From fdec0104c7d3fc26e5e44cce8c4b4d6ad016328d Mon Sep 17 00:00:00 2001 From: yokochi47 Date: Tue, 15 Oct 2024 16:46:51 +0900 Subject: [PATCH] DAOTHER-9354, 9714: Revise mapping information of content type and format --- wwpdb/utils/nmr/README.md | 50 ++++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 24 deletions(-) diff --git a/wwpdb/utils/nmr/README.md b/wwpdb/utils/nmr/README.md index 7e9cc944..fc430e58 100644 --- a/wwpdb/utils/nmr/README.md +++ b/wwpdb/utils/nmr/README.md @@ -61,7 +61,7 @@ check_auth_seq|param|Boolean value. False for OneDep system. validation_server|param|Boolean value. False for OneDep system. True for standalone validation server. transl_pseudo_name|param|Boolean value. False for OneDep system. Whether to convert pseudo atom nomenclature in NMR unified data file. tolerant_seq_align|param|Boolean value. Set True for 'nmr-str-consistency-check', 'nmr-str2str-deposit', 'nmr-str2cif-deposit', 'nmr-str2nef-release', and 'nmr-str2cif-annotate' workflow operations. Whether to ignore sequence alignment error due to residue variant. -fix_format_issue|param|Boolean value. True for legacy separated file data file deposition or release mode. +fix_format_issue|param|Boolean value. True for legacy separated file data file deposition or release mode. excl_missing_data|param|Boolean value. True for legacy separated file data file deposition. Whether to exclude missing mandatory data. cmpl_missing_data|param|Boolean value. True for legacy separated file data file deposition. Whether to complement missing data. (add missing pseudo atoms in NMR restraints in actual) trust_pdbx_nmr_ens|param|Boolean value. True for release mode. Whether to trust pdbx_nmr_ensemble to get total number of models. @@ -89,7 +89,7 @@ leave_intl_note|param|Boolean value. True by default. Whether to leave internal reduced_atom_notation|param|Boolean value. True by default. Whether to use reduced atom notation in warning/error message. 5. Invoke defined workflow operation - + After the input and output resources are complete, calling **op()** for a particular workflow operation performs a series of data processing. workflow operation|role @@ -168,8 +168,8 @@ As for NMR-STAR (NMR unified data) to CIF formatted NMR-STAR file conversion util.addInput(name='nonblk_bad_nterm', value=True, type='param') util.addInput(name='resolve_conflict', value=True, type='param') util.addInput(name='check_mandatory_tag', value=True, type='param') - util.setLog(data_dir_path + entry_id '-str2cif-deposit-log.json') # report file for data conversion - util.setDestination(data_dir_path + entry_id '-next.str') # the primary destination is the converted NMR-STAR file of the original data source + util.setLog(data_dir_path + entry_id '-str2cif-deposit-log.json') # report file for data conversion + util.setDestination(data_dir_path + entry_id '-next.str') # the primary destination is the converted NMR-STAR file of the original data source util.addOutput(name='nmr_cif_file_path', value=data_dir_path + entry_id + '-str2cif.cif', type='file') # converted CIF formatted NMR-STAR file util.addOutput(name='report_file_path', value=data_dir_path + entry_id + '-str2cif-str-deposit-log.json', type='file') # report file for the obtained NMR-STAR file util.addOutput(name='entry_id', value=entry_id, type='param') @@ -217,24 +217,26 @@ Structure of NmrDpUtility’s report file is defined in [JSON Schema file](../te The codes used for specifying each file type in NmrDpUtility are compatible with OneDep system as follows: -NmrDpUtility|OneDep|description +NmrDpUtility|OneDep (content type/format)|description ------------|------|----------- -nmr-star|nm-shi or nm-uni-str|NMR data in NMR-STAR format -nef|nm-uni-nef|NMR data in NEF (NMR Exchange Format) -pdbx|co-cif|Coordinates in PDBx/mmCIF format -nm-res-amb|nm-res-amb|Restraint file in AMBER format -nm-aux-amb|nm-aux-amb|Topology file in AMBER format -nm-res-ari|nm-res-ari|Restraint file in ARIA format -nm-res-bio|nm-res-bio|Restraint file in BIOSYM format -nm-res-cha|nm-res-cha|Restraint file in CHARMM format -nm-res-cns|nm-res-cns|Restraint file in CNS format -nm-res-cya|nm-res-cya|Restraint file in CYANA format -nm-res-dyn|nm-res-dyn|Restraint file in DYNAMO/PALES/TALOS format -nm-res-gro|nm-res-gro|Restraint file in GROMACS format -nm-aux-gro|nm-aux-gro|Topology file in GROMACS format -nm-res-isd|nm-res-isd|Restraint file in ISD format -nm-res-ros|nm-res-ros|Restraint file in ROSETTA format -nm-res-syb|nm-res-syb|Restraint file in SYBYL format -nm-res-xpl|nm-res-xpl|Restraint file in XPLOR-NIH format -nm-res-oth|nm-res-oth|Restraint file in other format -nm-pea-any|nm-pea-any|Any spectral peak list file +nmr-star|nmr-chemical-shifts/[nmr-star|pdbx] or nmr-data-str/[nmr-star|pdbx]|NMR data in NMR-STAR format +nef|nmr-data-nef/[nmr-star|pdbx]|NMR data in NEF (NMR Exchange Format) +pdbx|model/pdbx|Coordinates in PDBx/mmCIF format +nm-res-amb|nmr-restraints/amber|Restraint file in AMBER format +nm-aux-amb|nmr-restraints/any|Topology file in AMBER format +nm-res-ari|nmr-restraints/aria|Restraint file in ARIA format +nm-res-bio|nmr-restraints/biosym|Restraint file in BIOSYM format +nm-res-cha|nmr-restraints/charmm|Restraint file in CHARMM format +nm-res-cns|nmr-restraints/cns|Restraint file in CNS format +nm-res-cya|nmr-restraints/cyana|Restraint file in CYANA format +nm-res-dyn|nmr-restraints/dynamo|Restraint file in DYNAMO/PALES/TALOS format +nm-res-gro|nmr-restraints/gromacs|Restraint file in GROMACS format +nm-aux-gro|nmr-restraints/any|Topology file in GROMACS format +nm-res-isd|nmr-restraints/isd|Restraint file in ISD format +nm-res-ros|nmr-restraints/rosetta|Restraint file in ROSETTA format +nm-res-syb|nmr-restraints/sybyl|Restraint file in SYBYL format +nm-res-xpl|nmr-restraints/xplor-nih|Restraint file in XPLOR-NIH format +nm-res-oth|nmr-restraints/any|Restraint file in other format +nm-res-mr|nmr-restraints/pdb-mr|Restraint file in PDB-MR format +nm-res-sax|nmr-restraints/any|SAX CSV file +nm-pea-any|nmr-peaks/any|Any spectral peak list file