moorhen 0.8.4 → 0.9.0

package/baby-gru/CootWorker.js

@@ -1 +1 @@
-var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var a,r=1,t=arguments.length;r<t;r++)for(var o in a=arguments[r])Object.prototype.hasOwnProperty.call(a,o)&&(e[o]=a[o]);return e},__assign.apply(this,arguments)};importScripts("./wasm/moorhen.js"),importScripts("./wasm/web_example.js");var guid=function(){var e=Date.now();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,(function(a){var r=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===a?r:3&r|8).toString(16)}))},print=function(e){console.log(e),postMessage({consoleMessage:JSON.stringify(e)})},instancedMeshToMeshData=function(e,a,r,t){void 0===r&&(r=!1),void 0===t&&(t=1e4);for(var o=[],s=[],n=[],i=[],c=[],_=[],l=[],u=[],d=[],m=e.geom,p=e.markup,g=m.size(),h=0;h<g;h++){var f=r,v=[],y=[],S=[],b=[],M=[],z=[],T=[],x=m.get(h);"spherical-atoms"===x.name&&(f=!0);for(var A=x.vertices,F=x.triangles,w=F.size(),k=0;k<w;k++){var I=F.get(k).point_id;a?(v.push(I[0]),v.push(I[2]),v.push(I[1])):(v.push(I[0]),v.push(I[1]),v.push(I[2]))}F.delete();for(var J=A.size(),D=0;D<J;D++){var C=A.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;S.push(R[0]),S.push(R[1]),S.push(R[2])}A.delete();var P=x.instancing_data_A,E=P.size();if(E>0)for(var U=0;U<E;U++){var L=(q=P.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=q.size;b.push(B[0]),b.push(B[1]),b.push(B[2]),T.push.apply(T,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}P.delete();var j=x.instancing_data_B,V=j.size();if(V>0)for(U=0;U<V;U++){var q;if(!((B=(q=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=q.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=q.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;T.push(H[0][0]),T.push(H[0][1]),T.push(H[0][2]),T.push(H[0][3]),T.push(H[1][0]),T.push(H[1][1]),T.push(H[1][2]),T.push(H[1][3]),T.push(H[2][0]),T.push(H[2][1]),T.push(H[2][2]),T.push(H[2][3]),T.push(H[3][0]),T.push(H[3][1]),T.push(H[3][2]),T.push(H[3][3])}}j.delete(),n.push(S),s.push(y),o.push(v),i.push(b),_.push(z),l.push(T),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var K=simpleMeshToMeshData(p);return K.idx_tri.length>0&&K.idx_tri[0].length>0&&K.idx_tri[0][0].length>0?r?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[_,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[s,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d],idx_tri:[o],vert_tri:[s],norm_tri:[n],col_tri:[c],instance_use_colors:[u],instance_sizes:[i],instance_origins:[_],instance_orientations:[l]}},simpleMeshToMeshData=function(e,a){void 0===a&&(a=!1),performance.now();var r=e.vertices,t=e.triangles,o=r.size(),s=t.size(),n=new Uint32Array(3*s),i=new Float32Array(3*o),c=new Float32Array(3*o),_=new Float32Array(4*o);cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getColoursFromSimpleMesh2(e,_),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,c),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,n)):(cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getTriangleIndicesFromSimpleMesh2(e,n)),performance.now();var l=i,u=_,d=c,m=n;return r.delete(),t.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[m]],vert_tri:[[l]],norm_tri:[[d]],col_tri:[[u]]}},SuperposeResultsToJSArray=function(e){for(var a=e.aligned_pairs,r=a.size(),t=[],o=0;o<r;o++){var s=a.get(o),n=s.first,i=n.residue_spec,c=s.second,_=c.residue_spec,l={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:_.chain_id,insCode:_.ins_code,seqNum:_.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(l)}return a.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}a.push(n),o.delete()}return e.delete(),a},floatArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},mapMoleculeCentreInfoToJSObject=function(e){var a=e.updated_centre,r={updated_centre:[a.x(),a.y(),a.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return a.delete(),r},textureAsFloatsToJSTextureAsFloats=function(e){var a=[],r=e.image_data.size();console.log(r);for(var t=0;t<r;t++){var o=e.image_data.get(t);a.push(o)}return e.image_data.delete(),{width:e.width,height:e.height,x_size:e.x_size,y_size:e.y_size,z_position:e.z_position,image_data:a}},fitLigandInfoArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(__assign({},o))}return e.delete(),a},intArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},export_map_as_gltf=function(e,a,r,t,o,s){var n="".concat(guid(),".glb");molecules_container.export_map_molecule_as_gltf(e,a,r,t,o,s,n);var i=cootModule.FS.readFile(n,{encoding:"binary"});return cootModule.FS_unlink(n),i.buffer},export_molecule_as_gltf=function(e,a,r,t,o,s,n,i,c){var _="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,a,r,t,o,s,n,i,c,_);var l=cootModule.FS.readFile(_,{encoding:"binary"});return cootModule.FS_unlink(_),l.buffer},symmetryToJSData=function(e){for(var a=[],r=e.first,t=e.second,o=r.symm_trans,s=o.size(),n=0;n<s;n++){var i=o.get(n),c=i.first,_=i.second,l=t.get(n);a.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:_.us,ws:_.ws,vs:_.vs,matrix:l}),c.delete()}return o.delete(),t.delete(),a},mmrrccStatsToJSArray=function(e){var a=function(e){for(var a=[],r=e.keys(),t=r.size(),o=0;o<t;o++){var s=r.get(o),n=e.get(s);a.push({resNum:s.res_no,insCode:s.ins_code,modelNumber:s.model_number,chainId:s.chain_id,n:n.n,correlation:n.correlation()}),n.delete()}return r.delete(),a},r=e.first,t=e.second,o={"All atoms":a(r),"Side-chains":a(t)};return r.delete(),t.delete(),o},atomSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({chain_id:o.chain_id,res_no:o.res_no,ins_code:o.ins_code,atom_name:o.atom_name,alt_conf:o.alt_conf,int_user_data:o.int_user_data,float_user_data:o.float_user_data,string_user_data:o.string_user_data,model_number:o.model_number})}return e.delete(),a},residueSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({resNum:o.res_no,insCode:o.ins_code,modelNumber:o.model_number,chainId:o.chain_id,intUserData:o.int_user_data})}return e.delete(),a},stringPairVectorToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({first:o.first,second:o.second})}return e.delete(),a},validationDataToJSArray=function(e,a){void 0===a&&(a=null);for(var r=[],t=e.cviv,o=t.size(),s=0;s<o;s++){var n=t.get(s);if(null!==a&&n.chain_id!==a);else{for(var i=n.rviv,c=i.size(),_=0;_<c;_++){var l=i.get(_),u=l.residue_spec;r.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:l.function_value})}i.delete()}}return t.delete(),e.delete(),r},linesBoxToJSArray=function(e){for(var a=[],r=e.line_segments,t=r.size(),o=0;o<t;o++){for(var s=[],n=r.get(o),i=n.size(),c=0;c<i;c++){var _=n.get(c),l=_.getStart(),u=_.getFinish(),d=_.amplitude(),m={x:l.x(),y:l.y(),z:l.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),l.delete(),u.delete(),_.delete()}n.delete(),a.push(s)}return r.delete(),a},vectorHBondToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({hb_hydrogen:o.hb_hydrogen,donor:o.donor,acceptor:o.acceptor,donor_neigh:o.donor_neigh,acceptor_neigh:o.acceptor_neigh,angle_1:o.angle_1,angle_2:o.angle_2,angle_3:o.angle_3,dist:o.dist,ligand_atom_is_donor:o.ligand_atom_is_donor,hydrogen_is_ligand_atom:o.hydrogen_is_ligand_atom,bond_has_hydrogen_flag:o.bond_has_hydrogen_flag})}return e.delete(),a},interestingPlaceDataToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.residue_spec;a.push({intUserData:s.int_user_data,modelNumber:s.model_number,chainId:s.chain_id,insCode:s.ins_code,resNum:s.res_no,featureType:o.feature_type,featureValue:o.feature_value,buttonLabel:o.button_label,badness:o.badness,coordX:o.x,coordY:o.y,coordZ:o.z})}return e.delete(),a},histogramInfoToJSData=function(e){var a=e.counts;return{counts:intArrayToJSArray(a),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({idx:o.idx,F:o.F,phi:o.phi,w:o.w,weights_used:o.weights_used,Rfree:o.Rfree?o.Rfree.split("/")[3]:"",F_obs:o.F_obs?o.F_obs.split("/")[3]:"",sigF_obs:o.sigF_obs?o.sigF_obs.split("/")[3]:""})}if(e.delete(),a.some((function(e){return-1===e.idx}))){var s=a.find((function(e){return-1===e.idx}));s&&s.F_obs&&s.Rfree&&s.sigF_obs&&a.forEach((function(e){e.F_obs=s.F_obs,e.sigF_obs=s.sigF_obs,e.Rfree=s.Rfree})),a=a.filter((function(e){return-1!==e.idx}))}return a},ramachandranDataToJSArray=function(e,a){for(var r=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===a&&r.push({chainId:n.chain_id,insCode:n.ins_code,seqNum:n.residue_number,restype:s.residue_name(),isOutlier:!s.is_allowed_flag,phi:n.phi(),psi:n.psi(),is_pre_pro:"PRO"===s.residue_name()}),s.delete(),n.delete()}return e.delete(),r},vectorPairStringIntToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s={residue:o.first,slice:o.second};a.push(s)}return e.delete(),a},vectorPairClipperCoordFloatToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),a.push({value:s,coord:i})}return e.delete(),a},simpleMeshToLineMeshData=function(e,a){performance.now();var r=e.vertices,t=e.triangles,o=t.size(),s=r.size(),n=new Uint32Array(6*o),i=new Float32Array(3*s),c=new Float32Array(3*s),_=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),performance.now();var l=n,u=i,d=c,m=_;return r.delete(),t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],norm_tri:[[d]],col_tri:[[m]]}},auto_open_mtz=function(e){var a=guid(),r=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(a,".mtz"),r,!0,!0);var t="./".concat(a,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,a,r){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(a);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,r.F,r.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(o),i},new_positions_for_residue_atoms=function(e,a){var r=0,t=new cootModule.Vectormoved_residue_t;return a.forEach((function(e){if(e.length>0){var a=e[0],r=new cootModule.moved_residue_t(a.chain_id,parseInt(a.res_no),"");e.forEach((function(e){var a=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);r.add_atom(a),a.delete()})),t.push_back(r),r.delete()}})),r+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),r},read_mtz=function(e,a,r){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,r.F,r.PHI,"",!1,r.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,a,r,t,o){var s=new Uint8Array(a.data);cootModule.FS_createDataFile(".","".concat(a.fileName,".mtz"),s,!0,!0);var n="./".concat(a.fileName,".mtz"),i=[e,n,r,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,a,r){var t=guid(),o=new Uint8Array(e),s="";a.endsWith(".map.gz")?s="map.gz":a.