Coverage for biobb_amber/pdb4amber/pdb4amber_run.py: 76%

1#!/usr/bin/env python3 

2 

3"""Module containing the Pdb4amber class and the command line interface.""" 

4import argparse 

5from biobb_common.generic.biobb_object import BiobbObject 

6from biobb_common.configuration import settings 

7from biobb_common.tools import file_utils as fu 

8from biobb_common.tools.file_utils import launchlogger 

9from biobb_amber.pdb4amber.common import check_input_path, check_output_path 

10 

11 

12class Pdb4amberRun(BiobbObject): 

13 """ 

14 | biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun 

15 | Wrapper of the `AmberTools (AMBER MD Package) pdb4amber tool <https://ambermd.org/AmberTools.php>`_ module. 

16 | Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package. 

17 

18 Args: 

19 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/pdb4amber/1aki_fixed.pdb>`_. Accepted formats: pdb (edam:format_1476). 

20 output_pdb_path (str): Output 3D structure PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pdb4amber/structure.pdb4amber.pdb>`_. Accepted formats: pdb (edam:format_1476). 

21 properties (dict - Python dictionary object containing the tool parameters, not input/output files): 

22 * **remove_hydrogens** (*bool*) - (False) Remove hydrogen atoms from the PDB file. 

23 * **remove_waters** (*bool*) - (False) Remove water molecules from the PDB file. 

24 * **constant_pH** (*bool*) - (False) Rename ionizable residues e.g. GLU,ASP,HIS for constant pH simulation. 

25 * **binary_path** (*str*) - ("pdb4amber") Path to the pdb4amber executable binary. 

26 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. 

27 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 

28 * **container_path** (*str*) - (None) Container path definition. 

29 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. 

30 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. 

31 * **container_working_dir** (*str*) - (None) Container working directory definition. 

32 * **container_user_id** (*str*) - (None) Container user_id definition. 

33 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. 

34 

35 Examples: 

36 This is a use example of how to use the building block from Python:: 

37 

38 from biobb_amber.pdb4amber.pdb4amber_run import pdb4amber_run 

39 prop = { 

40 'remove_tmp': True 

41 } 

42 pdb4amber_run(input_pdb_path='/path/to/structure.pdb', 

43 output_pdb_path='/path/to/newStructure.pdb', 

44 properties=prop) 

45 

46 Info: 

47 * wrapped_software: 

48 * name: AmberTools pdb4amber 

49 * version: >20.9 

50 * license: LGPL 2.1 

51 * ontology: 

52 * name: EDAM 

53 * schema: http://edamontology.org/EDAM.owl 

54 

55 """ 

56 def __init__(self, input_pdb_path: str, output_pdb_path: str, 

57 properties: dict, **kwargs): 

58 

59 properties = properties or {} 

60 

61 # Call parent class constructor 

62 super().__init__(properties) 

63 self.locals_var_dict = locals().copy() 

64 

65 # Input/Output files 

66 self.io_dict = { 

67 'in': {'input_pdb_path': input_pdb_path}, 

68 'out': {'output_pdb_path': output_pdb_path} 

69 } 

70 

71 # Properties specific for BB 

72 self.properties = properties 

73 self.remove_hydrogens = properties.get('remove_hydrogens', False) 

74 self.remove_waters = properties.get('remove_waters', False) 

75 self.constant_pH = properties.get('constant_pH', False) 

76 self.binary_path = properties.get('binary_path', 'pdb4amber') 

77 

78 # Check the properties 

79 self.check_properties(properties) 

80 self.check_arguments() 

81 

82 def check_data_params(self, out_log, err_log): 

83 """ Checks input/output paths correctness """ 

84 

85 # Check input(s) 

86 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__) 

87 

88 # Check output(s) 

89 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__) 

90 

91 @launchlogger 

92 def launch(self): 

93 """Launches the execution of the Pdb4amberRun module.""" 

94 

95 # check input/output paths and parameters 

96 self.check_data_params(self.out_log, self.err_log) 

97 

98 # Setup Biobb 

99 if self.check_restart(): 

100 return 0 

101 self.stage_files() 

102 

103 # Creating temporary folder 

104 self.tmp_folder = fu.create_unique_dir() 

105 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) 

106 

107 # Command line 

108 # sander -O -i mdin/min.mdin -p $1.cpH.prmtop -c ph$i/$1.inpcrd -r ph$i/$1.min.rst7 -o ph$i/$1.min.o 

109 self.cmd = [self.binary_path, 

110 '-i', self.stage_io_dict['in']['input_pdb_path'], 

111 '-o', self.stage_io_dict['out']['output_pdb_path'] 

112 ] 

113 

114 if self.remove_hydrogens: 

115 self.cmd.append("-y ") 

116 if self.remove_waters: 

117 self.cmd.append("-d ") 

118 if self.constant_pH: 

119 self.cmd.append("--constantph ") 

120 

121 # Run Biobb block 

122 self.run_biobb() 

123 

124 # Copy files to host 

125 self.copy_to_host() 

126 

127 # remove temporary folder(s) 

128 self.tmp_files.extend([ 

129 self.stage_io_dict.get("unique_dir"), 

130 self.tmp_folder 

131 ]) 

132 self.remove_tmp_files() 

133 

134 self.check_arguments(output_files_created=True, raise_exception=False) 

135 

136 return self.return_code 

137 

138 

139def pdb4amber_run(input_pdb_path: str, output_pdb_path: str, 

140 properties: dict = None, **kwargs) -> int: 

141 """Create :class:`Pdb4amberRun <pdb4amber.pdb4amber_run.Pdb4amberRun>`pdb4amber.pdb4amber_run.Pdb4amberRun class and 

142 execute :meth:`launch() <pdb4amber.pdb4amber_run.Pdb4amberRun.launch>` method""" 

143 

144 return Pdb4amberRun(input_pdb_path=input_pdb_path, 

145 output_pdb_path=output_pdb_path, 

146 properties=properties).launch() 

147 

148 

149def main(): 

150 parser = argparse.ArgumentParser(description='Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

151 parser.add_argument('--config', required=False, help='Configuration file') 

152 

153 # Specific args 

154 required_args = parser.add_argument_group('required arguments') 

155 required_args.add_argument('--input_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.') 

156 required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file. Accepted formats: pdb.') 

157 

158 args = parser.parse_args() 

159 config = args.config if args.config else None 

160 properties = settings.ConfReader(config=config).get_prop_dic() 

161 

162 # Specific call 

163 pdb4amber_run(input_pdb_path=args.input_pdb_path, 

164 output_pdb_path=args.output_pdb_path, 

165 properties=properties) 

166 

167 

168if __name__ == '__main__': 

169 main()