Merge pull request #23 from stan-donarise/fixes-1

fixed support for optimade, poscar and some cifs; error styles

matinfio/cell/cell.ts

@@ -34,12 +34,9 @@ namespace $ {
 	}
 
 	/** 3x3 matrix to crystalline cell parameters */
-	export function $mpds_cifplayer_matinfio_cell_params_from_matrix( matrix: number[] ) {
-		const norms: number[] = []
+	export function $mpds_cifplayer_matinfio_cell_params_from_matrix( matrix: number[][] ) {
+		const norms: number[] = matrix.map( vec => math.norm( vec ) )
 		const angles = []
-		matrix.forEach( function( vec ) {
-			norms.push( math.norm( vec ) )
-		} )
 		let j = -1
 		let k = -2
 		for( let i = 0; i < 3; i++ ) {

matinfio/cif/cif.ts

@@ -83,9 +83,14 @@ namespace $ {
 				}
 				continue
 
-			} else if( fingerprt.startsWith( '_symmetry_space_group_name_h-m' ) || fingerprt.startsWith( '_space_group.patterson_name_h-m' ) ) {
+			} else if( 
+				fingerprt.startsWith( '_symmetry_space_group_name_h-m' ) 
+				|| fingerprt.startsWith( '_space_group.patterson_name_h-m' )
+				|| fingerprt.startsWith( '_space_group_name_h-m_alt' )
+			) {
 				loop_active = false
-				cur_structure.sg_name = lines[ i ].trim().substr( 31 ).replace( /"/g, '' ).replace( /'/g, '' )
+				const match = cur_line.match( /"(.*)"|'(.*)'/ )
+				cur_structure.sg_name = match?.[1] || match?.[2]
 				continue
 
 			} else if( fingerprt.startsWith( '_space_group.it_number' ) || fingerprt.startsWith( '_space_group_it_number' ) || fingerprt.startsWith( '_symmetry_int_tables_number' ) ) {

matinfio/player/player.web.ts

@@ -15,6 +15,16 @@ namespace $ {
 
 		} else {
 			cell_matrix = crystal.cell_matrix // for POSCAR and OPTIMADE
+
+			const params = $mpds_cifplayer_matinfio_cell_params_from_matrix( cell_matrix! )
+			descr = {
+				'a': params[0],
+				'b': params[1],
+				'c': params[2],
+				'alpha': params[3],
+				'beta': params[4],
+				'gamma': params[5],
+			}
 		}
 
 		if( !crystal.atoms.length ) this.$mpds_cifplayer_matinfio_log.warning( "Note: no atomic coordinates supplied" )

matinfio/spacegroup/spacegroup.web.ts

@@ -8,10 +8,10 @@ namespace $ {
 			super()
 		}
 
-		@ $mol_mem_key
-		static by_name_and_num( name: string, num: number ) {
-			const spacegroup = $mpds_cifplayer_matinfio_spacegroup.by_num( num )
-				?? $mpds_cifplayer_matinfio_spacegroup.by_name( name )
+		static by_name_or_num( name: string, num: number ) {
+			const spacegroup = num
+				? $mpds_cifplayer_matinfio_spacegroup.by_num( num )
+				: name ? $mpds_cifplayer_matinfio_spacegroup.by_name( name ) : null
 			return spacegroup ? spacegroup : $mpds_cifplayer_matinfio_spacegroup.unknown()
 		}
 

player/player.view.css.ts

@@ -99,6 +99,21 @@ namespace $.$$ {
 			height: '2rem',
 		},
 
+		Message: {
+			position: 'absolute',
+			zIndex: 1,
+			top: '6rem',
+			left: 0,
+			right: 0,
+		},
+
+		Message_card: {
+			background: {
+				color: $mol_theme.back,
+			},
+			margin: 'auto',
+		},
+
 	} )
 
 }

player/player.view.tree

@@ -70,10 +70,15 @@ $mpds_cifplayer_player $mol_view
 			sub <= overlays_sub /
 				<= Switch_overlay $mol_switch
 					value? <=> overlay? \S
-					options <= available_overlays *
+					options <= available_overlays *string
 						\
 							\display none
 						S \elements
+		^ message_visible / <= Message $mol_view
+			sub /
+				<= Message_card $mol_card
+					theme \$mol_theme_special
+					title <= message \
 	colors_light *
 		a \#990000
 		b \#009900

player/player.view.web.ts

@@ -8,14 +8,14 @@ namespace $.$$ {
 
 	export class $mpds_cifplayer_player extends $.$mpds_cifplayer_player {
 
-		@ $mol_mem
-		render(): void {
-			super.render()
-			this.structure_3d_data() //for bubbling errors into view
-		}
-
 		@ $mol_mem
 		available_overlays() {
+			try {
+				this.structure_3d_data()
+			} catch (error) {
+				return {}
+			}
+
 			return {
 				...super.available_overlays(),
 				...this.structure_3d_data().overlayed
@@ -91,6 +91,22 @@ namespace $.$$ {
 			this.camera().position.add( this.camera_distance().multiplyScalar( this.zoom_scale_step() ) )
 		}
 
+		@ $mol_mem
+		message_visible() {
+			return this.message() ? super.message_visible() : []
+		}
+
+		@ $mol_mem
+		message(): string {
+			try {
+				this.structure_3d_data()
+				return ''
+
+			} catch ( error: any ) {
+				return error.message || error
+			}
+		}
+
 		@ $mol_mem
 		structure_3d_data() {
 			return new $mpds_cifplayer_matinfio( this.data() ).player()
@@ -153,7 +169,7 @@ namespace $.$$ {
 		spacegroup() {
 			const { sg_name, ng_name } = this.structure_3d_data()
 
-			return $mpds_cifplayer_matinfio_spacegroup.by_name_and_num( sg_name, ng_name )
+			return $mpds_cifplayer_matinfio_spacegroup.by_name_or_num( sg_name, ng_name )
 		}
 
 		@ $mol_mem
@@ -444,7 +460,12 @@ namespace $.$$ {
 
 		@ $mol_mem
 		left_panel(): readonly any[] {
-			console.log('this.structure_3d_data()', this.structure_3d_data())
+			try {
+				this.structure_3d_data()
+			} catch (error) {
+				return []
+			}
+
 			return this.structure_3d_data().cell_matrix ? super.left_panel() : []
 		}