Coverage for biobb_chemistry/babelm/babel_minimize.py: 86%

1#!/usr/bin/env python3 

2 

3"""Module containing the BabelMinimize 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.file_utils import launchlogger 

10from biobb_chemistry.babelm.common import check_minimize_property, check_input_path_minimize, check_output_path_minimize 

11 

12 

13class BabelMinimize(BiobbObject): 

14 """ 

15 | biobb_chemistry BabelMinimize 

16 | This class is a wrapper of the Open Babel tool. 

17 | Energetically minimizes small molecules. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. `Visit the official page <http://openbabel.org/wiki/Main_Page>`_. 

18 

19 Args: 

20 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/babel/babel.minimize.pdb>`_. Accepted formats: pdb (edam:format_1476), mol2 (edam:format_3816). 

21 output_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/babel/ref_babel.minimize.pdb>`_. Accepted formats: pdb (edam:format_1476), mol2 (edam:format_3816). 

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

23 * **criteria** (*float*) - (1e-6) Convergence criteria 

24 * **method** (*str*) - ("cg") Method. Values: cg (conjugate gradients algorithm), sd (steepest descent algorithm). 

25 * **force_field** (*str*) - (None) Force field. Values: GAFF (General Amber Force Field), Ghemical (Ghemical force field), MMFF94 (MMFF94 force field), MMFF94s (MMFF94s force field), UFF (Universal Force Field). 

26 * **hydrogens** (*bool*) - (False) Add hydrogen atoms. 

27 * **steps** (*int*) - (2500) [0~5000|1] Maximum number of steps. 

28 * **cutoff** (*bool*) - (False) Use cut-off. 

29 * **rvdw** (*float*) - (6.0) [0~50|1.0] VDW cut-off distance. 

30 * **rele** (*float*) - (10.0) [0~50|1.0] Electrostatic cut-off distance. 

31 * **frequency** (*int*) - (10) [0~50|1] Frequency to update the non-bonded pairs. 

32 * **binary_path** (*str*) - ("obminimize") Path to the obminimize executable binary. 

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

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

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

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

37 * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition. 

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

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

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

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

42 

43 Examples: 

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

45 

46 from biobb_chemistry.babelm.babel_minimize import babel_minimize 

47 prop = { 

48 'criteria': 1e-6, 

49 'method': 'cg', 

50 'force_field': 'GAFF' 

51 } 

52 babel_minimize(input_path='/path/to/myStructure.mol2', 

53 output_path='/path/to/newStructure.mol2', 

54 properties=prop) 

55 

56 Info: 

57 * wrapped_software: 

58 * name: Open Babel 

59 * version: 2.4.1 

60 * license: GNU 

61 * ontology: 

62 * name: EDAM 

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

64 

65 """ 

66 

67 def __init__(self, input_path, output_path, 

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

69 properties = properties or {} 

70 

71 # Call parent class constructor 

72 super().__init__(properties) 

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

74 

75 # Input/Output files 

76 self.io_dict = { 

77 "in": {"input_path": input_path}, 

78 "out": {"output_path": output_path} 

79 } 

80 

81 # Properties specific for BB 

82 self.criteria = properties.get('criteria', '') 

83 self.method = properties.get('method', '') 

84 self.force_field = properties.get('force_field', '') 

85 self.hydrogens = properties.get('hydrogens', '') 

86 self.steps = properties.get('steps', '') 

87 self.cutoff = properties.get('cutoff', '') 

88 self.rvdw = properties.get('rvdw', '') 

89 self.rele = properties.get('rele', '') 

90 self.frequency = properties.get('frequency', '') 

91 self.binary_path = properties.get('binary_path', 'obminimize') 

92 self.properties = properties 

93 

94 # Check the properties 

95 self.check_properties(properties) 

96 self.check_arguments() 

97 

98 def check_data_params(self, out_log, err_log): 

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

100 self.io_dict["in"]["input_path"] = check_input_path_minimize(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__) 

101 self.io_dict["out"]["output_path"] = check_output_path_minimize(self.io_dict["out"]["output_path"], out_log, self.__class__.__name__) 

