diff --git a/modules/io/doc/profile.rst b/modules/io/doc/profile.rst index 8df9254e5aaf1ba3554b1e4fc8c9d39b442ed764..11d5779fab15f8bca07b920f25d7045baae3f20e 100644 --- a/modules/io/doc/profile.rst +++ b/modules/io/doc/profile.rst @@ -45,7 +45,7 @@ STRICT IOProfile(dialect='PDB', strict_hydrogens=False, quack_mode=False, fault_tolerant=False, join_spread_atom_records=False, - no_hetatms=False) + no_hetatms=False, bond_feasibility_check=True) SLOPPY: @@ -55,7 +55,7 @@ SLOPPY: IOProfile(dialect='PDB', strict_hydrogens=False, quack_mode=True, fault_tolerant=True, join_spread_atom_records=False, - no_hetatms=False) + no_hetatms=False, bond_feasibility_check=True) CHARMM: @@ -66,7 +66,7 @@ CHARMM: IOProfile(dialect='CHARMM', strict_hydrogens=False, quack_mode=True, fault_tolerant=True, join_spread_atom_records=True, - no_hetatms=False) + no_hetatms=False, bond_feasibility_check=True) The IOProfile Class @@ -123,3 +123,18 @@ The IOProfile Class If set to true, atom records belonging to the same residue are joined, even if they do not appear sequentially in the PDB file. + + .. attribute:: calpha_only + + When set to true, forces the importers to only load atoms named CA. This is + most useful in combination with protein-only PDB files to speed up subsequent + processing and importing. + + .. attribute:: bond_feasibility_check + + When set to true, adds an additional distance feasibility to figure out if + two atoms should be connected. Atoms are only connected if they are within a + certain distance range. Set this to false to completely disable distance + checks for intra-residual bonds. Peptide bonds as well as bonds between + nucleotides involving more than one residue still make use of the distance + check to figure out of if the two residues should be connected.