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Handle multiline TITLE and new-style EXPDTA record
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ModBase will now split long model titles over multiple
TITLE records, and uses a standards-compliant EXPDTA
record, moving Modeller version information to a REMARK.
Capture this information and convert to mmCIF.
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@benmwebb
benmwebb committed Jan 12, 2024
1 parent 0015b4d commit 33bb712
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Showing 4 changed files with 401 additions and 3 deletions.
8 changes: 5 additions & 3 deletions modbase_pdb_to_cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,9 +182,11 @@ def _read_pdb(self, fh):
elif line.startswith('REMARK') and line.count(':') == 1:
key, val = [x.strip() for x in line[11:].split(':')]
self.remarks[key] = val
elif line.startswith('TITLE '):
self.title = line[10:].strip()
elif line.startswith('EXPDTA '):
elif line.startswith('TITLE '):
txt = line[10:].rstrip()
self.title = self.title + txt if self.title else txt
elif (line.startswith('EXPDTA ')
or line.startswith('REMARK 6 PRODUCED BY MODELLER')):
self.expdta = line[10:].strip()
elif line.startswith('ATOM') or line.startswith('HETATM'):
self.atoms.append(line)
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325 changes: 325 additions & 0 deletions test/input/test_multi_expdta.cif
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Original file line number Diff line number Diff line change
@@ -0,0 +1,325 @@
data_model_66b8fbc891f519c1ba8d8ad2e62c6caa
_entry.id model_66b8fbc891f519c1ba8d8ad2e62c6caa
_struct.entry_id model_66b8fbc891f519c1ba8d8ad2e62c6caa
_struct.pdbx_model_details .
_struct.pdbx_structure_determination_methodology computational
_struct.title 'Model of S54091 hypothetical protein YPR070w - yeast (Saccharomyces cerevisiae)'
_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/base/mmcif_ma-core.dic
_audit_conform.dict_name mmcif_ma.dic
_audit_conform.dict_version 1.4.5
_database_2.database_code 66b8fbc891f519c1ba8d8ad2e62c6caa
_database_2.database_id MODBASE
#
loop_
_citation.id
_citation.title
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation.pdbx_database_id_PubMed
_citation.pdbx_database_id_DOI
primary
'ModBase, a database of annotated comparative protein structure models and associated resources'
'Nucleic Acids Res' 42 D336 D346 2014 24271400 10.1093/nar/gkt1144
2 'Comparative protein modelling by satisfaction of spatial restraints.'
'J Mol Biol' 234 779 815 1993 8254673 10.1006/jmbi.1993.1626
#
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Pieper, U.' 1
primary 'Webb, B.M.' 2
primary 'Dong, G.Q.' 3
primary 'Schneidman-Duhovny, D.' 4
primary 'Fan, H.' 5
primary 'Kim, S.J.' 6
primary 'Khuri, N.' 7
primary 'Spill, Y.G.' 8
primary 'Weinkam, P.' 9
primary 'Hammel, M.' 10
primary 'Tainer, J.A.' 11
primary 'Nilges, M.' 12
primary 'Sali, A.' 13
2 'Sali, A.' 14
2 'Blundell, T.L.' 15
#
#
loop_
_software.pdbx_ordinal
_software.name
_software.classification
_software.description
_software.version
_software.type
_software.location
_software.citation_id
1 ModPipe 'comparative modeling' 'Comparative modeling pipeline' SVN.r1693:r1694
program https://salilab.org/modpipe/ .
2 MODELLER 'comparative modeling'
'Comparative modeling by satisfaction of spatial restraints' SVN program
https://salilab.org/modeller/ 2
3 modbase_pdb_to_cif.py 'format conversion'
'Conversion of ModBase PDB and alignment files to mmCIF format' 0.4 program
https://github.com/salilab/modbase_utils .
#
#
loop_
_ma_software_group.ordinal_id
_ma_software_group.group_id
_ma_software_group.software_id
_ma_software_group.parameter_group_id
1 1 1 .
2 2 2 .
#
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Pieper, U.' 1
'Webb, B.' 2
'Narayanan, E.' 3
'Sali, A.' 4
#
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.name
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.ma_provenance
GLU 'L-peptide linking' 'GLUTAMIC ACID' 'C5 H9 N O4' 147.130 'CCD Core'
THR 'L-peptide linking' THREONINE 'C4 H9 N O3' 119.120 'CCD Core'
#
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.details
1 polymer man Target 266.250 1 .
#
#
loop_
_ma_target_ref_db_details.target_entity_id
_ma_target_ref_db_details.db_name
_ma_target_ref_db_details.db_name_other_details
_ma_target_ref_db_details.db_code
_ma_target_ref_db_details.db_accession
_ma_target_ref_db_details.seq_db_isoform
_ma_target_ref_db_details.seq_db_align_begin
_ma_target_ref_db_details.seq_db_align_end
_ma_target_ref_db_details.ncbi_taxonomy_id
_ma_target_ref_db_details.organism_scientific
_ma_target_ref_db_details.seq_db_sequence_version_date
_ma_target_ref_db_details.seq_db_sequence_checksum
1 UNP . B5VTL7_YEAS6 B5VTL7 ? 9 10 . . . .
1 Other RefSeq NP_015395.1 NP_015395 ? 9 10 . . . .
#
#
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
1 polypeptide(L) no no A ET ET
#
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 GLU .
1 2 THR .
#
#
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 'Model subunit'
#
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
A 1 1 GLU 9 9 GLU GLU A .
A 1 2 THR 10 10 THR THR A .
