tilde-lab · blokhin · Feb 13, 2024 · Jan 3, 2024 · Jan 7, 2024 · Jan 13, 2024
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+*	-text
diff --git a/.github/workflows/mpds_cifplayer.yml b/.github/workflows/mpds_cifplayer.yml
@@ -0,0 +1,23 @@
+name: $mpds_cifplayer
+
+on:
+  workflow_dispatch:
+  push:
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: hyoo-ru/mam_build@master2
+      with:
+        package: 'mpds/cifplayer'
+        modules: 'demo'
+
+    - uses: JamesIves/github-pages-deploy-action@4.1.7
+      with:
+        branch: gh-pages
+        folder: 'mpds/cifplayer/demo/-'
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1 @@
-/src/js/libs/*.custom.js
-/node_modules
-/three.js-r72
-/_work
+-*
diff --git a/app/app.view.css.ts b/app/app.view.css.ts
@@ -0,0 +1,54 @@
+namespace $.$$ {
+
+	$mol_style_define( $mpds_cifplayer_app, {
+
+		contain: 'none', //otherwise in fullscreen 'fixed' positions plot relative to parent not to the viewport
+
+		'@': {
+			mol_drop_status: {
+				drag: {
+					background: {
+						color: $mol_theme.hover,
+					},
+				},
+			},
+		},
+
+		Start: {
+			background: {
+				color: $mol_theme.back,
+			},
+			padding: {
+				top: '6rem',
+			},
+			flex: {
+				grow: 1,
+				direction: 'column',
+			},
+			align: {
+				items: 'center',
+			},
+		},
+
+		Menu: {
+			Body_content: {
+				gap: $mol_gap.block,
+				maxWidth: '25rem',
+			},
+			Head: {
+				justify: {
+					content: 'flex-start'
+				},
+			},
+		},
+
+		Player: {
+			flex: {
+				grow: 1,
+				basis: '30rem',
+			},
+		},
+
+	} )
+
+}
diff --git a/app/app.view.tree b/app/app.view.tree
@@ -0,0 +1,36 @@
+$mpds_cifplayer_app $mol_drop
+	receive? <=> drop_file? null
+	Sub <= Book $mol_book2
+		plugins /
+			<= Theme $mol_theme_auto
+		pages <= pages
+		Placeholder null
+	pages /
+		<= Menu $mol_page
+			title \3d-crystals web-viewer
+			tools /
+				<= Source $mol_link_source
+					uri \https://github.com/tilde-lab/cifplayer
+				<= Lights $mol_lights_toggle
+			body <= menu_body /
+				<= Upload $mol_button_open
+					Icon => Upload_icon
+					Native => Upload_native
+					sub /
+						<= Upload_icon
+						<= Upload_native
+						\Choose file
+				<= Data_text $mol_textarea
+					value? <=> data_str?
+					hint \Paste here...
+		<= Player $mpds_cifplayer_player
+			data <= data_str? \
+			vibrate? => vibrate?
+			unvibrate => unvibrate
+	Start $mol_view
+		sub /
+			<= Start_message $mol_text
+				text \Choose or paste a CIF, POSCAR, or Optimade file. No remote server is used.
