moorhen 0.9.0 → 0.9.1

package/README.md

@@ -43,11 +43,21 @@ Binaries are available on the releases page. Please read the instructions there
 * git
 * curl
 * patch
-* emsdk (Steps 1 and 2 below)
+* ninja
+* meson
 * cmake
+* flex
+* bison
 * A *native* C++ compiler. (This is required for part of the `boost` build system).
 * `autoconf`,`autotools`
 * `libtool`
+* emsdk/emscripten (Steps 1 and 2 below)
+\
+\
+Most of these (except emscripten) can be installed by somelike like `sudo apt install git cmake curl patch meson ninja-build autoconf automake libtool flex bison g++` on a Debian like system. All of these should be available through Homebrew or Ports on macOS.
+\
+\
+Moorhen should build on any reasonably recent version of macOS (Intel or Arm64) and any reasonly recent Linux distribution (x86_64 or aarch64). Tested on Ubuntu 22.04 x86_64, Raspberry Pi OS Bookworm/Debian 12 on Pi5, macOS Monteray and Sonama and others.
 
 1. Install emscripten (following  [https://emscripten.org/docs/getting_started/downloads.html](https://emscripten.org/docs/getting_started/downloads.html)):  
 `git clone https://github.com/emscripten-core/emsdk.git`  

