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javascript
/
three.js
-ын хуулбар https://github.com/tazdij/three.js.git
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Эх сурвалжийг харах

CSS3DRenderer: added molecules example.

alteredq 12 жил өмнө
parent
20029be18b
commit
48324702ed
21 өөрчлөгдсөн 3319 нэмэгдсэн , 0 устгасан
Өөрчлөлтийг ялгаж харах Өөрчлөлтийн статистик харах
  1. 337 0
      examples/css3d_molecules.html
  2. 237 0
      examples/js/loaders/PDBLoader.js
  3. 3 0
      examples/models/molecules/.htaccess
  4. 287 0
      examples/models/molecules/Al2O3.pdb
  5. 40 0
      examples/models/molecules/aspirin.pdb
  6. 122 0
      examples/models/molecules/buckyball.pdb
  7. 49 0
      examples/models/molecules/caf2.pdb
  8. 44 0
      examples/models/molecules/caffeine.pdb
  9. 237 0
      examples/models/molecules/cholesterol.pdb
  10. 119 0
      examples/models/molecules/cocaine.pdb
  11. 155 0
      examples/models/molecules/cu.pdb
  12. 30 0
      examples/models/molecules/cubane.pdb
  13. 665 0
      examples/models/molecules/diamond.pdb
  14. 18 0
      examples/models/molecules/ethanol.pdb
  15. 59 0
      examples/models/molecules/glucose.pdb
  16. 403 0
      examples/models/molecules/graphite.pdb
  17. 79 0
      examples/models/molecules/lsd.pdb
  18. 90 0
      examples/models/molecules/lycopene.pdb
  19. 133 0
      examples/models/molecules/nacl.pdb
  20. 62 0
      examples/models/molecules/nicotine.pdb
  21. 150 0
      examples/models/molecules/ybco.pdb

+ 337 - 0
examples/css3d_molecules.html
Файл харах 

@@ -0,0 +1,337 @@
 
+<!DOCTYPE html>
 
+<html>
 
+	<head>
 
+		<meta charset="utf-8">
 
+		<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
 
+		<title>three.js css3d - molecules</title>
 
+		<style>
 
+			html, body {
 
+				height: 100%;
 
+			}
 
+
 
+			body {
 
+				background-color: #000000;
 
+				margin: 0;
 
+				font-family: Arial;
 
+				overflow: hidden;
 
+			}
 
+
 
+			a {
 
+				color: #ffffff;
 
+			}
 
+
 
+			#info {
 
+				position: absolute;
 
+				width: 100%;
 
+				color: #ffffff;
 
+				padding: 5px;
 
+				font-family: Monospace;
 
+				font-size: 13px;
 
+				font-weight: bold;
 
+				text-align: center;
 
+				z-index: 100;
 
+			}
 
+
 
+			#menu {
 
+				position: absolute;
 
+				bottom: 20px;
 
+				width: 100%;
 
+				text-align: center;
 
+				padding: 0;
 
+				margin: 0;
 
+			}
 
+
 
+			button {
 
+				color: rgb(255,255,255);
 
+				background: transparent;
 
+				border: 0px;
 
+				padding: 5px 10px;
 
+				cursor: pointer;
 
+			}
 
+			button:hover {
 
+				background-color: rgba(0,255,255,0.5);
 
+			}
 
+			button:active {
 
+				color: #000000;
 
+				background-color: rgba(0,255,255,1);
 
+			}
 
+		</style>
 
+	</head>
 
+	<body>
 
+		<script src="../build/three.min.js"></script>
 
+		<script src="js/controls/TrackballControls.js"></script>
 
+		<script src="js/renderers/CSS3DRenderer.js"></script>
 
+		<script src="js/loaders/PDBLoader.js"></script>
 
+
 
+		<div id="container"></div>
 
+		<div id="info"><a href="http://threejs.org" target="_blank">three.js css3d</a> - molecules</div>
 
+		<div id="menu"></div>
 
+
 
+		<script>
 
+			var camera, scene, renderer;
 
+			var controls;
 
+
 
+			var objects = [];
 
+
 
+			var MOLECULES = {
 
+			"Ethanol"   :"ethanol.pdb",
 
+			"Aspirin"   :"aspirin.pdb",
 
+			"Caffeine"  :"caffeine.pdb",
 
+			"Nicotine"  :"nicotine.pdb",
 
+			"LSD"  		:"lsd.pdb",
 
+			"Cocaine"  		:"cocaine.pdb",
 
+			"Cholesterol"  :"cholesterol.pdb",
 
+			"Lycopene"  :"lycopene.pdb",
 
+			"Glucose"   : "glucose.pdb",
 
+			"Aluminium oxide":"Al2O3.pdb",
 
+			"Cubane"	:"cubane.pdb",
 
+			"Copper"    :"cu.pdb",
 
+			"Fluorite"  :"caf2.pdb",
 
+			"Salt"      :"nacl.pdb",
 
+			"YBCO superconductor":"ybco.pdb",
 
+			"Buckyball" : "buckyball.pdb",
 
+			//"Diamond"   :"diamond.pdb",
 
+			"Graphite"  :"graphite.pdb"
 
+			};
 
+
 
+			var loader = new THREE.PDBLoader();
 
+			var colorSpriteMap = {};
 
+			var baseSprite = document.createElement( 'img' );
 
+
 
+			var menu = document.getElementById( "menu" );
 
+
 
+			init();
 
+			animate();
 
+
 
+			function init() {
 
+
 
+				camera = new THREE.PerspectiveCamera( 50, window.innerWidth / window.innerHeight, 1, 5000 );
 
+				camera.position.z = 1800;
 
+
 
+				scene = new THREE.Scene();
 
+
 
+				//
 
+
 
+				renderer = new THREE.CSS3DRenderer();
 
+				renderer.setSize( window.innerWidth, window.innerHeight );
 
+				renderer.domElement.style.position = 'absolute';
 
+				renderer.domElement.style.top = 0;
 
+				document.getElementById( 'container' ).appendChild( renderer.domElement );
 
+
 
+				//
 
+
 
+				controls = new THREE.TrackballControls( camera, renderer.domElement );
 
+				controls.rotateSpeed = 0.5;
 
+				controls.addEventListener( 'change', render );
 
+
 
+				//
 
+
 
+				baseSprite.onload = function () {
 
+
 
+					loadMolecule( "models/molecules/caffeine.pdb" );
 
+
 
+					function generateButtonCallback( url ) {
 
+
 
+						return function ( event ) {
 
+
 
+							loadMolecule( url );
 
+
 
+						}
 
+
 
+					}
 
+
 
+					for ( var m in MOLECULES ) {
 
+
 
+						var button = document.createElement( 'button' );
 
+						button.innerHTML = m;
 
+						menu.appendChild( button );
 
+
 
+						var url = "models/molecules/" +  MOLECULES[ m ];
 
+
 
+						button.addEventListener( 'click', generateButtonCallback( url ), false );
 
+
 
+					}
 
+
 
+				};
 
+
 
+				baseSprite.src = 'textures/sprites/ball.png';
 
+
 
+				//
 
+
 
+				window.addEventListener( 'resize', onWindowResize, false );
 
+
 
+			}
 
+
 
+			//
 
+
 
+			function parseColor( colorString ) {
 
+
 
+				// default to white opaque
 
+
 
+				var r, g, b, a;
 
+				r = g = b = a = 1;
 
+
 
+				var matchRGBA = reRGBA.exec( colorString );
 
+
 
+				if ( matchRGBA ) {
 
+
 
+					r = parseInt( matchRGBA[ 1 ] ) / 255;
 
+					g = parseInt( matchRGBA[ 2 ] ) / 255;
 
+					b = parseInt( matchRGBA[ 3 ] ) / 255;
 
+					a = parseFloat( matchRGBA[ 4 ] );
 
+
 
+				} else {
 
+
 
+					var matchRGB = reRGB.exec( colorString );
 
+
 
+					if ( matchRGB ) {
 
+
 
+						r = parseInt( matchRGB[ 1 ] ) / 255;
 
+						g = parseInt( matchRGB[ 2 ] ) / 255;
 
+						b = parseInt( matchRGB[ 3 ] ) / 255;
 
+
 
+					}
 
+
 
+				}
 
+
 
+				return { "r": r, "g": g, "b": b, "a": a };
 
+
 
+			}
 
+
 
+			function colorify( ctx, width, height, color, a ) {
 
+
 
+				var r = color.r;
 
+				var g = color.g;
 
+				var b = color.b;
 
+
 
+				var imageData = ctx.getImageData( 0, 0, width, height );
 
+				var data = imageData.data;
 
+
 
+				for ( var y = 0; y < height; y ++ ) {
 
+
 
+					for ( var x = 0; x < width; x ++ ) {
 
+
 
+						var index = ( y * width + x ) * 4;
 
+
 
+						data[ index ]     *= r;
 
+						data[ index + 1 ] *= g;
 
+						data[ index + 2 ] *= b;
 
+						data[ index + 3 ] *= a;
 
+
 
+					}
 
+
 
+				}
 
+
 
+				ctx.putImageData( imageData, 0, 0 );
 
+
 
+			}
 
+
 
+			function imageToCanvas( image ) {
 
+
 
+				var width = image.width;
 
+				var height = image.height;
 
+
 
+				var canvas = document.createElement( 'canvas' );
 
+
 
+				canvas.width = width;
 
+				canvas.height = height;
 
+
 
+				var context = canvas.getContext( '2d' );
 
+				context.drawImage( image, 0, 0, width, height );
 
+
 
+				return canvas;
 
+
 
+			}
 
+
 
+			//
 
+
 
+			function loadMolecule( url ) {
 
+
 
+				//console.log( "loading", url );
 
+
 
+				for ( var i = 0; i < objects.length; i ++ ) {
 
+
 
+					scene.remove( objects[ i ] );
 
+					renderer.cameraElement.removeChild( objects[ i ].element );
 
+
 
+				}
 
+
 
+				objects = [];
 
+
 
+				loader.load( url, function ( geometry ) {
 
+
 
+					THREE.GeometryUtils.center( geometry );
 
+
 
+					for ( var i = 0; i < geometry.vertices.length; i ++ ) {
 
+
 
+						var position = geometry.vertices[ i ];
 
+						var color = geometry.colors[ i ];
 
+						var element = geometry.elements[ i ];
 
+
 
+						if ( !colorSpriteMap[ element ] ) {
 
+
 
+							var canvas = imageToCanvas( baseSprite );
 
+							var context = canvas.getContext( '2d' );
 
+
 
+							colorify( context, canvas.width, canvas.height, color, 1 );
 
+
 
+							var dataUrl = canvas.toDataURL();
 
+
 
+							colorSpriteMap[ element ] = dataUrl;
 
+
 
+						}
 
+
 
+						colorSprite = colorSpriteMap[ element ];
 
+
 
+						var atom = document.createElement( 'img' );
 
+						atom.src = colorSprite;
 
+
 
+						var object = new THREE.CSS3DObject( atom );
 
+						object.position.copy( position );
 
+						object.position.multiplyScalar( 50 );
 
+						object.billboard = true;
 
+						scene.add( object );
 
+
 
+						objects.push( object );
 
+
 
+					}
 
+
 
+					//console.log( "atoms", geometry.vertices.length );
 
+
 
+					render();
 
+
 
+				} );
 
+
 
+
 
+			}
 
+
 
+			//
 
+
 
+			function onWindowResize() {
 
+
 
+				camera.aspect = window.innerWidth / window.innerHeight;
 
+				camera.updateProjectionMatrix();
 
+
 
+				renderer.setSize( window.innerWidth, window.innerHeight );
 
+
 
+				render();
 
+
 
+			}
 
+
 
+			function animate() {
 
+
 
+				requestAnimationFrame( animate );
 
+				controls.update();
 
+
 
+			}
 
+
 
+			function render() {
 
+
 
+				renderer.render( scene, camera );
 
+
 
+			}
 
+
 
+    </script>
 
+  </body>
 
+
 
+</html>

+ 237 - 0
examples/js/loaders/PDBLoader.js
Файл харах 

@@ -0,0 +1,237 @@
 
+/**
 
+ * @author alteredq / http://alteredqualia.com/
 
+ */
 
+
 
+THREE.PDBLoader = function ( showStatus ) {
 
+
 
+	THREE.Loader.call( this, showStatus );
 
+
 
+};
 
+
 
+THREE.PDBLoader.prototype = new THREE.Loader();
 
+THREE.PDBLoader.prototype.constructor = THREE.PDBLoader;
 
+THREE.PDBLoader.prototype.supr = THREE.Loader.prototype;
 
+
 
+THREE.PDBLoader.prototype.load = function ( url, callback ) {
 
+
 
+	var worker, scope = this;
 
+
 
+	this.onLoadStart();
 
+	this.loadAjaxPDB( this, url, callback );
 
+
 
+};
 
+
 
+THREE.PDBLoader.prototype.loadAjaxPDB = function ( context, url, callback, callbackProgress ) {
 
+
 
+	var xhr = new XMLHttpRequest();
 
+
 
+	var length = 0;
 
+
 
+	xhr.onreadystatechange = function () {
 
+
 
+		if ( xhr.readyState === xhr.DONE ) {
 
+
 
+			if ( xhr.status === 200 || xhr.status === 0 ) {
 
+
 
+				if ( xhr.responseText ) {
 
+
 
+					var json = context.parsePDB( xhr.responseText );
 
+					context.createModel( json, callback );
 
+
 
+				} else {
 
+
 
+					console.warn( "THREE.PDBLoader: [" + url + "] seems to be unreachable or file there is empty" );
 
+
 
+				}
 
+
 
+				// in context of more complex asset initialization
 
+				// do not block on single failed file
 
+				// maybe should go even one more level up
 
+
 
+				context.onLoadComplete();
 
+
 
+			} else {
 
+
 
+				console.error( "THREE.PDBLoader: Couldn't load [" + url + "] [" + xhr.status + "]" );
 
+
 
+			}
 
+
 
+		} else if ( xhr.readyState === xhr.LOADING ) {
 
+
 
+			if ( callbackProgress ) {
 
+
 
+				if ( length === 0 ) {
 
+
 
+					length = xhr.getResponseHeader( "Content-Length" );
 
+
 
+				}
 
+
 
+				callbackProgress( { total: length, loaded: xhr.responseText.length } );
 
+
 
+			}
 
+
 
+		} else if ( xhr.readyState === xhr.HEADERS_RECEIVED ) {
 
+
 
+			length = xhr.getResponseHeader( "Content-Length" );
 
+
 
+		}
 
+
 
+	};
 
+
 
+	xhr.open( "GET", url, true );
 
+	if ( xhr.overrideMimeType ) xhr.overrideMimeType( "text/plain; charset=x-user-defined" );
 
+	xhr.setRequestHeader( "Content-Type", "text/plain" );
 
+	xhr.send( null );
 
+
 
+};
 
+
 
+// Based on CanvasMol PDB parser
 
+
 
+THREE.PDBLoader.prototype.parsePDB = function ( text ) {
 
+
 
+	function trim( text ) {
 
+
 
+		return text.replace(/^\s\s*/, '').replace(/\s\s*$/, '');
 
+
 
+	}
 
+
 
+	function capitalize( text ) {
 
+
 
+		return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase();
 
+
 
+	}
 
+
 
+    function hash( s, e ) {
 
+
 
+        return "s" + Math.min( s, e ) + "e" + Math.max( s, e );
 
+
 
+    }
 
+
 
+    function parseBond( start, length ) {
 
+
 
+        var eatom = parseInt( lines[ i ].substr( start, length ) );
 
+
 
+        if( eatom ) {
 
+
 
+            var h = hash( satom, eatom );
 
+
 
+            if ( bhash[ h ] == undefined ) {
 
+
 
+                bonds.push( [ satom - 1, eatom - 1, 1 ] );
 
+                bhash[ h ] = bonds.length - 1;
 
+
 
+			} else {
 
+
 
+                // doesn't really work as almost all PDBs
 
+                // have just normal bonds appearing multiple
 
+                // times instead of being double/triple bonds
 
+                //bonds[bhash[h]][2] += 1;
 