+			<= Paste_example $mol_button_minor
+				title \Show example
+				click? <=> paste_example? null
diff --git a/app/app.view.web.ts b/app/app.view.web.ts
@@ -0,0 +1,33 @@
+namespace $.$$ {
+	export class $mpds_cifplayer_app extends $.$mpds_cifplayer_app {
+
+		@ $mol_mem
+		pages(): readonly any[] {
+			return this.data_str()
+				? super.pages()
+				: [ this.Menu(), this.Start() ]
+		}
+
+		@ $mol_action
+		files_read(next: readonly File[]) {
+			const data = $mol_wire_sync( this.$ ).$mol_blob_text( next[0] )
+			this.data_str( data )
+		}
+
+		@ $mol_action
+		drop_file(transfer: any) {
+			this.files_read( transfer.files )
+		}
+
+		@ $mol_action
+		paste_example() {
+			this.data_str( this.data_example() )
+		}
+
+		data_example() {
+			return `# CIF file\n# This file was generated by FINDSYM\n# Harold T. Stokes, Branton J. Campbell, Dorian M. Hatch\n# Brigham Young University, Provo, Utah, USA\n \ndata_findsym-output\n \n_symmetry_space_group_name_H-M "I 4/m 2/c 2/m"\n_symmetry_Int_Tables_number 140\n \n_cell_length_a       5.51665\n_cell_length_b       5.51665\n_cell_length_c       7.80171\n_cell_angle_alpha   90.00000\n_cell_angle_beta    90.00000\n_cell_angle_gamma   90.00000\n \nloop_\n_space_group_symop_operation_xyz\nx,y,z\nx,-y,-z+1/2\n-x,y,-z+1/2\n-x,-y,z\n-y,-x,-z+1/2\n-y,x,z\ny,-x,z\ny,x,-z+1/2\n-x,-y,-z\n-x,y,z+1/2\nx,-y,z+1/2\nx,y,-z\ny,x,z+1/2\ny,-x,-z\n-y,x,-z\n-y,-x,z+1/2\nx+1/2,y+1/2,z+1/2\nx+1/2,-y+1/2,-z\n-x+1/2,y+1/2,-z\n-x+1/2,-y+1/2,z+1/2\n-y+1/2,-x+1/2,-z\n-y+1/2,x+1/2,z+1/2\ny+1/2,-x+1/2,z+1/2\ny+1/2,x+1/2,-z\n-x+1/2,-y+1/2,-z+1/2\n-x+1/2,y+1/2,z\nx+1/2,-y+1/2,z\nx+1/2,y+1/2,-z+1/2\ny+1/2,x+1/2,z\ny+1/2,-x+1/2,-z+1/2\n-y+1/2,x+1/2,-z+1/2\n-y+1/2,-x+1/2,z\n \nloop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n_atom_site_occupancy\nTi1 Ti   0.00000   0.00000   0.00000   1.00000\nO1 O   0.23602   0.73602   0.00000   1.00000\nO2 O   0.00000   0.00000   0.25000   1.00000\nSr1 Sr   0.00000   0.50000   0.25000   1.00000\n `
+		}
+
+	}
+
+}
diff --git a/app/index.html b/app/index.html
@@ -0,0 +1,13 @@
+<!doctype html>
+<html mol_view_root>
+	<head>
+		<meta charset="utf-8" />
+		<meta name="viewport" content="width=device-width, height=device-height, initial-scale=1">
+		<meta name="mobile-web-app-capable" content="yes">
+		<meta name="apple-mobile-web-app-capable" content="yes">
+	</head>
+	<body mol_view_root>
+		<div mol_view_root="$mpds_cifplayer_app"></div>
+		<script src="web.js" charset="utf-8"></script>
+	</body>
+</html>
diff --git a/build.sh b/build.sh
diff --git a/comparison/cifs/H20.cif b/comparison/cifs/H20.cif
@@ -0,0 +1,177 @@
+data_H20
+# 
+_chem_comp.id                                    H20 
+_chem_comp.name                                  "6-CHLORO-4-(CYCLOHEXYLOXY)-3-ISOPROPYLQUINOLIN-2(1H)-ONE" 
+_chem_comp.type                                  NON-POLYMER 
+_chem_comp.pdbx_type                             HETAIN 
+_chem_comp.formula                               "C18 H22 Cl N O2" 
+_chem_comp.mon_nstd_parent_comp_id               ? 
+_chem_comp.pdbx_synonyms                         ? 
+_chem_comp.pdbx_formal_charge                    0 
+_chem_comp.pdbx_initial_date                     2004-07-22 
+_chem_comp.pdbx_modified_date                    2011-06-04 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.pdbx_replaced_by                      ? 
+_chem_comp.pdbx_replaces                         ? 
