diff --git a/src/reader/cif/schema.ts b/src/reader/cif/schema.ts
index 28f2afca2d78d3956ce2ac46fd1d8bfa11f0585d..8b390a4862a022e49ddb34717ddba7d6509f91d1 100644
--- a/src/reader/cif/schema.ts
+++ b/src/reader/cif/schema.ts
@@ -101,6 +101,7 @@ export namespace Field {
}
}
+ // spec argument is to allow for specialised implementation for undefined fields
function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field, category: Data.Category, key: string) => Column.Column<T>): Schema<T> {
return { type: 0 as any, ctor, undefinedField: (spec && spec.undefinedField) || Data.DefaultUndefinedField, alias: spec && spec.alias };
}
diff --git a/src/reader/cif/schema/ddl.ts b/src/reader/cif/schema/ddl.ts
new file mode 100644
index 0000000000000000000000000000000000000000..562133592a0ecb811f45af4ff26eccd6896a9c62
--- /dev/null
+++ b/src/reader/cif/schema/ddl.ts
@@ -0,0 +1,2 @@
+
+// TODO save frame schema for ddl http://mmcif.wwpdb.org/dictionaries/mmcif_ddl.dic/Index/
diff --git a/src/reader/cif/schema/dic.ts b/src/reader/cif/schema/dic.ts
new file mode 100644
index 0000000000000000000000000000000000000000..96f8d19c8b514aa3aee3750320db8401cd525f1c
--- /dev/null
+++ b/src/reader/cif/schema/dic.ts
@@ -0,0 +1,73 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Field, Block } from '../schema'
+
+const str = Field.str()
+const float = Field.float()
+
+const datablock = {
+ id: str,
+ description: str
+}
+
+const dictionary = {
+ title: str,
+ datablock_id: str,
+ version: str
+}
+
+const dictionary_history = {
+ version: str,
+ update: str,
+ revision: str
+}
+
+const sub_category = {
+ id: str,
+ description: str
+}
+
+const category_group_list = {
+ id: str,
+ parent_id: str,
+ description: str
+}
+
+const item_type_list = {
+ code: str,
+ primitive_code: str,
+ construct: str,
+ detail: str
+}
+
+const item_units_list = {
+ code: str,
+ detail: str
+}
+
+const item_units_conversion = {
+ from_code: str,
+ to_code: str,
+ operator: str,
+ factor: float
+}
+
+// TODO save frame dic schema
+
+const dic = {
+ datablock,
+ dictionary,
+ dictionary_history,
+ sub_category,
+ category_group_list,
+ item_type_list,
+ item_units_list,
+ item_units_conversion
+}
+
+type dic = Block.Instance<typeof dic>
+export default dic
diff --git a/src/reader/cif/schema/utils.ts b/src/reader/cif/schema/utils.ts
new file mode 100644
index 0000000000000000000000000000000000000000..42093d8391390b99cc3a7f6e5efb2161dd362af1
--- /dev/null
+++ b/src/reader/cif/schema/utils.ts
@@ -0,0 +1,100 @@
+
+// import dic from './dic'
+import { Field, Category } from '../schema'
+import * as Data from '../data-model'
+
+const pooledStr = Field.pooledStr()
+const str = Field.str()
+const int = Field.int()
+const float = Field.float()
+
+function getFieldType (type: string) {
+ switch (type) {
+ case 'code':
+ case 'ucode':
+ case 'line':
+ case 'uline':
+ case 'text':
+ case 'name':
+ case 'idname':
+ case 'any':
+ case 'atcode':
+ case 'fax':
+ case 'phone':
+ case 'email':
+ case 'code30':
+ case 'ec-type':
+ case 'seq-one-letter-code':
+ case 'author':
+ case 'orcid_id':
+ case 'sequence_dep':
+ case 'pdb_id':
+ case 'emd_id':
+ // todo, consider adding specialised fields
+ case 'yyyy-mm-dd':
+ case 'yyyy-mm-dd:hh:mm':
+ case 'yyyy-mm-dd:hh:mm-flex':
+ case 'int-range':
+ case 'float-range':
+ case 'binary':
+ case 'operation_expression':
+ case 'ucode-alphanum-csv':
+ case 'point_symmetry':
+ case 'id_list':
+ case '4x3_matrix':
+ case 'point_group':
+ case 'point_group_helical':
+ case 'boolean':
+ case 'symmetry_operation':
+ case 'date_dep':
+ return str
+ case 'uchar3':
+ case 'uchar1':
+ case 'symop':
+ return pooledStr
+ case 'int':
+ case 'non_negative_int':
+ case 'positive_int':
+ return int
+ case 'float':
+ return float
+ }
+ console.log(`unknown type '${type}'`)
+ return str
+}
+
+export function getSchema (dic: Data.Block) { // todo Block needs to be specialized with safe frames as well
+ const schema: { [category: string]: Category.Schema } = {}
+
+ dic.saveFrames.forEach(d => {
+ if (d.header[0] !== '_') {
+ schema[d.header] = {}
+ } else {
+ const categoryName = d.header.substring(1, d.header.indexOf('.'))
+ const itemName = d.header.substring(d.header.indexOf('.') + 1)
+ let fields
+ if (categoryName in schema) {
+ fields = schema[categoryName]
+ } else {
+ fields = {}
+ schema[categoryName] = fields
+ }
+ // console.log(util.inspect(d.categories, {showHidden: false, depth: 1}))
+ const item_type = d.categories['_item_type']
+ if (item_type) {
+ const code = item_type.getField('code')
+ if (code) {
+ fields[itemName] = getFieldType(code.str(0))
+ } else {
+ console.log(`item_type.code not found for '${d.header}'`)
+ }
+ } else {
+ // TODO check for _item_linked.parent_name and use its type
+ console.log(`item_type not found for '${d.header}'`)
+ }
+
+ }
+ })
+
+ return schema
+}
diff --git a/src/script.ts b/src/script.ts
index 724767d15e7d62088e67cd2cd27ef6ec260647e0..06868a492c54fa9971cfd113a919448c5a9051f8 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -11,6 +11,8 @@ import * as fs from 'fs'
import Gro from './reader/gro/parser'
import CIF from './reader/cif/index'
+import { getSchema } from './reader/cif/schema/utils'
+
const file = '1crn.gro'
// const file = 'water.gro'
// const file = 'test.gro'
@@ -148,8 +150,9 @@ async function runDic(input: string | Uint8Array) {
return;
}
- const data = parsed.result.blocks[0];
- console.log(util.inspect(data.saveFrames, {showHidden: false, depth: 3}))
+ const schema = getSchema(parsed.result.blocks[0])
+ // console.log(util.inspect(schema, {showHidden: false, depth: 1}))
+ console.log(util.inspect(Object.keys(schema).length, {showHidden: false, depth: 1}))
}
export function _dic() {