'dock_rescore' con YASARA para complejos receptor-ligando.
Podemos calcular el valor de ΔG, Kcal/mol de la unión de un ligando cristaligráfico con receptor usando el macro 'dock_rescore' de YASARA. Igualmente, podemos hacer ese cálculo cuando disponemos de poses de ligandos calculadas con cualquier porgrama de 'docking'. Para el cálculo de muchos complejos receptor-ligando, el uso de Linux nos ahorra muchos dolores de cabeza.
Disponemos de dos ficheros de datos: '6M91mod-peptide-repair_tres_ligand.sdf' (con 1001 ligandos) y '6M91mod-peptide-repair_tres_receptor.pdb'. Estos ficheros se encuentran en la ruta /home/jant/runRESCORE/.
Editamos el fichero dock_rescore.mcr según nuestros intereses, en este ejemplo según los valores que se ven en la imagen justo debajo, localizado en la ruta /home/jant/yasara-26.05.05/mcr/.
Los scripts de Python que se muestran a continuación se encuentran en la ruta /home/jant/py-linux/16_rescore-YAS/ y se ejecutan secuencialmente.
Para comprender la construcción de cada script es necesario ver la apertura que hace YASARA de los ficheros '6M91mod-peptide-repair_tres_ligand.sdf' (con 1001 ligandos) y '6M91mod-peptide-repair_tres_receptor.pdb' y eso se muestra eb la imagen justo debajo. El 'Obj 1' corresponde al receptor y los siguientes 1001 corresponden a los ligandos y secuencialmente se nombran como 'A_J97_601', 'tres__1', 'tres__2', 'tres__3', etc.
En vista de estos datos, necesitamos crear un fichero de texto (_lista-4-variables-en-4-columnas.txt en nuestro ejemplo) con dos variables separadas por tabuladores. Las columnas 3 y 4 son repetición de la columna 2 pero mantengo esa estructura por comodidad.
Mi primer script de Python para procesar los datos de rescoring se llama 160_recalcular-deltaG-dos-variables.py y tiene la siguiente estructura:
# -*- coding: utf-8 -*-
import os
from pathlib import Path
# --- CONFIGURACION DE RUTAS ---
base_path = Path('/home/jant/py-linux/16_rescore-YAS')
lista_path = base_path / '_lista-4-variables-en-4-columnas.txt'
template_path = base_path / 'run-macro_template_SCORE.mcr'
# Ahora la salida es la misma carpeta base que indicaste
output_dir = Path('/home/jant/py-linux/16_rescore-YAS')
# Crear carpeta si no existe (aunque ya deberia existir)
output_dir.mkdir(parents=True, exist_ok=True)
# Leer plantilla
try:
template = template_path.read_text(encoding='utf-8')
except FileNotFoundError:
print(f"Error: No se encontro la plantilla en {template_path}")
exit()
# Leer variables y generar macros
if not lista_path.exists():
print(f"Error: No se encontro el archivo de variables en {lista_path}")
exit()
with open(lista_path, 'r', encoding='utf-8') as f:
for line in f:
line = line.strip()
if not line:
continue
partes = line.split('\t')
if len(partes) < 2:
print(f"Linea omitida (formato incorrecto): {line}")
continue
variable_1 = partes[0]
variable_2 = partes[1]
# Reemplazo encadenado para asegurar que ambas variables se apliquen
contenido = template.replace('[variable-1]', variable_1).replace('[variable-2]', variable_2)
# Nombre del archivo de salida usando la variable_2
output_file = output_dir / f'{variable_2}.mcr'
# Guardar
output_file.write_text(contenido, encoding='utf-8')
print(f'Generado: {output_file.name}')
