Source code for leap.leap_solvate

#!/usr/bin/env python3

"""Module containing the LeapSolvate class and the command line interface."""

import os
import argparse
import re
from pathlib import PurePath
from typing import List, Optional

from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger

from biobb_amber.leap.common import _from_string_to_list


[docs] class LeapSolvate(BiobbObject): """ | biobb_amber LeapSolvate | Wrapper of the `AmberTools (AMBER MD Package) leap tool <https://ambermd.org/AmberTools.php>`_ module. | Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package. Args: input_pdb_path (str): Input 3D structure PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.leap.pdb>`_. Accepted formats: pdb (edam:format_1476). input_lib_path (str) (Optional): Input ligand library parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib>`_. Accepted formats: lib (edam:format_3889), zip (edam:format_3987). input_frcmod_path (str) (Optional): Input ligand frcmod parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod>`_. Accepted formats: frcmod (edam:format_3888), zip (edam:format_3987). input_params_path (str) (Optional): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987). input_prep_path (str) (Optional): Additional leap parameter files to load with loadAmberPrep Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/heme_all.in>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987). input_source_path (str) (Optional): Additional leap command files to load with source Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987). output_pdb_path (str): Output 3D structure PDB file matching the topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.pdb>`_. Accepted formats: pdb (edam:format_1476). output_top_path (str): Output topology file (AMBER ParmTop). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.top>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). output_crd_path (str): Output coordinates file (AMBER crd). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **forcefield** (*list*) - (["protein.ff14SB","DNA.bsc1","gaff"]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. "/path/to/leaprc.protein.ff14SB" or "protein.ff14SB"). Default values: ["protein.ff14SB","DNA.bsc1","gaff"]. * **water_type** (*str*) - ("TIP3PBOX") Water molecule parameters to be used for the topology. Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX. * **box_type** (*str*) - ("truncated_octahedron") Type for the MD system box. Values: cubic, truncated_octahedron. * **ions_type** (*str*) - ("ionsjc_tip3p") Ions type. Values: ionsjc_tip3p, ionsjc_spce, ionsff99_tip3p, ions_charmm22, ionsjc_tip4pew, None. * **neutralise** (*bool*) - ("False") Energetically neutralise the system adding the necessary counterions. * **iso** (*bool*) - ("False") Make the box isometric. * **positive_ions_number** (*int*) - (0) Number of additional positive ions to include in the system box. * **negative_ions_number** (*int*) - (0) Number of additional negative ions to include in the system box. * **positive_ions_type** (*str*) - ("Na+") Type of additional positive ions to include in the system box. Values: Na+,K+. * **negative_ions_type** (*str*) - ("Cl-") Type of additional negative ions to include in the system box. Values: Cl-. * **distance_to_molecule** (*float*) - ("8.0") Size for the MD system box -in Angstroms-, defined such as the minimum distance between any atom originally present in solute and the edge of the periodic box is given by this distance parameter. * **closeness** (*float*) - ("1.0") How close, in Å, solvent ATOMs may come to solute ATOMs. * **binary_path** (*str*) - ("tleap") Path to the tleap executable binary. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. * **container_path** (*str*) - (None) Container path definition. * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. * **container_working_dir** (*str*) - (None) Container working directory definition. * **container_user_id** (*str*) - (None) Container user_id definition. * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. Examples: This is a use example of how to use the building block from Python:: from biobb_amber.leap.leap_solvate import leap_solvate prop = { 'forcefield': ['protein.ff14SB'], 'water_type': 'TIP3PBOX', 'box_type': 'truncated_octahedron', 'neutralise' : True } leap_solvate(input_pdb_path='/path/to/structure.pdb', output_pdb_path='/path/to/newStructure.pdb', output_top_path='/path/to/newTopology.top', output_crd_path='/path/to/newCoordinates.crd', properties=prop) Info: * wrapped_software: * name: AmberTools tLeap * version: >20.9 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__( self, input_pdb_path: str, output_pdb_path: str, output_top_path: str, output_crd_path: str, input_lib_path: Optional[str] = None, input_frcmod_path: Optional[str] = None, input_params_path: Optional[str] = None, input_prep_path: Optional[str] = None, input_source_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs, ): properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { "in": { "input_pdb_path": input_pdb_path, "input_lib_path": input_lib_path, "input_frcmod_path": input_frcmod_path, "input_params_path": input_params_path, "input_prep_path": input_prep_path, "input_source_path": input_source_path, }, "out": { "output_pdb_path": output_pdb_path, "output_top_path": output_top_path, "output_crd_path": output_crd_path, }, } # # Ligand Parameter lists # self.ligands_lib_list = [] # if input_lib_path: # self.ligands_lib_list.append(input_lib_path) # # self.ligands_frcmod_list = [] # if input_frcmod_path: # self.ligands_frcmod_list.append(input_frcmod_path) # Set default forcefields amber_home_path = os.getenv("AMBERHOME") protein_ff14SB_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.protein.ff14SB') dna_bsc1_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.DNA.bsc1') gaff_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.gaff') # Properties specific for BB self.properties = properties self.forcefield = _from_string_to_list( properties.get("forcefield", [protein_ff14SB_path, dna_bsc1_path, gaff_path]) ) # Find the paths of the leaprc files if only the force field names are provided self.forcefield = self.find_leaprc_paths(self.forcefield) self.water_type = properties.get("water_type", "TIP3PBOX") self.box_type = properties.get("box_type", "truncated_octahedron") self.ions_type = properties.get("ions_type", "ionsjc_tip3p") self.neutralise = properties.get("neutralise", False) self.iso = properties.get("iso", False) self.positive_ions_number = properties.get("positive_ions_number", 0) self.positive_ions_type = properties.get("positive_ions_type", "Na+") self.negative_ions_number = properties.get("negative_ions_number", 0) self.negative_ions_type = properties.get("negative_ions_type", "Cl-") self.distance_to_molecule = properties.get("distance_to_molecule", 8.0) self.closeness = properties.get("closeness", 1.0) self.binary_path = properties.get("binary_path", "tleap") # Check the properties self.check_properties(properties) self.check_arguments()
[docs] def find_leaprc_paths(self, forcefields: List[str]) -> List[str]: """ Find the leaprc paths for the force fields provided. For each item in the forcefields list, the function checks if the str is a path to an existing file. If not, it tries to find the file in the $AMBERHOME/dat/leap/cmd/ directory or the $AMBERHOME/dat/leap/cmd/oldff/ directory with and without the leaprc prefix. Args: forcefields (List[str]): List of force fields to find the leaprc files for. Returns: List[str]: List of leaprc file paths. """ leaprc_paths = [] for forcefield in forcefields: num_paths = len(leaprc_paths) # Check if the forcefield is a path to an existing file if os.path.exists(forcefield): leaprc_paths.append(forcefield) continue # Check if the forcefield is in the leaprc directory leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"leaprc.{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue # Check if the forcefield is in the oldff directory leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"leaprc.{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue # Check if the forcefield is in the leaprc directory without the leaprc prefix leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue # Check if the forcefield is in the oldff directory without the leaprc prefix leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue new_num_paths = len(leaprc_paths) if new_num_paths == num_paths: raise ValueError(f"Force field {forcefield} not found. Check the $AMBERHOME/dat/leap/cmd/ directory for available force fields or provide the path to an existing leaprc file.") return leaprc_paths
# def check_data_params(self, out_log, err_log): # """ Checks input/output paths correctness """ # # Check input(s) # self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", False, out_log, self.__class__.__name__) # self.io_dict["in"]["input_lib_path"] = check_input_path(self.io_dict["in"]["input_lib_path"], "input_lib_path", True, out_log, self.__class__.__name__) # self.io_dict["in"]["input_frcmod_path"] = check_input_path(self.io_dict["in"]["input_frcmod_path"], "input_frcmod_path", True, out_log, self.__class__.__name__) # # self.io_dict["in"]["input_params_path"] = check_input_path(self.io_dict["in"]["input_params_path"], "input_params_path", True, out_log, self.__class__.__name__) # # self.io_dict["in"]["input_source_path"] = check_input_path(self.io_dict["in"]["input_source_path"], "input_source_path", True, out_log, self.__class__.__name__) # # Check output(s) # self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__) # self.io_dict["out"]["output_top_path"] = check_output_path(self.io_dict["out"]["output_top_path"], "output_top_path", False, out_log, self.