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,r],c=-1;try{c=molecules_container.read_ccp4_map.apply(molecules_container,i)}catch(e){console.warn(e)}finally{cootModule.FS_unlink(n)}return c},setUserDefinedBondColours=function(e,a,r){void 0===r&&(r=!1);var t=new cootModule.MapIntFloat3,o=new cootModule.VectorStringUInt_pair;a.forEach((function(e,a){t.set(a+51,e.rgb);var r={first:e.cid,second:a+51};o.push_back(r)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,r),o.delete(),t.delete()},privateerValidationToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=[],n=o.torsions,i=n.size(),c=0;c<i;c++)s.push(n.get(c));n.delete();var _={torsions:s,svg:o.svg.replace(/: *32/g,""),id:o.id.replace(/: *32/g,""),chain:o.chain,wurcs:o.wurcs,glyconnect_id:o.glyconnect_id,glytoucan_id:o.glytoucan_id,torsion_err:o.torsion_err,anomer_err:o.anomer_err,conformation_err:o.conformation_err,puckering_err:o.puckering_err,chirality_err:o.chirality_err};a.push(_)}return e.delete(),a},doCootCommand=function(e){var a=e.returnType,r=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(r){case"shim_new_positions_for_residue_atoms":i=new_positions_for_residue_atoms.apply(void 0,t);break;case"shim_read_mtz":i=read_mtz.apply(void 0,t);break;case"shim_auto_open_mtz":i=auto_open_mtz.apply(void 0,t);break;case"shim_read_ccp4_map":i=read_ccp4_map.apply(void 0,t);break;case"shim_associate_data_mtz_file_with_map":i=associate_data_mtz_file_with_map.apply(void 0,t);break;case"shim_replace_map_by_mtz_from_file":i=replace_map_by_mtz_from_file.apply(void 0,t);break;case"shim_set_bond_colours":i=setUserDefinedBondColours.apply(void 0,t);break;case"shim_export_map_as_gltf":i=export_map_as_gltf.apply(void 0,t);break;case"shim_export_molecule_as_gltf":i=export_molecule_as_gltf.apply(void 0,t);break;default:i=molecules_container[r].apply(molecules_container,t)}var c=void 0;switch(a){case"texture_as_floats_t":c=textureAsFloatsToJSTextureAsFloats(i);break;case"fit_ligand_info_array":c=fitLigandInfoArrayToJSArray(i);break;case"string_array_array":c=stringArrayArrayToJSArray(i);break;case"instanced_mesh_perm":c=instancedMeshToMeshData(i,!0);break;case"histogram_info_t":c=histogramInfoToJSData(i);break;case"symmetry":c=symmetryToJSData(i);break;case"mmrrcc_stats":c=mmrrccStatsToJSArray(i);break;case"colour_rules":c=colourRulesToJSArray(i);break;case"instanced_mesh_perfect_spheres":c=instancedMeshToMeshData(i,!1,!0);break;case"instanced_mesh":c=instancedMeshToMeshData(i,!1,!1,5);break;case"mesh_perm":c=simpleMeshToMeshData(i,!0);break;case"mesh":c=simpleMeshToMeshData(i);break;case"lit_lines_mesh":c=simpleMeshToLineMeshData(i,!0);break;case"lines_mesh":c=simpleMeshToLineMeshData(i,!1);break;case"float_array":c=floatArrayToJSArray(i);break;case"int_array":c=intArrayToJSArray(i);break;case"auto_read_mtz_info_array":c=autoReadMtzInfoVectToJSArray(i);break;case"map_molecule_centre_info_t":c=mapMoleculeCentreInfoToJSObject(i);break;case"string_array":c=stringArrayToJSArray(i);break;case"residue_specs":c=residueSpecToJSArray(i);break;case"atom_specs":c=atomSpecToJSArray(i);break;case"ramachandran_data":c=ramachandranDataToJSArray(i,e.chainID);break;case"validation_data":c=validationDataToJSArray(i,e.chainID);break;case"interesting_places_data":c=interestingPlaceDataToJSArray(i);break;case"superpose_results":c=SuperposeResultsToJSArray(i);break;case"generic_3d_lines_bonds_box":c=linesBoxToJSArray(i);break;case"vector_hbond":c=vectorHBondToJSArray(i);break;case"status_instanced_mesh_pair":c={status:i.first,mesh:instancedMeshToMeshData(i.second,!1,!1,5)};break;case"string_string_pair_vector":c=stringPairVectorToJSArray(i);break;case"void":c=null;break;case"vector_pair_clipper_coord_float":c=vectorPairClipperCoordFloatToJSArray(i);break;case"vector_pair_string_int":c=vectorPairStringIntToJSArray(i);break;case"privateer_results":c=privateerValidationToJSArray(i);break;default:c=i}try{i.delete()}catch(e){}return{messageId:o,messageSendTime:Date.now(),command:r,consoleMessage:"Completed ".concat(r," in ").concat(Date.now()-s," ms"),result:{status:"Completed",result:c}}}catch(e){return console.log(e),{messageId:o,myTimeStamp:s,message:n,consoleMessage:"EXCEPTION RAISED IN ".concat(r,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({locateFile:function(e){return"./wasm/".concat(e)},onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(a){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=a).molecules_container_js(!1)).set_use_gemmi(!1),molecules_container.set_show_timings(!1),molecules_container.set_refinement_is_verbose(!1),molecules_container.fill_rotamer_probability_tables(),molecules_container.set_map_sampling_rate(1.7),molecules_container.set_map_is_contoured_with_thread_pool(!0),molecules_container.set_max_number_of_threads(3),cootModule.FS.mkdir("COOT_BACKUP")})).catch((function(e){console.log(e),print(e)})),createCCP4Module({locateFile:function(e){return"./wasm/".concat(e)},onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"web_example.js",print,printErr:print}).then((function(e){ccp4Module=e})).catch((function(e){console.log(e),print(e)}));else if("close"===e.data.message)null==molecules_container||molecules_container.delete(),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Closed molecules container",message:e.data.message,result:{}});else if("get_mtz_data"===e.data.message){var a=cootModule.FS.readFile(e.data.fileName,{encoding:"binary"});postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched mtz data for map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mtzData:a}})}else if("get_map"===e.data.message){var r=guid(),t="./".concat(r,".map");molecules_container.writeCCP4Map(e.data.molNo,t);var o=cootModule.FS.readFile(t,{encoding:"binary"});cootModule.FS_unlink(t),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched map of map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mapData:o.buffer}})}else if("delete_file_name"===e.data.message){var s=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:s})}else if("coot_command_list"===e.data.message){var n=e.data.commandList.map((function(a){return doCootCommand(__assign(__assign({},e.data),a))}));postMessage({messageId:e.data.messageId,resultList:n})}"coot_command"===e.data.message&&(s=doCootCommand(e.data),postMessage(s))};
+var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var a,r=1,t=arguments.length;r<t;r++)for(var o in a=arguments[r])Object.prototype.hasOwnProperty.call(a,o)&&(e[o]=a[o]);return e},__assign.apply(this,arguments)};importScripts("./moorhen.js"),importScripts("./web_example.js");var guid=function(){var e=Date.now();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,(function(a){var r=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===a?r:3&r|8).toString(16)}))},print=function(e){console.log(e),postMessage({consoleMessage:JSON.stringify(e)})},instancedMeshToMeshData=function(e,a,r,t){void 0===r&&(r=!1),void 0===t&&(t=1e4);for(var o=[],s=[],n=[],i=[],c=[],_=[],l=[],u=[],d=[],m=e.geom,p=e.markup,g=m.size(),h=0;h<g;h++){var f=r,v=[],y=[],S=[],b=[],M=[],z=[],x=[],T=m.get(h);"spherical-atoms"===T.name&&(f=!0);for(var A=T.vertices,F=T.triangles,w=F.size(),k=0;k<w;k++){var I=F.get(k).point_id;a?(v.push(I[0]),v.push(I[2]),v.push(I[1])):(v.push(I[0]),v.push(I[1]),v.push(I[2]))}F.delete();for(var J=A.size(),D=0;D<J;D++){var C=A.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;S.push(R[0]),S.push(R[1]),S.push(R[2])}A.delete();var P=T.instancing_data_A,E=P.size();if(E>0)for(var U=0;U<E;U++){var L=(q=P.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=q.size;b.push(B[0]),b.push(B[1]),b.push(B[2]),x.push.apply(x,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}P.delete();var j=T.instancing_data_B,V=j.size();if(V>0)for(U=0;U<V;U++){var q;if(!((B=(q=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=q.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=q.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;x.push(H[0][0]),x.push(H[0][1]),x.push(H[0][2]),x.push(H[0][3]),x.push(H[1][0]),x.push(H[1][1]),x.push(H[1][2]),x.push(H[1][3]),x.push(H[2][0]),x.push(H[2][1]),x.push(H[2][2]),x.push(H[2][3]),x.push(H[3][0]),x.push(H[3][1]),x.push(H[3][2]),x.push(H[3][3])}}j.delete(),n.push(S),s.push(y),o.push(v),i.push(b),_.push(z),l.push(x),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var K=simpleMeshToMeshData(p);return K.idx_tri.length>0&&K.idx_tri[0].length>0&&K.idx_tri[0][0].length>0?r?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[_,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[s,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d],idx_tri:[o],vert_tri:[s],norm_tri:[n],col_tri:[c],instance_use_colors:[u],instance_sizes:[i],instance_origins:[_],instance_orientations:[l]}},simpleMeshToMeshData=function(e,a){void 0===a&&(a=!1),performance.now();var r=e.vertices,t=e.triangles,o=r.size(),s=t.size(),n=new Uint32Array(3*s),i=new Float32Array(3*o),c=new Float32Array(3*o),_=new Float32Array(4*o);cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getColoursFromSimpleMesh2(e,_),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,c),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,n)):(cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getTriangleIndicesFromSimpleMesh2(e,n)),performance.now();var l=i,u=_,d=c,m=n;return r.delete(),t.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[m]],vert_tri:[[l]],norm_tri:[[d]],col_tri:[[u]]}},SuperposeResultsToJSArray=function(e){for(var a=e.aligned_pairs,r=a.size(),t=[],o=0;o<r;o++){var s=a.get(o),n=s.first,i=n.residue_spec,c=s.second,_=c.residue_spec,l={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:_.chain_id,insCode:_.ins_code,seqNum:_.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(l)}return a.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}a.push(n),o.delete()}return e.delete(),a},floatArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},mapMoleculeCentreInfoToJSObject=function(e){var a=e.updated_centre,r={updated_centre:[a.x(),a.y(),a.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return a.delete(),r},textureAsFloatsToJSTextureAsFloats=function(e){var a=e.width*e.height,r=new Float32Array(a),t=performance.now();cootModule.getTextureArray(e,r);var o=performance.now();return console.log("Time to convert texture array to JS",o-t),{width:e.width,height:e.height,x_size:e.x_size,y_size:e.y_size,z_position:e.z_position,image_data:r}},fitLigandInfoArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(__assign({},o))}return e.delete(),a},intArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},export_map_as_gltf=function(e,a,r,t,o,s){var n="".concat(guid(),".glb");molecules_container.export_map_molecule_as_gltf(e,a,r,t,o,s,n);var i=cootModule.FS.readFile(n,{encoding:"binary"});return cootModule.FS_unlink(n),i.buffer},export_molecular_represenation_as_gltf=function(e,a,r,t){var o="".concat(guid(),".glb");molecules_container.export_molecular_represenation_as_gltf(e,a,r,t,o);var s=cootModule.FS.readFile(o,{encoding:"binary"});return cootModule.FS_unlink(o),s.buffer},export_molecule_as_gltf=function(e,a,r,t,o,s,n,i,c){var _="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,a,r,t,o,s,n,i,c,_);var l=cootModule.FS.readFile(_,{encoding:"binary"});return cootModule.FS_unlink(_),l.buffer},symmetryToJSData=function(e){for(var a=[],r=e.first,t=e.second,o=r.symm_trans,s=o.size(),n=0;n<s;n++){var i=o.get(n),c=i.first,_=i.second,l=t.get(n);a.