############################################################################## # # # cif_cml.dic # # version 0.0.01 -- beta # # by # # Herbert J. Bernstein # # yaya@bernstein-plus-sons.com # # 15 July 2000 # # (C) Copyright 2000 All Rights Reserved # # # ############################################################################## # # # General Notice # # # # Creative endeavors depend on the lively exchange of ideas. There are laws # # and customs which establish rights and responsibilities for authors and # # the users of what authors create. This notice is not intended to prevent # # you from using the software and documents in this package, but to ensure # # that there are no misunderstandings about terms and conditions of such # # use. # # # # Please read the following notice carefully. 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Do not give anyone the impression that the original author(s) are # # providing a warranty of any kind. # # # # If you use major portions of this document in some other document, make # # modifications to this document, or in some other way make what a lawyer # # would call a "derived work", you are not only permitted to do so, you are # # encouraged to do so, provided that, in addition to adhering to the three # # conditions stated above, you also do the following: # # # # 4. Explain in your documentation how what you do differs from this # # version of this document; and # # 5. Make your revised document available on an open-source basis. # # # # This document is not in the public domain, but is given freely to the # # community in the hope of advancing science. If you make changes please # # make them in a responsible manner, and please offer us the opportunity to # # include thos changes in in future versions of this document. # # # ############################################################################## # # # PRELIMINARY DRAFT -- SUBJECT TO CHANGE WITHOUT NOTICE # # # ############################################################################## ############################################################################## # # # This dictionary provides proposed translations from mmCIF to CML and is # # intended to be used an an extension to the mmCIF dictionary (cif_mm.dic) # # by P.M.D. Fitzgerald et. al. and to assist in producing XML documents # # intended to conform to CML DTD-1999-05-15 by P. Murray Rust and H. Rzepa # # # # Some portions of this mapping were derived from examination of pdb2xml by # # Adam Moore, BioDOM, March 1999 # # ############################################################################## data_cif_cml.dic _dictionary.title cif_cml.dic _dictionary.version 0.0.01 _dictionary.datablock_id cif_cml.dic ################ # DATA_ # ################ save_DATA_ _xml_mapping.description ; Data items in the DATA_ mapping record specify the mapping of data blocks to XML. ; _xml_mapping.token 'data_%' _xml_mapping.token_type 'data' _xml_mapping.target 'molecule id="%"' save_ ################ # ATOM_SITE # ################ save_ATOM_SITE _xml_mapping.description ; Data items in the ATOM_SITE mapping records specify the mapping of the category ATOM_SITE to XML. ; _xml_mapping.token 'ATOM_SITE' _xml_mapping.token_type 'category' _xml_mapping.target 'atomArray' save_ save__atom_site.B_iso_or_equiv _xml_mapping.description ; The B value (temperature factor) is mapped to B ; _xml_mapping.token '_atom_site.B_iso_or_equiv' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray title="B" convention="PDB"' save_ save__atom_site.Cartn_x _xml_mapping.description ; The x atom coordinate is mapped to the builtin value x3 ; _xml_mapping.token '_atom_site.Cartn_x' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="x3"' save_ save__atom_site.Cartn_y _xml_mapping.description ; The y atom coordinate is mapped to the builtin value y3 ; _xml_mapping.token '_atom_site.Cartn_y' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="y3"' save_ save__atom_site.Cartn_z _xml_mapping.description ; The z atom coordinate is mapped to the builtin value z3 ; _xml_mapping.token '_atom_site.Cartn_z' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="z3"' save_ save__atom_site.label_atom_id _xml_mapping.description ; The label_atom_id is mapped to ; _xml_mapping.token '_atom_site.label_atom_id' _xml_mapping.token_type 'item' _xml_mapping.target 'stringArray title="atomName"' save_ save__atom_site.label_comp_id _xml_mapping.description ; The label_comp_id is mapped to There is a problem here. For het groups the mapping should be to ; _xml_mapping.token '_atom_site.label_comp_id' _xml_mapping.token_type 