fix: commands download, log generation, trjconv echo

app/blueprints/download/routes.py

@@ -67,7 +67,7 @@ def commandsdownload(mode, protein, folder):
     #move os arquivos .xvg para a pasta graficos.
     for folder, subfolders, files in os.walk(folder_run_path):
         for file in files:
-            if file.endswith('_PBC.xtc') or file.endswith('complx_pr.tpr'):
+            if file.endswith('_PBC.xtc') or file.endswith('_pr.tpr'):
                 zf.write(os.path.join(folder, file), file, compress_type=zipfile.ZIP_DEFLATED)
 
     zf.close()

app/blueprints/dynamic/executors/acpype.py

@@ -79,7 +79,7 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
 
             ## comando 1
             comando_gerar_molecula_complexada = 'cat {}_livre.top | sed \'/forcefield\.itp\"/a\#include "{}"\' >| {}1_complx.top'.format(mol,itpname,mol)
-            with open(os.path.join(folder, "run", "logs", f"dynamic-log.log"), 'a') as f:
+            with open(os.path.join(folder, "run", "logs", f"linux-commands.log"), 'a') as f:
                 subprocess.call(comando_gerar_molecula_complexada, shell=True, stdin=f, stdout=f, stderr=f)
 
             with open(os.path.join(RunFolder, f"{mol}1_complx.top"), "r") as f:
@@ -104,7 +104,7 @@ def execute(folder, CommandsFileName, username, filename, itpname, groname, mol)
 
             #aqui vai o echo ligand 1
             comando_moleculetype = 'echo "{}" >> {}_complx.top'.format(molecula,mol)
-            with open(os.path.join(folder, "run", "logs", f"dynamic-log.log"), 'a') as f:
+            with open(os.path.join(folder, "run", "logs", f"linux-commands.log"), 'a') as f:
                 subprocess.call(comando_moleculetype, shell=True, stdin=f, stdout=f, stderr=f)
 
     with open(os.path.join(folder, 'status'), 'w') as f:

app/blueprints/dynamic/executors/apo.py

@@ -24,7 +24,7 @@ def execute(folder, CommandsFileName, username, filename):
         f.write(f"{folder}\n")
 
     with open(os.path.join(Config.UPLOAD_FOLDER, username, "log_dir"), "w") as f:
-        f.write(os.path.join(folder, "run", "logs", f"dynamic-log.log"))
+        f.write(os.path.join(folder, "run", "logs", f"gmx-commands.log"))
 
     #abrir arquivo
     with open(CommandsFileName) as f: #CODIGO PARA A PRODUÇÃO
@@ -39,7 +39,7 @@ def execute(folder, CommandsFileName, username, filename):
             WriteUserDynamics(l, username)
         else:
             os.chdir(RunFolder)
-            rcode = run_dynamics_command(l, os.path.join(folder, "run", "logs", f"dynamic-log.log"))
+            rcode = run_dynamics_command(l, os.path.join(folder, "run", "logs", f"gmx-commands.log"))
 
             if rcode != 0:
                 with open(os.path.join(folder, 'status'), 'w') as f:

app/blueprints/dynamic/generators/acpype.py

@@ -53,7 +53,7 @@ def generate(folder, file_orig, file_itp_orig, file_gro_orig, force_field, water
         f"{gmx} grompp -f md_pr.mdp -c \"{filename}_complx_npt.gro\" -p \"{filename}_complx.top\" -o \"{filename}_complx_pr.tpr\" -maxwarn 20\n",
         f"{gmx} mdrun -v -s \"{filename}_complx_pr.tpr\" -deffnm \"{filename}_complx_pr\"\n\n",
         "#analyzemd\n",
-        f"echo \"1 0\" | {gmx} trjconv -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr.xtc\" -o \"{filename}_complx_pr_PBC.xtc\" -pbc mol -center\n",
+        f"echo \"1 17\" | {gmx} trjconv -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr.xtc\" -o \"{filename}_complx_pr_PBC.xtc\" -pbc mol -center\n",
         f"echo \"4 4\" | {gmx} rms -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr_PBC.xtc\" -o \"{filename}_complx_rmsd_prod.xvg\" -tu ns\n",
         f"{grace} -nxy \"{filename}_complx_rmsd_prod\".xvg -hdevice PNG -hardcopy -printfile \"../graficos/{filename}_complx_rmsd_prod.png\"\n",
         f"echo \"4 4\" | {gmx} rms -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr_PBC.xtc\" -o \"{filename}_complx_rmsd_cris.xvg\" -tu ns\n",

