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amudhakumariamudhakumari
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rfam to schema
1 parent f53fe37 commit 86a26db

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2 files changed

+20
-16
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2 files changed

+20
-16
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‎EMICSS/EMICSS.py

Lines changed: 18 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
# -*- coding: utf-8 -*-
33

44
#
5-
# Generated Tue Jun 14 21:14:10 2022 by generateDS.py version 2.38.6.
5+
# Generated Thu Aug 1 15:07:22 2024 by generateDS.py version 2.38.6.
66
# Python 3.7.6 (default, Dec 30 2019, 19:38:28) [Clang 11.0.0 (clang-1100.0.33.16)]
77
#
88
# Command line options:
@@ -973,6 +973,7 @@ class provenance_type(str, Enum):
973973
database"""
974974
EMDB='EMDB'
975975
UNI_PROT='UniProt'
976+
UNI_PROT_KB='UniProtKB'
976977
PD_BE='PDBe'
977978
PD_BEKB='PDBe-KB'
978979
ALPHA_FOLDDB='AlphaFold DB'
@@ -993,20 +994,23 @@ class provenance_type(str, Enum):
993994
CATH='CATH'
994995
SCOP='SCOP'
995996
SCOP_2='SCOP2'
997+
SCOP_2_B='SCOP2B'
998+
RFAM='Rfam'
996999

9971000

9981001
class sample_kind(str, Enum):
9991002
COMPLEX='complex'
10001003
PROTEIN='protein'
10011004
LIGAND='ligand'
1005+
RNA='rna'
10021006

10031007

10041008
class emicss(GeneratedsSuper):
10051009
"""EMDB entry idEMICSS schema version"""
10061010
__hash__ = GeneratedsSuper.__hash__
10071011
subclass = None
10081012
superclass = None
1009-
def __init__(self, emdb_id=None, version='0.9.3', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, gds_collector_=None, **kwargs_):
1013+
def __init__(self, emdb_id=None, version='0.9.5', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, gds_collector_=None, **kwargs_):
10101014
self.gds_collector_ = gds_collector_
10111015
self.gds_elementtree_node_ = None
10121016
self.original_tagname_ = None
@@ -1124,7 +1128,7 @@ def exportAttributes(self, outfile, level, already_processed, namespaceprefix_='
11241128
if self.emdb_id is not None and 'emdb_id' not in already_processed:
11251129
already_processed.add('emdb_id')
11261130
outfile.write(' emdb_id=%s' % (self.gds_encode(self.gds_format_string(quote_attrib(self.emdb_id), input_name='emdb_id')), ))
1127-
if self.version != "0.9.3" and 'version' not in already_processed:
1131+
if self.version != "0.9.5" and 'version' not in already_processed:
11281132
already_processed.add('version')
11291133
outfile.write(' version=%s' % (self.gds_encode(self.gds_format_string(quote_attrib(self.version), input_name='version')), ))
11301134
if self.schema_location is not None and 'schema_location' not in already_processed:
@@ -1295,7 +1299,7 @@ def validate_provenance_type(self, value):
12951299
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
12961300
return False
12971301
value = value
1298-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1302+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
12991303
if value not in enumerations:
13001304
lineno = self.gds_get_node_lineno_()
13011305
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -1580,7 +1584,7 @@ def validate_provenance_type(self, value):
15801584
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
15811585
return False
15821586
value = value
1583-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1587+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
15841588
if value not in enumerations:
15851589
lineno = self.gds_get_node_lineno_()
15861590
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -1807,7 +1811,7 @@ def validate_provenance_type(self, value):
18071811
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
18081812
return False
18091813
value = value
1810-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1814+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
18111815
if value not in enumerations:
18121816
lineno = self.gds_get_node_lineno_()
18131817
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -1952,7 +1956,7 @@ def validate_provenance_type(self, value):
19521956
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
19531957
return False
19541958
value = value
1955-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1959+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
19561960
if value not in enumerations:
19571961
lineno = self.gds_get_node_lineno_()
19581962
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -2095,7 +2099,7 @@ def validate_provenance_type(self, value):
20952099
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
20962100
return False
20972101
value = value
2098-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
2102+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
20992103
if value not in enumerations:
21002104
lineno = self.gds_get_node_lineno_()
21012105
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -2336,7 +2340,7 @@ def validate_provenance_type(self, value):
23362340
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
23372341
return False
23382342
value = value
2339-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
2343+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
23402344
if value not in enumerations:
23412345
lineno = self.gds_get_node_lineno_()
23422346
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -2590,7 +2594,7 @@ def validate_provenance_type(self, value):
25902594
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
25912595
return False
25922596
value = value
2593-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
2597+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
25942598
if value not in enumerations:
25952599
lineno = self.gds_get_node_lineno_()
25962600
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3100,7 +3104,7 @@ def validate_sample_kind(self, value):
31003104
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
31013105
return False
31023106
value = value
3103-
enumerations = ['complex', 'protein', 'ligand']
3107+
enumerations = ['complex', 'protein', 'ligand', 'rna']
31043108
if value not in enumerations:
31053109
lineno = self.gds_get_node_lineno_()
31063110
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on sample_kind' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3113,7 +3117,7 @@ def validate_provenance_type(self, value):
31133117
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
31143118
return False
31153119
value = value
3116-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
3120+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
31173121
if value not in enumerations:
31183122
lineno = self.gds_get_node_lineno_()
31193123
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3510,7 +3514,7 @@ def validate_sample_kind(self, value):
35103514
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
35113515
return False
35123516
value = value
3513-
enumerations = ['complex', 'protein', 'ligand']
3517+
enumerations = ['complex', 'protein', 'ligand', 'rna']
35143518
if value not in enumerations:
35153519
lineno = self.gds_get_node_lineno_()
35163520
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on sample_kind' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3523,7 +3527,7 @@ def validate_provenance_type(self, value):
35233527
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
35243528
return False
35253529
value = value
3526-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
3530+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
35273531
if value not in enumerations:
35283532
lineno = self.gds_get_node_lineno_()
35293533
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )

‎EMICSS/EMICSSsub.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
#!/usr/bin/env python
22

33
#
4-
# Generated Tue Jun 14 21:14:10 2022 by generateDS.py version 2.38.6.
4+
# Generated Thu Aug 1 15:07:24 2024 by generateDS.py version 2.38.6.
55
# Python 3.7.6 (default, Dec 30 2019, 19:38:28) [Clang 11.0.0 (clang-1100.0.33.16)]
66
#
77
# Command line options:
@@ -62,7 +62,7 @@ def parsexmlstring_(instring, parser=None, **kwargs):
6262

6363

6464
class emicssSub(supermod.emicss):
65-
def __init__(self, emdb_id=None, version='0.9.3', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, **kwargs_):
65+
def __init__(self, emdb_id=None, version='0.9.5', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, **kwargs_):
6666
super(emicssSub, self).__init__(emdb_id, version, schema_location, dbs, entry_ref_dbs, primary_citation, weights, sample, **kwargs_)
6767
supermod.emicss.subclass = emicssSub
6868
# end class emicssSub

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