package/baby-gru/CootWorker.js

@@ -1 +1 @@
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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 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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))};
+var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var r,a=1,t=arguments.length;a<t;a++)for(var o in r=arguments[a])Object.prototype.hasOwnProperty.call(r,o)&&(e[o]=r[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(r){var a=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===r?a:3&a|8).toString(16)}))},print=function(e){console.log(e)},parseMonLibListCif=function(e){for(var r=cootModule.parse_mon_lib_list_cif(e),a=r.size(),t=[],o=0;o<a;o++){var s=r.get(o);t.push({three_letter_code:s.three_letter_code,name:s.name.replaceAll("'","").toLowerCase()})}return r.delete(),t},instancedMeshToMeshData=function(e,r,a,t){void 0===a&&(a=!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=a,v=[],y=[],b=[],S=[],M=[],z=[],A=[],T=m.get(h);"spherical-atoms"===T.name&&(f=!0);for(var x=T.vertices,F=T.triangles,k=F.size(),w=0;w<k;w++){var I=F.get(w).point_id;r?(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=x.size(),D=0;D<J;D++){var C=x.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;b.push(R[0]),b.push(R[1]),b.push(R[2])}x.delete();var P=T.instancing_data_A,L=P.size();if(L>0)for(var E=0;E<L;E++){var U=(q=P.get(E)).position;z.push(U[0]),z.push(U[1]),z.push(U[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var j=q.size;S.push(j[0]),S.push(j[1]),S.push(j[2]),A.push.apply(A,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}P.delete();var B=T.instancing_data_B,V=B.size();if(V>0)for(E=0;E<V;E++){var q;if(!((j=(q=B.get(E)).size)[2]>t)){S.push(j[0]),S.push(j[1]),S.push(j[2]),U=q.position,z.push(U[0]),z.push(U[1]),z.push(U[2]),O=q.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;A.push(H[0][0]),A.push(H[0][1]),A.push(H[0][2]),A.push(H[0][3]),A.push(H[1][0]),A.push(H[1][1]),A.push(H[1][2]),A.push(H[1][3]),A.push(H[2][0]),A.push(H[2][1]),A.push(H[2][2]),A.push(H[2][3]),A.push(H[3][0]),A.push(H[3][1]),A.push(H[3][2]),A.push(H[3][3])}}B.delete(),n.push(b),s.push(y),o.push(v),i.push(S),l.push(z),_.push(A),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?a?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[l,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:[l,null],instance_orientations:[_,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:[l,null],instance_orientations:[_,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:[l],instance_orientations:[_]}},simpleMeshToMeshData=function(e,r,a){void 0===r&&(r=!1),void 0===a&&(a=!1);var t=(performance.now(),e.vertices),o=e.triangles,s=t.size(),n=o.size(),i=new Uint32Array(3*n),c=new Float32Array(3*s),l=new Float32Array(3*s),_=new Float32Array(4*s);cootModule.getPositionsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),r?(a?cootModule.getReversedNormalsFromSimpleMesh3(e,l):cootModule.getReversedNormalsFromSimpleMesh2(e,l),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,i)):(cootModule.getNormalsFromSimpleMesh2(e,l),cootModule.getTriangleIndicesFromSimpleMesh2(e,i)),performance.now();var u=c,d=_,m=l,p=i;return t.delete(),o.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[p]],vert_tri:[[u]],norm_tri:[[m]],col_tri:[[d]]}},SuperposeResultsToJSArray=function(e){for(var r=e.aligned_pairs,a=r.size(),t=[],o=0;o<a;o++){var s=r.get(o),n=s.first,i=n.residue_spec,c=s.second,l=c.residue_spec,_={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:l.chain_id,insCode:l.ins_code,seqNum:l.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(_)}return r.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},stringArrayArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}r.push(n),o.delete()}return e.delete(),r},floatArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},mapMoleculeCentreInfoToJSObject=function(e){var r=e.updated_centre,a={updated_centre:[r.x(),r.y(),r.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return r.delete(),a},textureAsFloatsToJSTextureAsFloats=function(e){var r=e.width*e.height,a=new Float32Array(r),t=performance.now();cootModule.getTextureArray(e,a);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:a}},fitLigandInfoArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(__assign({},o))}return e.delete(),r},intArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},stringArrayToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push(o)}return e.delete(),r},export_map_as_gltf=function(e,r,a,t,o,s){var n="".concat(guid(),".glb");molecules_container.export_map_molecule_as_gltf(e,r,a,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,r,a,t){var o="".concat(guid(),".glb");molecules_container.export_molecular_represenation_as_gltf(e,r,a,t,o);var s=cootModule.FS.readFile(o,{encoding:"binary"});return cootModule.FS_unlink(o),s.buffer},export_molecule_as_gltf=function(e,r,a,t,o,s,n,i,c){var l="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,r,a,t,o,s,n,i,c,l);var _=cootModule.FS.readFile(l,{encoding:"binary"});return cootModule.FS_unlink(l),_.buffer},symmetryToJSData=function(e){for(var r=[],a=e.first,t=e.second,o=a.symm_trans,s=o.size(),n=0;n<s;n++){var i=o.get(n),c=i.first,l=i.second,_=t.get(n);r.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:l.us,ws:l.ws,vs:l.vs,matrix:_}),c.delete()}return o.delete(),t.delete(),r},mmrrccStatsToJSArray=function(e){var r=function(e){for(var r=[],a=e.keys(),t=a.size(),o=0;o<t;o++){var s=a.get(o),n=e.get(s);r.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 a.delete(),r},a=e.first,t=e.second,o={"All atoms":r(a),"Side-chains":r(t)};return a.delete(),t.delete(),o},atomSpecToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.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(),r},residueSpecToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.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(),r},stringPairVectorToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.push({first:o.first,second:o.second})}return e.delete(),r},validationDataToJSArray=function(e,r){void 0===r&&(r=null);for(var a=[],t=e.cviv,o=t.size(),s=0;s<o;s++){var n=t.get(s);if(null!==r&&n.chain_id!==r);else{for(var i=n.rviv,c=i.size(),l=0;l<c;l++){var _=i.get(l),u=_.residue_spec;a.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:_.function_value})}i.delete()}}return t.delete(),e.delete(),a},linesBoxToJSArray=function(e){for(var r=[],a=e.line_segments,t=a.size(),o=0;o<t;o++){for(var s=[],n=a.get(o),i=n.size(),c=0;c<i;c++){var l=n.get(c),_=l.getStart(),u=l.getFinish(),d=l.amplitude(),m={x:_.x(),y:_.y(),z:_.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),_.delete(),u.delete(),l.delete()}n.delete(),r.push(s)}return a.delete(),r},vectorHBondToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.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(),r},interestingPlaceDataToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t),s=o.residue_spec;r.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(),r},histogramInfoToJSData=function(e){var r=e.counts;return{counts:intArrayToJSArray(r),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t);r.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(),r.some((function(e){return-1===e.idx}))){var s=r.find((function(e){return-1===e.idx}));s&&s.F_obs&&s.Rfree&&s.sigF_obs&&r.forEach((function(e){e.F_obs=s.F_obs,e.sigF_obs=s.sigF_obs,e.Rfree=s.Rfree})),r=r.filter((function(e){return-1!==e.idx}))}return r},ramachandranDataToJSArray=function(e,r){for(var a=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===r&&a.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(),a},vectorPairStringIntToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t),s={residue:o.first,slice:o.second};r.push(s)}return e.delete(),r},vectorPairClipperCoordFloatToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),r.push({value:s,coord:i})}return e.delete(),r},simpleMeshToLineMeshData=function(e,r){var a=(performance.now(),e.vertices),t=e.triangles,o=t.size(),s=a.size(),n=new Uint32Array(6*o),i=new Float32Array(3*s),c=new Float32Array(3*s),l=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,l),performance.now();var _=n,u=i,d=c,m=l;return a.delete(),t.delete(),r?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[_]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[_]],vert_tri:[[u]],norm_tri:[[d]],col_tri:[[m]]}},auto_read_mtz=function(e){var r=guid(),a=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(r,".mtz"),a,!0,!0);var t="./".concat(r,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,r,a){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(r);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,a.F,a.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,r){var a=0,t=new cootModule.Vectormoved_residue_t;return r.forEach((function(e){if(e.length>0){var r=e[0],a=new cootModule.moved_residue_t(r.chain_id,parseInt(r.res_no),"");e.forEach((function(e){var r=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);a.add_atom(r),r.delete()})),t.push_back(a),a.delete()}})),a+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),a},read_mtz=function(e,r,a){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,a.F,a.PHI,"",!1,a.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,r,a,t,o){var s=new Uint8Array(r.data);cootModule.FS_createDataFile(".","".concat(r.fileName,".mtz"),s,!0,!0);var n="./".concat(r.fileName,".mtz"),i=[e,n,a,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,r,a){var t=guid(),o=new Uint8Array(e),s="";r.endsWith(".map.gz")?s="map.gz":r.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,a],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,r,a){void 0===a&&(a=!1);var t=new cootModule.MapIntFloat4,o=new cootModule.VectorStringUInt_pair;r.forEach((function(e,r){t.set(r+51,e.rgba);var a={first:e.cid,second:r+51};o.push_back(a)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,a),o.delete(),t.delete()},privateerValidationToJSArray=function(e){for(var r=[],a=e.size(),t=0;t<a;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 l={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};r.push(l)}return e.delete(),r},headerInfoAsJSObject=function(e){var r=e.author_lines,a=stringArrayToJSArray(r),t=e.compound_lines,o=stringArrayToJSArray(t),s=e.journal_lines,n=stringArrayToJSArray(s);return{title:e.title,author_lines:a,compound_lines:o,journal_lines:n}},doCootCommand=function(e){var r=e.returnType,a=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(a){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;case"parse_mon_lib_list_cif":i=parseMonLibListCif.apply(void 0,t);break;default:i=molecules_container[a].apply(molecules_container,t)}var c=void 0;switch(r){case"header_info_t":c=headerInfoAsJSObject(i);break;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_perm3":c=simpleMeshToMeshData(i,!0,!0);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:a,consoleMessage:"Completed ".concat(a," 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(a,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(r){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=r).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 r=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:r}})}else if("get_map"===e.data.message){var a=guid(),t="./".concat(a,".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(r){return doCootCommand(__assign(__assign({},e.data),r))}));postMessage({messageId:e.data.messageId,resultList:n})}"coot_command"===e.data.message&&(s=doCootCommand(e.data),postMessage(s))};

