Atom order library

  Spock's atom order file lives in $SPOCK/aalib/atom.lib. $SPOCK/lib/atom.lib might arguably be a better place for it, but it might not either! This file is used by spock to resort ``PDB'' files written by such abominations as XPLOR which--surely for low and evil purposes--don't use the proper atom ordering as set forth by the wise prophets of the Protein Data Bank and given unto us in the Holy PDB Format Specification. See also §6.7.1. This file also specifies the default hydrogen bond donors and acceptors. Here's the format, taken from the header of the file:

• Lines beginning with '#' are comments and are ignored. There should be no blank lines. Comments may only be inserted between records, not within a record.
• A single line giving the names of the residues. The order of these elements must not be changed. However, it is permissible to add additional residue types after the VAL of the residue name line. There are three characters per residue name, and each residue name must be followed by a space.
• A series of records for each residue, listed in the same order as the residue list line described above. This consists of three lines. The first line should contain (in order) the names of all atoms in the residue, with exactly 4 characters per atom, and no additional spaces. If there are spaces in the atom name, they must be present in this file. Note that this means that trailing white space is significant.
• The second line is a list of all hydrogen bond donor atoms in the same format, and the third line is all hydrogen bond acceptors. If there are either no donors or no acceptors, the corresponding line # should contain only a single space.