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:_.us,ws:_.ws,vs:_.vs,matrix:l}),c.delete()}return o.delete(),t.delete(),a},mmrrccStatsToJSArray=function(e){var a=function(e){for(var a=[],r=e.keys(),t=r.size(),o=0;o<t;o++){var s=r.get(o),n=e.get(s);a.push({resNum:s.res_no,insCode:s.ins_code,modelNumber:s.model_number,chainId:s.chain_id,n:n.n,correlation:n.correlation()}),n.delete()}return r.delete(),a},r=e.first,t=e.second,o={"All atoms":a(r),"Side-chains":a(t)};return r.delete(),t.delete(),o},atomSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({chain_id:o.chain_id,res_no:o.res_no,ins_code:o.ins_code,atom_name:o.atom_name,alt_conf:o.alt_conf,int_user_data:o.int_user_data,float_user_data:o.float_user_data,string_user_data:o.string_user_data,model_number:o.model_number})}return e.delete(),a},residueSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({resNum:o.res_no,insCode:o.ins_code,modelNumber:o.model_number,chainId:o.chain_id,intUserData:o.int_user_data})}return e.delete(),a},stringPairVectorToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({first:o.first,second:o.second})}return e.delete(),a},validationDataToJSArray=function(e,a){void 0===a&&(a=null);for(var r=[],t=e.cviv,o=t.size(),s=0;s<o;s++){var n=t.get(s);if(null!==a&&n.chain_id!==a);else{for(var i=n.rviv,c=i.size(),_=0;_<c;_++){var l=i.get(_),u=l.residue_spec;r.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:l.function_value})}i.delete()}}return t.delete(),e.delete(),r},linesBoxToJSArray=function(e){for(var a=[],r=e.line_segments,t=r.size(),o=0;o<t;o++){for(var s=[],n=r.get(o),i=n.size(),c=0;c<i;c++){var _=n.get(c),l=_.getStart(),u=_.getFinish(),d=_.amplitude(),m={x:l.x(),y:l.y(),z:l.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),l.delete(),u.delete(),_.delete()}n.delete(),a.push(s)}return r.delete(),a},vectorHBondToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({hb_hydrogen:o.hb_hydrogen,donor:o.donor,acceptor:o.acceptor,donor_neigh:o.donor_neigh,acceptor_neigh:o.acceptor_neigh,angle_1:o.angle_1,angle_2:o.angle_2,angle_3:o.angle_3,dist:o.dist,ligand_atom_is_donor:o.ligand_atom_is_donor,hydrogen_is_ligand_atom:o.hydrogen_is_ligand_atom,bond_has_hydrogen_flag:o.bond_has_hydrogen_flag})}return e.delete(),a},interestingPlaceDataToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.residue_spec;a.push({intUserData:s.int_user_data,modelNumber:s.model_number,chainId:s.chain_id,insCode:s.ins_code,resNum:s.res_no,featureType:o.feature_type,featureValue:o.feature_value,buttonLabel:o.button_label,badness:o.badness,coordX:o.x,coordY:o.y,coordZ:o.z})}return e.delete(),a},histogramInfoToJSData=function(e){var a=e.counts;return{counts:intArrayToJSArray(a),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({idx:o.idx,F:o.F,phi:o.phi,w:o.w,weights_used:o.weights_used,Rfree:o.Rfree?o.Rfree.split("/")[3]:"",F_obs:o.F_obs?o.F_obs.split("/")[3]:"",sigF_obs:o.sigF_obs?o.sigF_obs.split("/")[3]:""})}if(e.delete(),a.some((function(e){return-1===e.idx}))){var s=a.find((function(e){return-1===e.idx}));s&&s.F_obs&&s.Rfree&&s.sigF_obs&&a.forEach((function(e){e.F_obs=s.F_obs,e.sigF_obs=s.sigF_obs,e.Rfree=s.Rfree})),a=a.filter((function(e){return-1!==e.idx}))}return a},ramachandranDataToJSArray=function(e,a){for(var r=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===a&&r.push({chainId:n.chain_id,insCode:n.ins_code,seqNum:n.residue_number,restype:s.residue_name(),isOutlier:!s.is_allowed_flag,phi:n.phi(),psi:n.psi(),is_pre_pro:"PRO"===s.residue_name()}),s.delete(),n.delete()}return e.delete(),r},vectorPairStringIntToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s={residue:o.first,slice:o.second};a.push(s)}return e.delete(),a},vectorPairClipperCoordFloatToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),a.push({value:s,coord:i})}return e.delete(),a},simpleMeshToLineMeshData=function(e,a){performance.now();var r=e.vertices,t=e.triangles,o=t.size(),s=r.size(),n=new Uint32Array(6*o),i=new Float32Array(3*s),c=new Float32Array(3*s),_=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),performance.now();var l=n,u=i,d=c,m=_;return r.delete(),t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],norm_tri:[[d]],col_tri:[[m]]}},auto_read_mtz=function(e){var a=guid(),r=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(a,".mtz"),r,!0,!0);var t="./".concat(a,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,a,r){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(a);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,r.F,r.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(o),i},new_positions_for_residue_atoms=function(e,a){var r=0,t=new cootModule.Vectormoved_residue_t;return a.forEach((function(e){if(e.length>0){var a=e[0],r=new cootModule.moved_residue_t(a.chain_id,parseInt(a.res_no),"");e.forEach((function(e){var a=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);r.add_atom(a),a.delete()})),t.push_back(r),r.delete()}})),r+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),r},read_mtz=function(e,a,r){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,r.F,r.PHI,"",!1,r.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,a,r,t,o){var s=new Uint8Array(a.data);cootModule.FS_createDataFile(".","".concat(a.fileName,".mtz"),s,!0,!0);var n="./".concat(a.fileName,".mtz"),i=[e,n,r,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,a,r){var t=guid(),o=new Uint8Array(e),s="";a.endsWith(".map.gz")?s="map.gz":a.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,r],c=-1;try{c=molecules_container.read_ccp4_map.apply(molecules_container,i)}catch(e){console.warn(e)}finally{cootModule.FS_unlink(n)}return c},setUserDefinedBondColours=function(e,a,r){void 0===r&&(r=!1);var t=new cootModule.MapIntFloat3,o=new cootModule.VectorStringUInt_pair;a.forEach((function(e,a){t.set(a+51,e.rgb);var r={first:e.cid,second:a+51};o.push_back(r)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,r),o.delete(),t.delete()},privateerValidationToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=[],n=o.torsions,i=n.size(),c=0;c<i;c++)s.push(n.get(c));n.delete();var _={torsions:s,svg:o.svg.replace(/: *32/g,""),id:o.id.replace(/: *32/g,""),chain:o.chain,wurcs:o.wurcs,glyconnect_id:o.glyconnect_id,glytoucan_id:o.glytoucan_id,torsion_err:o.torsion_err,anomer_err:o.anomer_err,conformation_err:o.conformation_err,puckering_err:o.puckering_err,chirality_err:o.chirality_err};a.push(_)}return e.delete(),a},doCootCommand=function(e){var a=e.returnType,r=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(r){case"shim_new_positions_for_residue_atoms":i=new_positions_for_residue_atoms.apply(void 0,t);break;case"shim_read_mtz":i=read_mtz.apply(void 0,t);break;case"shim_auto_read_mtz":i=auto_read_mtz.apply(void 0,t);break;case"shim_read_ccp4_map":i=read_ccp4_map.apply(void 0,t);break;case"shim_associate_data_mtz_file_with_map":i=associate_data_mtz_file_with_map.apply(void 0,t);break;case"shim_replace_map_by_mtz_from_file":i=replace_map_by_mtz_from_file.apply(void 0,t);break;case"shim_set_bond_colours":i=setUserDefinedBondColours.apply(void 0,t);break;case"shim_export_map_as_gltf":i=export_map_as_gltf.apply(void 0,t);break;case"shim_export_molecule_as_gltf":i=export_molecule_as_gltf.apply(void 0,t);break;case"shim_export_molecular_represenation_as_gltf":i=export_molecular_represenation_as_gltf.apply(void 0,t);break;default:i=molecules_container[r].apply(molecules_container,t)}var c=void 0;switch(a){case"texture_as_floats_t":c=textureAsFloatsToJSTextureAsFloats(i);break;case"fit_ligand_info_array":c=fitLigandInfoArrayToJSArray(i);break;case"string_array_array":c=stringArrayArrayToJSArray(i);break;case"instanced_mesh_perm":c=instancedMeshToMeshData(i,!0);break;case"histogram_info_t":c=histogramInfoToJSData(i);break;case"symmetry":c=symmetryToJSData(i);break;case"mmrrcc_stats":c=mmrrccStatsToJSArray(i);break;case"colour_rules":c=colourRulesToJSArray(i);break;case"instanced_mesh_perfect_spheres":c=instancedMeshToMeshData(i,!1,!0);break;case"instanced_mesh":c=instancedMeshToMeshData(i,!1,!1,5);break;case"mesh_perm":c=simpleMeshToMeshData(i,!0);break;case"mesh":c=simpleMeshToMeshData(i);break;case"lit_lines_mesh":c=simpleMeshToLineMeshData(i,!0);break;case"lines_mesh":c=simpleMeshToLineMeshData(i,!1);break;case"float_array":c=floatArrayToJSArray(i);break;case"int_array":c=intArrayToJSArray(i);break;case"auto_read_mtz_info_array":c=autoReadMtzInfoVectToJSArray(i);break;case"map_molecule_centre_info_t":c=mapMoleculeCentreInfoToJSObject(i);break;case"string_array":c=stringArrayToJSArray(i);break;case"residue_specs":c=residueSpecToJSArray(i);break;case"atom_specs":c=atomSpecToJSArray(i);break;case"ramachandran_data":c=ramachandranDataToJSArray(i,e.chainID);break;case"validation_data":c=validationDataToJSArray(i,e.chainID);break;case"interesting_places_data":c=interestingPlaceDataToJSArray(i);break;case"superpose_results":c=SuperposeResultsToJSArray(i);break;case"generic_3d_lines_bonds_box":c=linesBoxToJSArray(i);break;case"vector_hbond":c=vectorHBondToJSArray(i);break;case"status_instanced_mesh_pair":c={status:i.first,mesh:instancedMeshToMeshData(i.second,!1,!1,5)};break;case"string_string_pair_vector":c=stringPairVectorToJSArray(i);break;case"void":c=null;break;case"vector_pair_clipper_coord_float":c=vectorPairClipperCoordFloatToJSArray(i);break;case"vector_pair_string_int":c=vectorPairStringIntToJSArray(i);break;case"privateer_results":c=privateerValidationToJSArray(i);break;default:c=i}try{i.delete()}catch(e){}return{messageId:o,messageSendTime:Date.now(),command:r,consoleMessage:"Completed ".concat(r," in ").concat(Date.now()-s," ms"),result:{status:"Completed",result:c}}}catch(e){return console.log(e),{messageId:o,myTimeStamp:s,message:n,consoleMessage:"EXCEPTION RAISED IN ".concat(r,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(a){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=a).molecules_container_js(!1)).set_use_gemmi(!1),molecules_container.set_show_timings(!1),molecules_container.set_refinement_is_verbose(!1),molecules_container.fill_rotamer_probability_tables(),molecules_container.set_map_sampling_rate(1.7),molecules_container.set_map_is_contoured_with_thread_pool(!0),molecules_container.set_max_number_of_threads(3),cootModule.FS.mkdir("COOT_BACKUP")})).catch((function(e){console.log(e),print(e)})),createCCP4Module({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"web_example.js",print,printErr:print}).then((function(e){ccp4Module=e})).catch((function(e){console.log(e),print(e)}));else if("close"===e.data.message)null==molecules_container||molecules_container.delete(),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Closed molecules container",message:e.data.message,result:{}});else if("get_mtz_data"===e.data.message){var a=cootModule.FS.readFile(e.data.fileName,{encoding:"binary"});postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched mtz data for map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mtzData:a}})}else if("get_map"===e.data.message){var r=guid(),t="./".concat(r,".map");molecules_container.writeCCP4Map(e.data.molNo,t);var o=cootModule.FS.readFile(t,{encoding:"binary"});cootModule.FS_unlink(t),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched map of map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mapData:o.buffer}})}else if("delete_file_name"===e.data.message){var s=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:s})}else if("coot_command_list"===e.data.message){var n=e.data.commandList.map((function(a){return doCootCommand(__assign(__assign({},e.data),a))}));postMessage({messageId:e.data.messageId,resultList:n})}"coot_command"===e.data.message&&(s=doCootCommand(e.data),postMessage(s))};