package/baby-gru/CootWorker.ts

@@ -24,7 +24,24 @@ const guid = () => {
 // @ts-ignore
 let print = (stuff) => {
     console.log(stuff)
-    postMessage({ consoleMessage: JSON.stringify(stuff) })
+}
+
+const parseMonLibListCif = (fileContents: string): libcootApi.compoundInfo[] => {
+    const table = cootModule.parse_mon_lib_list_cif(fileContents)
+    const tableSize = table.size()
+
+    let result: libcootApi.compoundInfo[] = []
+    for (let i = 0; i < tableSize; i++) {
+        const compound = table.get(i)
+        result.push({
+            three_letter_code: compound.three_letter_code,
+            // @ts-ignore
+            name: compound.name.replaceAll("'", "").toLowerCase()
+        })
+    }
+
+    table.delete()
+    return result
 }
 
 const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm: boolean, toSpheres: boolean = false, maxZSize: number = 10000.): libcootApi.InstancedMeshJS => {
@@ -226,7 +243,7 @@ const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm:
     }
 }
 
-const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean = false): libcootApi.SimpleMeshJS => {
+const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean = false, keepNorm: boolean = false): libcootApi.SimpleMeshJS => {
 
     const print_timing = false
     const ts = performance.now()
@@ -246,7 +263,11 @@ const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean
     cootModule.getColoursFromSimpleMesh2(simpleMesh,totCol_C)
 
     if (perm){
-        cootModule.getReversedNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+        if(keepNorm){
+            cootModule.getReversedNormalsFromSimpleMesh3(simpleMesh,totNorm_C)
+        } else {
+            cootModule.getReversedNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+        }
         cootModule.getPermutedTriangleIndicesFromSimpleMesh2(simpleMesh,totIdxs_C)
     } else {
         cootModule.getNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
@@ -956,12 +977,12 @@ const read_ccp4_map = (mapData: ArrayBufferLike, name: string, isDiffMap: boolea
     return molNo
 }
 
