Coverage for biobb_amber/parmed/parmed_hmassrepartition.py: 75%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from typing import Optional 

6from pathlib import PurePath 

7from biobb_common.generic.biobb_object import BiobbObject 

8from biobb_common.configuration import settings 

9from biobb_common.tools import file_utils as fu 

10from biobb_common.tools.file_utils import launchlogger 

11from biobb_amber.parmed.common import check_input_path, check_output_path 

12 

13 

14class ParmedHMassRepartition(BiobbObject): 

15 """ 

16 | biobb_amber ParmedHMassRepartition 

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

18 | Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package. 

19 

20 Args: 

21 input_top_path (str): Input AMBER topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/parmed/input.hmass.prmtop>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). 

22 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/parmed/output.hmass.prmtop>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). 

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

24 * **binary_path** (*str*) - ("parmed") Path to the parmed executable binary. 

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

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

27 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 

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.parmed.parmed_hmassrepartition import parmed_hmassrepartition 

39 parmed_hmassrepartition(input_top_path='/path/to/topology.top', 

40 output_top_path='/path/to/newTopology.top') 

41 

42 Info: 

43 * wrapped_software: 

44 * name: AmberTools parmed 

45 * version: >20.9 

46 * license: LGPL 2.1 

47 * ontology: 

48 * name: EDAM 

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

50 

51 """ 

52 

53 def __init__(self, input_top_path, output_top_path, properties=None, **kwargs) -> None: 

54 

55 properties = properties or {} 

56 

57 # Call parent class constructor 

58 super().__init__(properties) 

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

60 

61 # Input/Output files 

62 self.io_dict = { 

63 'in': {'input_top_path': input_top_path}, 

64 'out': {'output_top_path': output_top_path} 

65 } 

66 

67 # Properties specific for BB 

68 self.properties = properties 

69 self.binary_path = properties.get('binary_path', 'parmed') 

70 

71 # Check the properties 

72 self.check_properties(properties) 

73 self.check_arguments() 

74 

75 def check_data_params(self, out_log, err_log): 

76 """ Checks input/output paths correctness """ 

77 

78 # Check input(s) 

79 self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], "input_top_path", False, out_log, self.__class__.__name__) 

80 

81 # Check output(s) 

82 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__) 

83 

84 @launchlogger 

85 def launch(self): 

86 """Launches the execution of the ParmedHMassRepartition module.""" 

87 

88 # check input/output paths and parameters 

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

90 

91 # Setup Biobb 

92 if self.check_restart(): 

93 return 0 

94 self.stage_files() 

95 

96 # Creating temporary folder & Parmed configuration (instructions) file 

97 if self.container_path: 

98 instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("parmed.in")) 

99 instructions_file_path = str(PurePath(self.container_volume_path).joinpath("parmed.in")) 

100 self.tmp_folder = None 

101 else: 

102 self.tmp_folder = fu.create_unique_dir() 

103 instructions_file = str(PurePath(self.tmp_folder).joinpath("parmed.in")) 

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

105 instructions_file_path = instructions_file 

106 

107 with open(instructions_file, 'w') as parmedin: 

108 parmedin.write("hmassrepartition\n") 

109 parmedin.write("outparm " + self.stage_io_dict['out']['output_top_path'] + "\n") 

110 

111 self.cmd = [self.binary_path, 

112 '-p', self.stage_io_dict['in']['input_top_path'], 

113 '-i', instructions_file_path, 

114 '-O' # Overwrite output files 

115 ] 

116 

117 # Run Biobb block 

118 self.run_biobb() 

119 

120 # Copy files to host 

121 self.copy_to_host() 

122 

123 # remove temporary folder(s) 

124 self.tmp_files.extend([ 

125 # self.stage_io_dict.get("unique_dir", ""), 

126 str(self.tmp_folder) 

127 ]) 

128 self.remove_tmp_files() 

129 

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

131 

132 return self.return_code 

133 

134 

135def parmed_hmassrepartition(input_top_path: str, 

136 output_top_path: Optional[str] = None, 

137 properties: Optional[dict] = None, **kwargs) -> int: 

138 """Create :class:`ParmedHMassRepartition <parmed.parmed_hmassrepartition.ParmedHMassRepartition>`parmed.parmed_hmassrepartition.ParmedHMassRepartition class and 

139 execute :meth:`launch() <parmed.parmed_hmassrepartition.ParmedHMassRepartition.launch>` method""" 

140 

141 return ParmedHMassRepartition(input_top_path=input_top_path, 

142 output_top_path=output_top_path, 

143 properties=properties).launch() 

144 

145 parmed_hmassrepartition.__doc__ = ParmedHMassRepartition.__doc__ 

146 

147 

148def main(): 

149 parser = argparse.ArgumentParser(description='Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

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

151 

152 # Specific args 

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

154 required_args.add_argument('--input_top_path', required=True, help='Input AMBER topology file. Accepted formats: top, parmtop, prmtop.') 

155 required_args.add_argument('--output_top_path', required=False, help='Output topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.') 

156 

157 args = parser.parse_args() 

158 config = args.config if args.config else None 

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

160 

161 # Specific call 

162 parmed_hmassrepartition(input_top_path=args.input_top_path, 

163 output_top_path=args.output_top_path, 

164 properties=properties) 

165 

166 

167if __name__ == '__main__': 

168 main()