Bio.PDB.NACCESS module

Interface for the program NACCESS.

See: http://wolf.bms.umist.ac.uk/naccess/ Atomic Solvent Accessible Area Calculations

errors likely to occur with the binary: default values are often due to low default settings in accall.pars - e.g. max cubes error: change in accall.pars and recompile binary

use naccess -y, naccess -h or naccess -w to include HETATM records

Bio.PDB.NACCESS.run_naccess(model, pdb_file, probe_size=None, z_slice=None, naccess='naccess', temp_path='/tmp/')

Run naccess for a pdb file.

Bio.PDB.NACCESS.process_rsa_data(rsa_data)

Process the .rsa output file: residue level SASA data.

Bio.PDB.NACCESS.process_asa_data(rsa_data)

Process the .asa output file: atomic level SASA data.

class Bio.PDB.NACCESS.NACCESS(model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp')

Bases: Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap

Define NACCESS class for residue properties map.

__init__(self, model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp')

Initialize the class.

class Bio.PDB.NACCESS.NACCESS_atomic(model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp')

Bases: Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap

Define NACCESS atomic class for atom properties map.

__init__(self, model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp')

Initialize the class.