app/blueprints/dynamic/generators/apo.py

@@ -40,7 +40,7 @@ def generate(folder, file_orig, force_field, water_model, box_type, box_distance
     if neutralize:
         commands.extend([
             f"echo 'SOL' | {gmx} genion -s \"{filename}_charged.tpr\" -o \"{filename}_charged\" -p \"{filename}.top\" -neutral\n\n",
-            "#minimizationsteepdesc\n\n",
+            "#minimizationsteepdesc\n",
             f"{gmx} grompp -f PME_em.mdp -c \"{filename}_charged.gro\" -p \"{filename}.top\" -o \"{filename}_charged\" -maxwarn 2\n",
             f"{gmx} mdrun -v -s \"{filename}_charged.tpr\" -deffnm \"{filename}_sd_em\"\n",
             f"echo '10 0' | {gmx} energy -f \"{filename}_sd_em.edr\" -o \"{filename}_potentialsd.xvg\"\n",
@@ -67,7 +67,7 @@ def generate(folder, file_orig, force_field, water_model, box_type, box_distance
         f"{gmx} grompp -f md_pr.mdp -c \"{filename}_npt.gro\" -p \"{filename}.top\" -o \"{filename}_pr\" -maxwarn 2\n",
         f"{gmx} mdrun -v -s \"{filename}_pr.tpr\" -deffnm \"{filename}_pr\"\n\n",
         "#analyzemd\n",
-        f"echo '1 0' | {gmx} trjconv -s \"{filename}_pr.tpr\" -f \"{filename}_pr.xtc\" -o \"{filename}_pr_PBC.xtc\" -pbc mol -center\n",
+        f"echo '1 16' | {gmx} trjconv -s \"{filename}_pr.tpr\" -f \"{filename}_pr.xtc\" -o \"{filename}_pr_PBC.xtc\" -pbc mol -center\n",
         f"echo '4 4' | {gmx} rms -s \"{filename}_pr.tpr\" -f \"{filename}_pr_PBC.xtc\" -o \"{filename}_rmsd_prod.xvg\" -tu ns\n",
         f"{grace} -nxy \"{filename}_rmsd_prod.xvg\" -hdevice PNG -hardcopy -printfile \"../graficos/{filename}_rmsd_prod.png\"\n",
         f"echo '4 4' | {gmx} rms -s \"{filename}_charged.tpr\" -f \"{filename}_pr_PBC.xtc\" -o \"{filename}_rmsd_cris.xvg\" -tu ns\n",

app/blueprints/dynamic/generators/prodrg.py

@@ -24,7 +24,7 @@ def generate(folder, file_orig, file_itp_orig, file_gro_orig, force_field, water
     commands = [
         "#topology\n",
         f"{gmx} pdb2gmx -f \"{filename}{ext}\" -o \"{filename}_livre.gro\" -p \"{filename}_livre.top\" -ff gromos53a6 -water {water_model} -ignh -missing\n\n",
-        "#break\n\n",
+        "#break\n",
         f"{gmx} editconf -f \"{filename}_complx.gro\" -c -d 1 -bt {box_type} -o \"{filename}_complx.gro\"\n",
         "#solvate\n",
         f"{gmx} solvate -cp \"{filename}_complx.gro\" -cs spc216.gro -p \"{filename}_complx.top\" -o \"{filename}_complx_box.gro\"\n\n",
@@ -55,7 +55,7 @@ def generate(folder, file_orig, file_itp_orig, file_gro_orig, force_field, water
         f"{gmx} grompp -f md_pr.mdp -c \"{filename}_complx_npt.gro\" -p \"{filename}_complx.top\" -o \"{filename}_complx_pr.tpr\" -maxwarn 2\n",
         f"{gmx} mdrun -v -s \"{filename}_complx_pr.tpr\" -deffnm \"{filename}_complx_pr\"\n\n",
         "#analyzemd\n",
-        f"echo \"1 0\" | {gmx} trjconv -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr.xtc\" -o \"{filename}_complx_pr_PBC.xtc\" -pbc mol -center\n",
+        f"echo \"1 17\" | {gmx} trjconv -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr.xtc\" -o \"{filename}_complx_pr_PBC.xtc\" -pbc mol -center\n",
         f"echo \"4 4\" | {gmx} rms -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr_PBC.xtc\" -o \"{filename}_complx_rmsd_prod.xvg\" -tu ns\n",
         f"{grace} -nxy \"{filename}_complx_rmsd_prod.xvg\" -hdevice PNG -hardcopy -printfile \"../graficos/{filename}_complx_rmsd_prod.png\"\n",
         f"echo \"4 4\" | {gmx} rms -s \"{filename}_complx_pr.tpr\" -f \"{filename}_complx_pr_PBC.xtc\" -o \"{filename}_complx_rmsd_cris.xvg\"\n",

app/blueprints/dynamic/routes.py

@@ -35,11 +35,10 @@ def apo():
         if request.form.get('download') == 'Download':
             return redirect(
                 url_for(
-                    'DownloadRoutes.commandsdownload',
-                    filename={
-                        "complete": CompleteFileName,
-                        "name": filename
-                    }
+                    'DownloadRoutes.dynamiccomandsdownload',
+                    folder=f"{timestamp}",
+                    mode="apo",
+                    protein=filename
                 )
             )
 
@@ -113,11 +112,10 @@ def prodrg():
         if request.form.get('download') == 'Download':
             return redirect(
                 url_for(
-                    'DownloadRoutes.commandsdownload',
-                    filename={
-                        "complete": CompleteFileName,
-                        "name": name
-                    }
+                    'DownloadRoutes.dynamiccomandsdownload',
+                    folder=f"{timestamp}",
+                    mode="prodrg",
+                    protein=f"{filename}_{fileitpname}_{filegroname}"
                 )
             )
 
@@ -189,11 +187,10 @@ def acpype():
         if request.form.get('download') == 'Download':
             return redirect(
                 url_for(
-                    'DownloadRoutes.commandsdownload',
-                    filename={
-                        "complete": CompleteFileName,
-                        "name": name
-                    }
+                    'DownloadRoutes.dynamiccomandsdownload',
+                    folder=f"{timestamp}",
+                    mode="acpype",
+                    protein=f"{filename}_{fileitpname}_{filegroname}"
                 )
             )