print("\n>>> Macros generados exitosamente en /home/jant/py-linux/16_rescore-YAS/")
El script anterior necesita el fichero 'run-macro_template_SCORE.mcr' como plantilla (justo debajo), a partir de la cual se genera un macro por cada ligando (en nuestro ejemplo 1001 ficheros *.mcr):
Clear
LoadPDB "/home/jant/runRESCORE/6M91mod-peptide-repair_tres_receptor.pdb"
Loadsdf "/home/jant/runRESCORE/6M91mod-peptide-repair_tres_ligand.sdf",Transfer=yes
SaveYOb 1,/home/jant/runRESCORE/[variable-2]_receptor.yob
SaveSDF [variable-1],/home/jant/runRESCORE/[variable-2]_ligand.sdf,Transform=Yes,DativeBonds=No
MacroTarget /home/jant/runRESCORE/[variable-2]_receptor.yob,Remove=FromUnderscore
Include /home/jant/yasara-26.05.05/mcr/dock_runlocal.mcr
ExitEl siguiente script de Python genera 1001 ficheros *.sbatch para lanzar a la cola de SLURM 1001 'jobs', se llama 161_template_variable_DOCKING.py y tiene la siguiente estructura:
# -*- coding: iso-8859-1 -*-
import os
# Ruta y nombre de archivo de la lista de variables
var_file_path = '/home/jant/py-linux/16_rescore-YAS/_lista-4-variables-en-4-columnas.txt'
# Ruta y nombre de archivo de la plantilla de configuración
template_file_path = '/home/jant/py-linux/16_rescore-YAS/_15-template-config-UMH_DOCKING.txt'
# Abrir el archivo de variables y leer las líneas
with open(var_file_path, 'r') as var_file:
var_lines = var_file.readlines()
# Para cada línea de variables, generar una nueva plantilla con las variables sustituidas
for line in var_lines:
# Separar las variables por tabuladores y eliminar cualquier espacio en blanco
variables = [var.strip() for var in line.split('\t')]
# Leer la plantilla de configuración y sustituir las variables
with open(template_file_path, 'r') as template_file:
template = template_file.read()
for i in range(len(variables)):
template = template.replace(f'[variable-{i+1}]', variables[i])
# Guardar el archivo de configuración generado con el nombre de la primera variable
# y la extensión ".sbatch"
output_file_path = f"/home/jant/py-linux/16_rescore-YAS/_RES{variables[1]}.sbatch"
with open(output_file_path, 'w') as output_file:
output_file.write(template)
print("Proceso completado con éxito!")
ExitEl script anterior necesita el fichero de plantilla: '_15-template-config-UMH_DOCKING.txt'. Va a generar 1001 ficheros *.sbatch. El siguiente script de Python (162_template_docking_sh.py) genera un script de shell para cada job.
# -*- coding: utf-8 -*-
import os
import glob
import re
folder_path = "/home/jant/py-linux/16_rescore-YAS/"
file_pattern = "_RES"
# Función para extraer números y texto para orden natural
def natural_key(string_):
""" Convierte "archivo10" en ["archivo", 10] para ordenar correctamente """
return [int(s) if s.isdigit() else s.lower() for s in re.split(r'(\d+)', string_)]
# Obtener archivos
files = glob.glob(os.path.join(folder_path, file_pattern + "*"))
# --- ORDEN NATURAL ---
files.sort(key=natural_key)
with open("163_alanzar-DOCK.sh", "w") as f:
for filename in files:
# Usamos os.path.basename para que el nombre sea más limpio si es necesario
# pero mantenemos la lógica de sbatch
if os.path.isfile(filename):
f.write(f"sbatch {filename}\n")
# Establecer permisos 777
os.chmod("163_alanzar-DOCK.sh", 0o777)
print(f"Script generado con {len(files)} archivos en orden natural.")