+
 
+            }
 
+
 
+        }
 
+
 
+    }
 
+
 
+	var CPK = {"h":[255,255,255],"he":[217,255,255],"li":[204,128,255],"be":[194,255,0],"b":[255,181,181],"c":[144,144,144],"n":[48,80,248],"o":[255,13,13],"f":[144,224,80],"ne":[179,227,245],"na":[171,92,242],"mg":[138,255,0],"al":[191,166,166],"si":[240,200,160],"p":[255,128,0],"s":[255,255,48],"cl":[31,240,31],"ar":[128,209,227],"k":[143,64,212],"ca":[61,255,0],"sc":[230,230,230],"ti":[191,194,199],"v":[166,166,171],"cr":[138,153,199],"mn":[156,122,199],"fe":[224,102,51],"co":[240,144,160],"ni":[80,208,80],"cu":[200,128,51],"zn":[125,128,176],"ga":[194,143,143],"ge":[102,143,143],"as":[189,128,227],"se":[255,161,0],"br":[166,41,41],"kr":[92,184,209],"rb":[112,46,176],"sr":[0,255,0],"y":[148,255,255],"zr":[148,224,224],"nb":[115,194,201],"mo":[84,181,181],"tc":[59,158,158],"ru":[36,143,143],"rh":[10,125,140],"pd":[0,105,133],"ag":[192,192,192],"cd":[255,217,143],"in":[166,117,115],"sn":[102,128,128],"sb":[158,99,181],"te":[212,122,0],"i":[148,0,148],"xe":[66,158,176],"cs":[87,23,143],"ba":[0,201,0],"la":[112,212,255],"ce":[255,255,199],"pr":[217,255,199],"nd":[199,255,199],"pm":[163,255,199],"sm":[143,255,199],"eu":[97,255,199],"gd":[69,255,199],"tb":[48,255,199],"dy":[31,255,199],"ho":[0,255,156],"er":[0,230,117],"tm":[0,212,82],"yb":[0,191,56],"lu":[0,171,36],"hf":[77,194,255],"ta":[77,166,255],"w":[33,148,214],"re":[38,125,171],"os":[38,102,150],"ir":[23,84,135],"pt":[208,208,224],"au":[255,209,35],"hg":[184,184,208],"tl":[166,84,77],"pb":[87,89,97],"bi":[158,79,181],"po":[171,92,0],"at":[117,79,69],"rn":[66,130,150],"fr":[66,0,102],"ra":[0,125,0],"ac":[112,171,250],"th":[0,186,255],"pa":[0,161,255],"u":[0,143,255],"np":[0,128,255],"pu":[0,107,255],"am":[84,92,242],"cm":[120,92,227],"bk":[138,79,227],"cf":[161,54,212],"es":[179,31,212],"fm":[179,31,186],"md":[179,13,166],"no":[189,13,135],"lr":[199,0,102],"rf":[204,0,89],"db":[209,0,79],"sg":[217,0,69],"bh":[224,0,56],"hs":[230,0,46],"mt":[235,0,38],
 
+           "ds":[235,0,38],"rg":[235,0,38],"cn":[235,0,38],"uut":[235,0,38],"uuq":[235,0,38],"uup":[235,0,38],"uuh":[235,0,38],"uus":[235,0,38],"uuo":[235,0,38]};
 
+
 
+
 
+    var atoms = [];
 
+    var bonds = [];
 
+    var histogram = {};
 
+
 
+    var bhash = {};
 
+
 
+    var lines = text.split( "\n" );
 
+
 
+    var x, y, z, e;
 
+
 
+    for( var i = 0, il = lines.length; i < il; ++ i ) {
 
+
 
+        if( lines[i].substr(0,4)=="ATOM" || lines[i].substr(0,6)=="HETATM" ) {
 
+
 
+            x = parseFloat( lines[i].substr(30,7) );
 
+            y = parseFloat( lines[i].substr(38,7) );
 
+            z = parseFloat( lines[i].substr(46,7) );
 
+
 
+            e = trim( lines[i].substr(76,2) ).toLowerCase();
 
+
 
+            if ( e=="" ) e = trim(lines[i].substr(12,2)).toLowerCase();
 
+            atoms.push( [ x,y,z, CPK[e], capitalize(e) ] );
 
+
 
+            if (histogram[e]==undefined) histogram[e] = 1;
 
+            else histogram[e] += 1;
 
+
 
+        } else if(lines[i].substr(0,6)=="CONECT") {
 
+
 
+            var satom = parseInt( lines[i].substr(6,5) );
 
+
 
+            parseBond(11,5);
 
+            parseBond(16,5);
 
+            parseBond(21,5);
 
+            parseBond(26,5);
 
+
 
+        }
 
+
 
+    }
 
+
 
+    return { "ok": true, "atoms": atoms, "bonds": bonds, "histogram": histogram };
 
+
 
+};
 
+
 
+THREE.PDBLoader.prototype.createModel = function ( json, callback ) {
 
+
 
+	var scope = this,
 
+	geometryAtoms = new THREE.Geometry(),
 
+	geometryBonds = new THREE.Geometry();
 
+
 
+	geometryAtoms.elements = [];
 
+
 
+	var atoms = json.atoms;
 
+	var bonds = json.bonds;
 
+
 
+	for ( var i = 0; i < atoms.length; i ++ ) {
 
+
 
+		var atom = atoms[ i ];
 
+
 
+		var x = atom[ 0 ];
 
+		var y = atom[ 1 ];
 
+		var z = atom[ 2 ];
 
+
 
+		var position = new THREE.Vector3( x, y, z );
 
+		geometryAtoms.vertices.push( position );
 
+
 
+		var r = atom[ 3 ][ 0 ] / 255;
 
+		var g = atom[ 3 ][ 1 ] / 255;
 
+		var b = atom[ 3 ][ 2 ] / 255;
 
+		var color = new THREE.Color();
 
+		color.setRGB( r, g, b );
 
+
 
+		geometryAtoms.colors.push( color );
 
+
 
+		geometryAtoms.elements.push( atom[ 4 ] );
 
+
 
+	}
 
+
 
+/*
 
+	for ( var i = 0; i < bonds.length; i ++ ) {
 
+
 
+		var bond = bonds[ i ];
 
+
 
+		var start = bond[ 0 ];
 
+		var end = bond[ 1 ];
 
+
 
+		var vertex1 = geometryAtoms.vertices[ start ];
 
+		var vertex2 = geometryAtoms.vertices[ end ];
 
+
 
+		geometryBonds.vertices.push( vertex1.clone() );
 
+		geometryBonds.vertices.push( vertex2.clone() );
 
+
 
+	}
 
+*/
 
+
 
+	callback( geometryAtoms, geometryBonds );
 
+
 
+};
 
