msms – Calculating Molecular Surfaces

class MsmsProcessError(returncode, command)

Python 2.4 and older do not include the CalledProcessError exception. This class substitutes it.

CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False, no_hydrogens=False, no_hetatoms=False, no_waters=False, selection='', msms_exe=None, msms_env=None, keep_files=False, attach_asa=None, attach_esa=None)

Calculates molecular surface by using the external MSMS program

This method calculates a molecular surface by invoking the external program MSMS. First, it is checked if the MSMS executable is present, then, the necessary files are prepared in a temporary directory and MSMS is executed. The last step is to remove the temporary directory.

Parameters:

  • entity – Entity for which the surface is to be calculated

  • density – Surface point density

  • radius – Surface probe radius

  • all_surf – Calculate surface for all cavities (returns multiple surfaces as a list)

  • no_hydrogens – Calculate surface only for heavy atoms

  • selection – Calculate surface for subset of entity

  • msms_exe – msms executable (full path to executable)

  • msms_env – msms environment variable

  • keep_files – Do not delete temporary files

  • attach_asa – Attaches per atom SASA to specified FloatProp at atom level

  • attach_esa – Attaches per atom SESA to specified FloatProp at atom level

Returns:

list of SurfaceHandle objects

CalculateSurfaceArea(entity, density=1.0, radius=1.5, all_surf=False, no_hydrogens=False, no_hetatoms=False, no_waters=False, selection='', msms_exe=None, msms_env=None, keep_files=False, attach_asa=None, attach_esa=None)

Calculates analytical solvent excluded and solvent accessible surface area by using the external MSMS program.

This method calculates the molecular surface areas by invoking the external program MSMS. First, it is checked if the MSMS executable is present, then, the necessary files are prepared in a temporary directory and MSMS is executed. The last step is to remove the temporary directory.

Parameters:

  • entity – OST entity to calculate surface

  • density – Surface point density

  • radius – Surface probe radius

  • all_surf – Calculate surface area for all cavities (returns multiple surfaces areas as a list)

  • no_hydrogens – Calculate surface only for hevy atoms

  • selection – Calculate surface for subset of entity

  • msms_exe – msms executable (full path to executable)

  • msms_env – msms environment variable

  • keep_files – Do not delete temporary files

  • attach_asa – Attaches per atom SASA to specified FloatProp at atom level

  • attach_esa – Attaches per atom SESA to specified FloatProp at atom level

Returns:

Tuple of lists for (SES, SAS)

CalculateSurfaceVolume(entity, density=1.0, radius=1.5, all_surf=False, no_hydrogens=False, no_hetatoms=False, no_waters=False, selection='', msms_exe=None, msms_env=None, keep_files=False, attach_asa=None, attach_esa=None)

Calculates the volume of the solvent excluded surface by using the external MSMS program.

This method calculates the volume of the molecular surface by invoking the external program MSMS. First, it is checked if the MSMS executable is present, then, the necessary files are prepared in a temporary directory and MSMS is executed. The last step is to remove the temporary directory.

Parameters:

  • entity – OST entity to calculate surface

  • density – Surface point density

  • radius – Surface probe radius

  • all_surf – Calculate surface area for all cavities (returns multiple surfaces areas as a list)

  • no_hydrogens – Calculate surface only for hevy atoms

  • selection – Calculate surface for subset of entity

  • msms_exe – msms executable (full path to executable)

  • msms_env – msms environment variable

  • keep_files – Do not delete temporary files

  • attach_asa – Attaches per atom SASA to specified FloatProp at atom level

  • attach_esa – Attaches per atom SESA to specified FloatProp at atom level

Returns:

Tuple of lists for (SES, SAS)

GetVersion(msms_exe=None, msms_env=None)

Get version of MSMS executable