#
#
loop_
_ma_data.id
_ma_data.name
_ma_data.content_type
_ma_data.content_type_other_details
1 Target target .
2 'Target Template Alignment' 'target-template alignment' .
3 'Target Structure' 'model coordinates' .
4 'ModPipe sequence and structure database' 'reference database' .
#
#
loop_
_ma_data_group.ordinal_id
_ma_data_group.group_id
_ma_data_group.data_id
1 1 1
2 1 4
3 2 2
4 2 1
5 3 3
6 4 2
#
#
loop_
_ma_data_ref_db.data_id
_ma_data_ref_db.name
_ma_data_ref_db.location_url
_ma_data_ref_db.version
_ma_data_ref_db.release_date
4 'ModPipe sequence and structure database'
https://salilab.org/modpipe/doc/databases.html . .
#
#
loop_
_ma_target_entity.entity_id
_ma_target_entity.data_id
_ma_target_entity.origin
1 1 'reference database'
#
#
loop_
_ma_target_entity_instance.asym_id
_ma_target_entity_instance.entity_id
_ma_target_entity_instance.details
A 1 'Model subunit'
#
#
loop_
_ma_alignment_info.alignment_id
_ma_alignment_info.data_id
_ma_alignment_info.software_group_id
_ma_alignment_info.alignment_length
_ma_alignment_info.alignment_type
_ma_alignment_info.alignment_mode
1 2 1 . 'target-template pairwise alignment' global
#
#
loop_
_ma_protocol_step.ordinal_id
_ma_protocol_step.protocol_id
_ma_protocol_step.step_id
_ma_protocol_step.method_type
_ma_protocol_step.step_name
_ma_protocol_step.details
_ma_protocol_step.software_group_id
_ma_protocol_step.input_data_group_id
_ma_protocol_step.output_data_group_id
1 1 1 'template search' ModPipe . 1 1 4
2 1 2 modeling . . 2 2 3
3 1 3 'model selection' . . 1 3 3
#
#
loop_
_ma_model_list.ordinal_id
_ma_model_list.model_id
_ma_model_list.model_group_id
_ma_model_list.model_name
_ma_model_list.model_group_name
_ma_model_list.data_id
_ma_model_list.model_type
_ma_model_list.model_type_other_details
1 1 1 'Target Structure' 'All models' 3 'Homology model' .
#
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.label_entity_id
_atom_site.auth_asym_id
_atom_site.auth_comp_id
_atom_site.B_iso_or_equiv
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . GLU 1 9 ? A 6.074 25.683 -20.291 1.00 1 A GLU 77.44 1
ATOM 2 C CA . GLU 1 9 ? A 4.616 25.924 -20.396 1.00 1 A GLU 77.44 1
ATOM 3 C CB . GLU 1 9 ? A 4.343 27.032 -21.429 1.00 1 A GLU 77.44 1
ATOM 4 C CG . GLU 1 9 ? A 4.806 28.417 -20.968 1.00 1 A GLU 77.44 1
ATOM 5 C CD . GLU 1 9 ? A 4.505 29.414 -22.078 1.00 1 A GLU 77.44 1
ATOM 6 O OE1 . GLU 1 9 ? A 4.239 28.958 -23.221 1.00 1 A GLU 77.44 1
ATOM 7 O OE2 . GLU 1 9 ? A 4.543 30.643 -21.801 1.00 1 A GLU 77.44 1
ATOM 8 C C . GLU 1 9 ? A 3.913 24.679 -20.823 1.00 1 A GLU 77.44 1
ATOM 9 O O . GLU 1 9 ? A 2.695 24.664 -20.996 1.00 1 A GLU 77.44 1
ATOM 10 N N . THR 2 10 ? A 4.681 23.587 -20.989 1.00 1 A THR 99.59 1
ATOM 11 C CA . THR 2 10 ? A 4.114 22.350 -21.432 1.00 1 A THR 99.59 1
ATOM 12 C CB . THR 2 10 ? A 5.149 21.289 -21.688 1.00 1 A THR 99.59 1
ATOM 13 O OG1 . THR 2 10 ? A 4.531 20.137 -22.243 1.00 1 A THR 99.59 1
ATOM 14 C CG2 . THR 2 10 ? A 5.868 20.931 -20.374 1.00 1 A THR 99.59 1
ATOM 15 C C . THR 2 10 ? A 3.151 21.826 -20.414 1.00 1 A THR 99.59 1
ATOM 16 O O . THR 2 10 ? A 2.048 21.407 -20.759 1.00 1 A THR 99.59 1
#
#
loop_
_atom_type.symbol
C
N
O
#
#
loop_
_ma_qa_metric.id
_ma_qa_metric.name
_ma_qa_metric.description
_ma_qa_metric.type
_ma_qa_metric.mode
_ma_qa_metric.type_other_details
_ma_qa_metric.software_group_id
1 GA341 'GA341 fold reliability score' 'normalized score' global . 2
2 MPQS 'ModPipe Quality Score' other global
'composite score, values >1.1 are considered reliable' 1
3 zDOPE 'Normalized DOPE' zscore global . 2
4 'TSVMod RMSD' 'TSVMod predicted RMSD (MSALL)' distance global . .
5 'TSVMod NO35' 'TSVMod predicted native overlap (MSALL)' 'normalized score'
global . .
#
#
loop_
_ma_qa_metric_global.ordinal_id
_ma_qa_metric_global.model_id
_ma_qa_metric_global.metric_id
_ma_qa_metric_global.metric_value
1 1 1 0.82
2 1 2 0.853452
3 1 3 0.31
4 1 4 12.996
5 1 5 0.143
#
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