package/baby-gru/CootWorker.ts

@@ -3,9 +3,9 @@ import { emscriptem } from "../../src/types/emscriptem"
 import { privateer } from "../../src/types/privateer";
 
 // @ts-ignore
-importScripts('./wasm/moorhen.js')
+importScripts('./moorhen.js')
 // @ts-ignore
-importScripts('./wasm/web_example.js')
+importScripts('./web_example.js')
 
 let cootModule: libcootApi.CootModule;
 let molecules_container: libcootApi.MoleculesContainerJS;
@@ -381,16 +381,14 @@ const mapMoleculeCentreInfoToJSObject = (mapMoleculeCentreInfo: libcootApi.MapMo
 
 const textureAsFloatsToJSTextureAsFloats = (data:libcootApi.textureAsFloats): libcootApi.textureAsFloatsJS => {
 
-    let image_data = []
+    const imageDataVecSize = data.width * data.height
 
-    const imageDataVecSize = data.image_data.size()
-    console.log(imageDataVecSize);
-    for (let i = 0; i < imageDataVecSize; i++) {
-        const texVal = data.image_data.get(i)
-        image_data.push(texVal)
-    }
+    let image_data = new Float32Array(imageDataVecSize)
 
-    data.image_data.delete()
+    const t1 = performance.now()
+    cootModule.getTextureArray(data,image_data)
+    const t2 = performance.now()
+    console.log("Time to convert texture array to JS",t2-t1)
 
     return {
         width:data.width,
@@ -445,6 +443,14 @@ const export_map_as_gltf = (imol: number, x: number, y: number, z: number, radiu
     return fileContents.buffer
 }
 
+const export_molecular_represenation_as_gltf = (imol: number, cid: string, colourScheme: string, style: string) => {
+    const fileName = `${guid()}.glb`
+    molecules_container.export_molecular_represenation_as_gltf(imol, cid, colourScheme, style, fileName)
+    const fileContents = cootModule.FS.readFile(fileName, { encoding: 'binary' }) as Uint8Array
+    cootModule.FS_unlink(fileName)
+    return fileContents.buffer
+}
+
 const export_molecule_as_gltf = (
     imol: number, cid: string, mode: string, isDark: boolean, bondWidth: number, 
     atomRadius: number, bondSmoothness: number, drawHydrogens: boolean, drawMissingResidues: boolean
@@ -863,7 +869,7 @@ const simpleMeshToLineMeshData = (simpleMesh: libcootApi.SimpleMeshT, normalLigh
 
 }
 
-const auto_open_mtz = (mtzData: ArrayBufferLike) => {
+const auto_read_mtz = (mtzData: ArrayBufferLike) => {
     const theGuid = guid()
     const asUint8Array = new Uint8Array(mtzData)
     cootModule.FS_createDataFile(".", `${theGuid}.mtz`, asUint8Array, true, true);
@@ -1035,8 +1041,8 @@ const doCootCommand = (messageData: {
             case 'shim_read_mtz':
                 cootResult = read_mtz(...commandArgs as [ArrayBufferLike, string, { F: string; PHI: string; isDifference: boolean; }])
                 break
-            case 'shim_auto_open_mtz':
-                cootResult = auto_open_mtz(...commandArgs as [ArrayBuffer])
+            case 'shim_auto_read_mtz':
+                cootResult = auto_read_mtz(...commandArgs as [ArrayBuffer])
                 break
             case 'shim_read_ccp4_map':
                 cootResult = read_ccp4_map(...commandArgs as [ArrayBuffer, string, boolean])
@@ -1056,6 +1062,9 @@ const doCootCommand = (messageData: {
             case 'shim_export_molecule_as_gltf':
                 cootResult = export_molecule_as_gltf(...commandArgs as [number, string, string, boolean, number, number, number, boolean, boolean])
                 break
+            case 'shim_export_molecular_represenation_as_gltf':
+                cootResult = export_molecular_represenation_as_gltf(...commandArgs as [number, string, string, string])
+                break
             default:
                 cootResult = molecules_container[command](...commandArgs)
                 break
@@ -1194,7 +1203,6 @@ const doCootCommand = (messageData: {
 onmessage = function (e) {
     if (e.data.message === 'CootInitialize') {
         createRSRModule({
-            locateFile: (file) => `./wasm/${file}`,
             onRuntimeInitialized: () => { },
             mainScriptUrlOrBlob: "moorhen.js",
             print: print,
@@ -1219,7 +1227,6 @@ onmessage = function (e) {
             });
         