+

+ 3 - 0
examples/models/molecules/.htaccess
Файл харах 

@@ -0,0 +1,3 @@
 
+<Files *.pdb>
 
+SetOutputFilter DEFLATE
 
+</Files>

+ 287 - 0
examples/models/molecules/Al2O3.pdb
Файл харах 

@@ -0,0 +1,287 @@
 
+HEADER    CSD ENTRY GLOBAL
 
+CRYST1   4.7589   4.7589  12.9912  90.00  90.00 120.00      R-3c
 
+SCALE1      0.210133  0.121320 -0.000000       0.000000
 
+SCALE2      0.000000  0.242640 -0.000000       0.000000
 
+SCALE3      0.000000  0.000000  0.076975       0.000000
 
+HETATM    1 Al   UNK 0   1       2.379   4.121   4.573  1.00  0.00
 
+HETATM    2 O    UNK 0   1       3.835   4.121   3.248  1.00  0.00
 
+HETATM    3 Al   UNK 0   1       2.379   4.121   1.923  1.00  0.00
 
+HETATM    4 O    UNK 0   1       1.652   5.382   3.248  1.00  0.00
 
+HETATM    5 O    UNK 0   1       1.652   2.861   3.248  1.00  0.00
 
+HETATM    6 Al   UNK 0   1      -0.000   2.748   4.088  1.00  0.00
 
+HETATM    7 Al   UNK 0   1       4.759   2.748   4.088  1.00  0.00
 
+HETATM    8 O    UNK 0   1       3.303   2.748   5.413  1.00  0.00
 
+HETATM    9 Al   UNK 0   1       2.379   6.869   4.088  1.00  0.00
 
+HETATM   10 O    UNK 0   1       3.107   5.608   5.413  1.00  0.00
 
+HETATM   11 O    UNK 0   1       0.728   4.008   5.413  1.00  0.00
 
+HETATM   12 Al   UNK 0   1       4.759   5.495   2.408  1.00  0.00
 
+HETATM   13 Al   UNK 0   1       2.379   1.374   2.408  1.00  0.00
 
+HETATM   14 Al   UNK 0   1       0.000   5.495   2.408  1.00  0.00
 
+HETATM   15 O    UNK 0   1       0.728   4.234   1.083  1.00  0.00
 
+HETATM   16 O    UNK 0   1       3.303   5.495   1.083  1.00  0.00
 
+HETATM   17 O    UNK 0   1       3.107   2.634   1.083  1.00  0.00
 
+HETATM   18 Al   UNK 0   1      -2.379   4.121   4.573  1.00  0.00
 
+HETATM   19 O    UNK 0   1      -3.107   5.382   3.248  1.00  0.00
 
+HETATM   20 Al   UNK 0   1      -2.379   4.121   1.923  1.00  0.00
 
+HETATM   21 O    UNK 0   1      -3.107   2.861   3.248  1.00  0.00
 
+HETATM   22 O    UNK 0   1      -0.924   4.121   3.248  1.00  0.00
 
+HETATM   23 Al   UNK 0   1      -2.379   6.869   4.088  1.00  0.00
 
+HETATM   24 O    UNK 0   1      -1.652   5.608   5.413  1.00  0.00
 
+HETATM   25 Al   UNK 0   1      -4.759   2.748   4.088  1.00  0.00
 
+HETATM   26 O    UNK 0   1      -4.031   4.008   5.413  1.00  0.00
 
+HETATM   27 O    UNK 0   1      -1.456   2.748   5.413  1.00  0.00
 
+HETATM   28 Al   UNK 0   1      -4.759   5.495   2.408  1.00  0.00
 
+HETATM   29 Al   UNK 0   1      -2.379   1.374   2.408  1.00  0.00
 
+HETATM   30 O    UNK 0   1      -1.652   2.634   1.083  1.00  0.00
 
+HETATM   31 O    UNK 0   1      -4.031   4.234   1.083  1.00  0.00
 
+HETATM   32 O    UNK 0   1      -1.456   5.495   1.083  1.00  0.00
 
+HETATM   33 Al   UNK 0   1       0.000   0.000   4.573  1.00  0.00
 
+HETATM   34 O    UNK 0   1      -0.728  -1.261   3.248  1.00  0.00
 
+HETATM   35 Al   UNK 0   1       0.000   0.000   1.923  1.00  0.00
 
+HETATM   36 O    UNK 0   1       1.456   0.000   3.248  1.00  0.00
 
+HETATM   37 O    UNK 0   1      -0.728   1.261   3.248  1.00  0.00
 
+HETATM   38 Al   UNK 0   1      -2.379  -1.374   4.088  1.00  0.00
 
+HETATM   39 O    UNK 0   1      -1.652  -0.113   5.413  1.00  0.00
 
+HETATM   40 Al   UNK 0   1       2.379  -1.374   4.088  1.00  0.00
 
+HETATM   41 O    UNK 0   1       0.924  -1.374   5.413  1.00  0.00
 
+HETATM   42 O    UNK 0   1       0.728   1.487   5.413  1.00  0.00
 
+HETATM   43 Al   UNK 0   1      -0.000  -2.748   2.408  1.00  0.00
 
+HETATM   44 O    UNK 0   1       0.924   1.374   1.083  1.00  0.00
 
+HETATM   45 O    UNK 0   1       0.728  -1.487   1.083  1.00  0.00
 
+HETATM   46 O    UNK 0   1      -1.652   0.113   1.083  1.00  0.00
 
+HETATM   47 Al   UNK 0   1       4.759   0.000   4.573  1.00  0.00
 
+HETATM   48 O    UNK 0   1       4.031  -1.261   3.248  1.00  0.00
 
+HETATM   49 Al   UNK 0   1       4.759   0.000   1.923  1.00  0.00
 
+HETATM   50 O    UNK 0   1       6.215   0.000   3.248  1.00  0.00
 
+HETATM   51 O    UNK 0   1       4.031   1.261   3.248  1.00  0.00
 
+HETATM   52 O    UNK 0   1       3.107  -0.113   5.413  1.00  0.00
 
+HETATM   53 Al   UNK 0   1       7.138  -1.374   4.088  1.00  0.00
 
+HETATM   54 O    UNK 0   1       5.683  -1.374   5.413  1.00  0.00
 
+HETATM   55 O    UNK 0   1       5.487   1.487   5.413  1.00  0.00
 
+HETATM   56 Al   UNK 0   1       4.759  -2.748   2.408  1.00  0.00
 
+HETATM   57 Al   UNK 0   1       7.138   1.374   2.408  1.00  0.00
 
+HETATM   58 O    UNK 0   1       5.683   1.374   1.083  1.00  0.00
 
+HETATM   59 O    UNK 0   1       5.487  -1.487   1.083  1.00  0.00
 
+HETATM   60 O    UNK 0   1       3.107   0.113   1.083  1.00  0.00
 
+HETATM   61 Al   UNK 0   1      -0.000   2.748  13.234  1.00  0.00
 
+HETATM   62 O    UNK 0   1       1.456   2.748  11.909  1.00  0.00
 
+HETATM   63 Al   UNK 0   1      -0.000   2.748  10.583  1.00  0.00
 
+HETATM   64 O    UNK 0   1      -0.728   4.008  11.909  1.00  0.00
 
+HETATM   65 O    UNK 0   1      -0.728   1.487  11.909  1.00  0.00
 
+HETATM   66 Al   UNK 0   1      -2.379   1.374  12.749  1.00  0.00
 
+HETATM   67 Al   UNK 0   1       2.379   1.374  12.749  1.00  0.00
 
+HETATM   68 O    UNK 0   1       0.924   1.374  14.074  1.00  0.00
 
+HETATM   69 Al   UNK 0   1      -0.000   5.495  12.749  1.00  0.00
 
+HETATM   70 O    UNK 0   1       0.728   4.234  14.074  1.00  0.00
 
+HETATM   71 O    UNK 0   1      -1.652   2.634  14.074  1.00  0.00
 
+HETATM   72 Al   UNK 0   1       2.379   4.121  11.069  1.00  0.00
 
+HETATM   73 Al   UNK 0   1       0.000   0.000  11.069  1.00  0.00
 
+HETATM   74 Al   UNK 0   1      -2.379   4.121  11.069  1.00  0.00
 
+HETATM   75 O    UNK 0   1      -1.652   2.861   9.743  1.00  0.00
 
+HETATM   76 O    UNK 0   1       0.924   4.121   9.743  1.00  0.00
 
+HETATM   77 O    UNK 0   1       0.728   1.261   9.743  1.00  0.00
 
+HETATM   78 Al   UNK 0   1       2.379   1.374   8.903  1.00  0.00
 
+HETATM   79 O    UNK 0   1       3.835   1.374   7.578  1.00  0.00
 
+HETATM   80 Al   UNK 0   1       2.379   1.374   6.253  1.00  0.00
 
+HETATM   81 O    UNK 0   1       1.652   2.634   7.578  1.00  0.00
 
+HETATM   82 O    UNK 0   1       1.652   0.113   7.578  1.00  0.00
 
+HETATM   83 Al   UNK 0   1       0.000   0.000   8.418  1.00  0.00
 
+HETATM   84 Al   UNK 0   1       4.759   0.000   8.418  1.00  0.00
 
+HETATM   85 O    UNK 0   1       3.303   0.000   9.743  1.00  0.00
 
+HETATM   86 Al   UNK 0   1       2.379   4.121   8.418  1.00  0.00
 
+HETATM   87 O    UNK 0   1       3.107   2.861   9.743  1.00  0.00
 
+HETATM   88 Al   UNK 0   1       4.759   2.748   6.738  1.00  0.00
 
+HETATM   89 Al   UNK 0   1       2.379  -1.374   6.738  1.00  0.00
 
+HETATM   90 Al   UNK 0   1       0.000   2.748   6.738  1.00  0.00
 
+HETATM   91 O    UNK 0   1      -1.456   0.000   9.743  1.00  0.00
 
+HETATM   92 O    UNK 0   1       0.728  -1.261   9.743  1.00  0.00
 
+HETATM   93 Al   UNK 0   1      -2.379   1.374   8.903  1.00  0.00
 
+HETATM   94 O    UNK 0   1      -0.924   1.374   7.578  1.00  0.00
 
+HETATM   95 Al   UNK 0   1       0.000  -2.748   8.903  1.00  0.00
 
+HETATM   96 O    UNK 0   1      -0.728  -1.487   7.578  1.00  0.00
 
+HETATM   97 Al   UNK 0   1      -2.379  -1.374  10.583  1.00  0.00
 
+HETATM   98 Al   UNK 0   1       2.379  -1.374  10.583  1.00  0.00
 
+HETATM   99 O    UNK 0   1       1.652  -0.113  11.909  1.00  0.00
 
+HETATM  100 O    UNK 0   1      -0.924  -1.374  11.909  1.00  0.00
 
+HETATM  101 Al   UNK 0   1      -2.379   4.121   8.418  1.00  0.00
 
+HETATM  102 O    UNK 0   1      -3.835   4.121   9.743  1.00  0.00
 
+HETATM  103 O    UNK 0   1      -1.652   5.382   9.743  1.00  0.00
 
+HETATM  104 Al   UNK 0   1       0.000   5.495   8.903  1.00  0.00
 
+HETATM  105 Al   UNK 0   1      -4.759   5.495   8.903  1.00  0.00
 
+HETATM  106 O    UNK 0   1      -3.303   5.495   7.578  1.00  0.00
 
+HETATM  107 O    UNK 0   1      -3.107   2.634   7.578  1.00  0.00
 
+HETATM  108 O    UNK 0   1      -0.728   4.234   7.578  1.00  0.00
 
+HETATM  109 Al   UNK 0   1      -4.759   2.748  10.583  1.00  0.00
 
+HETATM  110 Al   UNK 0   1      -2.379   6.869  10.583  1.00  0.00
 
+HETATM  111 O    UNK 0   1      -3.303   2.748  11.909  1.00  0.00
 
+HETATM  112 O    UNK 0   1      -3.107   5.608  11.909  1.00  0.00
 
+HETATM  113 Al   UNK 0   1       4.759   0.000  11.069  1.00  0.00
 
+HETATM  114 O    UNK 0   1       5.487  -1.261   9.743  1.00  0.00
 
+HETATM  115 O    UNK 0   1       5.487   1.261   9.743  1.00  0.00
 
+HETATM  116 Al   UNK 0   1       7.138   1.374   8.903  1.00  0.00
 
+HETATM  117 Al   UNK 0   1       4.759  -2.748   8.903  1.00  0.00
 
+HETATM  118 O    UNK 0   1       4.031  -1.487   7.578  1.00  0.00
 
+HETATM  119 O    UNK 0   1       6.410   0.113   7.578  1.00  0.00
 
+HETATM  120 Al   UNK 0   1       4.759   2.748  10.583  1.00  0.00
 
+HETATM  121 Al   UNK 0   1       7.138  -1.374  10.583  1.00  0.00
 
+HETATM  122 O    UNK 0   1       6.410  -0.113  11.909  1.00  0.00
 
+HETATM  123 O    UNK 0   1       3.835  -1.374  11.909  1.00  0.00
 
+HETATM  124 O    UNK 0   1       4.031   1.487  11.909  1.00  0.00
 
+HETATM  125 O    UNK 0   1       3.107   5.382   9.743  1.00  0.00
 
+HETATM  126 Al   UNK 0   1       4.759   5.495   8.903  1.00  0.00
 
+HETATM  127 O    UNK 0   1       1.456   5.495   7.578  1.00  0.00
 
+HETATM  128 O    UNK 0   1       4.031   4.234   7.578  1.00  0.00
 
+HETATM  129 Al   UNK 0   1       2.379   6.869  10.583  1.00  0.00
 
+HETATM  130 O    UNK 0   1       4.031   4.008  11.909  1.00  0.00
 
+HETATM  131 O    UNK 0   1       1.652   5.608  11.909  1.00  0.00
 
+HETATM  132 Al   UNK 0   1      -2.379   1.374   6.253  1.00  0.00
 
+HETATM  133 Al   UNK 0   1      -0.000   5.495   6.253  1.00  0.00
 
+HETATM  134 Al   UNK 0   1       2.379   1.374  -0.243  1.00  0.00
 
+HETATM  135 Al   UNK 0   1       4.759   2.748   0.243  1.00  0.00
 
+HETATM  136 Al   UNK 0   1       0.000   2.748   0.243  1.00  0.00
 
+HETATM  137 O    UNK 0   1       1.456   2.748  -1.083  1.00  0.00
 
+HETATM  138 Al   UNK 0   1       2.379  -1.374   0.243  1.00  0.00
 
+HETATM  139 O    UNK 0   1       1.652  -0.113  -1.083  1.00  0.00
 
+HETATM  140 O    UNK 0   1       4.031   1.487  -1.083  1.00  0.00
 
+CONECT    1    2    3    4
 
+CONECT    2    3    7   12
 
+CONECT    3    4    5   12
 
+CONECT    4    9   14
 
+CONECT    5    1    6   13
 
+CONECT    6    1   11   18
 
+CONECT    7    1   47   51
 
+CONECT    8    1   80
 
+CONECT    9    1
 
+CONECT   10    1
 
+CONECT   11    1   90  133
 
+CONECT   12
 
+CONECT   13    3   17   35
 
+CONECT   14    3   20   22
 
+CONECT   15    3
 
+CONECT   16    3
 
+CONECT   17    3  134  135
 
+CONECT   18   19   20   21
 
+CONECT   19   20   23   28
 
+CONECT   20   21   22   28
 
+CONECT   21   25   29
 
+CONECT   22    6   18
 
+CONECT   23   18
 
+CONECT   24   18
 
+CONECT   25   18
 
+CONECT   26   18
 
+CONECT   27    6   18   90
 
+CONECT   28
 
+CONECT   29   20   35   37
 
+CONECT   30   20
 
+CONECT   31   20
 
+CONECT   32   20
 
+CONECT   33    6   34   35
 
+CONECT   34   35   38   43
 
+CONECT   35   36   37   43
 
+CONECT   36   13   33   40
 
+CONECT   37    6   33
 
+CONECT   38   33
 
+CONECT   39   33
 
+CONECT   40   33   47   48
 
+CONECT   41   33
 
+CONECT   42    6   33   80
 
+CONECT   43
 
+CONECT   44   13   35  134
 
+CONECT   45   35
 
+CONECT   46   35
 
+CONECT   47   48   49   50
 
+CONECT   48   49   56
 
+CONECT   49   13   50   51
 
+CONECT   50   53   57
 
+CONECT   51   13   47
 
+CONECT   52   47   80
 
+CONECT   53   47
 
+CONECT   54   47
 
+CONECT   55   47
 
+CONECT   56   49
 
+CONECT   57   49
 
+CONECT   58   49
 
+CONECT   59   49
 
+CONECT   60   13   49  134
 
+CONECT   61   62   63   64
 
+CONECT   62   63   67   72
 
+CONECT   63   64   65   72
 
+CONECT   64   69   74
 
+CONECT   65   61   66   73
 
+CONECT   66   61
 
+CONECT   67   61
 
+CONECT   68   61
 
+CONECT   69   61
 
+CONECT   70   61
 
+CONECT   71   61
 
+CONECT   72   76   86   87
 
+CONECT   73   63   77   83
 
+CONECT   74   63   75  101
 
+CONECT   75   63   93  101
 
+CONECT   76   63   86  104
 
+CONECT   77   63   78   83
 
+CONECT   78   79   80   81
 
+CONECT   79   80   84   88
 
+CONECT   80   81   82   88
 
+CONECT   81   86   90
 
+CONECT   82   78   83   89
 
+CONECT   83   78   91   92
 
+CONECT   84   78   85  113
 
+CONECT   85   78   98  113
 
+CONECT   86   78   87  104
 
+CONECT   87   78  120
 
+CONECT   88
 
+CONECT   89   80
 
+CONECT   90    6   42   80
 
+CONECT   91   73   93   97
 
+CONECT   92   73   95   98
 
+CONECT   93   83  101
 
+CONECT   94   83   90
 
+CONECT   95   83
 
+CONECT   96   83
 
+CONECT   97   73
 
+CONECT   98   73  113
 
+CONECT   99   73
 
+CONECT  100   73
 
+CONECT  101  102  103  104
 
+CONECT  102   74  105  109
 
+CONECT  103   74  104  110
 
+CONECT  104
 
+CONECT  105  101
 
+CONECT  106  101
 
+CONECT  107  101
 
+CONECT  108   90  101
 
+CONECT  109   74
 
+CONECT  110   74
 
+CONECT  111   74
 
+CONECT  112   74
 
+CONECT  113  114  115  120
 
+CONECT  114   84  117  121
 
+CONECT  115   84  116  120
 
+CONECT  116   84
 
+CONECT  117   84
 
+CONECT  118   84
 
+CONECT  119   84
 
+CONECT  120   72
 
+CONECT  121  113
 
+CONECT  122  113
 
+CONECT  123  113
 
+CONECT  124  113
 
+CONECT  125   72   86  126
 
+CONECT  126   86
 
+CONECT  127   86
 
+CONECT  128   86
 
+CONECT  129   72  125
 
+CONECT  130   72
 
+CONECT  131   72
 
+CONECT  132   27   90
 
+CONECT  133   90
 
+CONECT  134   13  135  136
 
+CONECT  135
 
+CONECT  136   44
 
+CONECT  137  134
 
+CONECT  138   60  134
 
+CONECT  139  134
 
+CONECT  140  134
 
+MASTER    0    0    0    0    0    0    0    0    3  140    0  140    0
 
+END

+ 40 - 0
examples/models/molecules/aspirin.pdb
Файл харах 

@@ -0,0 +1,40 @@
 
+HEADER    NONAME 22-Apr-10                                              NONE   1
 
+TITLE                                                                   NONE   2
 
+AUTHOR    Chemical Structure Services at http://cactus.nci.nih.gov      NONE   3
 
+REVDAT   1  22-Apr-10     0                                             NONE   4
 
+ATOM      1  C           0       2.154   1.017  -0.012  0.00  0.00           C+0
 
+ATOM      2  C           0      -0.545   1.675   0.087  0.00  0.00           C+0
 
+ATOM      3  C           0       1.761   2.338   0.015  0.00  0.00           C+0
 
+ATOM      4  C           0       0.416   2.666   0.064  0.00  0.00           C+0
 
+ATOM      5  C           0      -3.466  -1.377   0.133  0.00  0.00           C+0
 
+ATOM      6  C           0       1.192   0.004   0.010  0.00  0.00           C+0
 
+ATOM      7  C           0      -0.168   0.341   0.060  0.00  0.00           C+0
 
+ATOM      8  O           0       0.765  -2.290  -0.001  0.00  0.00           O+0
 
+ATOM      9  O           0      -2.733   0.825  -0.277  0.00  0.00           O+0
 
+ATOM     10  O           0       2.912  -1.731  -0.067  0.00  0.00           O+0
 
+ATOM     11  C           0       1.604  -1.411  -0.019  0.00  0.00           C+0
 
+ATOM     12  C           0      -2.411  -0.315  -0.036  0.00  0.00           C+0
 
+ATOM     13  O           0      -1.112  -0.634   0.081  0.00  0.00           O+0
 
+ATOM     14  H           0       3.183  -2.659  -0.086  0.00  0.00           H+0
 
+ATOM     15  H           0       3.203   0.765  -0.054  0.00  0.00           H+0
 
+ATOM     16  H           0      -1.591   1.939   0.125  0.00  0.00           H+0
 
+ATOM     17  H           0       2.506   3.120  -0.002  0.00  0.00           H+0
 
+ATOM     18  H           0       0.118   3.704   0.085  0.00  0.00           H+0
 
+ATOM     19  H           0      -3.762  -1.431   1.181  0.00  0.00           H+0
 
+ATOM     20  H           0      -4.334  -1.127  -0.477  0.00  0.00           H+0
 
+ATOM     21  H           0      -3.066  -2.340  -0.182  0.00  0.00           H+0
 
+CONECT    1    6    3   15    0                                         NONE  26
 
+CONECT    2    7    4   16    0                                         NONE  27
 
+CONECT    3    1    4   17    0                                         NONE  28
 
+CONECT    4    2    3   18    0                                         NONE  29
 
+CONECT    5   12   19   20   21                                         NONE  30
 
+CONECT    6    7    1   11    0                                         NONE  31
 
+CONECT    7    6    2   13    0                                         NONE  32
 
+CONECT    8   11    0    0    0                                         NONE  33
 
+CONECT    9   12    0    0    0                                         NONE  34
 
+CONECT   10   11   14    0    0                                         NONE  35
 
+CONECT   11    6   10    8    0                                         NONE  36
 
+CONECT   12   13    5    9    0                                         NONE  37
 
+CONECT   13    7   12    0    0                                         NONE  38
 
+END                                                                     NONE  39
 
+

+ 122 - 0
examples/models/molecules/buckyball.pdb
Файл харах 

@@ -0,0 +1,122 @@
 
+COMPND  bucky.pdb                                                               
+HETATM    1  C                 -3.4306  0.3484  0.3630                
+HETATM    2  C                 -3.1790  1.1810 -0.7334                
+HETATM    3  C                 -2.9160  0.3690 -1.8427                
+HETATM    4  C                 -3.0048 -0.9660 -1.4314                
+HETATM    5  C                 -3.3229 -0.9791 -0.0682                
+HETATM    6  C                 -1.9449  0.7442 -2.7732                
+HETATM    7  C                 -1.2332  1.9362 -2.5954                
+HETATM    8  C                 -1.4944  2.7485 -1.4902                
+HETATM    9  C                 -2.4680  2.3700 -0.5585                
+HETATM   10  C                 -2.0114  2.7298  0.7143                
+HETATM   11  C                 -2.2640  1.9005  1.8090                
+HETATM   12  C                 -2.9745  0.7074  1.6331                
+HETATM   13  C                 -2.4129 -0.2585  2.4753                
+HETATM   14  C                 -2.3071 -1.5829  2.0466                
+HETATM   15  C                 -2.7627 -1.9425  0.7730                
+HETATM   16  C                 -1.8823 -2.8972  0.2521                
+HETATM   17  C                 -1.5635 -2.8861 -1.1071                
+HETATM   18  C                 -2.1254 -1.9193 -1.9490                
+HETATM   19  C                 -1.1533 -1.5397 -2.8812                
+HETATM   20  C                 -1.0615 -0.2088 -3.2934                
+HETATM   21  C                  0.0879  1.7218 -3.0046                
+HETATM   22  C                 -0.4365  3.3422 -0.7917                
+HETATM   23  C                 -0.7555  3.3307  0.5716                
+HETATM   24  C                 -1.2619  1.6696  2.7586                
+HETATM   25  C                 -1.3534  0.3346  3.1711                
+HETATM   26  C                 -1.1426 -2.3137  2.3104                
+HETATM   27  C                 -0.8795 -3.1267  1.2011                
+HETATM   28  C                 -0.2429 -3.1010 -1.5184                
+HETATM   29  C                  0.0114 -2.2689 -2.6155                
+HETATM   30  C                  0.1936  0.3941 -3.4362                
+HETATM   31  C                  3.3266  0.9826  0.0695                
+HETATM   32  C                  3.0096  0.9706  1.4326                
+HETATM   33  C                  2.9177 -0.3640  1.8443                
+HETATM   34  C                  3.1778 -1.1770  0.7349                
+HETATM   35  C                  3.4306 -0.3451 -0.3621                
+HETATM   36  C                  1.9473 -0.7475  2.7721                
+HETATM   37  C                  1.0645  0.2062  3.2916                
+HETATM   38  C                  1.1547  1.5385  2.8834                
+HETATM   39  C                  2.1280  1.9203  1.9528                
+HETATM   40  C                  1.5657  2.8862  1.1107                
+HETATM   41  C                  1.8834  2.9000 -0.2489                
+HETATM   42  C                  2.7651  1.9463 -0.7707                
+HETATM   43  C                  2.3092  1.5866 -2.0437                
+HETATM   44  C                  2.4144  0.2631 -2.4755                
+HETATM   45  C                  2.9758 -0.7031 -1.6328                
+HETATM   46  C                  2.2666 -1.8962 -1.8100                
+HETATM   47  C                  2.0133 -2.7276 -0.7172                
+HETATM   48  C                  2.4693 -2.3670  0.5560                
+HETATM   49  C                  1.4973 -2.7481  1.4877                
+HETATM   50  C                  1.2349 -1.9394  2.5952                
+HETATM   51  C                 -0.1917 -0.3936  3.4362                
+HETATM   52  C                 -0.0088  2.2691  2.6153                
+HETATM   53  C                  0.2447  3.1026  1.5191                
+HETATM   54  C                  0.8815  3.1269 -1.2000                
+HETATM   55  C                  1.1442  2.3150 -2.3100                
+HETATM   56  C                  1.3558 -0.3333 -3.1706                
+HETATM   57  C                  1.2640 -1.6687 -2.7595                
+HETATM   58  C                  0.7577 -3.3290 -0.5712                
+HETATM   59  C                  0.4382 -3.3422  0.7920                
+HETATM   60  C                 -0.0856 -1.7214  3.0049                
+CONECT    1    2    5   12                                   
+CONECT    2    1    3    9                                   
+CONECT    3    2    4    6                                   
+CONECT    4    3    5   18                                   
+CONECT    5    1    4   15                                   
+CONECT    6    3    7   20                                   
+CONECT    7    6    8   21                                   
+CONECT    8    7    9   22                                   
+CONECT    9    2    8   10                                   
+CONECT   10    9   11   23                                   
+CONECT   11   10   12   24                                   
+CONECT   12    1   11   13                                   
+CONECT   13   12   14   25                                   
+CONECT   14   13   15   26                                   
+CONECT   15    5   14   16                                   
+CONECT   16   15   17   27                                   
+CONECT   17   16   18   28                                   
+CONECT   18    4   17   19                                   
+CONECT   19   18   20   29                                   
+CONECT   20    6   19   30                                   
+CONECT   21    7   30   55                                   
+CONECT   22    8   23   54                                   
+CONECT   23   10   22   53                                   
+CONECT   24   11   25   52                                   
+CONECT   25   13   24   51                                   
+CONECT   26   14   27   60                                   
+CONECT   27   16   26   59                                   
+CONECT   28   17   29   58                                   
+CONECT   29   19   28   57                                   
+CONECT   30   20   21   56                                   
+CONECT   31   32   35   42                                   
+CONECT   32   31   33   39                                   
+CONECT   33   32   34   36                                   
+CONECT   34   33   35   48                                   
+CONECT   35   31   34   45                                   
+CONECT   36   33   37   50                                   
+CONECT   37   36   38   51                                   
+CONECT   38   37   39   52                                   
+CONECT   39   32   38   40                                   
+CONECT   40   39   41   53                                   
+CONECT   41   40   42   54                                   
+CONECT   42   31   41   43                                   
+CONECT   43   42   44   55                                   
+CONECT   44   43   45   56                                   
+CONECT   45   35   44   46                                   
+CONECT   46   45   47   57                                   
+CONECT   47   46   48   58                                   
+CONECT   48   34   47   49                                   
+CONECT   49   48   50   59                                   
+CONECT   50   36   49   60                                   
+CONECT   51   25   37   60                                   
+CONECT   52   24   38   53                                   
+CONECT   53   23   40   52                                   
+CONECT   54   22   41   55                                   
+CONECT   55   21   43   54                                   
+CONECT   56   30   44   57                                   
+CONECT   57   29   46   56                                   
+CONECT   58   28   47   59                                   
+CONECT   59   27   49   58                                   
+CONECT   60   26   50   51                                   
+END

