_mod: 2,4,6,8
 source: ./input
-rosetta_version: /home/ochoadeo/Downloads/rosetta.binary.linux.release-296
+rosetta_version: ~/rosetta.binary.linux.release-296
 categories: NEUTRAL,HYDROPHOBIC,MEDIUM

src/general.py

@@ -430,8 +430,7 @@ def mutation_random(self,residues_mod,mutation_document,score_dictionary_total,m
 
             # Relax the generated structure
             os.system("{}/main/source/bin/relax.static.linuxgccrelease -database {}/main/database \
-                                                          -in:file:s {}/complex_{}_0001.pdb -relax:thorough -out:path:all {} \
-                                                          -relax:bb_move false".format(self.rosetta_path,
+                                                          -in:file:s {}/complex_{}_0001.pdb -relax:thorough -out:path:all {}".format(self.rosetta_path,
                                                                                        self.rosetta_path, self.path,
                                                                                        last_good_iteration, self.path))
 

src/internal_AA.txt

@@ -1,14 +1,3 @@
-ORN
-DAL
-DAS
-DHI
-DIL
-DPR
-DGN
-DAR
-DTR
-DTY
-DME
 ALA
 SER
 HIS

src/list_ncaa

@@ -1 +1 @@
-060 0A1 0AR 0EH 0JY 1E3 1TX 28J 2JN 2MR 2TL 41H 4DB 4FO 4WQ 54C 5CT 5GG 5GM 5OL 66D 6D6 6ZS 73C 85G 85J 9DW 9FZ 9G2 ABA ACB AHO ALO ALY AN6 API B8R BTK BWV C1J C4G D11 DA2 DBB DI7 DIV DLE DLY DTH DVA EEP ELY F7P F7V G5G HLX IIL ILO ILX J7H KCR KHB KJW LV8 LYH LYO M3L MK8 MKD ML3 MLY MLZ MYK NLE NMM NVA OAS ONL P2J PRK PRR TBG TPO TS9 UZA VR0 WPA WVL YTH ZS8
+060 0A1 0AR 0EH 0JY 1E3 1TX 28J 2JN 2MR 2TL 41H 4DB 4FO 4WQ 54C 5CT 5GG 5GM 5OL 66D 6D6 6ZS 73C 85G 85J 9DW 9FZ 9G2 ABA ACB AHO ALO ALY AN6 API B8R BTK BWV C1J C4G D11 DA2 DBB DI7 DIV DLE DLY DTH DVA EEP ELY F7P F7V G5G HLX IIL ILO ILX J7H KCR KHB KJW LV8 LYH LYO M3L MK8 MKD ML3 MLY MLZ MYK NLE NMM NVA OAS ONL P2J PRK PRR TBG TPO TS9 UZA VR0 WPA WVL YTH ZS8 ORN