-const setUserDefinedBondColours = (imol: number, colours: { cid: string; rgb: [number, number, number] }[], applyColourToNonCarbonAtoms: boolean = false) => {
-    let colourMap = new cootModule.MapIntFloat3()
+const setUserDefinedBondColours = (imol: number, colours: { cid: string; rgba: [number, number, number, number] }[], applyColourToNonCarbonAtoms: boolean = false) => {
+    let colourMap = new cootModule.MapIntFloat4()
     let indexedResiduesVec = new cootModule.VectorStringUInt_pair()
     
     colours.forEach((colour, index) => {
-        colourMap.set(index + 51, colour.rgb)
+        colourMap.set(index + 51, colour.rgba)
         const i = { first: colour.cid, second: index + 51 }
         indexedResiduesVec.push_back(i)
     })
@@ -1016,7 +1037,25 @@ const privateerValidationToJSArray = (results: emscriptem.vector<privateer.Resul
 
     results.delete();
     return data;
+}
+
+const headerInfoAsJSObject = (result: libcootApi.headerInfo): libcootApi.headerInfoJS => {
+
+    const authorLines = result.author_lines
+    const author_lines: string[] = stringArrayToJSArray(authorLines)
+
+    const compoundLines = result.compound_lines
+    const compound_lines: string[] = stringArrayToJSArray(compoundLines)
+
+    const journalLines = result.journal_lines
+    const journal_lines: string[] = stringArrayToJSArray(journalLines)
 
+    return {
+        title: result.title,
+        author_lines,
+        compound_lines,
+        journal_lines
+    }
 }
 
 const doCootCommand = (messageData: { 
@@ -1054,7 +1093,7 @@ const doCootCommand = (messageData: {
                 cootResult = replace_map_by_mtz_from_file(...commandArgs as [number, ArrayBufferLike, { F: string; PHI: string; }])
                 break
             case 'shim_set_bond_colours':
-                cootResult = setUserDefinedBondColours(...commandArgs as [number, { cid: string; rgb: [number, number, number] }[], boolean])
+                cootResult = setUserDefinedBondColours(...commandArgs as [number, { cid: string; rgba: [number, number, number, number] }[], boolean])
                 break
             case 'shim_export_map_as_gltf':
                 cootResult = export_map_as_gltf(...commandArgs as [number, number, number, number, number, number])
@@ -1065,6 +1104,9 @@ const doCootCommand = (messageData: {
             case 'shim_export_molecular_represenation_as_gltf':
                 cootResult = export_molecular_represenation_as_gltf(...commandArgs as [number, string, string, string])
                 break
+            case "parse_mon_lib_list_cif":
+                cootResult =  parseMonLibListCif(...commandArgs as [string])
+                break
             default:
                 cootResult = molecules_container[command](...commandArgs)
                 break
@@ -1072,6 +1114,9 @@ const doCootCommand = (messageData: {
 
         let returnResult;
         switch (returnType) {
+            case 'header_info_t':
+                returnResult = headerInfoAsJSObject(cootResult)
+                break
             case 'texture_as_floats_t':
                 returnResult = textureAsFloatsToJSTextureAsFloats(cootResult)
                 break;
@@ -1102,6 +1147,9 @@ const doCootCommand = (messageData: {
             case 'instanced_mesh':
                 returnResult = instancedMeshToMeshData(cootResult, false, false, 5)
                 break;
+            case 'mesh_perm3':
+                returnResult = simpleMeshToMeshData(cootResult, true, true)
+                break;
             case 'mesh_perm':
                 returnResult = simpleMeshToMeshData(cootResult, true)
                 break;

package/baby-gru/monomers/p/PRO.cif

@@ -7,34 +7,36 @@ _chem_comp.group
 _chem_comp.number_atoms_all
 _chem_comp.number_atoms_nh
 _chem_comp.desc_level
-PRO PRO PROLINE P-peptide 16 8 .
+PRO PRO PROLINE P-peptide 17 8 .
 
 data_comp_PRO
 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.type_energy
 _chem_comp_atom.charge
 _chem_comp_atom.x
 _chem_comp_atom.y
 _chem_comp_atom.z
-PRO N N NR15 0 39.037 37.549 83.040
-PRO CA C CH1 0 38.574 38.605 82.148
-PRO C C C 0 37.249 39.192 82.624
-PRO O O O 0 36.298 38.401 82.791
-PRO CB C CH2 0 38.459 37.920 80.773
-PRO CG C CH2 0 38.237 36.468 81.113
-PRO CD C CH2 0 39.066 36.257 82.367
-PRO OXT O OC -1 37.210 40.425 82.814
-PRO H H H 0 39.264 37.676 83.860
-PRO HA H H 0 39.261 39.316 82.107
-PRO HB3 H H 0 39.287 38.037 80.252
-PRO HB2 H H 0 37.701 38.283 80.256
-PRO HG3 H H 0 38.544 35.886 80.387
-PRO HG2 H H 0 37.289 36.288 81.286
-PRO HD3 H H 0 38.673 35.556 82.933
-PRO HD2 H H 0 39.987 36.001 82.137
+PRO N   N   N NT2 1  39.160 37.649 83.026
+PRO CA  CA  C CH1 0  38.550 38.680 82.125
+PRO C   C   C C   0  37.155 39.077 82.602
+PRO O   O   O O   0  36.450 38.196 83.146
+PRO CB  CB  C CH2 0  38.553 38.007 80.756
+PRO CG  CG  C CH2 0  38.265 36.558 81.098
+PRO CD  CD  C CH2 0  38.934 36.298 82.416
+PRO OXT OXT O OC  -1 36.821 40.268 82.409
+PRO H   H   H H   0  40.054 37.806 83.097
+PRO H2  H2  H H   0  38.800 37.681 83.862
+PRO HA  HA  H H   0  39.125 39.473 82.102
+PRO HB3 HB3 H H   0  39.422 38.100 80.320
+PRO HB2 HB2 H H   0  37.858 38.378 80.178
+PRO HG3 HG3 H H   0  38.625 35.964 80.410
+PRO HG2 HG2 H H   0  37.302 36.406 81.169
+PRO HD3 HD3 H H   0  38.363 35.755 82.994
+PRO HD2 HD2 H H   0  39.785 35.835 82.289
 
