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
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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.
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Bio.PDB.NACCESS.
process_rsa_data
(rsa_data)¶ Process the .rsa output file: residue level SASA data.
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Bio.PDB.NACCESS.
process_asa_data
(rsa_data)¶ Process the .asa output file: atomic level SASA data.
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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.
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__init__
(self, model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp')¶ Initialize the class.
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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.
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__init__
(self, model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp')¶ Initialize the class.
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