#!/usr/bin/env python3
"""Module containing the LeapAddIons class and the command line interface."""
import argparse
import shutil
import re
from decimal import Decimal
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_amber.leap.common import check_input_path, check_output_path
[docs]class LeapAddIons(BiobbObject):
"""
| biobb_amber LeapAddIons
| Wrapper of the `AmberTools (AMBER MD Package) leap tool <https://ambermd.org/AmberTools.php>`_ module.
| Adds counterions to 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.solv.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_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.ions.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.ions.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.ions.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"]) Forcefield to be used for the structure generation. Values: protein.ff14SB, protein.ff19SB, DNA.bsc1, DNA.OL15, RNA.OL3, 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*) - ("True") Energetically neutralise the system adding the necessary counterions.
* **ionic_concentration** (*float*) - (50) Additional ionic concentration to include in the system box. Units in Mol/L.
* **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-.
* **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.
* **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_add_ions import leap_add_ions
prop = {
'forcefield': ['protein.ff14SB'],
'water_type': 'TIP3PBOX',
'neutralise' : True
}
leap_add_ions(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: str = None, input_frcmod_path: str = None,
input_params_path: str = None, input_source_path: str = None,
properties: 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_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)
# Properties specific for BB
self.properties = properties
self.forcefield = properties.get('forcefield', ["protein.ff14SB", "DNA.bsc1", "gaff"])
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', True)
self.ionic_concentration = properties.get('ionic_concentration', 50)
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.binary_path = properties.get('binary_path', 'tleap')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] 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] def find_out_number_of_ions(self):
""" Computes the number of positive and negative ions from the input ionic
concentration and the number of water molecules in the system box."""
# Finding number of water molecules in the box
cnt = 0
with open(self.io_dict['in']['input_pdb_path']) as fp:
for line in fp:
# Water molecules are identified with different resids
# by different forcefields / MD packages
pq = re.compile((r'WAT|HOH|TP3|TIP3|SOL'), re.M)
if pq.search(line):
# Incrementing number of water molecules just in the water
# oxygen atom, ignoring hydrogen atoms
pq2 = re.compile(r"H", re.M)
if not pq2.search(line):
cnt = cnt + 1
# To get to X mM ions we need
# n(NaCl) = #waters / 55 Mol * X M
# where X M = X mM / 1000
self.nio = int((cnt / 55) * (self.ionic_concentration / 1000))
[docs] @launchlogger
def launch(self):
"""Launches the execution of the LeapAddIons 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()
# 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"
ions_command = ions_command + "addionsRand mol " + self.negative_ions_type + " 0 \n"
ions_command = ions_command + "addionsRand mol " + self.positive_ions_type + " 0 \n"
if self.ionic_concentration and self.negative_ions_number == 0 and self.positive_ions_number == 0:
self.find_out_number_of_ions()
nneg = self.nio # Update with function
npos = self.nio # Update with function
# ions_command = ions_command + "addions mol " + self.negative_ions_type + " " + str(nneg) + " \n"
# ions_command = ions_command + "addions mol " + self.positive_ions_type + " " + str(npos) + " \n"
ions_command = ions_command + "addionsRand mol " + self.negative_ions_type + " " + str(nneg) + " \n"
ions_command = ions_command + "addionsRand mol " + self.positive_ions_type + " " + str(npos) + " \n"
else:
if self.negative_ions_number != 0:
# ions_command = ions_command + "addions mol " + self.negative_ions_type + " " + str(self.negative_ions_number) + " \n"
ions_command = ions_command + "addionsRand 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"