 loop_
 _chem_comp_tree.comp_id
@@ -42,38 +44,40 @@ _chem_comp_tree.atom_id
 _chem_comp_tree.atom_back
 _chem_comp_tree.atom_forward
 _chem_comp_tree.connect_type
-PRO N n/a CA START
-PRO CA N C .
-PRO HA CA . .
-PRO CB CA CG .
-PRO HB3 CB . .
-PRO HB2 CB . .
-PRO CG CB CD .
-PRO HG3 CG . .
-PRO HG2 CG . .
-PRO CD CG HD2 .
-PRO HD3 CD . .
-PRO HD2 CD . .
-PRO C CA . END
-PRO O C . .
-PRO OXT C . .
-PRO H N . .
-PRO CD N . ADD
+PRO N   n/a CA  START
+PRO CA  N   C   .
+PRO HA  CA  .   .
+PRO CB  CA  CG  .
+PRO HB3 CB  .   .
+PRO HB2 CB  .   .
+PRO CG  CB  CD  .
+PRO HG3 CG  .   .
+PRO HG2 CG  .   .
+PRO CD  CG  HD2 .
+PRO HD3 CD  .   .
+PRO HD2 CD  .   .
+PRO C   CA  .   END
+PRO O   C   .   .
+PRO OXT C   .   .
+PRO H   N   .   .
+PRO H2  N   .   .
+PRO CD  N   .   ADD
 