+_chem_comp.formula_weight                        319.826 
+_chem_comp.one_letter_code                       ? 
+_chem_comp.three_letter_code                     H20 
+_chem_comp.pdbx_model_coordinates_details        ? 
+_chem_comp.pdbx_model_coordinates_missing_flag   N 
+_chem_comp.pdbx_ideal_coordinates_details        ? 
+_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
+_chem_comp.pdbx_model_coordinates_db_code        1TL3 
+_chem_comp.pdbx_subcomponent_list                ? 
+_chem_comp.pdbx_processing_site                  RCSB 
+# 
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_align 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.model_Cartn_x 
+_chem_comp_atom.model_Cartn_y 
+_chem_comp_atom.model_Cartn_z 
+_chem_comp_atom.pdbx_model_Cartn_x_ideal 
+_chem_comp_atom.pdbx_model_Cartn_y_ideal 
+_chem_comp_atom.pdbx_model_Cartn_z_ideal 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal 
+H20 CA   CA   C  0 1 N N N 1.747  -36.297 22.990 -1.853 -0.230 0.046  CA   H20 1  
+H20 CB   CB   C  0 1 N N N 3.298  -36.220 23.422 -2.539 0.533  1.180  CB   H20 2  
+H20 CC   CC   C  0 1 N N N 3.629  -35.017 24.291 -3.517 1.552  0.590  CC   H20 3  
+H20 CD   CD   C  0 1 N N N 2.881  -35.116 25.588 -4.571 0.822  -0.244 CD   H20 4  
+H20 CE   CE   C  0 1 N N N 1.381  -34.930 25.356 -3.884 0.058  -1.378 CE   H20 5  
+H20 CF   CF   C  0 1 N N N 0.779  -35.916 24.269 -2.907 -0.959 -0.788 CF   H20 6  
+H20 N1   N1   N  0 1 Y N N 0.708  -37.031 18.043 2.735  0.723  0.916  N1   H20 7  
+H20 C6   C6   C  0 1 Y N N 1.847  -37.693 18.482 2.038  0.372  2.010  C6   H20 8  
+H20 O2   O2   O  0 1 N N N 2.694  -38.080 17.657 2.502  0.615  3.112  O2   H20 9  
+H20 C5   C5   C  0 1 Y N N 2.049  -37.882 19.932 0.797  -0.277 1.921  C5   H20 10 
+H20 C4   C4   C  0 1 Y N N 1.108  -37.345 20.831 0.257  -0.560 0.699  C4   H20 11 
+H20 O4   O4   O  0 1 N N N 1.308  -37.473 22.257 -0.940 -1.181 0.598  O4   H20 12 
+H20 C2   C2   C  0 1 Y N N -0.218 -36.554 18.921 2.249  0.468  -0.350 C2   H20 13 
+H20 C3   C3   C  0 1 Y N N -0.030 -36.704 20.329 1.009  -0.175 -0.502 C3   H20 14 
+H20 C7   C7   C  0 1 Y N N -1.081 -36.293 21.184 0.511  -0.436 -1.781 C7   H20 15 
+H20 C8   C8   C  0 1 Y N N -2.268 -35.764 20.670 1.242  -0.060 -2.886 C8   H20 16 
+H20 C9   C9   C  0 1 Y N N -2.441 -35.623 19.296 2.468  0.574  -2.735 C9   H20 17 
+H20 C10  C10  C  0 1 Y N N -1.409 -36.019 18.415 2.971  0.839  -1.480 C10  H20 18 
+H20 CL   CL   CL 0 0 N N N -3.492 -35.284 21.715 0.628  -0.383 -4.478 CL   H20 19 
+H20 C11  C11  C  0 1 N N N 3.166  -38.860 20.343 0.056  -0.656 3.177  C11  H20 20 
+H20 C12  C12  C  0 1 N N N 4.529  -38.203 20.602 0.891  -1.655 3.980  C12  H20 21 