'item' _xml_mapping.target 'stringArray title="atomresName"' save_ save__atom_site.label_asym_id _xml_mapping.description ; The label_asym_id is mapped to ; _xml_mapping.token '_atom_site.label_asym_id' _xml_mapping.token_type 'item' _xml_mapping.target 'stringArray title="chain"' save_ save__atom_site.fract_x _xml_mapping.description ; The fractional x atom coordinate is mapped to the builtin value xfract ; _xml_mapping.token '_atom_site.fract_x' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="xfract"' save_ save__atom_site.fract_y _xml_mapping.description ; The fractional y atom coordinate is mapped to the builtin value yfract ; _xml_mapping.token '_atom_site.fract_y' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="yfract"' save_ save__atom_site.fract_z _xml_mapping.description ; The fractional z atom coordinate is mapped to the builtin value zfract ; _xml_mapping.token '_atom_site.fract_z' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="zfract"' save_ save__atom_site.id _xml_mapping.description ; The id is mapped to the builtin value atomId ; _xml_mapping.token '_atom_site.id' _xml_mapping.token_type 'item' _xml_mapping.target 'stringArray builtin="atomId"' save_ save__atom_site.occupancy _xml_mapping.description ; The occupancy is mapped to the builtin value occupancy ; _xml_mapping.token '_atom_site.occupancy' _xml_mapping.token_type 'item' _xml_mapping.target 'floatArray builtin="occupancy"' save_ save__atom_site.type_symbol _xml_mapping.description ; The type symbol is mapped to the builtin value elementType ; _xml_mapping.token '_atom_site.type_symbol' _xml_mapping.token_type 'item' _xml_mapping.target 'stringArray builtin="elementType"' save_ ################ # AUDIT_AUTHOR # ################ save_AUDIT_AUTHOR _xml_mapping.description ; Data items in the AUDIT_AUTHOR mapping records specify the mapping of the category AUDIT_AUTHOT to XML. These items refer to the authorship of the entry per se ; _xml_mapping.token 'AUDIT_AUTHOR' _xml_mapping.token_type 'category' _xml_mapping.target 'list title="AUTHORS"' save_ save__audit_author.name _xml_mapping.description ; The author name is mapped to To conform pdb2xml conventions, the name itself should also be parsed into initials and a surname. We do not consider this issues at this time. ; _xml_mapping.token '_audit_author.name' _xml_mapping.token_type 'item' _xml_mapping.target 'person title="author"' save_ ################ # ATOM_SITES # ################ save_ATOM_SITES _xml_mapping.description ; Data items in the ATOM_SITES mapping records specify the mapping of the category ATOM_SITES to XML. Note that we also map the categories CELL and SYMMETRY to crystal We treat DATABASE_PDB_MATRIX as part of ATOM_SITES ; _xml_mapping.token 'ATOM_SITES' _xml_mapping.token_type 'category' _xml_mapping.target 'crystal' save_ save_DATABASE_PDB_MATRIX _xml_mapping.token 'DATABASE_PDB_MATRIX' _xml_mapping.token_type 'category' _xml_mapping.target 'crystal' save_ save__database_pdb_matrix.origx[1][1] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[1][1]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[1][1]"'' save_ save__database_pdb_matrix.origx[1][2] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[1][2]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[1][2]"'' save_ save__database_pdb_matrix.origx[1][3] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[1][3]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[1][3]"'' save_ save__database_pdb_matrix.origx[2][1] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[2][1]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[2][1]"'' save_ save__database_pdb_matrix.origx[2][2] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[2][2]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[2][2]"'' save_ save__database_pdb_matrix.origx[2][3] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[2][3]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[2][3]"'' save_ save__database_pdb_matrix.origx[3][1] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[3][1]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[3][1]"'' save_ save__database_pdb_matrix.origx[3][2] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[3][2]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[3][2]"'' save_ save__database_pdb_matrix.origx[3][3] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_database_pdb_matrix.origx[3][3]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="origx[3][3]"'' save_ save__atom_sites.fract_transf_matrix[1][1] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[1][1]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[1][1]"'' save_ save__atom_sites.fract_transf_matrix[1][2] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[1][2]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[1][2]"'' save_ save__atom_sites.fract_transf_matrix[1][3] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[1][3]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[1][3]"'' save_ save__atom_sites.fract_transf_matrix[2][1] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[2][1]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[2][1]"'' save_ save__atom_sites.fract_transf_matrix[2][2] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[2][2]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[2][2]"'' save_ save__atom_sites.fract_transf_matrix[2][3] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[2][3]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[2][3]"'' save_ save__atom_sites.fract_transf_matrix[3][1] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[3][1]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[3][1]"'' save_ save__atom_sites.fract_transf_matrix[3][2] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[3][2]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[3][2]"'' save_ save__atom_sites.fract_transf_matrix[3][3] _xml_mapping.description ; The matrix elements are mapped to individual matrix elements to avoid any assumptions on order dependence ; _xml_mapping.token '_atom_sites.fract_transf_matrix[3][3]' _xml_mapping.token_type 'item' _xml_mapping.target 'float title="scale[3][3]"'' save_ ################ # CELL # ################ save_CELL _xml_mapping.description ; Data items in the CELL mapping records specify the mapping of the category CELL to XML. Note that we also map the categories ATOM_SITES and SYMMETRY to crystal ; _xml_mapping.token 'CELL' _xml_mapping.token_type 'category' _xml_mapping.target 'crystal' save_ save__cell.length_a _xml_mapping.description ; The length of cell edge a is mapped to the builtin acell ; _xml_mapping.token '_cell.length_a' _xml_mapping.token_type 'item' _xml_mapping.target 'float builtin="acell"'' save_ save__cell.length_b _xml_mapping.description ; The length of cell edge b is mapped to the builtin bcell ; _xml_mapping.token '_cell.length_b' _xml_mapping.token_type 'item' _xml_mapping.target 'float builtin="bcell"'' save_ save__cell.length_c _xml_mapping.description ; The length of cell edge c is mapped to the builtin ccell ; _xml_mapping.token '_cell.length_c' _xml_mapping.token_type 'item' _xml_mapping.target 'float builtin="ccell"'' save_ save__cell.angle_alpha _xml_mapping.description ; The cell edge angle alpha is mapped to the builtin alpha ; _xml_mapping.token '_cell.angle_alpha' _xml_mapping.token_type 'item' _xml_mapping.target 'float builtin="alpha"'' save_ save__cell.angle_beta _xml_mapping.description ; The cell edge angle beta is mapped to the builtin beta ; _xml_mapping.token '_cell.angle_beta' _xml_mapping.token_type 'item' _xml_mapping.target 'float builtin="beta"'' save_ save__cell.angle_gamma _xml_mapping.description ; The cell edge angle gamma is mapped to the builtin gamma ; _xml_mapping.token '_cell.angle_gamma' _xml_mapping.token_type 'item' _xml_mapping.target 'float builtin="gamma"'' save_ save__cell.Z_PDB _xml_mapping.description ; The PDB Z value is mapped to the builtin z ; _xml_mapping.token '_cell.Z_PDB' _xml_mapping.token_type 'item' _xml_mapping.target 'integer builtin="z"'' save_ save__cell_formula_units_Z _xml_mapping.description ; The cor CIF Z value is mapped to the builtin z ; _xml_mapping.token '_cell_formula_units_Z' _xml_mapping.token_type 'item' _xml_mapping.target 'integer builtin="z"'' save_ save_SYMMETRY _xml_mapping.description ; Data items in the SYMMETRY mapping records specify the mapping of the category SYMMETRY to XML. Note that we also map the categories ATOM_SITES and CELL to crystal ; _xml_mapping.token 'SYMMETRY' _xml_mapping.token_type 'category' _xml_mapping.target 'crystal' save_ save__symmetry.space_group_name_H-M _xml_mapping.description ; The space group is mapped to the builtin spaegroup ; _xml_mapping.token '_symmetry.space_group_name_H-M' _xml_mapping.token_type 'item' _xml_mapping.target 'string builtin="spacegroup"'' save_ save__entry.id _xml_mapping.description ; The entry id is mapped to ID ; _xml_mapping.token '_entry.id' _xml_mapping.token_type 'item' _xml_mapping.target 'string title="ID"' save_ save__struct_biol.details _xml_mapping.description ; This is used as the detail for classification ; _xml_mapping.token '_struct_biol.details' _xml_mapping.token_type 'item' _xml_mapping.target 'string title="CLASSIFICATION"' save_