+ 49 - 0
examples/models/molecules/caf2.pdb
Файл харах 

@@ -0,0 +1,49 @@
 
+HEADER    MOLECULE
 
+COMPND    CAF2 (FLUORITE), VIEW CENTERED ON ANIONS
 
+AUTHOR    A. W. MAVERICK
 
+ATOM      1  F     UNK   1      -1.366  -1.366  -1.366  1.00  0.00 
+ATOM      2  F     UNK   1      -1.366  -1.366   1.366  1.00  0.00 
+ATOM      3  F     UNK   1      -1.366   1.366  -1.366  1.00  0.00 
+ATOM      4  F     UNK   1      -1.366   1.366   1.366  1.00  0.00 
+ATOM      5  F     UNK   1       1.366  -1.366  -1.366  1.00  0.00 
+ATOM      6  F     UNK   1       1.366  -1.366   1.366  1.00  0.00 
+ATOM      7  F     UNK   1       1.366   1.366  -1.366  1.00  0.00 
+ATOM      8  F     UNK   1       1.366   1.366   1.366  1.00  0.00 
+ATOM      9 CA     UNK   1      -2.732  -2.732  -2.732  1.00  0.00 
+ATOM     10 CA     UNK   1       0.000   0.000  -2.732  1.00  0.00 
+ATOM     11 CA     UNK   1       0.000  -2.732   0.000  1.00  0.00 
+ATOM     12 CA     UNK   1      -2.732   0.000   0.000  1.00  0.00 
+ATOM     13 CA     UNK   1      -2.732  -2.732   2.732  1.00  0.00 
+ATOM     14 CA     UNK   1       0.000   0.000   2.732  1.00  0.00 
+ATOM     15 CA     UNK   1      -2.732   2.732  -2.732  1.00  0.00 
+ATOM     16 CA     UNK   1       0.000   2.732   0.000  1.00  0.00 
+ATOM     17 CA     UNK   1      -2.732   2.732   2.732  1.00  0.00 
+ATOM     18 CA     UNK   1       2.732  -2.732  -2.732  1.00  0.00 
+ATOM     19 CA     UNK   1       2.732   0.000   0.000  1.00  0.00 
+ATOM     20 CA     UNK   1       2.732  -2.732   2.732  1.00  0.00 
+ATOM     21 CA     UNK   1       2.732   2.732  -2.732  1.00  0.00 
+ATOM     22 CA     UNK   1       2.732   2.732   2.732  1.00  0.00 
+CONECT    1    9   10   11   12
 
+CONECT    2   11   12   13   14
 
+CONECT    3   10   12   15   16
 
+CONECT    4   12   14   16   17
 
+CONECT    5   10   11   18   19
 
+CONECT    6   11   14   19   20
 
+CONECT    7   10   16   19   21
 
+CONECT    8   14   16   19   22
 
+CONECT    9    1
 
+CONECT   10    1    3    5    7
 
+CONECT   11    1    2    5    6
 
+CONECT   12    1    2    3    4
 
+CONECT   13    2
 
+CONECT   14    2    4    6    8
 
+CONECT   15    3
 
+CONECT   16    3    4    7    8
 
+CONECT   17    4
 
+CONECT   18    5
 
+CONECT   19    5    6    7    8
 
+CONECT   20    6
 
+CONECT   21    7
 
+CONECT   22    8
 
+MASTER        0    0    0    0    0    0    0    0   22    0   22    0
 
+END

+ 44 - 0
examples/models/molecules/caffeine.pdb
Файл харах 

@@ -0,0 +1,44 @@
 
+HEADER    NONAME 22-Apr-10                                              NONE   1
 
+TITLE                                                                   NONE   2
 
+AUTHOR    Chemical Structure Services at http://cactus.nci.nih.gov      NONE   3
 