+H20 C13  C13  C  0 1 N N N 2.758  -39.962 21.356 -0.192 0.595  4.020  C13  H20 22 
+H20 HA   HA   H  0 1 N N N 1.640  -35.519 22.198 -1.309 0.470  -0.586 HA   H20 23 
+H20 HB1  1HB  H  0 1 N N N 3.959  -36.252 22.525 -3.083 -0.167 1.813  HB1  H20 24 
+H20 HB2  2HB  H  0 1 N N N 3.616  -37.165 23.920 -1.788 1.053  1.775  HB2  H20 25 
+H20 HC1  1HC  H  0 1 N N N 3.437  -34.052 23.766 -2.973 2.253  -0.042 HC1  H20 26 
+H20 HC2  2HC  H  0 1 N N N 4.727  -34.898 24.446 -4.006 2.096  1.398  HC2  H20 27 
+H20 HD1  1HD  H  0 1 N N N 3.275  -34.403 26.349 -5.267 1.548  -0.665 HD1  H20 28 
+H20 HD2  2HD  H  0 1 N N N 3.103  -36.069 26.123 -5.115 0.121  0.388  HD2  H20 29 
+H20 HE1  1HE  H  0 1 N N N 1.151  -33.870 25.097 -3.340 0.759  -2.011 HE1  H20 30 
+H20 HE2  2HE  H  0 1 N N N 0.821  -35.013 26.316 -4.636 -0.461 -1.973 HE2  H20 31 
+H20 HF1  1HF  H  0 1 N N N 0.433  -36.852 24.766 -2.418 -1.504 -1.596 HF1  H20 32 
+H20 HF2  2HF  H  0 1 N N N -0.190 -35.511 23.895 -3.451 -1.660 -0.155 HF2  H20 33 
+H20 HN1  HN1  H  0 1 N N N 0.547  -36.891 17.046 3.591  1.166  1.018  HN1  H20 34 
+H20 H7   H7   H  0 1 N N N -0.972 -36.387 22.278 -0.441 -0.931 -1.902 H7   H20 35 
+H20 H9   H9   H  0 1 N N N -3.385 -35.202 18.910 3.032  0.864  -3.609 H9   H20 36 
+H20 H10  H10  H  0 1 N N N -1.534 -35.910 17.325 3.926  1.333  -1.373 H10  H20 37 
+H20 H11  H11  H  0 1 N N N 3.334  -39.451 19.413 -0.898 -1.112 2.912  H11  H20 38 
+H20 H121 1H12 H  0 0 N N N 4.429  -37.389 21.358 0.376  -1.895 4.910  H121 H20 39 
+H20 H122 2H12 H  0 0 N N N 5.338  -38.911 20.900 1.030  -2.565 3.397  H122 H20 40 
+H20 H123 3H12 H  0 0 N N N 4.845  -37.605 19.716 1.863  -1.217 4.206  H123 H20 41 
+H20 H131 1H13 H  0 0 N N N 1.880  -40.529 20.967 0.761  1.050  4.286  H131 H20 42 
+H20 H132 2H13 H  0 0 N N N 3.567  -40.670 21.654 -0.788 1.306  3.448  H132 H20 43 
+H20 H133 3H13 H  0 0 N N N 2.308  -39.496 22.264 -0.729 0.320  4.929  H133 H20 44 
+# 
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal 
+H20 CA  CB   SING N N 1  
+H20 CA  CF   SING N N 2  
+H20 CA  O4   SING N N 3  
+H20 CA  HA   SING N N 4  
+H20 CB  CC   SING N N 5  
+H20 CB  HB1  SING N N 6  
+H20 CB  HB2  SING N N 7  
+H20 CC  CD   SING N N 8  
+H20 CC  HC1  SING N N 9  
+H20 CC  HC2  SING N N 10 
+H20 CD  CE   SING N N 11 
+H20 CD  HD1  SING N N 12 
+H20 CD  HD2  SING N N 13 
+H20 CE  CF   SING N N 14 
+H20 CE  HE1  SING N N 15 
+H20 CE  HE2  SING N N 16 
+H20 CF  HF1  SING N N 17 
+H20 CF  HF2  SING N N 18 
+H20 N1  C6   SING Y N 19 
+H20 N1  C2   SING Y N 20 
+H20 N1  HN1  SING N N 21 
+H20 C6  O2   DOUB N N 22 
+H20 C6  C5   SING Y N 23 
+H20 C5  C4   DOUB Y N 24 