         createCCP4Module({
-            locateFile: (file) => `./wasm/${file}`,
             onRuntimeInitialized: () => { },
             mainScriptUrlOrBlob: "web_example.js",
             print: print,

package/baby-gru/{wasm/moorhen.data → moorhen.data}

@@ -248008,86 +248008,86 @@ ATOM      4  O   VAL A 879       0.790  -0.922  -2.071  1.00 20.00           O
 ATOM      5  CB  VAL A 879      -0.945   1.215  -0.037  1.00 20.00           C  
 ATOM      6  CG1 VAL A 879      -1.704   1.260  -1.354  1.00 20.00           C  
 ATOM      7  CG2 VAL A 879      -1.908   1.177   1.140  1.00 20.00           C  
-ATOM      1  P    Gr A  14       2.827  -8.060   3.719  1.00 76.88           P  
-ATOM      2  O1P  Gr A  14       3.083  -8.927   4.896  1.00 78.59           O  
-ATOM      3  O2P  Gr A  14       1.855  -6.954   3.766  1.00 75.20           O  
-ATOM      4  O5*  Gr A  14       4.220  -7.417   3.279  1.00 78.76           O  
-ATOM      5  C5*  Gr A  14       5.490  -8.037   3.534  1.00 77.93           C  
-ATOM      6  C4*  Gr A  14       6.617  -7.075   3.190  1.00 78.66           C  
-ATOM      7  O4*  Gr A  14       6.505  -6.592   1.808  1.00 79.49           O  
-ATOM      8  C3*  Gr A  14       6.678  -5.807   4.033  1.00 78.23           C  
-ATOM      9  O3*  Gr A  14       7.315  -6.088   5.287  1.00 77.17           O  
-ATOM     10  C2*  Gr A  14       7.473  -4.888   3.087  1.00 79.34           C  
-ATOM     11  O2*  Gr A  14       8.870  -5.158   3.018  1.00 79.34           O  
-ATOM     12  C1*  Gr A  14       6.853  -5.219   1.725  1.00 78.22           C  
-ATOM     13  N9   Gr A  14       5.696  -4.394   1.332  1.00 78.19           N  
-ATOM     14  C8   Gr A  14       4.394  -4.807   1.165  1.00 77.84           C  
-ATOM     15  N7   Gr A  14       3.574  -3.845   0.802  1.00 78.55           N  
-ATOM     16  C5   Gr A  14       4.374  -2.712   0.715  1.00 78.01           C  
-ATOM     17  C6   Gr A  14       4.038  -1.373   0.382  1.00 77.95           C  
-ATOM     18  O6   Gr A  14       2.926  -0.912   0.076  1.00 77.77           O  
-ATOM     19  N1   Gr A  14       5.148  -0.527   0.422  1.00 77.73           N  
-ATOM     20  C2   Gr A  14       6.418  -0.922   0.750  1.00 77.58           C  
-ATOM     21  N2   Gr A  14       7.361   0.015   0.736  1.00 77.71           N  
-ATOM     22  N3   Gr A  14       6.743  -2.164   1.070  1.00 78.53           N  
-ATOM     23  C4   Gr A  14       5.680  -3.024   1.040  1.00 78.73           C  
-ATOM    101  P    Ad A   6      13.954  12.080  15.071  1.00 12.41           P  
-ATOM    102  O1P  Ad A   6      13.092  11.246  15.953  1.00 12.12           O  
-ATOM    103  O2P  Ad A   6      14.769  11.453  14.020  1.00 13.04           O  
-ATOM    104  O5*  Ad A   6      13.056  13.202  14.406  1.00 10.42           O  
-ATOM    105  C5*  Ad A   6      12.184  13.965  15.222  1.00  8.93           C  
-ATOM    106  C4*  Ad A   6      11.308  14.846  14.376  1.00  7.26           C  
-ATOM    107  O4*  Ad A   6      12.033  15.991  13.896  1.00  8.21           O  
-ATOM    108  C3*  Ad A   6      10.654  14.188  13.168  1.00  7.65           C  
-ATOM    109  O3*  Ad A   6       9.262  14.480  13.256  1.00  8.46           O  
-ATOM    110  C2*  Ad A   6      11.373  14.820  11.974  1.00  6.69           C  
-ATOM    111  C1*  Ad A   6      11.810  16.184  12.511  1.00  7.12           C  
-ATOM    112  N9   Ad A   6      13.051  16.742  11.953  1.00  9.06           N  
-ATOM    113  C8   Ad A   6      14.253  16.097  11.802  1.00  7.73           C  
-ATOM    114  N7   Ad A   6      15.197  16.853  11.305  1.00  8.04           N  
-ATOM    115  C5   Ad A   6      14.585  18.084  11.106  1.00  6.10           C  
-ATOM    116  C6   Ad A   6      15.066  19.322  10.605  1.00  5.87           C  
-ATOM    117  N6   Ad A   6      16.329  19.520  10.209  1.00  5.88           N  
-ATOM    118  N1   Ad A   6      14.198  20.357  10.535  1.00  5.73           N  
-ATOM    119  C2   Ad A   6      12.938  20.162  10.946  1.00  5.41           C  
-ATOM    120  N3   Ad A   6      12.370  19.048  11.444  1.00  9.07           N  
-ATOM    121  C4   Ad A   6      13.259  18.034  11.497  1.00  6.34           C  
-ATOM    122  P    Td A   7       8.258  14.006  12.104  1.00  8.61           P  
-ATOM    123  O1P  Td A   7       6.947  13.813  12.710  1.00  9.62           O  
-ATOM    124  O2P  Td A   7       8.856  12.940  11.281  1.00  9.62           O  
-ATOM    125  O5*  Td A   7       8.163  15.293  11.202  1.00  8.95           O  
-ATOM    126  C5*  Td A   7       7.907  16.566  11.799  1.00  7.95           C  
-ATOM    127  C4*  Td A   7       8.036  17.644  10.754  1.00  9.61           C  
-ATOM    128  O4*  Td A   7       9.413  17.875  10.402  1.00  9.78           O  
-ATOM    129  C3*  Td A   7       7.286  17.382   9.446  1.00 10.94           C  
-ATOM    130  O3*  Td A   7       6.228  18.341   9.347  1.00 11.97           O  
-ATOM    131  C2*  Td A   7       8.356  17.467   8.358  1.00  9.86           C  
-ATOM    132  C1*  Td A   7       9.471  18.252   9.036  1.00  8.76           C  
-ATOM    133  N1   Td A   7      10.850  18.009   8.588  1.00  7.75           N  
-ATOM    134  C2   Td A   7      11.576  19.096   8.121  1.00  7.10           C  
-ATOM    135  O2   Td A   7      11.113  20.233   8.017  1.00  8.86           O  
-ATOM    136  N3   Td A   7      12.874  18.803   7.780  1.00  7.27           N  
-ATOM    137  C4   Td A   7      13.507  17.588   7.844  1.00  6.07           C  
-ATOM    138  O4   Td A   7      14.687  17.499   7.508  1.00  7.68           O  
-ATOM    139  C5   Td A   7      12.689  16.491   8.322  1.00  6.88           C  
-ATOM    140  C5M  Td A   7      13.292  15.128   8.424  1.00  7.98           C  
-ATOM    141  C6   Td A   7      11.414  16.754   8.659  1.00  7.78           C  
-ATOM      4  O5*  Ur A   1       0.270  -7.725  -1.830  1.00 20.00           C  
-ATOM      5  O3*  Ur A   1       4.189  -7.682  -0.250  1.00 20.00           O  
-ATOM      6  C1*  Ur A   1       2.252  -5.410  -0.470  1.00 20.00           C  
-ATOM      7  C2*  Ur A   1       2.035  -6.740   0.240  1.00 20.00           C  
-ATOM      8  C3*  Ur A   1       2.818  -7.701  -0.640  1.00 20.00           C  
-ATOM      9  C4*  Ur A   1       2.608  -7.128  -2.040  1.00 20.00           C  
-ATOM     10  C5*  Ur A   1       1.364  -7.578  -2.770  1.00 20.00           C  
-ATOM     11  O4*  Ur A   1       2.530  -5.682  -1.830  1.00 20.00           O  
-ATOM     12  O4   Ur A   1      -2.039  -1.948  -0.270  1.00 20.00           O  
-ATOM     13  C4   Ur A   1      -1.112  -2.765  -0.320  1.00 20.00           C  
-ATOM     14  N3   Ur A   1       0.197  -2.352  -0.230  1.00 20.00           N  
-ATOM     15  C2   Ur A   1       1.320  -3.155  -0.270  1.00 20.00           C  
-ATOM     16  O2   Ur A   1       2.445  -2.697  -0.180  1.00 20.00           O  
-ATOM     17  N1   Ur A   1       1.073  -4.504  -0.420  1.00 20.00           N  
-ATOM     18  C6   Ur A   1      -0.201  -5.006  -0.520  1.00 20.00           C  
-ATOM     19  C5   Ur A   1      -1.273  -4.191  -0.470  1.00 20.00           C  
+ATOM      1  P     G A  14       2.827  -8.060   3.719  1.00 76.88           P  
+ATOM      2  O1P   G A  14       3.083  -8.927   4.896  1.00 78.59           O  
+ATOM      3  O2P   G A  14       1.855  -6.954   3.766  1.00 75.20           O  
+ATOM      4  O5'   G A  14       4.220  -7.417   3.279  1.00 78.76           O  
+ATOM      5  C5'   G A  14       5.490  -8.037   3.534  1.00 77.93           C  
+ATOM      6  C4'   G A  14       6.617  -7.075   3.190  1.00 78.66           C  
+ATOM      7  O4'   G A  14       6.505  -6.592   1.808  1.00 79.49           O  