+REVDAT   1  22-Apr-10     0                                             NONE   4
 
+ATOM      1  C           0      -2.561   1.251  -0.000  0.00  0.00           C+0
 
+ATOM      2  C           0      -3.261  -1.161  -0.000  0.00  0.00           C+0
 
+ATOM      3  C           0       1.534   2.629   0.000  0.00  0.00           C+0
 
+ATOM      4  C           0       2.247  -2.176  -0.000  0.00  0.00           C+0
 
+ATOM      5  O           0      -0.438  -2.428   0.000  0.00  0.00           O+0
 
+ATOM      6  O           0       2.994   0.384   0.000  0.00  0.00           O+0
 
+ATOM      7  C           0      -0.016  -1.285  -0.000  0.00  0.00           C+0
 
+ATOM      8  C           0       1.791   0.208   0.000  0.00  0.00           C+0
 
+ATOM      9  C           0      -0.911  -0.194  -0.000  0.00  0.00           C+0
 
+ATOM     10  C           0      -0.403   1.099  -0.000  0.00  0.00           C+0
 
+ATOM     11  N           0      -1.445   1.934  -0.000  0.00  0.00           N+0
 
+ATOM     12  N           0       0.971   1.277  -0.000  0.00  0.00           N+0
 
+ATOM     13  N           0       1.312  -1.048  -0.000  0.00  0.00           N+0
 
+ATOM     14  N           0      -2.286  -0.068   0.000  0.00  0.00           N+0
 
+ATOM     15  H           0      -3.552   1.680   0.004  0.00  0.00           H+0
 
+ATOM     16  H           0      -3.503  -1.433   1.028  0.00  0.00           H+0
 
+ATOM     17  H           0      -4.168  -0.840  -0.514  0.00  0.00           H+0
 
+ATOM     18  H           0      -2.839  -2.025  -0.514  0.00  0.00           H+0
 
+ATOM     19  H           0       1.673   2.965   1.028  0.00  0.00           H+0
 
+ATOM     20  H           0       2.495   2.623  -0.514  0.00  0.00           H+0
 
+ATOM     21  H           0       0.851   3.307  -0.514  0.00  0.00           H+0
 
+ATOM     22  H           0       2.478  -2.456  -1.028  0.00  0.00           H+0
 
+ATOM     23  H           0       3.164  -1.888   0.513  0.00  0.00           H+0
 
+ATOM     24  H           0       1.793  -3.024   0.514  0.00  0.00           H+0
 
+CONECT    1   14   11   15    0                                         NONE  29
 
+CONECT    2   14   16   17   18                                         NONE  30
 
+CONECT    3   12   19   20   21                                         NONE  31
 
+CONECT    4   13   22   23   24                                         NONE  32
 
+CONECT    5    7    0    0    0                                         NONE  33
 
+CONECT    6    8    0    0    0                                         NONE  34
 
+CONECT    7    9   13    5    0                                         NONE  35
 
+CONECT    8   12    6   13    0                                         NONE  36
 
+CONECT    9   10    7   14    0                                         NONE  37
 
+CONECT   10    9   12   11    0                                         NONE  38
 
+CONECT   11   10    1    0    0                                         NONE  39
 
+CONECT   12   10    8    3    0                                         NONE  40
 
+CONECT   13    7    4    8    0                                         NONE  41
 
+CONECT   14    9    1    2    0                                         NONE  42
 
+END                                                                     NONE  43
 
+

+ 237 - 0
examples/models/molecules/cholesterol.pdb
Файл харах 

@@ -0,0 +1,237 @@
 
+ORIGX1      1.000000  0.000000  0.000000        0.00000
 
+ORIGX2      0.000000  1.000000  0.000000        0.00000
 
+ORIGX3      0.000000  0.000000  1.000000        0.00000
 
+SCALE1      0.100000  0.000000  0.000000        0.00000
 
+SCALE2      0.000000  0.100000  0.000000        0.00000
 
+SCALE3      0.000000  0.000000  0.100000        0.00000
 
+ATOM      1  C           1      -7.323   0.716  -5.120  1.00  0.00
 
+ATOM      2  C           1      -8.580   0.025  -4.537  1.00  0.00
 
+ATOM      3  C           1      -9.814   0.931  -4.416  1.00  0.00
 
+ATOM      4  C           1      -9.476   2.171  -3.582  1.00  0.00
 
+ATOM      5  O           1     -10.603   3.009  -3.488  1.00  0.00
 
+ATOM      6  C           1      -7.105   2.022  -4.368  1.00  0.00
 
+ATOM      7  C           1      -8.298   2.936  -4.191  1.00  0.00
 
+ATOM      8  H           1      -9.230   1.870  -2.536  1.00  0.00
 
+ATOM      9  H           1     -10.862   3.297  -4.348  1.00  0.00
 
+ATOM     10  H           1     -10.173   1.239  -5.425  1.00  0.00
 
+ATOM     11  H           1     -10.653   0.372  -3.935  1.00  0.00
 
+ATOM     12  C           1      -5.905   2.409  -3.906  1.00  0.00
 
+ATOM     13  C           1      -4.641   1.613  -4.039  1.00  0.00
 
+ATOM     14  H           1      -8.856  -0.863  -5.151  1.00  0.00
 
+ATOM     15  H           1      -8.349  -0.350  -3.512  1.00  0.00
 
+ATOM     16  H           1      -8.053   3.806  -3.539  1.00  0.00
 
+ATOM     17  H           1      -8.589   3.360  -5.178  1.00  0.00
 
+ATOM     18  C           1      -7.556   1.063  -6.606  1.00  0.00
 
+ATOM     19  H           1      -6.656   1.519  -7.073  1.00  0.00
 
+ATOM     20  H           1      -7.847   0.176  -7.211  1.00  0.00
 
+ATOM     21  H           1      -8.382   1.793  -6.753  1.00  0.00
 
+ATOM     22  C           1      -6.098  -0.229  -4.938  1.00  0.00
 
+ATOM     23  C           1      -4.758   0.515  -5.105  1.00  0.00
 
+ATOM     24  H           1      -3.807   2.303  -4.306  1.00  0.00
 
+ATOM     25  H           1      -4.416   1.181  -3.036  1.00  0.00
 
+ATOM     26  H           1      -6.101  -0.569  -3.874  1.00  0.00
 
+ATOM     27  H           1      -4.726   1.004  -6.104  1.00  0.00
 
+ATOM     28  C           1      -6.149  -1.518  -5.786  1.00  0.00
 
+ATOM     29  C           1      -3.583  -0.466  -4.987  1.00  0.00
 
+ATOM     30  C           1      -3.610  -1.635  -5.997  1.00  0.00
 
+ATOM     31  C           1      -4.900  -2.410  -5.665  1.00  0.00
 
+ATOM     32  H           1      -7.038  -2.128  -5.500  1.00  0.00
 
+ATOM     33  H           1      -6.283  -1.269  -6.861  1.00  0.00
 
+ATOM     34  H           1      -4.850  -2.821  -4.629  1.00  0.00
 
+ATOM     35  H           1      -5.024  -3.287  -6.338  1.00  0.00
 
+ATOM     36  H           1      -3.640  -0.901  -3.959  1.00  0.00
 
+ATOM     37  C           1      -3.594  -1.172  -7.468  1.00  0.00
 
+ATOM     38  H           1      -3.716  -2.030  -8.165  1.00  0.00
 
+ATOM     39  H           1      -4.409  -0.460  -7.718  1.00  0.00
 
+ATOM     40  H           1      -2.644  -0.664  -7.746  1.00  0.00
 
+ATOM     41  C           1      -2.273  -2.341  -5.642  1.00  0.00
 
+ATOM     42  C           1      -1.314  -1.155  -5.356  1.00  0.00
 
+ATOM     43  C           1      -2.169   0.102  -5.114  1.00  0.00
 
+ATOM     44  H           1      -0.681  -1.369  -4.463  1.00  0.00
 
+ATOM     45  H           1      -0.630  -0.965  -6.217  1.00  0.00
 
+ATOM     46  H           1      -2.116   0.800  -5.982  1.00  0.00
 
+ATOM     47  H           1      -1.847   0.664  -4.206  1.00  0.00
 
+ATOM     48  H           1      -2.438  -2.878  -4.677  1.00  0.00
 
+ATOM     49  C           1      -1.661  -3.375  -6.619  1.00  0.00
 
+ATOM     50  C           1      -2.627  -4.529  -6.939  1.00  0.00
 
+ATOM     51  C           1      -0.337  -3.949  -6.059  1.00  0.00
 
+ATOM     52  C           1       0.515  -4.714  -7.088  1.00  0.00
 
+ATOM     53  C           1       1.887  -5.111  -6.518  1.00  0.00
 
+ATOM     54  C           1       2.733  -5.984  -7.466  1.00  0.00
 
+ATOM     55  C           1       4.014  -6.450  -6.753  1.00  0.00
 
+ATOM     56  C           1       3.101  -5.250  -8.766  1.00  0.00
 
+ATOM     57  H           1      -2.156  -5.315  -7.569  1.00  0.00
 
+ATOM     58  H           1      -2.994  -5.018  -6.008  1.00  0.00
 
+ATOM     59  H           1      -3.504  -4.190  -7.530  1.00  0.00
 
+ATOM     60  H           1       0.302  -3.122  -5.677  1.00  0.00
 
+ATOM     61  H           1      -0.560  -4.605  -5.185  1.00  0.00
 
+ATOM     62  H           1      -0.009  -5.640  -7.418  1.00  0.00
 
+ATOM     63  H           1       0.654  -4.067  -7.985  1.00  0.00
 
+ATOM     64  H           1       4.625  -7.113  -7.409  1.00  0.00
 
+ATOM     65  H           1       4.650  -5.583  -6.461  1.00  0.00
 
+ATOM     66  H           1       3.779  -7.028  -5.830  1.00  0.00
 
+ATOM     67  H           1       3.761  -5.877  -9.409  1.00  0.00
 
+ATOM     68  H           1       2.201  -5.009  -9.377  1.00  0.00
 
+ATOM     69  H           1       3.639  -4.299  -8.553  1.00  0.00
 
+ATOM     70  H           1       2.141  -6.894  -7.733  1.00  0.00
 
+ATOM     71  H           1       2.463  -4.192  -6.255  1.00  0.00
 
+ATOM     72  H           1       1.720  -5.673  -5.569  1.00  0.00
 
+ATOM     73  H           1      -1.419  -2.850  -7.574  1.00  0.00
 
+ATOM     74  H           1      -5.813   3.367  -3.367  1.00  0.00
 
+TER      75
 
+CONECT    1    2                                                                
+CONECT    2    1                                                                
+CONECT    2    3                                                                
+CONECT    3    2                                                                
+CONECT    3    4                                                                
+CONECT    4    3                                                                
+CONECT    4    5                                                                
+CONECT    5    4                                                                
+CONECT    1    6                                                                
+CONECT    6    1                                                                
+CONECT    6    7                                                                
+CONECT    7    6                                                                
+CONECT    7    4                                                                
+CONECT    4    7                                                                
+CONECT    4    8                                                                
+CONECT    8    4                                                                
+CONECT    5    9                                                                
+CONECT    9    5                                                                
+CONECT    3   10                                                                
+CONECT   10    3                                                                
+CONECT    3   11                                                                
+CONECT   11    3                                                                
+CONECT    6   12                                                                
+CONECT   12    6                                                                
+CONECT   12   13                                                                
+CONECT   13   12                                                                
+CONECT    2   14                                                                
+CONECT   14    2                                                                
+CONECT    2   15                                                                
+CONECT   15    2                                                                
+CONECT    7   16                                                                
+CONECT   16    7                                                                
+CONECT    7   17                                                                
+CONECT   17    7                                                                
+CONECT    1   18                                                                
+CONECT   18    1                                                                
+CONECT   18   19                                                                
+CONECT   19   18                                                                
+CONECT   18   20                                                                
+CONECT   20   18                                                                
+CONECT   18   21                                                                
+CONECT   21   18                                                                
+CONECT    1   22                                                                
+CONECT   22    1                                                                
+CONECT   22   23                                                                
+CONECT   23   22                                                                
+CONECT   23   13                                                                
+CONECT   13   23                                                                
+CONECT   13   24                                                                
+CONECT   24   13                                                                
+CONECT   13   25                                                                
+CONECT   25   13                                                                
+CONECT   22   26                                                                
+CONECT   26   22                                                                
+CONECT   23   27                                                                
+CONECT   27   23                                                                
+CONECT   22   28                                                                
+CONECT   28   22                                                                
+CONECT   23   29                                                                
+CONECT   29   23                                                                
+CONECT   29   30                                                                
+CONECT   30   29                                                                
+CONECT   28   31                                                                
+CONECT   31   28                                                                
+CONECT   31   30                                                                
+CONECT   30   31                                                                
+CONECT   28   32                                                                
+CONECT   32   28                                                                
+CONECT   28   33                                                                
+CONECT   33   28                                                                
+CONECT   31   34                                                                
+CONECT   34   31                                                                
+CONECT   31   35                                                                
+CONECT   35   31                                                                
+CONECT   29   36                                                                
+CONECT   36   29                                                                
+CONECT   30   37                                                                
+CONECT   37   30                                                                
+CONECT   37   38                                                                
+CONECT   38   37                                                                
+CONECT   37   39                                                                
+CONECT   39   37                                                                
+CONECT   37   40                                                                
+CONECT   40   37                                                                
+CONECT   30   41                                                                
+CONECT   41   30                                                                
+CONECT   41   42                                                                
+CONECT   42   41                                                                
+CONECT   42   43                                                                
+CONECT   43   42                                                                
+CONECT   43   29                                                                
+CONECT   29   43                                                                
+CONECT   42   44                                                                
+CONECT   44   42                                                                
+CONECT   42   45                                                                
+CONECT   45   42                                                                
+CONECT   43   46                                                                
+CONECT   46   43                                                                
+CONECT   43   47                                                                
+CONECT   47   43                                                                
+CONECT   41   48                                                                
+CONECT   48   41                                                                
+CONECT   41   49                                                                
+CONECT   49   41                                                                
+CONECT   49   50                                                                
+CONECT   50   49                                                                
+CONECT   49   51                                                                
+CONECT   51   49                                                                
+CONECT   51   52                                                                
+CONECT   52   51                                                                
+CONECT   52   53                                                                
+CONECT   53   52                                                                
+CONECT   53   54                                                                
+CONECT   54   53                                                                
+CONECT   54   55                                                                
+CONECT   55   54                                                                
+CONECT   54   56                                                                
+CONECT   56   54                                                                
+CONECT   50   57                                                                
+CONECT   57   50                                                                
+CONECT   50   58                                                                
+CONECT   58   50                                                                
+CONECT   50   59                                                                
+CONECT   59   50                                                                
+CONECT   51   60                                                                
+CONECT   60   51                                                                
+CONECT   51   61                                                                
+CONECT   61   51                                                                
+CONECT   52   62                                                                
+CONECT   62   52                                                                
+CONECT   52   63                                                                
+CONECT   63   52                                                                
+CONECT   55   64                                                                
+CONECT   64   55                                                                
+CONECT   55   65                                                                
+CONECT   65   55                                                                
+CONECT   55   66                                                                
+CONECT   66   55                                                                
+CONECT   56   67                                                                
+CONECT   67   56                                                                
+CONECT   56   68                                                                
+CONECT   68   56                                                                
+CONECT   56   69                                                                
+CONECT   69   56                                                                
+CONECT   54   70                                                                
+CONECT   70   54                                                                
+CONECT   53   71                                                                
+CONECT   71   53                                                                
+CONECT   53   72                                                                
+CONECT   72   53                                                                
+CONECT   49   73                                                                
+CONECT   73   49                                                                
+CONECT   12   74                                                                
+CONECT   74   12                                                                
+MASTER        0    0    0    0    0    0    0    6   74    1  154    0
 
+END

+ 119 - 0
examples/models/molecules/cocaine.pdb
Файл харах 

@@ -0,0 +1,119 @@
 
+COMPND                                                                
+REMARK   1 PDB to MMOD atom-numbering translation table; the mmod numbers
 
+REMARK   1 pertain to the .dat file from which this file was created,
 
+REMARK   1 not to one created from this file:
 
+REMARK   1  PDB:     1     2     3     4     5     6     7     8     9  
+REMARK   1 MMOD:     1     2     3     4     5     6     7     8    19 /
 
+REMARK   1  PDB:    10    11    12    13    14    15    16    17    18  
+REMARK   1 MMOD:    23    24    25    26    30    31    32    33    34 /
 
+REMARK   1  PDB:    19    20    21    22    23    24    25    26    27  
+REMARK   1 MMOD:    35    36    37    38     9    10    11    12    13 /
 
+REMARK   1  PDB:    28    29    30    31    32    33    34    35    36  
+REMARK   1 MMOD:    14    15    16    17    18    20    21    22    27 /
 
+REMARK   1  PDB:    37    38    39    40    41    42    43  
+REMARK   1 MMOD:    28    29    39    40    41    42    43 /
 
+HETATM    1  C01 UNK     0      -0.579  -1.681   0.616  0.00  0.00   0
 
+HETATM    2  C02 UNK     0      -1.566   0.560  -0.170  0.04  0.04   0
 
+HETATM    3  C03 UNK     0      -1.162   1.032   1.249  0.01  0.01   0
 
+HETATM    4  C04 UNK     0      -2.199   0.552   2.293  0.00  0.00   0
 
+HETATM    5  C05 UNK     0      -1.649  -0.811   2.760  0.00  0.00   0
 
+HETATM    6  C06 UNK     0      -0.340  -0.968   1.960  0.01  0.01   0
 
+HETATM    7  N07 UNK     0       0.044   0.417   1.782  0.19  0.19   0
 
+HETATM    8  C08 UNK     0      -1.653  -0.989  -0.246  0.07  0.07   0
 
+HETATM    9  C19 UNK     0       1.272   0.616   1.044  0.01  0.01   0
 
+HETATM   10  C23 UNK     0      -0.901   1.274  -1.354  0.38  0.38   0
 
+HETATM   11  O24 UNK     0      -0.195   2.368  -0.946  0.59  0.59   0
 
+HETATM   12  O25 UNK     0      -1.037   0.929  -2.512 -0.45 -0.45   0
 
+HETATM   13  C26 UNK     0       0.440   3.093  -1.986  0.07  0.07   0
 
+HETATM   14  O30 UNK     0      -1.609  -1.430  -1.593  0.59  0.59   0
 
+HETATM   15  C31 UNK     0      -1.789  -2.754  -1.882  0.42  0.42   0
 
+HETATM   16  O32 UNK     0      -2.125  -3.580  -1.053 -0.45 -0.45   0
 
+HETATM   17  C33 UNK     0      -1.523  -3.209  -3.279  0.00  0.00   0
 
+HETATM   18  C34 UNK     0      -0.997  -2.329  -4.230  0.00  0.00   0
 
+HETATM   19  C35 UNK     0      -0.765  -2.755  -5.540  0.00  0.00   0
 
+HETATM   20  C36 UNK     0      -1.059  -4.064  -5.914  0.00  0.00   0
 
+HETATM   21  C37 UNK     0      -1.581  -4.946  -4.971  0.00  0.00   0
 
+HETATM   22  C38 UNK     0      -1.813  -4.523  -3.662  0.00  0.00   0
 
+HETATM   23  H09 UNK     0      -0.884  -2.728   0.852  0.00  0.00   0
 
+HETATM   24  H10 UNK     0       0.374  -1.778   0.044  0.00  0.00   0
 
+HETATM   25  H11 UNK     0      -2.605   0.931  -0.328  0.00  0.00   0
 
+HETATM   26  H12 UNK     0      -1.090   2.146   1.298  0.00  0.00   0
 
+HETATM   27  H13 UNK     0      -2.229   1.262   3.154  0.00  0.00   0
 
+HETATM   28  H14 UNK     0      -3.233   0.480   1.883  0.00  0.00   0
 
+HETATM   29  H15 UNK     0      -1.434  -0.778   3.855  0.00  0.00   0
 
+HETATM   30  H16 UNK     0      -2.361  -1.651   2.584  0.00  0.00   0
 
+HETATM   31  H17 UNK     0       0.429  -1.522   2.552  0.00  0.00   0
 
+HETATM   32  H18 UNK     0      -2.651  -1.286   0.167  0.00  0.00   0
 
+HETATM   33  H20 UNK     0       1.203   0.272  -0.011  0.00  0.00   0
 
+HETATM   34  H21 UNK     0       1.546   1.695   1.056  0.00  0.00   0
 
+HETATM   35  H22 UNK     0       2.105   0.067   1.538  0.00  0.00   0
 
+HETATM   36  H27 UNK     0       1.178   3.787  -1.521  0.00  0.00   0
 
+HETATM   37  H28 UNK     0       0.992   2.401  -2.667  0.00  0.00   0
 
+HETATM   38  H29 UNK     0      -0.320   3.686  -2.550  0.00  0.00   0
 
+HETATM   39  H39 UNK     0      -0.751  -1.289  -3.968  0.00  0.00   0
 
+HETATM   40  H40 UNK     0      -0.350  -2.053  -6.284  0.00  0.00   0
 
+HETATM   41  H41 UNK     0      -0.880  -4.399  -6.951  0.00  0.00   0
 
+HETATM   42  H42 UNK     0      -1.815  -5.985  -5.264  0.00  0.00   0
 
+HETATM   43  H43 UNK     0      -2.228  -5.248  -2.942  0.00  0.00   0
 
+CONECT    1    6    8   23   24
 
+CONECT    2    3    8   25   10
 
+CONECT    3    2    4    7   26
 
+CONECT    4    3    5   27   28
 
+CONECT    5    4    6   29   30
 
+CONECT    6    5    1    7   31
 
+CONECT    7    6    3    9
 
+CONECT    8    2    1   32   14
 
+CONECT    9    7   33   34   35
 
+CONECT   10   11    2
 
+CONECT   10   12
 
+CONECT   10   12
 
+CONECT   11   10   13
 
+CONECT   12   10
 
+CONECT   12   10
 
+CONECT   13   11   36   37   38
 
+CONECT   14    8   15
 
+CONECT   15   14   17
 
+CONECT   15   16
 
+CONECT   15   16
 
+CONECT   16   15
 
+CONECT   16   15
 
+CONECT   17   22   15
 
+CONECT   17   18
 
+CONECT   17   18
 
+CONECT   18   19   39
 
+CONECT   18   17
 
+CONECT   18   17
 
+CONECT   19   18   40
 
+CONECT   19   20
 
+CONECT   19   20
 
+CONECT   20   21   41
 
+CONECT   20   19
 
+CONECT   20   19
 
+CONECT   21   20   42
 
+CONECT   21   22
 
+CONECT   21   22
 
+CONECT   22   17   43
 
+CONECT   22   21
 
+CONECT   22   21
 
+CONECT   23    1
 
+CONECT   24    1
 
+CONECT   25    2
 
+CONECT   26    3
 
+CONECT   27    4
 
+CONECT   28    4
 
+CONECT   29    5
 
+CONECT   30    5
 
+CONECT   31    6
 
+CONECT   32    8
 
+CONECT   33    9
 
+CONECT   34    9
 
+CONECT   35    9
 
+CONECT   36   13
 
+CONECT   37   13
 
+CONECT   38   13
 
+CONECT   39   18
 
+CONECT   40   19
 
+CONECT   41   20
 
+CONECT   42   21
 
+CONECT   43   22
 
+END

+ 155 - 0
examples/models/molecules/cu.pdb
Файл харах 

@@ -0,0 +1,155 @@
 
+HEADER    MOLECULE
 
+COMPND    COPPER, MULTILAYER
 
+AUTHOR    A. W. MAVERICK
 
+ATOM      1 CU     UNK   1      -1.278  -2.214  -6.261  1.00  0.00 
+ATOM      2 CU     UNK   1       1.278  -2.214  -6.261  1.00  0.00 
+ATOM      3 CU     UNK   1       0.000   0.000  -6.261  1.00  0.00 
+ATOM      4 CU     UNK   1       2.556   0.000  -6.261  1.00  0.00 
+ATOM      5 CU     UNK   1       1.278   2.214  -6.261  1.00  0.00 
+ATOM      6 CU     UNK   1      -1.278   2.214  -6.261  1.00  0.00 
+ATOM      7 CU     UNK   1      -2.556   0.000  -6.261  1.00  0.00 
+ATOM      8 CU     UNK   1       0.000  -1.476  -4.174  1.00  0.00 
+ATOM      9 CU     UNK   1       2.556  -1.476  -4.174  1.00  0.00 
+ATOM     10 CU     UNK   1       1.278   0.738  -4.174  1.00  0.00 
+ATOM     11 CU     UNK   1      -1.278   0.738  -4.174  1.00  0.00 
+ATOM     12 CU     UNK   1       0.000   2.951  -4.174  1.00  0.00 
+ATOM     13 CU     UNK   1      -2.556  -1.476  -4.174  1.00  0.00 
+ATOM     14 CU     UNK   1      -1.278  -0.738  -2.087  1.00  0.00 
+ATOM     15 CU     UNK   1      -2.556   1.476  -2.087  1.00  0.00 
+ATOM     16 CU     UNK   1       0.000   1.476  -2.087  1.00  0.00 
+ATOM     17 CU     UNK   1       1.278  -0.738  -2.087  1.00  0.00 
+ATOM     18 CU     UNK   1       2.556   1.476  -2.087  1.00  0.00 
+ATOM     19 CU     UNK   1       0.000  -2.951  -2.087  1.00  0.00 
+ATOM     20 CU     UNK   1      -1.278  -2.214   0.000  1.00  0.00 
+ATOM     21 CU     UNK   1       1.278  -2.214   0.000  1.00  0.00 
+ATOM     22 CU     UNK   1       0.000   0.000   0.000  1.00  0.00 
+ATOM     23 CU     UNK   1       2.556   0.000   0.000  1.00  0.00 
+ATOM     24 CU     UNK   1       1.278   2.214   0.000  1.00  0.00 
+ATOM     25 CU     UNK   1      -1.278   2.214   0.000  1.00  0.00 
+ATOM     26 CU     UNK   1      -2.556   0.000   0.000  1.00  0.00 
+ATOM     27 CU     UNK   1       0.000  -1.476   2.087  1.00  0.00 
+ATOM     28 CU     UNK   1       2.556  -1.476   2.087  1.00  0.00 
+ATOM     29 CU     UNK   1       1.278   0.738   2.087  1.00  0.00 
+ATOM     30 CU     UNK   1      -1.278   0.738   2.087  1.00  0.00 
+ATOM     31 CU     UNK   1       0.000   2.951   2.087  1.00  0.00 
+ATOM     32 CU     UNK   1      -2.556  -1.476   2.087  1.00  0.00 
+ATOM     33 CU     UNK   1      -1.278  -0.738   4.174  1.00  0.00 
+ATOM     34 CU     UNK   1      -2.556   1.476   4.174  1.00  0.00 
+ATOM     35 CU     UNK   1       0.000   1.476   4.174  1.00  0.00 
+ATOM     36 CU     UNK   1       1.278  -0.738   4.174  1.00  0.00 
+ATOM     37 CU     UNK   1       2.556   1.476   4.174  1.00  0.00 
+ATOM     38 CU     UNK   1       0.000  -2.951   4.174  1.00  0.00 
+ATOM     39 CU     UNK   1      -1.278  -2.214   6.261  1.00  0.00 
+ATOM     40 CU     UNK   1       1.278  -2.214   6.261  1.00  0.00 
+ATOM     41 CU     UNK   1       0.000   0.000   6.261  1.00  0.00 
+ATOM     42 CU     UNK   1       2.556   0.000   6.261  1.00  0.00 
+ATOM     43 CU     UNK   1       1.278   2.214   6.261  1.00  0.00 
+ATOM     44 CU     UNK   1      -1.278   2.214   6.261  1.00  0.00 
+ATOM     45 CU     UNK   1      -2.556   0.000   6.261  1.00  0.00 
+CONECT    1   13
 
