leonarski_f
e58453a693
A restraint dictionary carried in the binary, so refinement reads nothing from disk and needs no CLIBD_MON: the 20 amino acids and MSE, the DNA/RNA nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG fragments (PEG, PGE, PG4, 1PE), GOL, EDO, SO4, PO4, ACT, MPD, water and common ions - copied verbatim from the CCP4 Monomer Library (LGPL-3.0) - plus links_and_mods.cif cut down to the links and modifications those compounds can take (peptide, cis-peptide, proline, N-methyl, disulfide, nucleic-acid backbone, termini, metal-Cys/His) and ener_lib.cif cut to its atom-type table. monomers/update_monomers.py holds the compound list and regenerates the subset; CMake embeds every .cif of the directory as string pieces under MSVC's literal limit; EmbeddedMonomerLibrary() parses them from memory into a gemmi::MonLib once per process. About 0.7 MB of text in the binary. gemmi v0.7.5's monlib.cpp, topo.cpp and riding_h.cpp vendored verbatim (prepare_topology). Licence text in licenses/, rows and a note in THIRD_PARTY_NOTICES.md. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 38034718052c4a300691393b5b817f476c83dfc2)
31 lines
638 B
Plaintext
31 lines
638 B
Plaintext
data_comp_list
|
|
loop_
|
|
_chem_comp.id
|
|
_chem_comp.three_letter_code
|
|
_chem_comp.name
|
|
_chem_comp.group
|
|
_chem_comp.number_atoms_all
|
|
_chem_comp.number_atoms_nh
|
|
_chem_comp.desc_level
|
|
CL CL 'CHLORIDE ION ' NON-POLYMER 1 1 .
|
|
|
|
data_comp_CL
|
|
loop_
|
|
_chem_comp_atom.comp_id
|
|
_chem_comp_atom.atom_id
|
|
_chem_comp_atom.type_symbol
|
|
_chem_comp_atom.type_energy
|
|
_chem_comp_atom.partial_charge
|
|
_chem_comp_atom.x
|
|
_chem_comp_atom.y
|
|
_chem_comp_atom.z
|
|
CL CL CL CL -1.000 0.000 0.000 0.000
|
|
|
|
loop_
|
|
_chem_comp_tree.comp_id
|
|
_chem_comp_tree.atom_id
|
|
_chem_comp_tree.atom_back
|
|
_chem_comp_tree.atom_forward
|
|
_chem_comp_tree.connect_type
|
|
CL CL n/a . END
|