+H20 C5  C11  SING N N 25 
+H20 C4  O4   SING N N 26 
+H20 C4  C3   SING Y N 27 
+H20 C2  C3   SING Y N 28 
+H20 C2  C10  DOUB Y N 29 
+H20 C3  C7   DOUB Y N 30 
+H20 C7  C8   SING Y N 31 
+H20 C7  H7   SING N N 32 
+H20 C8  C9   DOUB Y N 33 
+H20 C8  CL   SING N N 34 
+H20 C9  C10  SING Y N 35 
+H20 C9  H9   SING N N 36 
+H20 C10 H10  SING N N 37 
+H20 C11 C12  SING N N 38 
+H20 C11 C13  SING N N 39 
+H20 C11 H11  SING N N 40 
+H20 C12 H121 SING N N 41 
+H20 C12 H122 SING N N 42 
+H20 C12 H123 SING N N 43 
+H20 C13 H131 SING N N 44 
+H20 C13 H132 SING N N 45 
+H20 C13 H133 SING N N 46 
+# 
+loop_
+_pdbx_chem_comp_descriptor.comp_id 
+_pdbx_chem_comp_descriptor.type 
+_pdbx_chem_comp_descriptor.program 
+_pdbx_chem_comp_descriptor.program_version 
+_pdbx_chem_comp_descriptor.descriptor 
+H20 SMILES           ACDLabs              10.04 "Clc3ccc2c(C(OC1CCCCC1)=C(C(=O)N2)C(C)C)c3"                                                                               
+H20 SMILES_CANONICAL CACTVS               3.341 "CC(C)C1=C(OC2CCCCC2)c3cc(Cl)ccc3NC1=O"                                                                                   
+H20 SMILES           CACTVS               3.341 "CC(C)C1=C(OC2CCCCC2)c3cc(Cl)ccc3NC1=O"                                                                                   
+H20 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)C1=C(c2cc(ccc2NC1=O)Cl)OC3CCCCC3"                                                                                   
+H20 SMILES           "OpenEye OEToolkits" 1.5.0 "CC(C)C1=C(c2cc(ccc2NC1=O)Cl)OC3CCCCC3"                                                                                   
+H20 InChI            InChI                1.03  "InChI=1S/C18H22ClNO2/c1-11(2)16-17(22-13-6-4-3-5-7-13)14-10-12(19)8-9-15(14)20-18(16)21/h8-11,13H,3-7H2,1-2H3,(H,20,21)" 
+H20 InChIKey         InChI                1.03  OQCFORGSZJSAEL-UHFFFAOYSA-N                                                                                               
+# 
+loop_
+_pdbx_chem_comp_identifier.comp_id 
+_pdbx_chem_comp_identifier.type 
+_pdbx_chem_comp_identifier.program 
+_pdbx_chem_comp_identifier.program_version 
+_pdbx_chem_comp_identifier.identifier 
+H20 "SYSTEMATIC NAME" ACDLabs              10.04 "6-chloro-4-(cyclohexyloxy)-3-(1-methylethyl)quinolin-2(1H)-one" 
+H20 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 6-chloro-4-cyclohexyloxy-3-propan-2-yl-1H-quinolin-2-one         
+# 
+loop_
+_pdbx_chem_comp_audit.comp_id 
+_pdbx_chem_comp_audit.action_type 
+_pdbx_chem_comp_audit.date 
+_pdbx_chem_comp_audit.processing_site 
+H20 "Create component"  2004-07-22 RCSB 
+H20 "Modify descriptor" 2011-06-04 RCSB 
+#