+ATOM      8  C3'   G A  14       6.678  -5.807   4.033  1.00 78.23           C  
+ATOM      9  O3'   G A  14       7.315  -6.088   5.287  1.00 77.17           O  
+ATOM     10  C2'   G A  14       7.473  -4.888   3.087  1.00 79.34           C  
+ATOM     11  O2'   G A  14       8.870  -5.158   3.018  1.00 79.34           O  
+ATOM     12  C1'   G A  14       6.853  -5.219   1.725  1.00 78.22           C  
+ATOM     13  N9    G A  14       5.696  -4.394   1.332  1.00 78.19           N  
+ATOM     14  C8    G A  14       4.394  -4.807   1.165  1.00 77.84           C  
+ATOM     15  N7    G A  14       3.574  -3.845   0.802  1.00 78.55           N  
+ATOM     16  C5    G A  14       4.374  -2.712   0.715  1.00 78.01           C  
+ATOM     17  C6    G A  14       4.038  -1.373   0.382  1.00 77.95           C  
+ATOM     18  O6    G A  14       2.926  -0.912   0.076  1.00 77.77           O  
+ATOM     19  N1    G A  14       5.148  -0.527   0.422  1.00 77.73           N  
+ATOM     20  C2    G A  14       6.418  -0.922   0.750  1.00 77.58           C  
+ATOM     21  N2    G A  14       7.361   0.015   0.736  1.00 77.71           N  
+ATOM     22  N3    G A  14       6.743  -2.164   1.070  1.00 78.53           N  
+ATOM     23  C4    G A  14       5.680  -3.024   1.040  1.00 78.73           C  
+ATOM    101  P    DA A   6      13.954  12.080  15.071  1.00 12.41           P  
+ATOM    102  O1P  DA A   6      13.092  11.246  15.953  1.00 12.12           O  
+ATOM    103  O2P  DA A   6      14.769  11.453  14.020  1.00 13.04           O  
+ATOM    104  O5'  DA A   6      13.056  13.202  14.406  1.00 10.42           O  
+ATOM    105  C5'  DA A   6      12.184  13.965  15.222  1.00  8.93           C  
+ATOM    106  C4'  DA A   6      11.308  14.846  14.376  1.00  7.26           C  
+ATOM    107  O4'  DA A   6      12.033  15.991  13.896  1.00  8.21           O  
+ATOM    108  C3'  DA A   6      10.654  14.188  13.168  1.00  7.65           C  
+ATOM    109  O3'  DA A   6       9.262  14.480  13.256  1.00  8.46           O  
+ATOM    110  C2'  DA A   6      11.373  14.820  11.974  1.00  6.69           C  
+ATOM    111  C1'  DA A   6      11.810  16.184  12.511  1.00  7.12           C  
+ATOM    112  N9   DA A   6      13.051  16.742  11.953  1.00  9.06           N  
+ATOM    113  C8   DA A   6      14.253  16.097  11.802  1.00  7.73           C  
+ATOM    114  N7   DA A   6      15.197  16.853  11.305  1.00  8.04           N  
+ATOM    115  C5   DA A   6      14.585  18.084  11.106  1.00  6.10           C  
+ATOM    116  C6   DA A   6      15.066  19.322  10.605  1.00  5.87           C  
+ATOM    117  N6   DA A   6      16.329  19.520  10.209  1.00  5.88           N  
+ATOM    118  N1   DA A   6      14.198  20.357  10.535  1.00  5.73           N  
+ATOM    119  C2   DA A   6      12.938  20.162  10.946  1.00  5.41           C  
+ATOM    120  N3   DA A   6      12.370  19.048  11.444  1.00  9.07           N  
+ATOM    121  C4   DA A   6      13.259  18.034  11.497  1.00  6.34           C  
+ATOM    122  P    DT A   7       8.258  14.006  12.104  1.00  8.61           P  
+ATOM    123  O1P  DT A   7       6.947  13.813  12.710  1.00  9.62           O  
+ATOM    124  O2P  DT A   7       8.856  12.940  11.281  1.00  9.62           O  
+ATOM    125  O5'  DT A   7       8.163  15.293  11.202  1.00  8.95           O  
+ATOM    126  C5'  DT A   7       7.907  16.566  11.799  1.00  7.95           C  
+ATOM    127  C4'  DT A   7       8.036  17.644  10.754  1.00  9.61           C  
+ATOM    128  O4'  DT A   7       9.413  17.875  10.402  1.00  9.78           O  
+ATOM    129  C3'  DT A   7       7.286  17.382   9.446  1.00 10.94           C  
+ATOM    130  O3'  DT A   7       6.228  18.341   9.347  1.00 11.97           O  
+ATOM    131  C2'  DT A   7       8.356  17.467   8.358  1.00  9.86           C  
+ATOM    132  C1'  DT A   7       9.471  18.252   9.036  1.00  8.76           C  
+ATOM    133  N1   DT A   7      10.850  18.009   8.588  1.00  7.75           N  
+ATOM    134  C2   DT A   7      11.576  19.096   8.121  1.00  7.10           C  
+ATOM    135  O2   DT A   7      11.113  20.233   8.017  1.00  8.86           O  
+ATOM    136  N3   DT A   7      12.874  18.803   7.780  1.00  7.27           N  
+ATOM    137  C4   DT A   7      13.507  17.588   7.844  1.00  6.07           C  
+ATOM    138  O4   DT A   7      14.687  17.499   7.508  1.00  7.68           O  
+ATOM    139  C5   DT A   7      12.689  16.491   8.322  1.00  6.88           C  
+ATOM    140  C5M  DT A   7      13.292  15.128   8.424  1.00  7.98           C  
+ATOM    141  C6   DT A   7      11.414  16.754   8.659  1.00  7.78           C  
+ATOM      4  O5'   U A   1       0.270  -7.725  -1.830  1.00 20.00           C  
+ATOM      5  O3'   U A   1       4.189  -7.682  -0.250  1.00 20.00           O  
+ATOM      6  C1'   U A   1       2.252  -5.410  -0.470  1.00 20.00           C  
+ATOM      7  C2'   U A   1       2.035  -6.740   0.240  1.00 20.00           C  
+ATOM      8  C3'   U A   1       2.818  -7.701  -0.640  1.00 20.00           C  
+ATOM      9  C4'   U A   1       2.608  -7.128  -2.040  1.00 20.00           C  
+ATOM     10  C5'   U A   1       1.364  -7.578  -2.770  1.00 20.00           C  
+ATOM     11  O4'   U A   1       2.530  -5.682  -1.830  1.00 20.00           O  
+ATOM     12  O4    U A   1      -2.039  -1.948  -0.270  1.00 20.00           O  
+ATOM     13  C4    U A   1      -1.112  -2.765  -0.320  1.00 20.00           C  
+ATOM     14  N3    U A   1       0.197  -2.352  -0.230  1.00 20.00           N  
+ATOM     15  C2    U A   1       1.320  -3.155  -0.270  1.00 20.00           C  
+ATOM     16  O2    U A   1       2.445  -2.697  -0.180  1.00 20.00           O  
+ATOM     17  N1    U A   1       1.073  -4.504  -0.420  1.00 20.00           N  
+ATOM     18  C6    U A   1      -0.201  -5.006  -0.520  1.00 20.00           C  
+ATOM     19  C5    U A   1      -1.273  -4.191  -0.470  1.00 20.00           C  
 ATOM      1  N   CIS A  21      67.090  -2.052   8.023  1.00  9.75           N  
 ATOM      2  CA  CIS A  21      66.837  -1.688   9.412  1.00 10.96           C  
 ATOM      3  C   CIS A  21      66.455  -2.909  10.241  1.00 12.66           C  
@@ -248104,109 +248104,109 @@ ATOM    147  N   TNS F  22      64.888  -1.819   9.413  1.00 12.20           N
 ATOM    148  CA  TNS F  22      63.583  -2.402   9.699  1.00 12.31           C  
 ATOM    153  C   TNS F  22      63.405  -3.736   8.983  1.00 13.23           C  
 ATOM    154  O   TNS F  22      63.020  -4.733   9.594  1.00 13.30           O  
-ATOM     93  P    Cd B   4      -0.807  -8.873  -2.081  1.00 20.00           P  
-ATOM     94  O1P  Cd B   4      -0.196 -10.199  -1.861  1.00 20.00           O  
-ATOM     95  O2P  Cd B   4      -2.030  -8.583  -1.291  1.00 20.00           O  
-ATOM     96  O5*  Cd B   4       0.270  -7.725  -1.831  1.00 20.00           O  
-ATOM     97  O3*  Cd B   4       4.189  -7.682  -0.251  1.00 20.00           O  
-ATOM     98  C1*  Cd B   4       2.252  -5.410  -0.471  1.00 20.00           C  
-ATOM     99  C2*  Cd B   4       2.035  -6.740   0.239  1.00 20.00           C  
-ATOM    100  C3*  Cd B   4       2.818  -7.701  -0.641  1.00 20.00           C  
-ATOM    101  C4*  Cd B   4       2.607  -7.128  -2.041  1.00 20.00           C  
-ATOM    102  C5*  Cd B   4       1.364  -7.578  -2.771  1.00 20.00           C  
-ATOM    103  O4*  Cd B   4       2.530  -5.682  -1.831  1.00 20.00           O  
-ATOM    104  N4   Cd B   4      -2.005  -1.896  -0.271  1.00 20.00           N  
-ATOM    105  C4   Cd B   4      -1.006  -2.763  -0.321  1.00 20.00           C  
-ATOM    106  N3   Cd B   4       0.245  -2.297  -0.221  1.00 20.00           N  
-ATOM    107  C2   Cd B   4       1.307  -3.139  -0.271  1.00 20.00           C  
