Coverage for biobb_flexserv / flexserv / nma_run.py: 87%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5import os 

6from pathlib import Path 

7from biobb_common.generic.biobb_object import BiobbObject 

8from biobb_common.tools.file_utils import launchlogger 

9 

10 

11class NMARun(BiobbObject): 

12 """ 

13 | biobb_flexserv NMARun 

14 | Wrapper of the Normal Mode Analysis tool from the FlexServ module. 

15 | Generates protein conformational structures using the Normal Mode Analysis (NMA) method. 

16 

17 Args: 

18 input_pdb_path (str): Input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/flexserv/structure.ca.pdb>`_. Accepted formats: pdb (edam:format_1476). 

19 output_log_path (str): Output log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/nma_run_out.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). 

20 output_crd_path (str): Output ensemble. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/nma_run_out.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878). 

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

22 * **binary_path** (*str*) - ("diaghess") NMA binary path to be used. 

23 * **frames** (*int*) - (1000) Number of frames in the final ensemble 

24 * **nvecs** (*int*) - (50) Number of vectors to take into account for the ensemble generation 

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 

29 Examples: 

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

31 

32 from biobb_flexserv.flexserv.bd_run import bd_run 

33 prop = { 

34 'binary_path': 'diaghess' 

35 } 

36 flexserv_run(input_pdb_path='/path/to/nma_input.pdb', 

37 output_log_path='/path/to/nma_log.log', 

38 output_crd_path='/path/to/nma_ensemble.crd', 

39 properties=prop) 

40 

41 Info: 

42 * wrapped_software: 

43 * name: FlexServ Normal Mode Analysis 

44 * version: >=1.0 

45 * license: Apache-2.0 

46 * ontology: 

47 * name: EDAM 

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

49 

50 """ 

51 

52 def __init__(self, input_pdb_path: str, output_log_path: str, 

53 output_crd_path: str, properties: Optional[dict] = 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_pdb_path': input_pdb_path}, 

64 'out': {'output_log_path': output_log_path, 

65 'output_crd_path': output_crd_path} 

66 } 

67 

68 # Properties specific for BB 

69 self.properties = properties 

70 self.binary_path = properties.get('binary_path', 'diaghess') 

71 self.frames = properties.get('frames', 1000) 

72 self.nvecs = properties.get('nvecs', 50) 

73 

74 # Check the properties 

75 self.check_properties(properties) 

76 self.check_arguments() 

77 

78 @launchlogger 

79 def launch(self): 

80 """Launches the execution of the FlexServ NMARun module.""" 

81 

82 # Setup Biobb 

83 if self.check_restart(): 

84 return 0 

85 self.stage_files() 

86 

87 # Internal file paths 

88 try: 

89 # Using rel paths to shorten the amount of characters due to fortran path length limitations 

90 input_pdb = str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())) 

91 output_crd = str(Path(self.stage_io_dict["out"]["output_crd_path"]).relative_to(Path.cwd())) 

92 output_log = str(Path(self.stage_io_dict["out"]["output_log_path"]).relative_to(Path.cwd())) 

93 except ValueError: 

94 # Container or remote case 

95 input_pdb = self.stage_io_dict["in"]["input_pdb_path"] 

96 output_crd = self.stage_io_dict["out"]["output_crd_path"] 

97 output_log = self.stage_io_dict["out"]["output_log_path"] 

98 

99 # Command line 

100 # nmanu.pl structure.ca.pdb hessian.dat 1 0 40 

101 # diaghess 

102 # mc-eigen.pl eigenvec.dat > file.proj 

103 # pca_anim_mc.pl -pdb structure.ca.pdb -evec eigenvec.dat -i file.proj -n 50 -pout traj.crd 

104 conda_path = os.getenv("CONDA_PREFIX") 

105 nmanu = str(conda_path) + "/bin/nmanu.pl" 

106 nma_eigen = str(conda_path) + "/bin/mc-eigen-mdweb.pl" 

107 pca_anim = str(conda_path) + "/bin/pca_anim_mc.pl" 

108 self.cmd = ["perl ", 

109 nmanu, 

110 input_pdb, 

111 "hessian.dat 1 0 40;", 

112 self.binary_path, 

113 "; perl", 

114 nma_eigen, 

115 "eigenvec.dat ", str(self.frames), " > file.proj", 

116 "; perl", 

117 pca_anim, 

118 "-pdb", 

119 input_pdb, 

120 " -evec eigenvec.dat -i file.proj -n ", 

121 str(self.nvecs), 

122 " -pout", output_crd, 

123 '>', output_log 

124 ] 

125 

126 # Run Biobb block 

127 self.run_biobb() 

128 

129 # Copy files to host 

130 self.copy_to_host() 

131 

132 # Remove temporary folder(s) 

133 self.remove_tmp_files() 

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

135 

136 return self.return_code 

137 

138 

139def nma_run(input_pdb_path: str, 

140 output_log_path: str, output_crd_path: str, 

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

142 """Create :class:`NMARun <flexserv.nma_run.NMARun>`flexserv.nma_run.NMARun class and 

143 execute :meth:`launch() <flexserv.nma_run.NMARun.launch>` method""" 

144 return NMARun(**dict(locals())).launch() 

145 

146 

147nma_run.__doc__ = NMARun.__doc__ 

148main = NMARun.get_main(nma_run, "Generates protein conformational structures using the Normal Mode Analysis method.") 

149 

150if __name__ == '__main__': 

151 main()