Coverage for biobb_chemistry / acpype / acpype_params_gmx.py: 93%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5from biobb_common.generic.biobb_object import BiobbObject 

6from biobb_common.tools.file_utils import launchlogger 

7from biobb_chemistry.acpype.common import get_binary_path, check_input_path, check_output_path, get_basename, get_charge, create_unique_name, get_default_value, process_output_gmx 

8 

9 

10class AcpypeParamsGMX(BiobbObject): 

11 """ 

12 | biobb_chemistry AcpypeParamsGMX 

13 | This class is a wrapper of `Acpype <https://github.com/alanwilter/acpype>`_ tool for generation of topologies for GROMACS. 

14 | Generation of topologies for GROMACS. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. `Visit the official page <https://github.com/alanwilter/acpype>`_. 

15 

16 Args: 

17 input_path (str): Path to the input file. File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/acpype/acpype.params.mol2>`_. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816). 

18 output_path_gro (str): Path to the GRO output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro>`_. Accepted formats: gro (edam:format_2033). 

19 output_path_itp (str): Path to the ITP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.itp>`_. Accepted formats: itp (edam:format_3883). 

20 output_path_top (str): Path to the TOP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top>`_. Accepted formats: top (edam:format_3880). 

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

22 * **basename** (*str*) - ("BBB") A basename for the project (folder and output files). 

23 * **charge** (*int*) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype. 

24 * **binary_path** (*str*) - ("acpype") Path to the acpype 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*) - ('acpype/acpype:2022.7.21') 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_chemistry.acpype.acpype_params_gmx import acpype_params_gmx 

39 prop = { 

40 'basename': 'BBB', 

41 'charge': 0 

42 } 

43 acpype_params_gmx(input_path='/path/to/myStructure.mol2', 

44 output_path_gro='/path/to/newGRO.gro', 

45 output_path_itp='/path/to/newITP.itp', 

46 output_path_top='/path/to/newTOP.top', 

47 properties=prop) 

48 

49 Info: 

50 * wrapped_software: 

51 * name: Acpype 

52 * version: 2019.10.05.12.26 

53 * license: GNU 

54 * ontology: 

55 * name: EDAM 

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

57 

58 """ 

59 

60 def __init__(self, input_path, output_path_gro, output_path_itp, output_path_top, 

61 properties=None, **kwargs) -> None: 

62 properties = properties or {} 

63 

64 # Call parent class constructor 

65 super().__init__(properties) 

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

67 

68 # Input/Output files 

69 self.io_dict = { 

70 "in": {"input_path": input_path}, 

71 "out": {"output_path_gro": output_path_gro, "output_path_itp": output_path_itp, "output_path_top": output_path_top} 

72 } 

73 

74 # Properties specific for BB 

75 self.basename = properties.get('basename', 'BBB') 

76 self.charge = properties.get('charge', '') 

77 self.binary_path = get_binary_path(properties, 'binary_path') 

78 self.properties = properties 

79 

80 # Check the properties 

81 self.check_properties(properties) 

82 self.check_arguments() 

83 

84 def check_data_params(self, out_log, err_log): 

85 """ Checks all the input/output paths and parameters """ 

86 self.io_dict["in"]["input_path"] = check_input_path(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__) 

87 self.io_dict["out"]["output_path_gro"] = check_output_path(self.io_dict["out"]["output_path_gro"], 'gro', out_log, self.__class__.__name__) 

88 self.io_dict["out"]["output_path_itp"] = check_output_path(self.io_dict["out"]["output_path_itp"], 'itp', out_log, self.__class__.__name__) 

89 self.io_dict["out"]["output_path_top"] = check_output_path(self.io_dict["out"]["output_path_top"], 'top', out_log, self.__class__.__name__) 

90 self.output_files = { 

91 'gro': self.io_dict["out"]["output_path_gro"], 

92 'itp': self.io_dict["out"]["output_path_itp"], 

93 'top': self.io_dict["out"]["output_path_top"], 

94 } 

95 

96 def create_cmd(self, container_io_dict, out_log, err_log): 

97 """Creates the command line instruction using the properties file settings""" 

98 instructions_list = [] 

99 

100 # generating output path 

101 if self.container_path: 

102 out_pth = self.container_volume_path + '/' + get_basename(self.basename, out_log) + '.' + self.unique_name 

103 else: 

104 out_pth = get_basename(self.basename, out_log) + '.' + self.unique_name 

105 

106 # executable path 

107 instructions_list.append(self.binary_path) 

108 

109 # generating input 

110 ipath = '-i ' + container_io_dict["in"]["input_path"] 

111 instructions_list.append(ipath) 

112 

113 # generating output 

114 basename = '-b ' + out_pth 

115 instructions_list.append(basename) 

116 

117 # adding charge if not None 

118 charge = get_charge(self.charge, out_log) 

119 if charge: 

120 charge = '-n ' + charge 

121 instructions_list.append(charge) 

122 

123 return instructions_list 

124 

125 @launchlogger 

126 def launch(self) -> int: 

127 """Execute the :class:`AcpypeParamsGMX <acpype.acpype_params_gmx.AcpypeParamsGMX>` acpype.acpype_params_gmx.AcpypeParamsGMX object.""" 

128 

129 # check input/output paths and parameters 

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

131 

132 # Setup Biobb 

133 if self.check_restart(): 

134 return 0 

135 self.stage_files() 

136 

137 # create unique name for temporary folder (created by acpype) 

138 self.unique_name = create_unique_name(6) 

139 

140 # create command line instruction 

141 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log) 

142 

143 # Run Biobb block 

144 self.run_biobb() 

145 

146 # Copy files to host 

147 self.copy_to_host() 

148 

149 # move files to output_path and removes temporary folder 

150 if self.container_path: 

151 process_output_gmx(self.unique_name, 

152 # self.stage_io_dict['unique_dir'], 

153 self.remove_tmp, 

154 self.basename, 

155 get_default_value(self.__class__.__name__), 

156 self.output_files, self.out_log) 

157 else: 

158 self.tmp_files.append(self.basename + "." + self.unique_name + ".acpype") 

159 process_output_gmx(self.unique_name, 

160 self.basename + "." + self.unique_name + ".acpype", 

161 self.remove_tmp, 

162 self.basename, 

163 get_default_value(self.__class__.__name__), 

164 self.output_files, self.out_log) 

165 

166 self.remove_tmp_files() 

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

168 

169 return self.return_code 

170 

171 

172def acpype_params_gmx(input_path: str, output_path_gro: str, output_path_itp: str, output_path_top: str, properties: Optional[dict] = None, **kwargs) -> int: 

173 """Create the :class:`AcpypeParamsGMX <acpype.acpype_params_gmx.AcpypeParamsGMX>` class and 

174 execute the :meth:`launch() <acpype.acpype_params_gmx.AcpypeParamsGMX.launch>` method.""" 

175 return AcpypeParamsGMX(**dict(locals())).launch() 

176 

177 

178acpype_params_gmx.__doc__ = AcpypeParamsGMX.__doc__ 

179main = AcpypeParamsGMX.get_main(acpype_params_gmx, "Small molecule parameterization for GROMACS MD package.") 

180 

181if __name__ == '__main__': 

182 main()