102 

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

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

105 instructions_list = [] 

106 

107 # executable path 

108 instructions_list.append(self.binary_path) 

109 

110 # check all properties 

111 if check_minimize_property("criteria", self.criteria, out_log): 

112 instructions_list.append('-c ' + str(self.criteria)) 

113 

114 if check_minimize_property("method", self.method, out_log): 

115 instructions_list.append('-' + self.method) 

116 

117 if check_minimize_property("force_field", self.force_field, out_log): 

118 instructions_list.append('-ff ' + self.force_field) 

119 

120 if check_minimize_property("hydrogens", self.hydrogens, out_log): 

121 instructions_list.append('-h') 

122 

123 if check_minimize_property("steps", self.steps, out_log): 

124 instructions_list.append('-n ' + str(self.steps)) 

125 

126 if check_minimize_property("cutoff", self.cutoff, out_log): 

127 instructions_list.append('-cut') 

128 

129 if check_minimize_property("rvdw", self.rvdw, out_log): 

130 instructions_list.append('-rvdw ' + str(self.rvdw)) 

131 

132 if check_minimize_property("rele", self.rele, out_log): 

133 instructions_list.append('-rele ' + str(self.rele)) 

134 

135 if check_minimize_property("frequency", self.frequency, out_log): 

136 instructions_list.append('-pf ' + str(self.frequency)) 

137 

138 iextension = PurePath(container_io_dict["in"]["input_path"]).suffix 

139 oextension = PurePath(container_io_dict["out"]["output_path"]).suffix 

140 

141 instructions_list.append('-i' + iextension[1:] + ' ' + container_io_dict["in"]["input_path"]) 

142 

143 instructions_list.append('-o' + oextension[1:]) 

144 

145 instructions_list.append('>') 

146 

147 instructions_list.append(container_io_dict["out"]["output_path"]) 

148 

149 return instructions_list 

150 

151 @launchlogger 

152 def launch(self) -> int: 

153 """Execute the :class:`BabelMinimize <babelm.babel_minimize.BabelMinimize>` babelm.babel_minimize.BabelMinimize object.""" 

154 

155 # check input/output paths and parameters 

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

157 

158 # Setup Biobb 

159 if self.check_restart(): 

160 return 0 

161 self.stage_files() 

162 

163 # create command line instruction 

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

165 

166 # Run Biobb block 

167 self.run_biobb() 

168 

169 # Copy files to host 

170 self.copy_to_host() 

171 

172 # remove temporary folder(s) 

173 '''self.tmp_files.extend([ 

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

175 ])''' 

176 self.remove_tmp_files() 

177 

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

179 

180 return self.return_code 

181 

182 

183def babel_minimize(input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs) -> int: 

184 """Execute the :class:`BabelMinimize <babelm.babel_minimize.BabelMinimize>` class and 

185 execute the :meth:`launch() <babelm.babel_minimize.BabelMinimize.launch>` method.""" 

186 

187 return BabelMinimize(input_path=input_path, 

188 output_path=output_path, 

189 properties=properties, **kwargs).launch() 

190 

191 babel_minimize.__doc__ = BabelMinimize.__doc__ 

192 

193 

194def main(): 

195 """Command line execution of this building block. Please check the command line documentation.""" 

196 parser = argparse.ArgumentParser(description="Energetically minimize small molecules.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

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

198 

199 # Specific args of each building block 

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

201 required_args.add_argument('--input_path', required=True, help='Path to the input file. Accepted formats: pdb, mol2.') 

202 required_args.add_argument('--output_path', required=True, help='Path to the output file. Accepted formats: pdb, mol2.') 

203 

204 args = parser.parse_args() 

205 args.config = args.config or "{}" 

206 properties = settings.ConfReader(config=args.config).get_prop_dic() 

207 

208 # Specific call of each building block 

209 babel_minimize(input_path=args.input_path, 

210 output_path=args.output_path, 

211 properties=properties) 

212 

213 

214if __name__ == '__main__': 

215 main()