__class__.__name__) # self.io_dict["out"]["output_crd_path"] = check_output_path(self.io_dict["out"]["output_crd_path"], "output_crd_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self): """Launches the execution of the LeapSolvate module.""" # check input/output paths and parameters # self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() box_command = "solvateOct" if self.box_type == "cubic": box_command = "solvateBox" # Forcefield # source_ff_command = "source leaprc." + self.forcefield # Water Type # leaprc.water.tip4pew, tip4pd, tip3p, spceb, spce, opc, fb4, fb3 # Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX. source_wat_command = "source leaprc.water.tip3p" if self.water_type == "TIP4PEWBOX": source_wat_command = "leaprc.water.tip4pew" if self.water_type == "TIP4PBOX": source_wat_command = "leaprc.water.tip4pd" if re.match(r"SPC", self.water_type): source_wat_command = "source leaprc.water.spce" if re.match(r"OPC", self.water_type): source_wat_command = "source leaprc.water.opc" # Counterions ions_command = "" if self.neutralise: ions_command = ( ions_command + "addions mol " + self.negative_ions_type + " 0 \n" ) ions_command = ( ions_command + "addions mol " + self.positive_ions_type + " 0 \n" ) if self.negative_ions_number != 0: ions_command = ( ions_command + "addions mol " + self.negative_ions_type + " " + str(self.negative_ions_number) + " \n" ) if self.positive_ions_number != 0: ions_command = ( ions_command + "addions mol " + self.positive_ions_type + " " + str(self.positive_ions_number) + " \n" ) # Creating temporary folder & Leap configuration (instructions) file if self.container_path: instructions_file = str( PurePath(self.stage_io_dict["unique_dir"]).joinpath("leap.in") ) instructions_file_path = str( PurePath(self.container_volume_path).joinpath("leap.in") ) self.tmp_folder = None else: self.tmp_folder = fu.create_unique_dir() instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in")) fu.log("Creating %s temporary folder" % self.tmp_folder, self.out_log) instructions_file_path = instructions_file ligands_lib_list = [] if self.io_dict["in"]["input_lib_path"] is not None: if self.io_dict["in"]["input_lib_path"].endswith(".zip"): ligands_lib_list = fu.unzip_list( self.stage_io_dict["in"]["input_lib_path"], dest_dir=self.tmp_folder, out_log=self.out_log, ) else: ligands_lib_list.append(self.stage_io_dict["in"]["input_lib_path"]) ligands_frcmod_list = [] if self.io_dict["in"]["input_frcmod_path"] is not None: if self.io_dict["in"]["input_frcmod_path"].endswith(".zip"): ligands_frcmod_list = fu.unzip_list( self.stage_io_dict["in"]["input_frcmod_path"], dest_dir=self.tmp_folder, out_log=self.out_log, ) else: ligands_frcmod_list.append( self.stage_io_dict["in"]["input_frcmod_path"] ) amber_params_list = [] if self.io_dict["in"]["input_params_path"] is not None: if self.io_dict["in"]["input_params_path"].endswith(".zip"): amber_params_list = fu.unzip_list( self.stage_io_dict["in"]["input_params_path"], dest_dir=self.tmp_folder, out_log=self.out_log, ) else: amber_params_list.append(self.stage_io_dict["in"]["input_params_path"]) amber_prep_list = [] if self.io_dict["in"]["input_prep_path"] is not None: if self.io_dict["in"]["input_prep_path"].endswith(".zip"): amber_prep_list = fu.unzip_list( self.stage_io_dict["in"]["input_prep_path"], dest_dir=self.tmp_folder, out_log=self.out_log, ) else: amber_prep_list.append(self.stage_io_dict["in"]["input_prep_path"]) leap_source_list = [] if self.io_dict["in"]["input_source_path"] is not None: if self.io_dict["in"]["input_source_path"].endswith(".zip"): leap_source_list = fu.unzip_list( self.stage_io_dict["in"]["input_source_path"], dest_dir=self.tmp_folder, out_log=self.out_log, ) else: leap_source_list.append(self.stage_io_dict["in"]["input_source_path"]) with open(instructions_file, "w") as leapin: # Forcefields loaded by default: # Protein: ff14SB (PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA) # leapin.write("source leaprc.protein.ff14SB \n") # DNA: parmBSC1 (ParmBSC1 (ff99 + bsc0 + bsc1) for DNA. Ivani et al. Nature Methods 13: 55, 2016) # leapin.write("source leaprc.DNA.bsc1 \n") # Ligands: GAFF (General Amber Force field, J. Comput. Chem. 2004 Jul 15;25(9):1157-74) # leapin.write("source leaprc.gaff \n") # Forcefields loaded from input forcefield property for t in self.forcefield: leapin.write("source {}\n".format(t)) # Additional Leap commands for leap_commands in leap_source_list: leapin.write("source " + leap_commands + "\n") # Ions Type if self.ions_type != "None": leapin.write("loadamberparams frcmod." + self.ions_type + "\n") # Additional Amber parameters for amber_params in amber_params_list: leapin.write("loadamberparams " + amber_params + "\n") # Additional Amber prep files for amber_prep in amber_prep_list: leapin.write("loadamberprep " + amber_prep + "\n") # Water Model loaded from input water_model property leapin.write(source_wat_command + " \n") # Ligand(s) libraries (if any) for amber_lib in ligands_lib_list: leapin.write("loadOff " + amber_lib + "\n") for amber_frcmod in ligands_frcmod_list: leapin.write("loadamberparams " + amber_frcmod + "\n") # Loading PDB file leapin.write( "mol = loadpdb " + self.stage_io_dict["in"]["input_pdb_path"] + " \n" ) # Generating box + adding water molecules leapin.write( box_command + " mol " + self.water_type + " " + str(self.distance_to_molecule) ) leapin.write( " iso " + str(self.closeness) + "\n" ) if self.iso else leapin.write(" " + str(self.closeness) + "\n") # Adding counterions leapin.write(ions_command) # Saving output PDB file, coordinates and topology leapin.write( "savepdb mol " + self.stage_io_dict["out"]["output_pdb_path"] + " \n" ) leapin.write( "saveAmberParm mol " + self.stage_io_dict["out"]["output_top_path"] + " " + self.stage_io_dict["out"]["output_crd_path"] + "\n" ) leapin.write("quit \n") # Command line self.cmd = [self.binary_path, "-f", instructions_file_path] # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # Saving octahedron box with all decimals in PDB file. Needed for the add_ions BB. # Getting octahedron box from generated crd file with open(self.io_dict["out"]["output_crd_path"], "r") as file: for line in file: pass # Adding box as a first line in the generated pdb file with OCTBOX tag octbox = "OCTBOX " + line with open(self.io_dict["out"]["output_pdb_path"], "r+") as f: content = f.read() f.seek(0, 0) f.write(octbox + content) # remove temporary folder(s) self.tmp_files.extend([ # self.stage_io_dict.get("unique_dir", ""), str(self.tmp_folder), "leap.log" ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs] def leap_solvate( input_pdb_path: str, output_pdb_path: str, output_top_path: str, output_crd_path: str, input_lib_path: Optional[str] = None, input_frcmod_path: Optional[str] = None, input_params_path: Optional[str] = None, input_prep_path: Optional[str] = None, input_source_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs, ) -> int: """Create :class:`LeapSolvate <leap.leap_solvate.LeapSolvate>`leap.leap_solvate.LeapSolvate class and execute :meth:`launch() <leap.leap_solvate.LeapSolvate.launch>` method""" return LeapSolvate( input_pdb_path=input_pdb_path, input_lib_path=input_lib_path, input_frcmod_path=input_frcmod_path, input_params_path=input_params_path, input_prep_path=input_prep_path, input_source_path=input_source_path, output_pdb_path=output_pdb_path, output_top_path=output_top_path, output_crd_path=output_crd_path, properties=properties, ).launch() leap_solvate.__doc__ = LeapSolvate.__doc__
[docs] def main(): parser = argparse.ArgumentParser( description="Generating and solvating a system box for an AMBER MD system. using tLeap program from AmberTools MD package.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999), ) parser.add_argument("--config", required=False, help="Configuration file") # Specific args required_args = parser.add_argument_group("required arguments") required_args.add_argument( "--input_pdb_path", required=True, help="Input 3D structure PDB file. Accepted formats: pdb.", ) required_args.add_argument( "--input_lib_path", required=False, help="Input ligand library parameters file. Accepted formats: lib, zip.", ) required_args.add_argument( "--input_frcmod_path", required=False, help="Input ligand frcmod parameters file. Accepted formats: frcmod, zip.", ) required_args.add_argument( "--input_params_path", required=False, help="Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.", ) required_args.add_argument( "--input_prep_path", required=False, help="Additional leap parameter files to load with loadAmberPrep Leap command. Accepted formats: leapin, in, txt, zip.", ) required_args.add_argument( "--input_source_path", required=False, help="Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.", ) required_args.add_argument( "--output_pdb_path", required=True, help="Output 3D structure PDB file matching the topology file. Accepted formats: pdb.", ) required_args.add_argument( "--output_top_path", required=True, help="Output topology file (AMBER ParmTop). Accepted formats: top.", ) required_args.add_argument( "--output_crd_path", required=True, help="Output coordinates file (AMBER crd). Accepted formats: crd.", ) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call leap_solvate( input_pdb_path=args.input_pdb_path, input_lib_path=args.input_lib_path, input_frcmod_path=args.input_frcmod_path, input_params_path=args.input_params_path, input_prep_path=args.input_prep_path, input_source_path=args.input_source_path, output_pdb_path=args.output_pdb_path, output_top_path=args.output_top_path, output_crd_path=args.output_crd_path, properties=properties, )
if __name__ == "__main__": main()