 loop_
 _chem_comp_acedrg.comp_id
 _chem_comp_acedrg.atom_id
 _chem_comp_acedrg.atom_type
-PRO N N[5](C[5]C[5]CH)(C[5]C[5]HH)(H){4|H<1>}
-PRO CA C[5](C[5]C[5]HH)(N[5]C[5]H)(COO)(H){4|H<1>}
-PRO C C(C[5]C[5]N[5]H)(O)2
-PRO O O(CC[5]O)
-PRO CB C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{3|H<1>}
-PRO CG C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,2|H<1>}
-PRO CD C[5](C[5]C[5]HH)(N[5]C[5]H)(H)2{1|C<3>,3|H<1>}
+PRO N   N[5](C[5]C[5]CH)(C[5]C[5]HH)(H)2{4|H<1>}
+PRO CA  C[5](C[5]C[5]HH)(N[5]C[5]HH)(COO)(H){4|H<1>}
+PRO C   C(C[5]C[5]N[5]H)(O)2
+PRO O   O(CC[5]O)
+PRO CB  C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{4|H<1>}
+PRO CG  C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,3|H<1>}
+PRO CD  C[5](C[5]C[5]HH)(N[5]C[5]HH)(H)2{1|C<3>,3|H<1>}
 PRO OXT O(CC[5]O)
-PRO H H(N[5]C[5]2)
-PRO HA H(C[5]C[5]N[5]C)
+PRO H   H(N[5]C[5]2H)
+PRO H2  H(N[5]C[5]2H)
+PRO HA  H(C[5]C[5]N[5]C)
 PRO HB3 H(C[5]C[5]2H)
 PRO HB2 H(C[5]C[5]2H)
 PRO HG3 H(C[5]C[5]2H)
@@ -85,28 +89,29 @@ loop_
 _chem_comp_bond.comp_id
 _chem_comp_bond.atom_id_1
 _chem_comp_bond.atom_id_2
-_chem_comp_bond.type
-_chem_comp_bond.aromatic
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
 _chem_comp_bond.value_dist_nucleus
 _chem_comp_bond.value_dist_nucleus_esd
 _chem_comp_bond.value_dist
 _chem_comp_bond.value_dist_esd
-PRO N CA SINGLE n 1.457 0.0100 1.457 0.0100
-PRO N CD SINGLE n 1.458 0.0200 1.458 0.0200
-PRO CA C SINGLE n 1.524 0.0159 1.524 0.0159
-PRO CA CB SINGLE n 1.534 0.0192 1.534 0.0192
-PRO C O DOUBLE n 1.248 0.0171 1.248 0.0171
-PRO C OXT SINGLE n 1.248 0.0171 1.248 0.0171
-PRO CB CG SINGLE n 1.509 0.0200 1.509 0.0200
-PRO CG CD SINGLE n 1.521 0.0187 1.521 0.0187
-PRO N H SINGLE n 1.018 0.0520 0.860 0.0100
-PRO CA HA SINGLE n 1.092 0.0100 0.990 0.0200
-PRO CB HB3 SINGLE n 1.092 0.0100 0.986 0.0200
-PRO CB HB2 SINGLE n 1.092 0.0100 0.986 0.0200
-PRO CG HG3 SINGLE n 1.092 0.0100 0.980 0.0127
-PRO CG HG2 SINGLE n 1.092 0.0100 0.980 0.0127
-PRO CD HD3 SINGLE n 1.092 0.0100 0.983 0.0176
-PRO CD HD2 SINGLE n 1.092 0.0100 0.983 0.0176
+PRO N  CA  SINGLE n 1.496 0.0142 1.496 0.0142
+PRO N  CD  SINGLE n 1.499 0.0135 1.499 0.0135
+PRO CA C   SINGLE n 1.525 0.0103 1.525 0.0103
+PRO CA CB  SINGLE n 1.526 0.0157 1.526 0.0157
+PRO C  O   DOUBLE n 1.252 0.0117 1.252 0.0117
+PRO C  OXT SINGLE n 1.252 0.0117 1.252 0.0117
+PRO CB CG  SINGLE n 1.516 0.0179 1.516 0.0179
+PRO CG CD  SINGLE n 1.497 0.0200 1.497 0.0200
+PRO N  H   SINGLE n 1.018 0.0520 0.910 0.0200
+PRO N  H2  SINGLE n 1.018 0.0520 0.910 0.0200
+PRO CA HA  SINGLE n 1.092 0.0100 0.980 0.0200
+PRO CB HB3 SINGLE n 1.092 0.0100 0.977 0.0145
+PRO CB HB2 SINGLE n 1.092 0.0100 0.977 0.0145
+PRO CG HG3 SINGLE n 1.092 0.0100 0.978 0.0181
+PRO CG HG2 SINGLE n 1.092 0.0100 0.978 0.0181
+PRO CD HD3 SINGLE n 1.092 0.0100 0.977 0.0199
+PRO CD HD2 SINGLE n 1.092 0.0100 0.977 0.0199
 
 loop_
 _chem_comp_angle.comp_id
@@ -115,36 +120,39 @@ _chem_comp_angle.atom_id_2
 _chem_comp_angle.atom_id_3
 _chem_comp_angle.value_angle
 _chem_comp_angle.value_angle_esd
-PRO CA N CD 110.881 3.00
-PRO CA N H 124.203 1.50
-PRO CD N H 124.916 3.00
-PRO N CA C 111.610 3.00
-PRO N CA CB 102.532 3.00
-PRO N CA HA 109.054 1.85
-PRO C CA CB 112.350 1.50
-PRO C CA HA 109.862 1.50
-PRO CB CA HA 109.576 1.50
-PRO CA C O 117.170 3.00
-PRO CA C OXT 117.170 3.00
-PRO O C OXT 125.661 1.52
-PRO CA CB CG 103.478 1.50
-PRO CA CB HB3 110.876 1.50
-PRO CA CB HB2 110.876 1.50
-PRO CG CB HB3 110.891 1.59
-PRO CG CB HB2 110.891 1.59
+PRO CA  N  CD  107.978 1.50
+PRO CA  N  H   109.889 3.00
+PRO CA  N  H2  109.889 3.00
+PRO CD  N  H   110.257 3.00
+PRO CD  N  H2  110.257 3.00
+PRO H   N  H2  108.772 3.00
+PRO N   CA C   110.397 1.50
+PRO N   CA CB  103.994 1.50
+PRO N   CA HA  109.579 1.50
+PRO C   CA CB  113.159 3.00
+PRO C   CA HA  109.687 1.50
+PRO CB  CA HA  109.910 1.89
+PRO CA  C  O   116.979 3.00
+PRO CA  C  OXT 116.979 3.00
+PRO O   C  OXT 126.043 1.52
+PRO CA  CB CG  101.701 3.00
+PRO CA  CB HB3 110.865 1.50
+PRO CA  CB HB2 110.865 1.50
+PRO CG  CB HB3 110.891 1.59
+PRO CG  CB HB2 110.891 1.59
 PRO HB3 CB HB2 108.880 2.25
-PRO CB CG CD 104.486 3.00
-PRO CB CG HG3 110.897 1.50
-PRO CB CG HG2 110.897 1.50
-PRO CD CG HG3 110.795 1.50
-PRO CD CG HG2 110.795 1.50
+PRO CB  CG CD  105.541 3.00
+PRO CB  CG HG3 110.897 1.50
+PRO CB  CG HG2 110.897 1.50
+PRO CD  CG HG3 110.621 1.50
+PRO CD  CG HG2 110.621 1.50
 PRO HG3 CG HG2 108.871 1.50
-PRO N CD CG 104.878 3.00
-PRO N CD HD3 110.854 1.50
-PRO N CD HD2 110.854 1.50
-PRO CG CD HD3 110.755 1.50
-PRO CG CD HD2 110.755 1.50
-PRO HD3 CD HD2 108.734 1.82
+PRO N   CD CG  104.386 2.30
+PRO N   CD HD3 110.569 1.50
+PRO N   CD HD2 110.569 1.50
+PRO CG  CD HD3 111.131 1.62
+PRO CG  CD HD2 111.131 1.62
+PRO HD3 CD HD2 109.116 1.50
 