-ATOM    108  O2   Cd B   4       2.474  -2.738  -0.181  1.00 20.00           O  
-ATOM    109  N1   Cd B   4       1.073  -4.504  -0.421  1.00 20.00           N  
-ATOM    110  C6   Cd B   4      -0.192  -4.986  -0.521  1.00 20.00           C  
-ATOM    111  C5   Cd B   4      -1.272  -4.160  -0.471  1.00 20.00           C  
-ATOM     93  P    Xr B   5      -0.449  -9.609   3.122  1.00 20.00           P
-ATOM     94  O1P  Xr B   5       0.162 -10.935   3.342  1.00 20.00           O
-ATOM     95  O2P  Xr B   5      -1.672  -9.319   3.912  1.00 20.00           O
-ATOM     96  O5*  Xr B   5       0.628  -8.461   3.372  1.00 20.00           O
-ATOM     97  O3*  Xr B   5       4.547  -8.418   4.952  1.00 20.00           O
-ATOM     98  C1*  Xr B   5       2.610  -6.146   4.732  1.00 20.00           C
-ATOM     99  C2*  Xr B   5       2.393  -7.476   5.442  1.00 20.00           C
-ATOM     99  O2*  Xr B   5       2.907  -7.413   6.758  1.00 20.00           O
-ATOM    100  C3*  Xr B   5       3.176  -8.437   4.562  1.00 20.00           C
-ATOM    101  C4*  Xr B   5       2.965  -7.864   3.162  1.00 20.00           C
-ATOM    102  C5*  Xr B   5       1.722  -8.314   2.432  1.00 20.00           C
-ATOM    103  O4*  Xr B   5       2.888  -6.418   3.372  1.00 20.00           O
-ATOM    104  N4   Xr B   5      -1.647  -2.632   4.932  1.00 20.00           N
-ATOM    105  C4   Xr B   5      -0.648  -3.499   4.882  1.00 20.00           C
-ATOM    106  N3   Xr B   5       0.603  -3.033   4.982  1.00 20.00           N
-ATOM    107  C2   Xr B   5       1.665  -3.875   4.932  1.00 20.00           C
-ATOM    108  O2   Xr B   5       2.832  -3.474   5.022  1.00 20.00           O
-ATOM    109  N1   Xr B   5       1.431  -5.240   4.782  1.00 20.00           N
-ATOM    110  C6   Xr B   5       0.166  -5.722   4.682  1.00 20.00           C
-ATOM    111  C5   Xr B   5      -0.914  -4.896   4.732  1.00 20.00           C
-ATOM     21  P    Cr Q   2      -6.082  -7.578   5.445  1.00 20.00      Q    P  
-ATOM     22  O1P  Cr Q   2      -7.533  -7.624   5.771  1.00 20.00      Q    O  
-ATOM     23  O2P  Cr Q   2      -5.156  -6.839   6.329  1.00 20.00      Q    O  
-ATOM     24  O5*  Cr Q   2      -5.573  -9.094   5.389  1.00 20.00      Q    O  
-ATOM     25  C5*  Cr Q   2      -6.453 -10.176   5.763  1.00 20.00      Q    C  
-ATOM     26  C4*  Cr Q   2      -5.695 -11.355   6.372  1.00 20.00      Q    C  
-ATOM     27  O4*  Cr Q   2      -4.841 -11.970   5.378  1.00 20.00      Q    O  
-ATOM     28  C1*  Cr Q   2      -3.715 -12.552   6.012  1.00 20.00      Q    C  
-ATOM     29  N1   Cr Q   2      -2.517 -11.849   5.539  1.00 20.00      Q    N  
-ATOM     30  C6   Cr Q   2      -2.608 -10.568   5.075  1.00 20.00      Q    C  
-ATOM     31  C2   Cr Q   2      -1.282 -12.505   5.564  1.00 20.00      Q    C  
-ATOM     32  O2   Cr Q   2      -1.229 -13.666   6.009  1.00 20.00      Q    O  
-ATOM     33  N3   Cr Q   2      -0.187 -11.859   5.106  1.00 20.00      Q    N  
-ATOM     34  C4   Cr Q   2      -0.292 -10.611   4.645  1.00 20.00      Q    C  
-ATOM     35  N4   Cr Q   2       0.815 -10.019   4.194  1.00 20.00      Q    N  
-ATOM     36  C5   Cr Q   2      -1.537  -9.920   4.625  1.00 20.00      Q    C  
-ATOM     37  C2*  Cr Q   2      -3.929 -12.413   7.517  1.00 20.00      Q    C  
-ATOM     38  O2*  Cr Q   2      -4.616 -13.546   7.991  1.00 20.00      Q    O  
-ATOM     39  C3*  Cr Q   2      -4.799 -11.168   7.591  1.00 20.00      Q    C  
-ATOM     40  O3*  Cr Q   2      -5.600 -11.193   8.766  1.00 20.00      Q    O  
-ATOM     41  P    Ar Q   3      -4.940 -11.446  10.232  1.00 20.00      Q    P  
-ATOM     42  O1P  Ar Q   3      -6.007 -12.136  11.012  1.00 20.00      Q    O  
-ATOM     43  O2P  Ar Q   3      -4.345 -10.197  10.770  1.00 20.00      Q    O  
-ATOM     44  O5*  Ar Q   3      -3.787 -12.546  10.091  1.00 20.00      Q    O  
-ATOM     45  C5*  Ar Q   3      -3.983 -13.848  10.656  1.00 20.00      Q    C  
-ATOM     46  C4*  Ar Q   3      -2.675 -14.512  11.030  1.00 20.00      Q    C  
-ATOM     47  O4*  Ar Q   3      -1.864 -14.738   9.853  1.00 20.00      Q    O  
-ATOM     48  C1*  Ar Q   3      -0.503 -14.773  10.233  1.00 20.00      Q    C  
-ATOM     49  N9   Ar Q   3       0.189 -13.720   9.488  1.00 20.00      Q    N  
-ATOM     50  C4   Ar Q   3       1.525 -13.615   9.179  1.00 20.00      Q    C  
-ATOM     51  N3   Ar Q   3       2.522 -14.454   9.499  1.00 20.00      Q    N  
-ATOM     52  C2   Ar Q   3       3.686 -14.006   9.027  1.00 20.00      Q    C  
-ATOM     53  N1   Ar Q   3       3.943 -12.897   8.322  1.00 20.00      Q    N  
-ATOM     54  C6   Ar Q   3       2.915 -12.078   8.016  1.00 20.00      Q    C  
-ATOM     55  N6   Ar Q   3       3.159 -10.968   7.311  1.00 20.00      Q    N  
-ATOM     56  C5   Ar Q   3       1.637 -12.436   8.457  1.00 20.00      Q    C  
-ATOM     57  N7   Ar Q   3       0.405 -11.826   8.317  1.00 20.00      Q    N  
-ATOM     58  C8   Ar Q   3      -0.418 -12.624   8.946  1.00 20.00      Q    C  
-ATOM     59  C2*  Ar Q   3      -0.451 -14.600  11.753  1.00 20.00      Q    C  
-ATOM     60  O2*  Ar Q   3      -0.415 -15.878  12.347  1.00 20.00      Q    O  
-ATOM     61  C3*  Ar Q   3      -1.743 -13.844  12.032  1.00 20.00      Q    C  
-ATOM     62  O3*  Ar Q   3      -2.242 -14.105  13.347  1.00 20.00      Q    O  
-ATOM      1  P    Gd R   1      -0.354  -9.215  -1.849  1.00 20.00           P
-ATOM      2  O1P  Gd R   1      -0.207 -10.499  -2.569  1.00 20.00           O
-ATOM      3  O2P  Gd R   1      -1.304  -9.104  -0.720  1.00 20.00           O
-ATOM      4  O5*  Gd R   1       1.084  -8.739  -1.333  1.00 20.00           O
-ATOM      5  O3*  Gd R   1       4.211  -6.835   0.518  1.00 20.00           O
-ATOM      6  C1*  Gd R   1       1.903  -5.330  -0.003  1.00 20.00           C
-ATOM      7  C2*  Gd R   1       1.811  -6.647   0.752  1.00 20.00           C
-ATOM      8  C3*  Gd R   1       2.971  -7.365   0.076  1.00 20.00           C
-ATOM      9  C4*  Gd R   1       2.757  -6.990  -1.386  1.00 20.00           C
-ATOM     10  C5*  Gd R   1       1.926  -7.975  -2.188  1.00 20.00           C
-ATOM     11  O4*  Gd R   1       2.086  -5.703  -1.354  1.00 20.00           O
-ATOM     12  N9   Gd R   1       0.728  -4.472   0.106  1.00 20.00           N
-ATOM     13  C8   Gd R   1      -0.586  -4.835   0.294  1.00 20.00           C
-ATOM     14  N7   Gd R   1      -1.409  -3.819   0.350  1.00 20.00           N
-ATOM     15  C5   Gd R   1      -0.599  -2.700   0.190  1.00 20.00           C
-ATOM     16  C4   Gd R   1       0.718  -3.092   0.039  1.00 20.00           C
-ATOM     17  N1   Gd R   1       0.231  -0.536  -0.024  1.00 20.00           N
-ATOM     18  C2   Gd R   1       1.512  -1.022  -0.166  1.00 20.00           C
-ATOM     19  N3   Gd R   1       1.813  -2.313  -0.141  1.00 20.00           N
-ATOM     20  C6   Gd R   1      -0.909  -1.319   0.162  1.00 20.00           C
-ATOM     21  O6   Gd R   1      -2.018  -0.779   0.278  1.00 20.00           O
-ATOM     22  N2   Gd R   1       2.491  -0.117  -0.337  1.00 20.00           N
+ATOM     93  P    DC B   4      -0.807  -8.873  -2.081  1.00 20.00           P  
+ATOM     94  O1P  DC B   4      -0.196 -10.199  -1.861  1.00 20.00           O  
+ATOM     95  O2P  DC B   4      -2.030  -8.583  -1.291  1.00 20.00           O  
+ATOM     96  O5'  DC B   4       0.270  -7.725  -1.831  1.00 20.00           O  
+ATOM     97  O3'  DC B   4       4.189  -7.682  -0.251  1.00 20.00           O  
+ATOM     98  C1'  DC B   4       2.252  -5.410  -0.471  1.00 20.00           C  
+ATOM     99  C2'  DC B   4       2.035  -6.740   0.239  1.00 20.00           C  
+ATOM    100  C3'  DC B   4       2.818  -7.701  -0.641  1.00 20.00           C  