+CONECT    1    2    3    7    8
 
+CONECT    2    9
 
+CONECT    2    1    3    4    8
 
+CONECT    3    1    2    4    5
 
+CONECT    3    6    7    8   10
 
+CONECT    3   11
 
+CONECT    4   10
 
+CONECT    4    2    3    5    9
 
+CONECT    5    3    4    6   10
 
+CONECT    5   12
 
+CONECT    6    3    5    7   11
 
+CONECT    6   12
 
+CONECT    7    1    3    6   11
 
+CONECT    7   13
 
+CONECT    8    1    2    3    9
 
+CONECT    8   17   19
 
+CONECT    8   10   11   13   14
 
+CONECT    9    2    4    8   10
 
+CONECT    9   17
 
+CONECT   10   17   18
 
+CONECT   10    3    4    5    8
 
+CONECT   10    9   11   12   16
 
+CONECT   11   10   12   13   14
 
+CONECT   11    3    6    7    8
 
+CONECT   11   15   16
 
+CONECT   12   16
 
+CONECT   12    5    6   10   11
 
+CONECT   13   14
 
+CONECT   13    1    7    8   11
 
+CONECT   14   22   26
 
+CONECT   14    8   11   13   15
 
+CONECT   14   16   17   19   20
 
+CONECT   15   11   14   16   25
 
+CONECT   15   26
 
+CONECT   16   24   25
 
+CONECT   16   10   11   12   14
 
+CONECT   16   15   17   18   22
 
+CONECT   17   16   18   19   21
 
+CONECT   17    8    9   10   14
 
+CONECT   17   22   23
 
+CONECT   18   24
 
+CONECT   18   10   16   17   23
 
+CONECT   19   21
 
+CONECT   19    8   14   17   20
 
+CONECT   20   14   19   21   22
 
+CONECT   20   26   27   32
 
+CONECT   21   17   19   20   22
 
+CONECT   21   23   27   28
 
+CONECT   22   26   27   29   30
 
+CONECT   22   21   23   24   25
 
+CONECT   22   14   16   17   20
 
+CONECT   23   17   18   21   22
 
+CONECT   23   24   28   29
 
+CONECT   24   25   29   31
 
+CONECT   24   16   18   22   23
 
+CONECT   25   15   16   22   24
 
+CONECT   25   26   30   31
 
+CONECT   26   14   15   20   22
 
+CONECT   26   25   30   32
 
+CONECT   27   36   38
 
+CONECT   27   29   30   32   33
 
+CONECT   27   20   21   22   28
 
+CONECT   28   21   23   27   29
 
+CONECT   28   36
 
+CONECT   29   36   37
 
+CONECT   29   28   30   31   35
 
+CONECT   29   22   23   24   27
 
+CONECT   30   29   31   32   33
 
+CONECT   30   34   35
 
+CONECT   30   22   25   26   27
 
+CONECT   31   35
 
+CONECT   31   24   25   29   30
 
+CONECT   32   33
 
+CONECT   32   20   26   27   30
 
+CONECT   33   35   36   38   39
 
+CONECT   33   41   45
 
+CONECT   33   27   30   32   34
 
+CONECT   34   45
 
+CONECT   34   30   33   35   44
 
+CONECT   35   29   30   31   33
 
+CONECT   35   34   36   37   41
 
+CONECT   35   43   44
 
+CONECT   36   27   28   29   33
 
+CONECT   36   35   37   38   40
 
+CONECT   36   41   42
 
+CONECT   37   43
 
+CONECT   37   29   35   36   42
 
+CONECT   38   40
 
+CONECT   38   27   33   36   39
 
+CONECT   39   33   38   40   41
 
+CONECT   39   45
 
+CONECT   40   36   38   39   41
 
+CONECT   40   42
 
+CONECT   41   33   35   36   39
 
+CONECT   41   45
 
+CONECT   41   40   42   43   44
 
+CONECT   42   36   37   40   41
 
+CONECT   42   43
 
+CONECT   43   35   37   41   42
 
+CONECT   43   44
 
+CONECT   44   34   35   41   43
 
+CONECT   44   45
 
+CONECT   45   33   34   39   41
 
+CONECT   45   44
 
+MASTER        0    0    0    0    0    0    0    0   45    0   45    0
 
+END

+ 30 - 0
examples/models/molecules/cubane.pdb
Файл харах 

@@ -0,0 +1,30 @@
 
+HEADER    NONAME 23-Apr-10                                              NONE   1
 
+TITLE                                                                   NONE   2
 
+AUTHOR    Chemical Structure Services at http://cactus.nci.nih.gov      NONE   3
 
+REVDAT   1  23-Apr-10     0                                             NONE   4
 
+ATOM      1  C           0       0.414   0.765   0.999  0.00  0.00           C+0
 
+ATOM      2  C           0       0.414  -0.765   0.999  0.00  0.00           C+0
 
+ATOM      3  C           0       0.999   0.765  -0.414  0.00  0.00           C+0
 
+ATOM      4  C           0      -1.000   0.765   0.414  0.00  0.00           C+0
 
+ATOM      5  C           0       0.999  -0.765  -0.414  0.00  0.00           C+0
 
+ATOM      6  C           0      -1.000  -0.765   0.414  0.00  0.00           C+0
 
+ATOM      7  C           0      -0.414   0.765  -1.000  0.00  0.00           C+0
 
+ATOM      8  C           0      -0.414  -0.765  -1.000  0.00  0.00           C+0
 
+ATOM      9  H           0       0.756   1.394   1.822  0.00  0.00           H+0
 
+ATOM     10  H           0       0.756  -1.394   1.822  0.00  0.00           H+0
 
+ATOM     11  H           0       1.823   1.394  -0.754  0.00  0.00           H+0
 
+ATOM     12  H           0      -1.822   1.394   0.756  0.00  0.00           H+0
 
+ATOM     13  H           0       1.823  -1.394  -0.754  0.00  0.00           H+0
 
+ATOM     14  H           0      -1.822  -1.394   0.756  0.00  0.00           H+0
 
+ATOM     15  H           0      -0.754   1.396  -1.821  0.00  0.00           H+0
 
+ATOM     16  H           0      -0.754  -1.396  -1.821  0.00  0.00           H+0
 
+CONECT    1    2    3    4    9                                         NONE  21
 
+CONECT    2    1    5    6   10                                         NONE  22
 
+CONECT    3    1    5    7   11                                         NONE  23
 
+CONECT    4    1    6    7   12                                         NONE  24
 
+CONECT    5    2    3    8   13                                         NONE  25
 
+CONECT    6    2    4    8   14                                         NONE  26
 
+CONECT    7    3    4    8   15                                         NONE  27
 
+CONECT    8    5    6    7   16                                         NONE  28
 
+END                                                                     NONE  29
 
+

+ 665 - 0
examples/models/molecules/diamond.pdb
Файл харах 

@@ -0,0 +1,665 @@
 
+HEADER
 
+REMARK Spartan exported Fri Jan 30 16:05:42 1998
 
+HETATM    1  C   UNK  0001       1.339   5.378  -4.149
 
+HETATM    2  C   UNK  0001      -1.079   1.746  -3.946
 
+HETATM    3  C   UNK  0001       1.441   1.816  -3.988
 
+HETATM    4  C   UNK  0001       0.149   3.619  -2.788
 
+HETATM    5  C   UNK  0001      -1.023  -0.984  -5.086
 
+HETATM    6  C   UNK  0001       0.206   0.890  -3.927
 
+HETATM    7  C   UNK  0001      -0.977  -1.816  -3.786
 
+HETATM    8  C   UNK  0001       1.543  -1.746  -3.828
 
+HETATM    9  C   UNK  0001       0.251   0.057  -2.628
 
+HETATM   10  C   UNK  0001      -0.921  -4.546  -4.925
 
+HETATM   11  C   UNK  0001       0.308  -2.672  -3.766
 
+HETATM   12  C   UNK  0001      -0.876  -5.378  -3.626
 
+HETATM   13  C   UNK  0001       0.353  -3.505  -2.468
 
+HETATM   14  C   UNK  0001      -1.143   5.422  -1.587
 
+HETATM   15  C   UNK  0001      -3.607   2.623  -2.684
 
+HETATM   16  C   UNK  0001      -1.085   2.693  -2.726
 
+HETATM   17  C   UNK  0001      -2.378   4.496  -1.526
 
+HETATM   18  C   UNK  0001      -3.562   1.790  -1.385
 
+HETATM   19  C   UNK  0001      -1.041   1.860  -1.427
 
+HETATM   20  C   UNK  0001      -2.333   3.663  -0.227
 
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+HETATM  294  C   UNK  0001       2.819   5.094   8.468
 
+HETATM  295  C   UNK  0001       1.635   2.388   8.608
 
+HETATM  296  C   UNK  0001       4.155   2.458   8.566
 
+HETATM  297  C   UNK  0001       2.864   4.261   9.767
 
+HETATM  298  C   UNK  0001       2.825   4.146   7.248
 
+HETATM  299  C   UNK  0001       2.882   1.418   6.108
 
+HETATM  300  C   UNK  0001       1.691  -0.341   7.469
 
+HETATM  301  C   UNK  0001       4.213  -0.271   7.427
 
+HETATM  302  C   UNK  0001       2.921   1.533   8.628
 
+HETATM  303  C   UNK  0001       1.737  -1.174   8.769
 
+HETATM  304  C   UNK  0001       4.257  -1.104   8.727
 
+HETATM  305  C   UNK  0001       2.966   0.699   9.927
 
+HETATM  306  C   UNK  0001       2.927   0.585   7.408
 
+HETATM  307  C   UNK  0001       2.984  -2.144   6.268
 
+HETATM  308  C   UNK  0001       1.793  -3.903   7.630
 
+HETATM  309  C   UNK  0001       4.315  -3.833   7.588
 
+HETATM  310  C   UNK  0001       3.023  -2.029   8.788
 
+HETATM  311  C   UNK  0001       1.839  -4.736   8.929
 
+HETATM  312  C   UNK  0001       3.067  -2.863  10.087
 
+HETATM  313  C   UNK  0001       3.029  -2.977   7.568
 
+HETATM  314  C   UNK  0001       0.298   5.024   8.509
 
+HETATM  315  C   UNK  0001      -0.893   3.265   9.870
 
+HETATM  316  C   UNK  0001       1.629   3.335   9.828
 
+HETATM  317  C   UNK  0001      -0.847   2.432  11.170
 
+HETATM  318  C   UNK  0001       1.673   2.503  11.128
 
+HETATM  319  C   UNK  0001       0.343   4.191   9.809
 
+HETATM  320  C   UNK  0001       0.400   1.462   8.669
 
+HETATM  321  C   UNK  0001      -0.791  -0.297  10.031
 
+HETATM  322  C   UNK  0001       1.731  -0.227   9.989
 
+HETATM  323  C   UNK  0001       0.439   1.577  11.189
 
+HETATM  324  C   UNK  0001      -0.745  -1.130  11.330
 
+HETATM  325  C   UNK  0001       1.775  -1.059  11.288
 
+HETATM  326  C   UNK  0001       0.445   0.629   9.970
 
+HETATM  327  C   UNK  0001       0.502  -2.100   8.830
 
+HETATM  328  C   UNK  0001      -0.689  -3.859  10.191
 
+HETATM  329  C   UNK  0001       1.833  -3.789  10.149
 
+HETATM  330  C   UNK  0001       0.540  -1.985  11.350
 
+HETATM  331  C   UNK  0001       0.546  -2.933  10.130
 
+CONECT    1   66
 
+CONECT    2    6   16   22
 
+CONECT    3    6   67   74
 
+CONECT    4   16   67   90
 
+CONECT    5    7
 
+CONECT    6    2    3    9
 
+CONECT    7    5   11   24   30
 
+CONECT    8   11   75   82
 
+CONECT    9    6   24   75   98
 
+CONECT   10   12
 
+CONECT   11    7    8   13
 
+CONECT   12   10   32
 
+CONECT   13   11   32   83  106
 
+CONECT   14   17   90
 
+CONECT   15   18   21
 
+CONECT   16    2    4   19   21
 
+CONECT   17   14   20   21
 
+CONECT   18   15   25   40   46
 
+CONECT   19   16   25   91   98
 
+CONECT   20   17   40   91  116
 
+CONECT   21   15   16   17
 
+CONECT   22    2   29
 
+CONECT   23   26   29
 
+CONECT   24    7    9   27   29
 
+CONECT   25   18   19   28   29
 
+CONECT   26   23   33   48   54
 
+CONECT   27   24   33   99  106
 
+CONECT   28   25   48   99  124
 
+CONECT   29   22   23   24   25
 
+CONECT   30    7   37
 
+CONECT   31   34   37
 
+CONECT   32   12   13   35   37
 
+CONECT   33   26   27   36   37
 
+CONECT   34   31   55
 
+CONECT   35   32  107
 
+CONECT   36   33   55  107  132
 
+CONECT   37   30   31   32   33
 
+CONECT   38   41  116
 
+CONECT   39   42   45
 
+CONECT   40   18   20   43   45
 
+CONECT   41   38   44   45
 
+CONECT   42   39   49   60
 
+CONECT   43   40   49  117  124
 
+CONECT   44   41   60  117  141
 
+CONECT   45   39   40   41
 
+CONECT   46   18   53
 
+CONECT   47   50   53
 
+CONECT   48   26   28   51   53
 
+CONECT   49   42   43   52   53
 
+CONECT   50   47   56   62
 
+CONECT   51   48   56  125  132
 
+CONECT   52   49   62  125  149
 
+CONECT   53   46   47   48   49
 
+CONECT   54   26   59
 
+CONECT   55   34   36   57   59
 
+CONECT   56   50   51   58   59
 
+CONECT   57   55  133
 
+CONECT   58   56  133  157
 
+CONECT   59   54   55   56
 
+CONECT   60   42   44   61
 
+CONECT   61   60  142  149
 
+CONECT   62   50   52   63
 
+CONECT   63   62  150  157
 
+CONECT   64   69   90
 
+CONECT   65   69  164
 
+CONECT   66    1   73
 
+CONECT   67    3    4   70   73
 
+CONECT   68   71   73
 
+CONECT   69   64   65   72   73
 
+CONECT   70   67   77   92   98
 
+CONECT   71   68   77  165  172
 
+CONECT   72   69   92  165  188
 
+CONECT   73   66   67   68   69
 
+CONECT   74    3   81
 
+CONECT   75    8    9   78   81
 
+CONECT   76   79   81
 
+CONECT   77   70   71   80   81
 
+CONECT   78   75   84  100  106
 
+CONECT   79   76   84  173  180
 
+CONECT   80   77  100  173  196
 
+CONECT   81   74   75   76   77
 
+CONECT   82    8   87
 
+CONECT   83   13   85   87
 
+CONECT   84   78   79   86   87
 
+CONECT   85   83  108
 
+CONECT   86   84  108  181  204
 
+CONECT   87   82   83   84
 
+CONECT   88   93  116
 
+CONECT   89   93  188
 
+CONECT   90    4   14   64   97
 
+CONECT   91   19   20   94   97
 
+CONECT   92   70   72   95   97
 
+CONECT   93   88   89   96   97
 
+CONECT   94   91  101  118  124
 
+CONECT   95   92  101  189  196
 
+CONECT   96   93  118  189  214
 
+CONECT   97   90   91   92   93
 
+CONECT   98    9   19   70  105
 
+CONECT   99   27   28  102  105
 
+CONECT  100   78   80  103  105
 
+CONECT  101   94   95  104  105
 
+CONECT  102   99  109  126  132
 
+CONECT  103  100  109  197  204
 
+CONECT  104  101  126  197  222
 
+CONECT  105   98   99  100  101
 
+CONECT  106   13   27   78  113
 
+CONECT  107   35   36  110  113
 
+CONECT  108   85   86  111  113
 
+CONECT  109  102  103  112  113
 
+CONECT  110  107  134
 
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+CONECT  116   20   38   88  123
 
