A subset of the YASARA soup can be obtained as a pdb

YASARA comes with a Python PDB file interface that can be found at yasara/plg/pdb_file.py. In addition, you can easily obtain any part of the YASARA soup as an instance of such a PDB file interface. This means that you can use the same piece of Python code to analyze a PDB file loaded from disk and the YASARA soup.


import pdb_file

pdb=pdb_file.interface("1crn.pdb")
for i in range(pdb.atoms):
  if (pdb.atom[i].name=="CA"): print pdb.atom[i]


Instance.crdsys	1 if the atom coordinates use a left-handed system (YASARA's default), and -1 otherwise (PDB file default).
Instance.atoms	the number of atoms
Instance.atom[i]	the ith atom
Instance.atom[i].element	the chemical element number of the ith atom
Instance.atom[i].name	the name of the ith atom with spaces stripped
Instance.atom[i].name4	the name of the ith atom as present in the PDB file, with all spaces
Instance.atom[i].num	the YASARA number of the ith atom (only present in the YASARA Python module)
Instance.atom[i].altloc	the alternate location indicator of the ith atom, None if empty
Instance.atom[i].pos.x/.y/.z	the position of the ith atom
Instance.atom[i].pos.c[j]	the jth 'c'omponent of the position vector of atom i
Instance.atom[i].occupancy	the occupancy of the ith atom
Instance.atom[i].bfactor	the B-factor of the ith atom
Instance.atom[i].resname	the name of the residue the ith atom belongs to
Instance.atom[i].resnum	the number of the residue the ith atom belongs to
Instance.atom[i].molname	the name of the molecule the ith atom belongs to
Instance.atom[i].segname	the name of the segment the ith atom belongs to
Instance.residues	the number of residues
Instance.residue[i]	the ith residue
Instance.residue[i].name	the name of the ith residue
Instance.residue[i].num	the number of the ith residue
Instance.residue[i].atoms	the number of atoms in the ith residue
Instance.residue[i].atom[j]	the jth atom in the ith residue with properties described above
Instance.residue[i].atomnamed["X"]	atom with name "X" in the ith residue with properties described above
Instance.molecules	the number of molecules (=chains)
Instance.molecule[i]	the ith molecule (=chain)
Instance.molecule[i].atoms	the number of atoms in the ith molecule
Instance.molecule[i].atom[j]	the jth atom in the ith molecule with properties described above
Instance.molecule[i].residues	the number of residues in the ith molecule
Instance.molecule[i].residue[j]	the jth residue in the ith molecule with properties described above
Instance.objects	the number of objects (=NMR MODELs)
Instance.object[i]	the ith object
Instance.object[i].name	the YASARA name of the ith object (only present in the YASARA Python module)
Instance.object[i].num	the YASARA number of the ith object (only present in the YASARA Python module)
Instance.object[i].atoms	the number of atoms in the ith object
Instance.object[i].atom[j]	the jth atom in the ith object with properties described above
Instance.object[i].residues	the number of residues in the ith object
Instance.object[i].residue[j]	the jth residue in the ith object with properties described above
Instance.object[i].molecules	the number of molecules in the ith object
Instance.object[i].molecule[j]	the jth molecule in the ith object with properties described above
Instance.object[i].molnamed["X"]	the molecule named "X" in the ith object with properties described above

The YASARA Python module provides five commands to extract selected portions of the YASARA soup as a PDB file instance: Atom, Residue , Molecule, Object and All. The first four take a selection as the only argument:


from yasara import *

# Load PDB file 5tim
LoadPDB("5tim")

# Get all atoms in molecule A that contact molecule B
contact=Atom("Mol A with distance<5 from Mol B")
print "There are %d contacts:"%contact.atoms
print contact

# Get all Arg residues that form a salt-bridge with Asp or Glu
bridge=Residue("Arg Atom NH? with distance<3.5 from Asp Glu Atom OD? OE?")
print "There are %d salt-bridged arginines"%bridge.residues
for i in range(bridge.residues):
  print bridge.residue[i].name,bridge.residue[i].num

# Get the protein molecules
protein=Molecule("Protein")
print "There are %d protein molecules containing %d atoms"%(protein.molecules,protein.atoms)

# Clear the YASARA soup and load an NMR structure bundle
Clear()
LoadPDB("3gb1")

# Get the first model (each model is stored in a separate object)
first=Object(1)
print "The first model contains %d atoms, %d residues and %d molecules"%(first.atoms,first.residues,first.molecules)

# Get the entire soup
soup=All()
print "The bundle contains %d models"%soup.objects

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A subset of the YASARA soup can be obtained as a pdb_file instance