/usr/lib/python2.7/dist-packages/cogent/app/msms.py is in python-cogent 1.9-9.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | #!/usr/bin/env python
"""Application controller and utility functions for MSMS (molecular surface
calculation)."""
import os
import tempfile
from cogent.app.util import CommandLineApplication, ResultPath
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.format.xyzrn import XYZRNWriter
from cogent.parse.msms import parse_VertFile
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class Msms(CommandLineApplication):
"""Application controller for MSMS. The default input is a ``Entity``
instance.
Supported parameters:
- probe_radius float : probe sphere radius, [1.5]
- density float : surface points density, [1.0]
- hdensity float : surface points high density, [3.0]
- surface <tses,ases>: triangulated or Analytical SES, [tses]
- no_area : turns off the analytical surface area computation
- noh : ignore atoms with radius 1.2
- no_rest_on_pbr : no restart if pb. during triangulation
- no_rest : no restart if pb. are encountered
- if filename : sphere input file
- of filename : output for triangulated surface
- af filename : area file
- no_header : do not add comment line to the output
- free_vertices : turns on computation for isolated RS vertices
- all_components : compute all the surfaces components
"""
_parameters = {
# -probe_radius float : probe sphere radius, [1.5]
'-probe_radius':ValuedParameter(Prefix='-', Name='probe_radius', Delimiter=' '),
# -density float : surface points density, [1.0]
'-density':ValuedParameter(Prefix='-', Name='density', Delimiter=' '),
# -hdensity float : surface points high density, [3.0]
'-hdensity':ValuedParameter(Prefix='-', Name='hdensity', Delimiter=' '),
# -surface <tses,ases>: triangulated or Analytical SES, [tses]
'-surface':ValuedParameter(Prefix='-', Name='surface', Delimiter=' '),
# -no_area : turns off the analytical surface area computation
'-no_area':FlagParameter(Prefix='-', Name='no_area', Value=False),
# -noh : ignore atoms with radius 1.2
'-noh':FlagParameter(Prefix='-', Name='noh', Value=False),
# -no_rest_on_pbr : no restart if pb. during triangulation
'-no_rest_on_pbr':FlagParameter(Prefix='-', Name='no_rest_on_pbr', Value=False),
# -no_rest : no restart if pb. are encountered
'-no_rest':FlagParameter(Prefix='-', Name='no_rest', Value=False),
# -if filename : sphere input file
'-if':ValuedParameter(Prefix='-', Name='if', Delimiter=' ', IsPath=True),
# -of filename : output for triangulated surface
'-of':ValuedParameter(Prefix='-', Name='of', Delimiter=' ', IsPath=True),
# -af filename : area file
'-af':ValuedParameter(Prefix='-', Name='af', Delimiter=' ', IsPath=True),
# -no_header : do not add comment line to the output
'-no_header':FlagParameter(Prefix='-', Name='no_header', Value=False),
# -free_vertices : turns on computation for isolated RS vertices
'-free_vertices':FlagParameter(Prefix='-', Name='free_vertices', Value=False),
# -all_components : compute all the surfaces components
'-all_components':FlagParameter(Prefix='-', Name='all_components', Value=False),
#######################
# -one_cavity #atoms at1 [at2][at3] : Compute the surface for an internal
# cavity for which at least one atom is specified
#######################
# -socketName servicename : socket connection from a client
# -socketPort portNumber : socket connection from a client
# -xdr : use xdr encoding over socket
# -sinetd : inetd server connectio
}
_command = "msms"
_input_handler = '_input_from_entity'
def _input_from_entity(self, data):
"""This allows to feed entities to msms."""
if data:
# create temporary files and names.
fd, self._input_filename = tempfile.mkstemp()
os.close(fd)
# write XYZR data
fh = open(self._input_filename, 'wb')
XYZRNWriter(fh, data)
fh.close()
#
self.Parameters['-if'].on(self._input_filename)
self.Parameters['-of'].on(self._input_filename) # msms appends .vert .face
self.Parameters['-af'].on(self._input_filename) # msms appends .area
if (not self.Parameters['-if'].isOn()) or \
(not self.Parameters['-of'].isOn()) or \
(not self.Parameters['-af'].isOn()):
raise ValueError('All of -if, -of and -af have to be specified.')
return ""
def _get_result_paths(self, data):
result = {}
vert_file = self.Parameters['-of'].Value + '.vert'
result['VertFile'] = ResultPath(Path=vert_file, IsWritten=True)
face_file = self.Parameters['-of'].Value + '.face'
result['FaceFile'] = ResultPath(Path=face_file, IsWritten=True)
if not self.Parameters['-no_area'].Value:
area_file = self.Parameters['-af'].Value + '.area'
result['AreaFile'] = ResultPath(Path=area_file, IsWritten=True)
return result
def surface_xtra(entity, **kwargs):
"""Runs the MSMS application to create the molecular surface, which is an
a numpy array of 3D-coordinates.
Arguments:
* entity - an ``Entity`` instance.
Additional keyworded arguments are for the ``Msms`` application controller.
Returns the numpy array and put it into entity.xtra['MSMS_SURFACE'].
"""
msms = Msms(**kwargs)
res = msms(entity)
surface = parse_VertFile(res['VertFile'])
entity.xtra['MSMS_SURFACE'] = surface
res.cleanUp() # remove all temporary files
return surface
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