+CONECT  117   43   44  120  123
 
+CONECT  118   94   96  121  123
 
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+CONECT  120  117  127  143  149
 
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+CONECT  122  119  143  215  239
 
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+CONECT  124   28   43   94  131
 
+CONECT  125   51   52  128  131
 
+CONECT  126  102  104  129  131
 
+CONECT  127  120  121  130  131
 
+CONECT  128  125  135  151  157
 
+CONECT  129  126  135  223  230
 
+CONECT  130  127  151  223  247
 
+CONECT  131  124  125  126  127
 
+CONECT  132   36   51  102  139
 
+CONECT  133   57   58  136  139
 
+CONECT  134  110  112  137  139
 
+CONECT  135  128  129  138  139
 
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+CONECT  137  134  231
 
+CONECT  138  135  158  231  255
 
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+CONECT  140  144  239
 
+CONECT  141   44  114  148
 
+CONECT  142   61  145  148
 
+CONECT  143  120  122  146  148
 
+CONECT  144  140  147  148
 
+CONECT  145  142  152
 
+CONECT  146  143  152  240  247
 
+CONECT  147  144  240
 
+CONECT  148  141  142  143  144
 
+CONECT  149   52   61  120  156
 
+CONECT  150   63  153  156
 
+CONECT  151  128  130  154  156
 
+CONECT  152  145  146  155  156
 
+CONECT  153  150  159
 
+CONECT  154  151  159  248  255
 
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+CONECT  156  149  150  151  152
 
+CONECT  157   58   63  128  162
 
+CONECT  158  136  138  160  162
 
+CONECT  159  153  154  161  162
 
+CONECT  160  158  256
 
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+CONECT  164   65  171
 
+CONECT  165   71   72  168  171
 
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+CONECT  167  163  170  171
 
+CONECT  168  165  175  190  196
 
+CONECT  169  166  175  263
 
+CONECT  170  167  190  263  268
 
+CONECT  171  164  165  166  167
 
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+CONECT  173   79   80  176  179
 
+CONECT  174  177  179
 
+CONECT  175  168  169  178  179
 
+CONECT  176  173  182  198  204
 
+CONECT  177  174  182  265
 
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+CONECT  179  172  173  174  175
 
+CONECT  180   79  185
 
+CONECT  181   86  183  185
 
+CONECT  182  176  177  184  185
 
+CONECT  183  181  206
 
+CONECT  184  182  206  284
 
+CONECT  185  180  181  182
 
+CONECT  186  191  214
 
+CONECT  187  191  268
 
+CONECT  188   72   89  163  195
 
+CONECT  189   95   96  192  195
 
+CONECT  190  168  170  193  195
 
+CONECT  191  186  187  194  195
 
+CONECT  192  189  199  216  222
 
+CONECT  193  190  199  269  276
 
+CONECT  194  191  216  269  291
 
+CONECT  195  188  189  190  191
 
+CONECT  196   80   95  168  203
 
+CONECT  197  103  104  200  203
 
+CONECT  198  176  178  201  203
 
+CONECT  199  192  193  202  203
 
+CONECT  200  197  207  224  230
 
+CONECT  201  198  207  277  284
 
+CONECT  202  199  224  277  299
 
+CONECT  203  196  197  198  199
 
+CONECT  204   86  103  176  211
 
+CONECT  205  111  112  208  211
 
+CONECT  206  183  184  209  211
 
+CONECT  207  200  201  210  211
 
+CONECT  208  205  232
 
+CONECT  209  206  285
 
+CONECT  210  207  232  285  307
 
+CONECT  211  204  205  206  207
 
+CONECT  212  217  239
 
+CONECT  213  217  291
 
+CONECT  214   96  115  186  221
 
+CONECT  215  121  122  218  221
 
+CONECT  216  192  194  219  221
 
+CONECT  217  212  213  220  221
 
+CONECT  218  215  225  241  247
 
+CONECT  219  216  225  292  299
 
+CONECT  220  217  241  292  314
 
+CONECT  221  214  215  216  217
 
+CONECT  222  104  121  192  229
 
+CONECT  223  129  130  226  229
 
+CONECT  224  200  202  227  229
 
+CONECT  225  218  219  228  229
 
+CONECT  226  223  233  249  255
 
+CONECT  227  224  233  300  307
 
+CONECT  228  225  249  300  320
 
+CONECT  229  222  223  224  225
 
+CONECT  230  112  129  200  237
 
+CONECT  231  137  138  234  237
 
+CONECT  232  208  210  235  237
 
+CONECT  233  226  227  236  237
 
+CONECT  234  231  257
 
+CONECT  235  232  308
 
+CONECT  236  233  257  308  327
 
+CONECT  237  230  231  232  233
 
+CONECT  238  242  314
 
+CONECT  239  122  140  212  246
 
+CONECT  240  146  147  243  246
 
+CONECT  241  218  220  244  246
 
+CONECT  242  238  245  246
 
+CONECT  243  240  250
 
+CONECT  244  241  250  315  320
 
+CONECT  245  242  315
 
+CONECT  246  239  240  241  242
 
+CONECT  247  130  146  218  254
 
+CONECT  248  154  155  251  254
 
+CONECT  249  226  228  252  254
 
+CONECT  250  243  244  253  254
 
+CONECT  251  248  258
 
+CONECT  252  249  258  321  327
 
+CONECT  253  250  321
 
+CONECT  254  247  248  249  250
 
+CONECT  255  138  154  226  262
 
+CONECT  256  160  161  259  262
 
+CONECT  257  234  236  260  262
 
+CONECT  258  251  252  261  262
 
+CONECT  259  256
 
+CONECT  260  257  328
 
+CONECT  261  258  328
 
+CONECT  262  255  256  257  258
 
+CONECT  263  169  170  264
 
+CONECT  264  263  270  276
 
+CONECT  265  177  178  266
 
+CONECT  266  265  278  284
 
+CONECT  267  271  291
 
+CONECT  268  170  187  275
 
+CONECT  269  193  194  272  275
 
+CONECT  270  264  273  275
 
+CONECT  271  267  274  275
 
+CONECT  272  269  279  293  299
 
+CONECT  273  270  279
 
+CONECT  274  271  293
 
+CONECT  275  268  269  270  271
 
+CONECT  276  178  193  264  283
 
+CONECT  277  201  202  280  283
 
+CONECT  278  266  281  283
 
+CONECT  279  272  273  282  283
 
+CONECT  280  277  286  301  307
 
+CONECT  281  278  286
 
+CONECT  282  279  301
 
+CONECT  283  276  277  278  279
 
+CONECT  284  184  201  266  289
 
+CONECT  285  209  210  287  289
 
+CONECT  286  280  281  288  289
 
+CONECT  287  285  309
 
+CONECT  288  286  309
 
+CONECT  289  284  285  286
 
+CONECT  290  294  314
 
+CONECT  291  194  213  267  298
 
+CONECT  292  219  220  295  298
 
+CONECT  293  272  274  296  298
 
+CONECT  294  290  297  298
 
+CONECT  295  292  302  316  320
 
+CONECT  296  293  302
 
+CONECT  297  294  316
 
+CONECT  298  291  292  293  294
 
+CONECT  299  202  219  272  306
 
+CONECT  300  227  228  303  306
 
+CONECT  301  280  282  304  306
 
+CONECT  302  295  296  305  306
 
+CONECT  303  300  310  322  327
 
+CONECT  304  301  310
 
+CONECT  305  302  322
 
+CONECT  306  299  300  301  302
 
+CONECT  307  210  227  280  313
 
+CONECT  308  235  236  311  313
 
+CONECT  309  287  288  313
 
+CONECT  310  303  304  312  313
 
+CONECT  311  308  329
 
+CONECT  312  310  329
 
+CONECT  313  307  308  309  310
 
+CONECT  314  220  238  290  319
 
+CONECT  315  244  245  317  319
 
+CONECT  316  295  297  318  319
 
+CONECT  317  315  323
 
+CONECT  318  316  323
 
+CONECT  319  314  315  316
 
+CONECT  320  228  244  295  326
 
+CONECT  321  252  253  324  326
 
+CONECT  322  303  305  325  326
 
+CONECT  323  317  318  326
 
+CONECT  324  321  330
 
+CONECT  325  322  330
 
+CONECT  326  320  321  322  323
 
+CONECT  327  236  252  303  331
 
+CONECT  328  260  261  331
 
+CONECT  329  311  312  331
 
+CONECT  330  324  325  331
 
+CONECT  331  327  328  329  330
 
+END

+ 18 - 0
examples/models/molecules/ethanol.pdb
Файл харах 

@@ -0,0 +1,18 @@
 
+HEADER    NONAME 23-Apr-10                                              NONE   1
 
+TITLE                                                                   NONE   2
 
+AUTHOR    Chemical Structure Services at http://cactus.nci.nih.gov      NONE   3
 
+REVDAT   1  23-Apr-10     0                                             NONE   4
 
+ATOM      1  C           0       0.011  -0.566   0.000  0.00  0.00           C+0
 
+ATOM      2  C           0      -1.285   0.246  -0.000  0.00  0.00           C+0
 
+ATOM      3  H           0       1.925  -0.229  -0.000  0.00  0.00           H+0
 
+ATOM      4  O           0       1.130   0.322   0.000  0.00  0.00           O+0
 
+ATOM      5  H           0       0.046  -1.195   0.890  0.00  0.00           H+0
 
+ATOM      6  H           0       0.046  -1.195  -0.890  0.00  0.00           H+0
 
+ATOM      7  H           0      -2.139  -0.432   0.000  0.00  0.00           H+0
 
+ATOM      8  H           0      -1.320   0.875   0.890  0.00  0.00           H+0
 
+ATOM      9  H           0      -1.320   0.875  -0.890  0.00  0.00           H+0
 
+CONECT    1    2    4    5    6                                         NONE  14
 
+CONECT    2    7    8    9    0                                       NONE  15
 
+CONECT    4    3    0    0    0                                         NONE  16
 
+END                                                                     NONE  17
 
+

+ 59 - 0
examples/models/molecules/glucose.pdb
Файл харах 

@@ -0,0 +1,59 @@
 
+COMPND                                                                
+REMARK   1 PDB to MMOD atom-numbering translation table; the mmod numbers
 
+REMARK   1 pertain to the .dat file from which this file was created,
 
+REMARK   1 not to one created from this file:
 
+REMARK   1  PDB:     1     2     3     4     5     6     7     8     9  
+REMARK   1 MMOD:     1     2     3     4     5     6     7     8     9 /
 
+REMARK   1  PDB:    10    11    12    13    14    15    16    17    18  
+REMARK   1 MMOD:    10    11    23    12    13    14    15    16    17 /
 