ions_command = ions_command + "addionsRand 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'])
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'])
# instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in"))
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 leaprc.{}\n".format(t))
# Additional Leap commands
for leap_commands in leap_source_list:
leapin.write("source " + leap_commands + "\n")
# Water Model loaded from input water_model property
leapin.write(source_wat_command + " \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")
# 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")
# Adding ions
leapin.write(ions_command)
# Generating box
leapin.write("setBox mol vdw \n")
# 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()
if self.box_type != "cubic":
fu.log('Fixing truncated octahedron Box in the topology and coordinates files', self.out_log, self.global_log)
# Taking box info from input PDB file, CRYST1 tag (first line)
with open(self.io_dict['in']['input_pdb_path']) as file:
lines = file.readlines()
pdb_line = lines[0]
if 'OCTBOX' not in pdb_line:
fu.log('WARNING: box info not found in input PDB file (OCTBOX). Needed to correctly assign the octahedron box. Assuming cubic box.', self.out_log, self.global_log)
else:
# PDB info: CRYST1 86.316 86.316 86.316 109.47 109.47 109.47 P 1
# PDB info: OCTBOX 86.1942924 86.1942924 86.1942924 109.4712190 109.4712190 109.4712190
# regex_box = 'CRYST1\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*P 1'
regex_box = r'OCTBOX\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)'
box = re.findall(regex_box, pdb_line)[0]
box_line = ""
for coord in box:
box_line += "{:12.7f}".format(float(coord))
# PRMTOP info: 1.09471219E+02 8.63157502E+01 8.63157502E+01 8.63157502E+01
top_box_line = ""
top_box_line += ' %.8E' % Decimal(float(box[3]))
top_box_line += ' %.8E' % Decimal(float(box[0]))
top_box_line += ' %.8E' % Decimal(float(box[1]))
top_box_line += ' %.8E' % Decimal(float(box[2]))
# Removing box generated by tleap from the crd file (last line)
with open(self.io_dict['out']['output_crd_path']) as file:
lines = file.readlines()
crd_lines = lines[:-1]
# Adding old box coordinates (taken from the input pdb)
crd_lines.append(box_line)
with open(self.io_dict['out']['output_crd_path'], 'w') as file:
for line in crd_lines:
file.write(str(line))
file.write("\n")
# Now fixing IFBOX param in prmtop.
box_flag = False
ifbox_flag = 0
# %FLAG BOX_DIMENSIONS
# %FORMAT(5E16.8)
# 1.09471219E+02 8.63157502E+01 8.63157502E+01 8.63157502E+01
tmp_parmtop = str(PurePath(self.tmp_folder).joinpath("top_temp.parmtop"))
shutil.copyfile(self.io_dict['out']['output_top_path'], tmp_parmtop)
with open(self.io_dict['out']['output_top_path'], 'w') as new_top:
with open(tmp_parmtop, 'r') as old_top:
for line in old_top:
if 'BOX_DIMENSIONS' in line:
box_flag = True
new_top.write(line)
elif box_flag and 'FORMAT' not in line:
new_top.write(top_box_line + "\n")
box_flag = False
elif 'FLAG POINTERS' in line or ifbox_flag == 1 or ifbox_flag == 2 or ifbox_flag == 3:
ifbox_flag += 1
new_top.write(line)
elif ifbox_flag == 4:
# new_top.write(top_box_line + "\n")
new_top.write(line[:56] + ' 2' + line[64:])
ifbox_flag += 1
else:
new_top.write(line)
# remove temporary folder(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
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_add_ions(input_pdb_path: str, output_pdb_path: str,
output_top_path: str, output_crd_path: str,
input_lib_path: str = None, input_frcmod_path: str = None,
input_params_path: str = None, input_source_path: str = None,
properties: dict = None, **kwargs) -> int:
"""Create :class:`LeapAddIons <leap.leap_add_ions.LeapAddIons>`leap.leap_add_ions.LeapAddIons class and
execute :meth:`launch() <leap.leap_add_ions.LeapAddIons.launch>` method"""
return LeapAddIons(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_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()
[docs]def main():
parser = argparse.ArgumentParser(description='Adds counterions to a system box for an AMBER MD system using tLeap.', 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_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_add_ions(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_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()