 loop_
 _chem_comp_tor.comp_id
@@ -156,12 +164,12 @@ _chem_comp_tor.atom_id_4
 _chem_comp_tor.value_angle
 _chem_comp_tor.value_angle_esd
 _chem_comp_tor.period
-PRO chi1 N CA CB CG -60.000 10.0 3
-PRO chi2 CA CB CG CD 180.000 10.0 3
-PRO sp3_sp3_1 CB CA N CD 60.000 10.0 3
-PRO sp3_sp3_25 N CD CG CB -60.000 10.0 3
-PRO sp3_sp3_34 CG CD N CA 180.000 10.0 3
-PRO sp2_sp3_1 O C CA N 0.000 10.0 6
+PRO chi1       N  CA CB CG -60.000 10.0 3
+PRO chi2       CA CB CG CD 180.000 10.0 3
+PRO sp3_sp3_1  CB CA N  CD 60.000  10.0 3
+PRO sp3_sp3_28 N  CD CG CB -60.000 10.0 3
+PRO sp3_sp3_37 CG CD N  CA 180.000 10.0 3
+PRO sp2_sp3_1  O  C  CA N  0.000   10.0 6
 
 loop_
 _chem_comp_chir.comp_id
@@ -172,21 +180,16 @@ _chem_comp_chir.atom_id_2
 _chem_comp_chir.atom_id_3
 _chem_comp_chir.volume_sign
 PRO chir_1 CA N C CB positive
-PRO chir_2 N CA CD H both
 
 loop_
 _chem_comp_plane_atom.comp_id
 _chem_comp_plane_atom.plane_id
 _chem_comp_plane_atom.atom_id
 _chem_comp_plane_atom.dist_esd
-PRO plan-1 CA 0.020
-PRO plan-1 CD 0.020
-PRO plan-1 H 0.020
-PRO plan-1 N 0.020
-PRO plan-2 C 0.020
-PRO plan-2 CA 0.020
-PRO plan-2 O 0.020
-PRO plan-2 OXT 0.020
+PRO plan-1 C   0.020
+PRO plan-1 CA  0.020
+PRO plan-1 O   0.020
+PRO plan-1 OXT 0.020
 
 loop_
 _pdbx_chem_comp_descriptor.comp_id
@@ -194,20 +197,20 @@ _pdbx_chem_comp_descriptor.type
 _pdbx_chem_comp_descriptor.program
 _pdbx_chem_comp_descriptor.program_version
 _pdbx_chem_comp_descriptor.descriptor
-PRO SMILES ACDLabs 10.04 O=C(O)C1NCCC1
-PRO SMILES_CANONICAL CACTVS 3.341 OC(=O)[C@@H]1CCCN1
-PRO SMILES CACTVS 3.341 OC(=O)[CH]1CCCN1
-PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1C[C@H](NC1)C(=O)O
-PRO SMILES "OpenEye OEToolkits" 1.5.0 C1CC(NC1)C(=O)O
-PRO InChI InChI 1.03 InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
-PRO InChIKey InChI 1.03 ONIBWKKTOPOVIA-BYPYZUCNSA-N
+PRO SMILES           ACDLabs              10.04 "O=C(O)C1NCCC1"
+PRO SMILES_CANONICAL CACTVS               3.341 "OC(=O)[C@@H]1CCCN1"
+PRO SMILES           CACTVS               3.341 "OC(=O)[CH]1CCCN1"
+PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H](NC1)C(=O)O"
+PRO SMILES           "OpenEye OEToolkits" 1.5.0 "C1CC(NC1)C(=O)O"
+PRO InChI            InChI                1.03  "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"
+PRO InChIKey         InChI                1.03  ONIBWKKTOPOVIA-BYPYZUCNSA-N
 
