#!/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()