+ATOM    101  C4'  DC B   4       2.607  -7.128  -2.041  1.00 20.00           C  
+ATOM    102  C5'  DC B   4       1.364  -7.578  -2.771  1.00 20.00           C  
+ATOM    103  O4'  DC B   4       2.530  -5.682  -1.831  1.00 20.00           O  
+ATOM    104  N4   DC B   4      -2.005  -1.896  -0.271  1.00 20.00           N  
+ATOM    105  C4   DC B   4      -1.006  -2.763  -0.321  1.00 20.00           C  
+ATOM    106  N3   DC B   4       0.245  -2.297  -0.221  1.00 20.00           N  
+ATOM    107  C2   DC B   4       1.307  -3.139  -0.271  1.00 20.00           C  
+ATOM    108  O2   DC B   4       2.474  -2.738  -0.181  1.00 20.00           O  
+ATOM    109  N1   DC B   4       1.073  -4.504  -0.421  1.00 20.00           N  
+ATOM    110  C6   DC B   4      -0.192  -4.986  -0.521  1.00 20.00           C  
+ATOM    111  C5   DC B   4      -1.272  -4.160  -0.471  1.00 20.00           C  
+ATOM     93  P     X B   5      -0.449  -9.609   3.122  1.00 20.00           P
+ATOM     94  O1P   X B   5       0.162 -10.935   3.342  1.00 20.00           O
+ATOM     95  O2P   X B   5      -1.672  -9.319   3.912  1.00 20.00           O
+ATOM     96  O5'   X B   5       0.628  -8.461   3.372  1.00 20.00           O
+ATOM     97  O3'   X B   5       4.547  -8.418   4.952  1.00 20.00           O
+ATOM     98  C1'   X B   5       2.610  -6.146   4.732  1.00 20.00           C
+ATOM     99  C2'   X B   5       2.393  -7.476   5.442  1.00 20.00           C
+ATOM     99  O2'   X B   5       2.907  -7.413   6.758  1.00 20.00           O
+ATOM    100  C3'   X B   5       3.176  -8.437   4.562  1.00 20.00           C
+ATOM    101  C4'   X B   5       2.965  -7.864   3.162  1.00 20.00           C
+ATOM    102  C5'   X B   5       1.722  -8.314   2.432  1.00 20.00           C
+ATOM    103  O4'   X B   5       2.888  -6.418   3.372  1.00 20.00           O
+ATOM    104  N4    X B   5      -1.647  -2.632   4.932  1.00 20.00           N
+ATOM    105  C4    X B   5      -0.648  -3.499   4.882  1.00 20.00           C
+ATOM    106  N3    X B   5       0.603  -3.033   4.982  1.00 20.00           N
+ATOM    107  C2    X B   5       1.665  -3.875   4.932  1.00 20.00           C
+ATOM    108  O2    X B   5       2.832  -3.474   5.022  1.00 20.00           O
+ATOM    109  N1    X B   5       1.431  -5.240   4.782  1.00 20.00           N
+ATOM    110  C6    X B   5       0.166  -5.722   4.682  1.00 20.00           C
+ATOM    111  C5    X B   5      -0.914  -4.896   4.732  1.00 20.00           C
+ATOM     21  P     C Q   2      -6.082  -7.578   5.445  1.00 20.00      Q    P  
+ATOM     22  O1P   C Q   2      -7.533  -7.624   5.771  1.00 20.00      Q    O  
+ATOM     23  O2P   C Q   2      -5.156  -6.839   6.329  1.00 20.00      Q    O  
+ATOM     24  O5'   C Q   2      -5.573  -9.094   5.389  1.00 20.00      Q    O  
+ATOM     25  C5'   C Q   2      -6.453 -10.176   5.763  1.00 20.00      Q    C  
+ATOM     26  C4'   C Q   2      -5.695 -11.355   6.372  1.00 20.00      Q    C  
+ATOM     27  O4'   C Q   2      -4.841 -11.970   5.378  1.00 20.00      Q    O  
+ATOM     28  C1'   C Q   2      -3.715 -12.552   6.012  1.00 20.00      Q    C  
+ATOM     29  N1    C Q   2      -2.517 -11.849   5.539  1.00 20.00      Q    N  
+ATOM     30  C6    C Q   2      -2.608 -10.568   5.075  1.00 20.00      Q    C  
+ATOM     31  C2    C Q   2      -1.282 -12.505   5.564  1.00 20.00      Q    C  
+ATOM     32  O2    C Q   2      -1.229 -13.666   6.009  1.00 20.00      Q    O  
+ATOM     33  N3    C Q   2      -0.187 -11.859   5.106  1.00 20.00      Q    N  
+ATOM     34  C4    C Q   2      -0.292 -10.611   4.645  1.00 20.00      Q    C  
+ATOM     35  N4    C Q   2       0.815 -10.019   4.194  1.00 20.00      Q    N  
+ATOM     36  C5    C Q   2      -1.537  -9.920   4.625  1.00 20.00      Q    C  
+ATOM     37  C2'   C Q   2      -3.929 -12.413   7.517  1.00 20.00      Q    C  
+ATOM     38  O2'   C Q   2      -4.616 -13.546   7.991  1.00 20.00      Q    O  
+ATOM     39  C3'   C Q   2      -4.799 -11.168   7.591  1.00 20.00      Q    C  
+ATOM     40  O3'   C Q   2      -5.600 -11.193   8.766  1.00 20.00      Q    O  
+ATOM     41  P     A Q   3      -4.940 -11.446  10.232  1.00 20.00      Q    P  
+ATOM     42  O1P   A Q   3      -6.007 -12.136  11.012  1.00 20.00      Q    O  
+ATOM     43  O2P   A Q   3      -4.345 -10.197  10.770  1.00 20.00      Q    O  
+ATOM     44  O5'   A Q   3      -3.787 -12.546  10.091  1.00 20.00      Q    O  
+ATOM     45  C5'   A Q   3      -3.983 -13.848  10.656  1.00 20.00      Q    C  
+ATOM     46  C4'   A Q   3      -2.675 -14.512  11.030  1.00 20.00      Q    C  
+ATOM     47  O4'   A Q   3      -1.864 -14.738   9.853  1.00 20.00      Q    O  
+ATOM     48  C1'   A Q   3      -0.503 -14.773  10.233  1.00 20.00      Q    C  
+ATOM     49  N9    A Q   3       0.189 -13.720   9.488  1.00 20.00      Q    N  
+ATOM     50  C4    A Q   3       1.525 -13.615   9.179  1.00 20.00      Q    C  
+ATOM     51  N3    A Q   3       2.522 -14.454   9.499  1.00 20.00      Q    N  
+ATOM     52  C2    A Q   3       3.686 -14.006   9.027  1.00 20.00      Q    C  
+ATOM     53  N1    A Q   3       3.943 -12.897   8.322  1.00 20.00      Q    N  
+ATOM     54  C6    A Q   3       2.915 -12.078   8.016  1.00 20.00      Q    C  
+ATOM     55  N6    A Q   3       3.159 -10.968   7.311  1.00 20.00      Q    N  
+ATOM     56  C5    A Q   3       1.637 -12.436   8.457  1.00 20.00      Q    C  
+ATOM     57  N7    A Q   3       0.405 -11.826   8.317  1.00 20.00      Q    N  
+ATOM     58  C8    A Q   3      -0.418 -12.624   8.946  1.00 20.00      Q    C  
+ATOM     59  C2'   A Q   3      -0.451 -14.600  11.753  1.00 20.00      Q    C  
+ATOM     60  O2'   A Q   3      -0.415 -15.878  12.347  1.00 20.00      Q    O  
+ATOM     61  C3'   A Q   3      -1.743 -13.844  12.032  1.00 20.00      Q    C  
+ATOM     62  O3'   A Q   3      -2.242 -14.105  13.347  1.00 20.00      Q    O  
+ATOM      1  P    DG R   1      -0.354  -9.215  -1.849  1.00 20.00           P
+ATOM      2  O1P  DG R   1      -0.207 -10.499  -2.569  1.00 20.00           O
+ATOM      3  O2P  DG R   1      -1.304  -9.104  -0.720  1.00 20.00           O
+ATOM      4  O5'  DG R   1       1.084  -8.739  -1.333  1.00 20.00           O
+ATOM      5  O3'  DG R   1       4.211  -6.835   0.518  1.00 20.00           O
+ATOM      6  C1'  DG R   1       1.903  -5.330  -0.003  1.00 20.00           C
+ATOM      7  C2'  DG R   1       1.811  -6.647   0.752  1.00 20.00           C
+ATOM      8  C3'  DG R   1       2.971  -7.365   0.076  1.00 20.00           C
+ATOM      9  C4'  DG R   1       2.757  -6.990  -1.386  1.00 20.00           C
+ATOM     10  C5'  DG R   1       1.926  -7.975  -2.188  1.00 20.00           C
+ATOM     11  O4'  DG R   1       2.086  -5.703  -1.354  1.00 20.00           O
+ATOM     12  N9   DG R   1       0.728  -4.472   0.106  1.00 20.00           N
+ATOM     13  C8   DG R   1      -0.586  -4.835   0.294  1.00 20.00           C
+ATOM     14  N7   DG R   1      -1.409  -3.819   0.350  1.00 20.00           N
+ATOM     15  C5   DG R   1      -0.599  -2.700   0.190  1.00 20.00           C
+ATOM     16  C4   DG R   1       0.718  -3.092   0.039  1.00 20.00           C
+ATOM     17  N1   DG R   1       0.231  -0.536  -0.024  1.00 20.00           N
+ATOM     18  C2   DG R   1       1.512  -1.022  -0.166  1.00 20.00           C
+ATOM     19  N3   DG R   1       1.813  -2.313  -0.141  1.00 20.00           N
+ATOM     20  C6   DG R   1      -0.909  -1.319   0.162  1.00 20.00           C
+ATOM     21  O6   DG R   1      -2.018  -0.779   0.278  1.00 20.00           O
+ATOM     22  N2   DG R   1       2.491  -0.117  -0.337  1.00 20.00           N
 END
 {
    "date_last_updated": "11/21/2022",