 loop_
 _pdbx_chem_comp_description_generator.comp_id
 _pdbx_chem_comp_description_generator.program_name
 _pdbx_chem_comp_description_generator.program_version
 _pdbx_chem_comp_description_generator.descriptor
-PRO acedrg 278 "dictionary generator"
-PRO acedrg_database 12 "data source"
-PRO rdkit 2019.09.1 "Chemoinformatics tool"
-PRO refmac5 5.8.0419 "optimization tool"
+PRO acedrg          281       "dictionary generator"
+PRO acedrg_database 12        "data source"
+PRO rdkit           2019.09.1 "Chemoinformatics tool"
+PRO refmac5         5.8.0419  "optimization tool"

package/baby-gru/monomers/t/TYR.cif

@@ -19,30 +19,30 @@ _chem_comp_atom.charge
 _chem_comp_atom.x
 _chem_comp_atom.y
 _chem_comp_atom.z
-TYR N N NT3 1 5.363 5.148 15.619
-TYR CA C CH1 0 5.352 6.374 16.467
-TYR C C C 0 4.808 7.551 15.649
-TYR O O O 0 4.011 8.328 16.222
-TYR CB C CH2 0 6.754 6.687 17.001
-TYR CG C CR6 0 7.337 5.635 17.936
-TYR CD1 C CR16 0 7.089 5.671 19.307
-TYR CD2 C CR16 0 8.139 4.603 17.449
-TYR CE1 C CR16 0 7.618 4.714 20.164
-TYR CE2 C CR16 0 8.674 3.642 18.296
-TYR CZ C CR6 0 8.413 3.697 19.657
-TYR OH O OH1 0 8.936 2.754 20.494
-TYR OXT O OC -1 5.198 7.654 14.465
-TYR H H H 0 6.035 5.195 15.019
-TYR H2 H H 0 4.582 5.061 15.177
-TYR H3 H H 0 5.479 4.415 16.133
-TYR HA H H 0 4.747 6.216 17.240
-TYR HB3 H H 0 6.719 7.546 17.478
-TYR HB2 H H 0 7.360 6.798 16.235
-TYR HD1 H H 0 6.549 6.359 19.662
-TYR HD2 H H 0 8.323 4.557 16.524
-TYR HE1 H H 0 7.439 4.755 21.088
-TYR HE2 H H 0 9.213 2.952 17.948
-TYR HH H H 0 9.793 2.799 20.487
+TYR N N NT3 1 5.311 5.160 15.589
+TYR CA C CH1 0 5.358 6.374 16.456
+TYR C C C 0 4.823 7.578 15.662
+TYR O O O 0 3.988 8.305 16.245
+TYR CB C CH2 0 6.763 6.679 16.994
+TYR CG C CR6 0 7.348 5.630 17.938
+TYR CD1 C CR16 0 7.096 5.672 19.314
+TYR CD2 C CR16 0 8.161 4.597 17.458
+TYR CE1 C CR16 0 7.628 4.720 20.176
+TYR CE2 C CR16 0 8.697 3.641 18.313
+TYR CZ C CR6 0 8.431 3.702 19.674
+TYR OH O OH1 0 8.982 2.738 20.476
+TYR OXT O OC -1 5.248 7.759 14.496
+TYR H H H 0 5.552 4.421 16.046
+TYR H2 H H 0 5.856 5.257 14.876
+TYR H3 H H 0 4.470 5.038 15.288
+TYR HA H H 0 4.756 6.220 17.232
+TYR HB3 H H 0 6.733 7.543 17.464
+TYR HB2 H H 0 7.369 6.788 16.227
+TYR HD1 H H 0 6.552 6.358 19.667
+TYR HD2 H H 0 8.350 4.543 16.534
+TYR HE1 H H 0 7.444 4.765 21.099
+TYR HE2 H H 0 9.240 2.953 17.971
+TYR HH H H 0 8.782 2.828 21.308
 
 loop_
 _chem_comp_tree.comp_id
@@ -205,7 +205,7 @@ TYR CONST_2 CG CD1 CE1 CZ 0.000 0.0 1
 TYR CONST_3 CZ CE2 CD2 CG 0.000 0.0 1
 TYR CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1
 TYR CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1
-TYR hh1 CE1 CZ OH HH 90.000 5.0 2
+TYR hh1 CE1 CZ OH HH 0.000 5.0 2
 TYR sp3_sp3_1 C CA N H 180.000 10.0 3
 TYR const_21 CE2 CD2 CG CD1 0.000 0.0 1
 TYR sp2_sp3_1 O C CA N 0.000 10.0 6
@@ -265,3 +265,4 @@ TYR acedrg 278 "dictionary generator"
 TYR acedrg_database 12 "data source"
 TYR rdkit 2019.09.1 "Chemoinformatics tool"
 TYR refmac5 5.8.0419 "optimization tool"
+TYR servalcat 0.4.57 'optimization tool'