Merge pull request #3 from Tianhao-Gu/add_KBaseStructure_spec

add KBaseStructure spec

Author: Tianhao-Gu

.gitignore

@@ -1,2 +1,3 @@
 test_local
 sdk.cfg
+lib/ProteinStructureUtils/ProteinStructureUtilsImpl.py.bak-*

KBaseStructure.spec

@@ -0,0 +1,112 @@
+
+/*
+@author chenry jmc jjeffryes tgu2
+*/
+module KBaseStructure {
+  typedef int bool;
+
+  /*
+    Reference to KBase genome
+    @id ws KBaseGenomes.Genome KBaseGenomeAnnotations.GenomeAnnotation
+  */
+  typedef string genome_ref;
+
+  /*
+    CDS ID
+    @id kb
+  */
+  typedef string cds_id;
+
+  /*
+    Molecule ID
+    @id external
+  */
+  typedef string mol_id;
+
+  /*
+    Uniref ID
+    @id external
+  */
+  typedef string uniref_id;
+
+  /*
+    Reference to a file handle in shock
+    @id handle
+  */
+  typedef string handle_ref;
+
+  /*
+    ProteinData
+    mol_id id: ID for the protein
+    string sequence: amino acid sequence
+    string md5: hash of the amino acid sequence
+    uniref_id uniref_id: from uniprot
+    genome_ref genome_ref: from a kbase genome
+    cds_id cds_id; from a kbase genome
+
+    @optional id uniref_id genome_ref cds_id
+  */
+  typedef structure {
+    mol_id id;
+    string sequence;
+    string md5;
+    uniref_id uniref_id;
+    genome_ref genome_ref;
+    cds_id cds_id;
+  } ProteinData;
+
+  /*
+    ExpProteinStructure
+    @optional mmcif_handle xml_handle
+  */
+  typedef structure {
+    /*Experimental header*/
+    string rcsb_id;
+    string name;
+    string deposition_date;
+    string head;
+    string release_date;
+    string structure_method;
+    float resolution;
+    string author;
+    list<string> compound;
+    list<string> source;
+
+    /*Structure metadata*/
+    int num_models;
+    int num_chains;
+    int num_residues;
+    int num_atoms;
+    int num_het_atoms;
+    int num_water_atoms;
+    int num_disordered_atoms;
+    int num_disordered_residues;
+
+    /*Protein links*/
+    list<ProteinData> proteins;
+
+    /*File links*/
+    handle_ref pdb_handle;
+    handle_ref mmcif_handle;
+    handle_ref xml_handle;
+  } ExperimentalProteinStructure;
+
+  /*
+    ModelProteinStructure
+    @optional
+  */
+  typedef structure {
+    string user_data;
+    string name;
+    int num_chains;
+    int num_residues;
+    int num_atoms;
+
+    /*Protein links*/
+    ProteinData protein;
+
+    /*File links*/
+    handle_ref pdb_handle;
+  } ModelProteinStructure;
+};
+

kbase.yml

@@ -8,7 +8,7 @@ service-language:
     python
 
 module-version:
-    0.0.1
+    0.0.2
 
 owners:
     [asedova, jjeffryes, tgu2]

lib/ProteinStructureUtils/ProteinStructureUtilsImpl.py

@@ -22,9 +22,9 @@ class ProteinStructureUtils:
     # state. A method could easily clobber the state set by another while
     # the latter method is running.
     ######################################### noqa
-    VERSION = "0.0.1"
-    GIT_URL = "https://github.com/kbaseapps/ProteinStructureUtils.git"
-    GIT_COMMIT_HASH = "c382ad991f24c7fb4e191b164413a95a6a33eaba"
+    VERSION = "0.0.2"
+    GIT_URL = "https://github.com/Tianhao-Gu/ProteinStructureUtils.git"
+    GIT_COMMIT_HASH = "7fb3a1f471f5f5832cbb415fadda86ff878fc0f7"
 
     #BEGIN_CLASS_HEADER
     logging.basicConfig(format='%(asctime)s %(levelname)-8s %(message)s',