Source code for leap.leap_add_ions

#!/usr/bin/env python3

"""Module containing the LeapAddIons class and the command line interface."""
import argparse
import shutil, re
from decimal import Decimal
from pathlib import Path, 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 *

[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-. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 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) # 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-") # Check the properties self.check_properties(properties)
[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() # Creating temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) # 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" 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.io_dict['in']['input_lib_path'], dest_dir=self.tmp_folder, out_log=self.out_log) else: ligands_lib_list.append(self.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.io_dict['in']['input_frcmod_path'], dest_dir=self.tmp_folder, out_log=self.out_log) else: ligands_frcmod_list.append(self.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.io_dict['in']['input_params_path'], dest_dir=self.tmp_folder, out_log=self.out_log) else: amber_params_list.append(self.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.io_dict['in']['input_source_path'], dest_dir=self.tmp_folder, out_log=self.out_log) else: leap_source_list.append(self.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.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.io_dict['out']['output_pdb_path'] + " \n") leapin.write("saveAmberParm mol " + self.io_dict['out']['output_top_path'] + " " + self.io_dict['out']['output_crd_path'] + "\n") leapin.write("quit \n"); # Command line self.cmd = ['tleap ', '-f', instructions_file ] # 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 = '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) if self.remove_tmp: self.tmp_files.append(self.tmp_folder) self.tmp_files.append("leap.log") self.remove_tmp_files() 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()