Exit163_alanzar-DOCK.sh
sbatch /home/jant/py-linux/16_rescore-YAS/_RESA_J97_601.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__1.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__2.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__3.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__4.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__5.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__6.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__7.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__8.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__9.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__10.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__11.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__12.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__13.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__14.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__15.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__16.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__17.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__18.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__19.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__20.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__21.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__22.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__23.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__24.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__25.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__26.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__27.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__28.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__29.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__30.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__31.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__32.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__33.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__34.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__35.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__36.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__37.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__38.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__39.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__40.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__41.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__42.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__43.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__44.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__45.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__46.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__47.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__48.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__49.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__50.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__51.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__52.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__53.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__54.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__55.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__56.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__57.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__58.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__59.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__60.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__61.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__62.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__63.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__64.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__65.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__66.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__67.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__68.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__69.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__70.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__71.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__72.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__73.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__74.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__75.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__76.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__77.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__78.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__79.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__80.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__81.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__82.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__83.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__84.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__85.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__86.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__87.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__88.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__89.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__90.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__91.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__92.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__93.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__94.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__95.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__96.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__97.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__98.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__99.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__100.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__101.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__102.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__103.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__104.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__105.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__106.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__107.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__108.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__109.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__110.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__111.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__112.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__113.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__114.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__115.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__116.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__117.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__118.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__119.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__120.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__121.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__122.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__123.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__124.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__125.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__126.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__127.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__128.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__129.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__130.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__131.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__132.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__133.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__134.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__135.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__136.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__137.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__138.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__139.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__140.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__141.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__142.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__143.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__144.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__145.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__146.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__147.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__148.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__149.sbatch
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sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__998.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__999.sbatch
sbatch /home/jant/py-linux/16_rescore-YAS/_REStres__1000.sbatchY para terminar, el script 164_analiza-logs.py rescata los valores de ΔG de generados con el dock_rescore.
# -*- coding: utf-8 -*-
from pathlib import Path
import re
# --- CONFIGURACION ---
ruta = Path("/home/jant/runRESCORE")
salida = ruta / "_resultados-TRES.txt"
def natural_key(text):
return [int(c) if c.isdigit() else c.lower() for c in re.split(r'(\d+)', text)]
def limpiar_numero(texto):
""" Convierte a float y luego a string para eliminar ceros a la izquierda """
try:
# Al convertir a float, 000007.8930 se convierte en 7.893
valor = float(texto.strip())
# Si prefieres mantener un numero fijo de decimales, usa: return f"{valor:.4f}"
return str(valor)
except ValueError:
return texto.strip()
# Buscar *.log
logs = sorted(ruta.glob("*.log"), key=lambda x: natural_key(x.stem))
print(f"Procesando {len(logs)} archivos en {ruta}...")
with open(salida, "w", encoding="utf-8") as fout:
# Cabecera
fout.write("Compound\tClu\tBind.energy[kcal/mol]\tDissoc. constant [pM]\tCon.Surf[A^2]\n")
for log_file in logs:
try:
linea_datos = None
with open(log_file, "r", encoding="utf-8", errors="ignore") as fin:
en_seccion_clusters = False
for line in fin:
if "After clustering" in line:
en_seccion_clusters = True
if en_seccion_clusters and line.strip().startswith("001 |"):
linea_datos = line.strip()
break
if linea_datos:
bloques = [x.strip() for x in linea_datos.split("|")]
# bloques[0] -> Cluster (ej: 001)
# bloques[1] -> Energia (ej: 000007.8930)
# bloques[2] -> Constante (ej: 00000001638152.3750)
# bloques[3] -> Superficie (ej: 000332.65)
nombre = log_file.stem
# Limpiamos los ceros de cada campo numerico
cluster = limpiar_numero(bloques[0])
energia = limpiar_numero(bloques[1])
constante = limpiar_numero(bloques[2])
superficie = limpiar_numero(bloques[3])
# Escribimos con tabuladores
fout.write(f"{nombre}\t{cluster}\t{energia}\t{constante}\t{superficie}\n")
else:
print(f"[AVISO] No se encontro el cluster 001 en: {log_file.name}")
except Exception as e:
print(f"[ERROR] En {log_file.name}: {e}")
print(f"\n>>> Hecho! Los resultados en {salida} ahora estan limpios para Excel.")