Coverage for biobb_flexserv/pcasuite/pcz_bfactor.py: 92%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5from pathlib import PurePath 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8 

9 

10class PCZbfactor(BiobbObject): 

11 """ 

12 | biobb_flexserv PCZbfactor 

13 | Extract residue bfactors x PCA mode from a compressed PCZ file. 

14 | Wrapper of the pczdump tool from the PCAsuite FlexServ module. 

15 

16 Args: 

17 input_pcz_path (str): Input compressed trajectory file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz>`_. Accepted formats: pcz (edam:format_3874). 

18 output_dat_path (str): Output Bfactor x residue x PCA mode file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/bfactors.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330), csv (edam:format_3752). 

19 output_pdb_path (str) (Optional): Output PDB with Bfactor x residue x PCA mode file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/bfactors.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

21 * **binary_path** (*str*) - ("pczdump") pczdump binary path to be used. 

22 * **eigenvector** (*int*) - (0) PCA mode (eigenvector) from which to extract bfactor values per residue (0 means average over all modes). 

23 * **pdb** (*bool*) - (False) Generate a PDB file with the computed bfactors (to be easily represented with colour scale) 

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

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

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

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

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

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

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

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

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

33 

34 Examples: 

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

36 

37 from biobb_flexserv.pcasuite.pcz_bfactor import pcz_bfactor 

38 prop = { 

39 'eigenvector': 1, 

40 'pdb': True 

41 } 

42 pcz_bfactor( input_pcz_path='/path/to/pcazip_input.pcz', 

43 output_dat_path='/path/to/bfactors_mode1.dat', 

44 output_pdb_path='/path/to/bfactors_mode1.pdb', 

45 properties=prop) 

46 

47 Info: 

48 * wrapped_software: 

49 * name: FlexServ PCAsuite 

50 * version: >=1.0 

51 * license: Apache-2.0 

52 * ontology: 

53 * name: EDAM 

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

55 

56 """ 

57 

58 def __init__(self, input_pcz_path: str, output_dat_path: str, 

59 output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> None: 

60 

61 properties = properties or {} 

62 

63 # Call parent class constructor 

64 super().__init__(properties) 

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

66 

67 # Input/Output files 

68 self.io_dict = { 

69 'in': {'input_pcz_path': input_pcz_path}, 

70 'out': {'output_dat_path': output_dat_path, 

71 'output_pdb_path': output_pdb_path} 

72 } 

73 

74 # Properties specific for BB 

75 self.properties = properties 

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

77 self.eigenvector = properties.get('eigenvector', 1) 

78 self.pdb = properties.get('pdb', False) 

79 

80 # Check the properties 

81 self.check_properties(properties) 

82 self.check_arguments() 

83 

84 @launchlogger 

85 def launch(self): 

86 """Launches the execution of the FlexServ pcz_bfactor module.""" 

87 

88 # Setup Biobb 

89 if self.check_restart(): 

90 return 0 

91 self.stage_files() 

92 

93 if self.container_path: 

94 working_dir = self.container_volume_path if self.container_volume_path else "/data" 

95 else: 

96 working_dir = self.stage_io_dict.get("unique_dir", "") 

97 

98 # Command line (1: dat file) 

99 # pczdump -i structure.ca.std.pcz --fluc=1 -o bfactor_1.dat 

100 # self.cmd = [self.binary_path, 

101 # "-i", input_pcz, 

102 # "-o", output_dat, 

103 # "--bfactor", 

104 # "--fluc={}".format(self.eigenvector) 

105 # ] 

106 

107 self.cmd = ['cd', working_dir, ';', 

108 self.binary_path, 

109 '-i', PurePath(self.stage_io_dict["in"]["input_pcz_path"]).name, 

110 '-o', PurePath(self.stage_io_dict["out"]["output_dat_path"]).name, 

111 "--bfactor", 

112 "--fluc={}".format(self.eigenvector) 

113 ] 

114 

115 # Run Biobb block 

116 self.run_biobb() 

117 

118 if self.pdb: 

119 # Command line (2: pdb file) 

120 # pczdump -i structure.ca.std.pcz --fluc=1 --pdb -o bfactor_1.pdb 

121 # self.cmd = [self.binary_path, 

122 # "-i", input_pcz, 

123 # "-o", output_pdb, 

124 # "--bfactor", 

125 # "--fluc={}".format(self.eigenvector), 

126 # "--pdb" 

127 # ] 

128 

129 self.cmd = ['cd', working_dir, ';', 

130 self.binary_path, 

131 '-i', PurePath(self.stage_io_dict["in"]["input_pcz_path"]).name, 

132 '-o', PurePath(self.stage_io_dict["out"]["output_pdb_path"]).name, 

133 "--bfactor", 

134 "--fluc={}".format(self.eigenvector), 

135 "--pdb" 

136 ] 

137 

138 # Run Biobb block 

139 self.run_biobb() 

140 

141 # Copy files to host 

142 self.copy_to_host() 

143 

144 # Remove temporary folder(s) 

145 self.remove_tmp_files() 

146 

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

148 

149 return self.return_code 

150 

151 

152def pcz_bfactor(input_pcz_path: str, output_dat_path: str, output_pdb_path: str, 

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

154 """Create :class:`PCZbfactor <flexserv.pcasuite.pcz_bfactor>`flexserv.pcasuite.PCZbfactor class and 

155 execute :meth:`launch() <flexserv.pcasuite.pcz_bfactor.launch>` method""" 

156 return PCZbfactor(**dict(locals())).launch() 

157 

158 

159pcz_bfactor.__doc__ = PCZbfactor.__doc__ 

160main = PCZbfactor.get_main(pcz_bfactor, "Extract residue bfactors x PCA mode from a compressed PCZ file.") 

161 

162if __name__ == '__main__': 

163 main()