+REMARK   1  PDB:    19    20    21    22    23    24  
+REMARK   1 MMOD:    18    19    20    21    22    24 /
 
+HETATM    1  C01 UNK A   1     -10.447   3.465   0.000  0.00  0.00   0
 
+HETATM    2  C02 UNK A   1     -11.071   4.006   1.273  0.00  0.00   0
 
+HETATM    3  C03 UNK A   1     -12.577   4.148   1.128  0.00  0.00   0
 
+HETATM    4  C04 UNK A   1     -12.891   4.988  -0.105  0.00  0.00   0
 
+HETATM    5  C05 UNK A   1     -12.200   4.411  -1.349  0.00  0.00   0
 
+HETATM    6  O06 UNK A   1     -10.802   4.239  -1.130  0.00  0.00   0
 
+HETATM    7  O07 UNK A   1     -10.803   3.104   2.323  0.00  0.00   0
 
+HETATM    8  O08 UNK A   1     -13.072   4.770   2.296  0.00  0.00   0
 
+HETATM    9  O09 UNK A   1     -14.294   4.984  -0.281  0.00  0.00   0
 
+HETATM   10  C10 UNK A   1     -12.311   5.317  -2.577  0.00  0.00   0
 
+HETATM   11  O11 UNK A   1     -13.660   5.466  -2.961  0.00  0.00   0
 
+HETATM   12  O23 UNK A   1      -9.045   3.478   0.138  0.00  0.00   0
 
+HETATM   13  H12 UNK A   1      -9.995   3.339   2.755  0.00  0.00   0
 
+HETATM   14  H13 UNK A   1     -12.863   4.206   3.024  0.00  0.00   0
 
+HETATM   15  H14 UNK A   1     -13.704   6.000  -3.739  0.00  0.00   0
 
+HETATM   16  H15 UNK A   1     -10.793   2.419  -0.156  0.00  0.00   0
 
+HETATM   17  H16 UNK A   1     -10.626   4.997   1.513  0.00  0.00   0
 
+HETATM   18  H17 UNK A   1     -13.037   3.141   1.020  0.00  0.00   0
 
+HETATM   19  H18 UNK A   1     -12.542   6.032   0.061  0.00  0.00   0
 
+HETATM   20  H19 UNK A   1     -12.653   3.423  -1.588  0.00  0.00   0
 
+HETATM   21  H20 UNK A   1     -14.475   5.505  -1.044  0.00  0.00   0
 
+HETATM   22  H21 UNK A   1     -11.886   6.317  -2.335  0.00  0.00   0
 
+HETATM   23  H22 UNK A   1     -11.738   4.866  -3.418  0.00  0.00   0
 
+HETATM   24  H24 UNK A   1      -8.822   2.951   0.906  0.00  0.00   0
 
+CONECT    1    2    6   12   16
 
+CONECT    2    1    3    7   17
 
+CONECT    3    2    4    8   18
 
+CONECT    4    3    5    9   19
 
+CONECT    5    4    6   10   20
 
+CONECT    6    5    1
 
+CONECT    7    2   13
 
+CONECT    8    3   14
 
+CONECT    9    4   21
 
+CONECT   10    5   11   22   23
 
+CONECT   11   10   15
 
+CONECT   12    1   24
 
+CONECT   13    7
 
+CONECT   14    8
 
+CONECT   15   11
 
+CONECT   16    1
 
+CONECT   17    2
 
+CONECT   18    3
 
+CONECT   19    4
 
+CONECT   20    5
 
+CONECT   21    9
 
+CONECT   22   10
 
+CONECT   23   10
 
+CONECT   24   12
 
+END

+ 403 - 0
examples/models/molecules/graphite.pdb
Файл харах 

@@ -0,0 +1,403 @@
 
+HEADER
 
+REMARK Spartan exported Fri Jan 30 16:10:52 1998
 
+HETATM    1  C   UNK  0001       4.141   3.305  -3.641
 
+HETATM    2  C   UNK  0001       3.254   3.762  -2.621
 
+HETATM    3  C   UNK  0001       1.962   0.786  -4.295
 
+HETATM    4  C   UNK  0001       2.087   0.286  -2.965
 
+HETATM    5  C   UNK  0001      -0.217  -1.734  -4.949
 
+HETATM    6  C   UNK  0001      -1.104  -1.278  -3.929
 
+HETATM    7  C   UNK  0001      -2.397  -4.254  -5.603
 
+HETATM    8  C   UNK  0001      -2.272  -4.753  -4.273
 
+HETATM    9  C   UNK  0001       2.265   4.743  -2.925
 
+HETATM   10  C   UNK  0001       1.378   5.199  -1.906
 
+HETATM   11  C   UNK  0001       0.085   2.223  -3.579
 
+HETATM   12  C   UNK  0001       0.210   1.724  -2.249
 
+HETATM   13  C   UNK  0001      -2.094  -0.297  -4.233
 
+HETATM   14  C   UNK  0001      -2.981   0.160  -3.214
 
+HETATM   15  C   UNK  0001      -4.273  -2.817  -4.887
 
+HETATM   16  C   UNK  0001      -4.148  -3.316  -3.557
 
+HETATM   17  C   UNK  0001       0.388   6.180  -2.210
 
+HETATM   18  C   UNK  0001      -0.499   6.636  -1.190
 
+HETATM   19  C   UNK  0001      -1.792   3.660  -2.864
 
+HETATM   20  C   UNK  0001      -1.666   3.161  -1.533
 
+HETATM   21  C   UNK  0001      -3.971   1.141  -3.518
 
+HETATM   22  C   UNK  0001      -4.858   1.597  -2.498
 
+HETATM   23  C   UNK  0001      -6.150  -1.379  -4.172
 
+HETATM   24  C   UNK  0001      -6.025  -1.878  -2.841
 
+HETATM   25  C   UNK  0001      -1.489   7.617  -1.494
 
+HETATM   26  C   UNK  0001      -2.376   8.074  -0.474
 
+HETATM   27  C   UNK  0001      -3.668   5.098  -2.148
 
+HETATM   28  C   UNK  0001      -3.543   4.598  -0.818
 
+HETATM   29  C   UNK  0001      -5.848   2.578  -2.802
 
+HETATM   30  C   UNK  0001      -6.734   3.034  -1.782
 
+HETATM   31  C   UNK  0001      -8.027   0.058  -3.456
 
+HETATM   32  C   UNK  0001      -7.902  -0.441  -2.126
 
+HETATM   33  C   UNK  0001      -3.366   9.055  -0.778
 
+HETATM   34  C   UNK  0001      -4.252   9.511   0.242
 
+HETATM   35  C   UNK  0001      -5.545   6.535  -1.432
 
+HETATM   36  C   UNK  0001      -5.420   6.036  -0.102
 
+HETATM   37  C   UNK  0001      -7.724   4.015  -2.086
 
+HETATM   38  C   UNK  0001      -8.611   4.472  -1.066
 
+HETATM   39  C   UNK  0001      -9.904   1.496  -2.740
 
+HETATM   40  C   UNK  0001      -9.779   0.996  -1.410
 
+HETATM   41  C   UNK  0001       5.300   1.876  -1.994
 
+HETATM   42  C   UNK  0001       4.413   2.332  -0.974
 
+HETATM   43  C   UNK  0001       3.121  -0.644  -2.648
 
+HETATM   44  C   UNK  0001       3.246  -1.143  -1.317
 
+HETATM   45  C   UNK  0001       0.941  -3.164  -3.302
 
+HETATM   46  C   UNK  0001       0.055  -2.707  -2.282
 
+HETATM   47  C   UNK  0001      -1.238  -5.684  -3.956
 
+HETATM   48  C   UNK  0001      -1.113  -6.183  -2.625
 
+HETATM   49  C   UNK  0001       3.423   3.313  -1.278
 
+HETATM   50  C   UNK  0001       2.536   3.769  -0.258
 
+HETATM   51  C   UNK  0001       1.244   0.793  -1.932
 
+HETATM   52  C   UNK  0001       1.369   0.294  -0.601
 
+HETATM   53  C   UNK  0001      -0.935  -1.727  -2.586
 
+HETATM   54  C   UNK  0001      -1.822  -1.270  -1.566
 
+HETATM   55  C   UNK  0001      -3.115  -4.246  -3.240
 
+HETATM   56  C   UNK  0001      -2.990  -4.746  -1.910
 
+HETATM   57  C   UNK  0001       1.546   4.750  -0.562
 
+HETATM   58  C   UNK  0001       0.660   5.207   0.458
 
+HETATM   59  C   UNK  0001      -0.633   2.231  -1.216
 
+HETATM   60  C   UNK  0001      -0.508   1.731   0.114
 
+HETATM   61  C   UNK  0001      -2.812  -0.289  -1.870
 
+HETATM   62  C   UNK  0001      -3.699   0.167  -0.850
 
+HETATM   63  C   UNK  0001      -4.991  -2.809  -2.524
 
+HETATM   64  C   UNK  0001      -4.866  -3.308  -1.194
 
+HETATM   65  C   UNK  0001      -0.330   6.188   0.154
 
+HETATM   66  C   UNK  0001      -1.217   6.644   1.173
 
+HETATM   67  C   UNK  0001      -2.510   3.668  -0.500
 
+HETATM   68  C   UNK  0001      -2.385   3.169   0.830
 
+HETATM   69  C   UNK  0001      -4.689   1.148  -1.154
 
+HETATM   70  C   UNK  0001      -5.576   1.605  -0.135
 
+HETATM   71  C   UNK  0001      -6.868  -1.371  -1.808
 
+HETATM   72  C   UNK  0001      -6.743  -1.871  -0.478
 
+HETATM   73  C   UNK  0001      -2.207   7.625   0.869
 
+HETATM   74  C   UNK  0001      -3.094   8.082   1.889
 
+HETATM   75  C   UNK  0001      -4.386   5.105   0.215
 
+HETATM   76  C   UNK  0001      -4.261   4.606   1.546
 
+HETATM   77  C   UNK  0001      -6.566   2.586  -0.439
 
+HETATM   78  C   UNK  0001      -7.452   3.042   0.581
 
+HETATM   79  C   UNK  0001      -8.745   0.066  -1.093
 
+HETATM   80  C   UNK  0001      -8.620  -0.433   0.238
 
+HETATM   81  C   UNK  0001       6.459   0.446  -0.346
 
+HETATM   82  C   UNK  0001       5.572   0.902   0.674
 
+HETATM   83  C   UNK  0001       4.279  -2.074  -1.000
 
+HETATM   84  C   UNK  0001       4.404  -2.573   0.330
 
+HETATM   85  C   UNK  0001       2.100  -4.594  -1.654
 
+HETATM   86  C   UNK  0001       1.213  -4.137  -0.634
 
+HETATM   87  C   UNK  0001      -0.079  -7.113  -2.308
 
+HETATM   88  C   UNK  0001       0.046  -7.613  -0.978
 
+HETATM   89  C   UNK  0001       4.582   1.883   0.370
 
+HETATM   90  C   UNK  0001       3.695   2.340   1.389
 
+HETATM   91  C   UNK  0001       2.403  -0.637  -0.284
 
+HETATM   92  C   UNK  0001       2.528  -1.136   1.046
 
+HETATM   93  C   UNK  0001       0.223  -3.156  -0.938
 
+HETATM   94  C   UNK  0001      -0.664  -2.700   0.081
 
+HETATM   95  C   UNK  0001      -1.956  -5.676  -1.592
 
+HETATM   96  C   UNK  0001      -1.831  -6.175  -0.262
 
+HETATM   97  C   UNK  0001       2.705   3.321   1.085
 
+HETATM   98  C   UNK  0001       1.818   3.777   2.105
 
+HETATM   99  C   UNK  0001       0.526   0.801   0.431
 
+HETATM  100  C   UNK  0001       0.651   0.302   1.762
 
+HETATM  101  C   UNK  0001      -1.653  -1.719  -0.223
 
+HETATM  102  C   UNK  0001      -2.540  -1.262   0.797
 
+HETATM  103  C   UNK  0001      -3.833  -4.239  -0.877
 
+HETATM  104  C   UNK  0001      -3.708  -4.738   0.454
 
+HETATM  105  C   UNK  0001       0.828   4.758   1.801
 
+HETATM  106  C   UNK  0001      -0.058   5.214   2.821
 
+HETATM  107  C   UNK  0001      -1.351   2.238   1.147
 
+HETATM  108  C   UNK  0001      -1.226   1.739   2.477
 
+HETATM  109  C   UNK  0001      -3.530  -0.281   0.493
 
+HETATM  110  C   UNK  0001      -4.417   0.175   1.513
 
+HETATM  111  C   UNK  0001      -5.710  -2.801  -0.161
 
+HETATM  112  C   UNK  0001      -5.584  -3.300   1.169
 
+HETATM  113  C   UNK  0001      -1.048   6.195   2.517
 
+HETATM  114  C   UNK  0001      -1.935   6.652   3.537
 
+HETATM  115  C   UNK  0001      -3.228   3.676   1.863
 
+HETATM  116  C   UNK  0001      -3.103   3.176   3.193
 
+HETATM  117  C   UNK  0001      -5.407   1.156   1.209
 
+HETATM  118  C   UNK  0001      -6.294   1.612   2.229
 
+HETATM  119  C   UNK  0001      -7.586  -1.364   0.555
 
+HETATM  120  C   UNK  0001      -7.461  -1.863   1.885
 
+HETATM  121  C   UNK  0001       7.617  -0.984   1.301
 
+HETATM  122  C   UNK  0001       6.730  -0.528   2.321
 
+HETATM  123  C   UNK  0001       5.438  -3.504   0.647
 
+HETATM  124  C   UNK  0001       5.563  -4.003   1.978
 
+HETATM  125  C   UNK  0001       3.259  -6.023  -0.007
 
+HETATM  126  C   UNK  0001       2.372  -5.567   1.013
 
+HETATM  127  C   UNK  0001       1.079  -8.543  -0.661
 
+HETATM  128  C   UNK  0001       1.204  -9.042   0.670
 
+HETATM  129  C   UNK  0001       5.740   0.453   2.017
 
+HETATM  130  C   UNK  0001       4.854   0.910   3.037
 
+HETATM  131  C   UNK  0001       3.561  -2.066   1.363
 
+HETATM  132  C   UNK  0001       3.686  -2.566   2.694
 
+HETATM  133  C   UNK  0001       1.382  -4.586   0.709
 
+HETATM  134  C   UNK  0001       0.495  -4.130   1.729
 
+HETATM  135  C   UNK  0001      -0.797  -7.106   0.055
 
+HETATM  136  C   UNK  0001      -0.672  -7.605   1.385
 
+HETATM  137  C   UNK  0001       3.864   1.891   2.733
 
+HETATM  138  C   UNK  0001       2.977   2.347   3.753
 
+HETATM  139  C   UNK  0001       1.684  -0.629   2.079
 
+HETATM  140  C   UNK  0001       1.809  -1.128   3.409
 
+HETATM  141  C   UNK  0001      -0.495  -3.149   1.425
 
+HETATM  142  C   UNK  0001      -1.382  -2.692   2.445
 
+HETATM  143  C   UNK  0001      -2.674  -5.668   0.771
 
+HETATM  144  C   UNK  0001      -2.549  -6.168   2.101
 
+HETATM  145  C   UNK  0001       1.987   3.328   3.449
 
+HETATM  146  C   UNK  0001       1.100   3.785   4.468
 
+HETATM  147  C   UNK  0001      -0.192   0.809   2.795
 
+HETATM  148  C   UNK  0001      -0.067   0.309   4.125
 
+HETATM  149  C   UNK  0001      -2.372  -1.711   2.141
 
+HETATM  150  C   UNK  0001      -3.258  -1.255   3.160
 
+HETATM  151  C   UNK  0001      -4.551  -4.231   1.487
 
+HETATM  152  C   UNK  0001      -4.426  -4.730   2.817
 
+HETATM  153  C   UNK  0001       0.110   4.766   4.164
 
+HETATM  154  C   UNK  0001      -0.777   5.222   5.184
 
+HETATM  155  C   UNK  0001      -2.069   2.246   3.510
 
+HETATM  156  C   UNK  0001      -1.944   1.747   4.841
 
+HETATM  157  C   UNK  0001      -4.248  -0.274   2.856
 
+HETATM  158  C   UNK  0001      -5.135   0.183   3.876
 
+HETATM  159  C   UNK  0001      -6.428  -2.794   2.202
 
+HETATM  160  C   UNK  0001      -6.303  -3.293   3.533
 
+HETATM  161  C   UNK  0001       8.776  -2.414   2.949
 
+HETATM  162  C   UNK  0001       7.889  -1.957   3.969
 
+HETATM  163  C   UNK  0001       6.597  -4.933   2.295
 
+HETATM  164  C   UNK  0001       6.722  -5.433   3.625
 
+HETATM  165  C   UNK  0001       4.417  -7.453   1.641
 
+HETATM  166  C   UNK  0001       3.531  -6.997   2.661
 
+HETATM  167  C   UNK  0001       2.238  -9.973   0.987
 
+HETATM  168  C   UNK  0001       2.363 -10.472   2.317
 
+HETATM  169  C   UNK  0001       6.899  -0.976   3.665
 
+HETATM  170  C   UNK  0001       6.012  -0.520   4.684
 
+HETATM  171  C   UNK  0001       4.720  -3.496   3.011
 
+HETATM  172  C   UNK  0001       4.845  -3.995   4.341
 
+HETATM  173  C   UNK  0001       2.541  -6.016   2.357
 
+HETATM  174  C   UNK  0001       1.654  -5.559   3.376
 
+HETATM  175  C   UNK  0001       0.361  -8.535   1.703
 
+HETATM  176  C   UNK  0001       0.486  -9.035   3.033
 
+HETATM  177  C   UNK  0001       5.022   0.461   4.380
 
+HETATM  178  C   UNK  0001       4.136   0.918   5.400
 
+HETATM  179  C   UNK  0001       2.843  -2.059   3.726
 
+HETATM  180  C   UNK  0001       2.968  -2.558   5.057
 
+HETATM  181  C   UNK  0001       0.664  -4.578   3.072
 
+HETATM  182  C   UNK  0001      -0.223  -4.122   4.092
 
+HETATM  183  C   UNK  0001      -1.515  -7.098   2.418
 
+HETATM  184  C   UNK  0001      -1.390  -7.597   3.749
 
+HETATM  185  C   UNK  0001       3.146   1.898   5.096
 
+HETATM  186  C   UNK  0001       2.259   2.355   6.116
 
+HETATM  187  C   UNK  0001       0.966  -0.621   4.442
 
+HETATM  188  C   UNK  0001       1.091  -1.120   5.772
 
+HETATM  189  C   UNK  0001      -1.213  -3.141   3.788
 
+HETATM  190  C   UNK  0001      -2.100  -2.685   4.808
 
+HETATM  191  C   UNK  0001      -3.392  -5.661   3.134
 
+HETATM  192  C   UNK  0001      -3.267  -6.160   4.464
 
+HETATM  193  C   UNK  0001       1.269   3.336   5.812
 
+HETATM  194  C   UNK  0001       0.382   3.792   6.832
 
+HETATM  195  C   UNK  0001      -0.910   0.816   5.158
 
+HETATM  196  C   UNK  0001      -0.785   0.317   6.488
 
+HETATM  197  C   UNK  0001      -3.090  -1.704   4.504
 
+HETATM  198  C   UNK  0001      -3.976  -1.247   5.524
 
+HETATM  199  C   UNK  0001      -5.269  -4.223   3.850
 
+HETATM  200  C   UNK  0001      -5.144  -4.723   5.180
 
+CONECT    1    2
 
+CONECT    2    1    9   49
 
+CONECT    3    4
 
+CONECT    4    3   43   51
 
+CONECT    5    6
 
+CONECT    6    5   13   53
 
+CONECT    7    8
 
+CONECT    8    7   47   55
 
+CONECT    9    2   10
 
+CONECT   10    9   17   57
 
+CONECT   11   12
 
+CONECT   12   11   51   59
 
+CONECT   13    6   14
 
+CONECT   14   13   21   61
 
+CONECT   15   16
 
+CONECT   16   15   55   63
 
+CONECT   17   10   18
 
+CONECT   18   17   25   65
 
+CONECT   19   20
 
+CONECT   20   19   59   67
 
+CONECT   21   14   22
 
+CONECT   22   21   29   69
 
+CONECT   23   24
 
+CONECT   24   23   63   71
 
+CONECT   25   18   26
 
+CONECT   26   25   33   73
 
+CONECT   27   28
 
+CONECT   28   27   67   75
 
+CONECT   29   22   30
 
+CONECT   30   29   37   77
 
+CONECT   31   32
 
+CONECT   32   31   71   79
 
+CONECT   33   26   34
 
+CONECT   34   33
 
+CONECT   35   36
 
+CONECT   36   35   75
 
+CONECT   37   30   38
 
+CONECT   38   37
 
+CONECT   39   40
 
+CONECT   40   39   79
 
+CONECT   41   42
 
+CONECT   42   41   49   89
 
+CONECT   43    4   44
 
+CONECT   44   43   83   91
 
+CONECT   45   46
 
+CONECT   46   45   53   93
 
+CONECT   47    8   48
 
+CONECT   48   47   87   95
 
+CONECT   49    2   42   50
 
+CONECT   50   49   57   97
 
+CONECT   51    4   12   52
 
+CONECT   52   51   91   99
 
+CONECT   53    6   46   54
 
+CONECT   54   53   61  101
 
+CONECT   55    8   16   56
 
+CONECT   56   55   95  103
 
+CONECT   57   10   50   58
 
+CONECT   58   57   65  105
 
+CONECT   59   12   20   60
 
+CONECT   60   59   99  107
 
+CONECT   61   14   54   62
 
+CONECT   62   61   69  109
 
+CONECT   63   16   24   64
 
+CONECT   64   63  103  111
 
+CONECT   65   18   58   66
 
+CONECT   66   65   73  113
 
+CONECT   67   20   28   68
 
+CONECT   68   67  107  115
 
+CONECT   69   22   62   70
 
+CONECT   70   69   77  117
 
+CONECT   71   24   32   72
 
+CONECT   72   71  111  119
 
+CONECT   73   26   66   74
 
+CONECT   74   73
 
+CONECT   75   28   36   76
 
+CONECT   76   75  115
 
+CONECT   77   30   70   78
 
+CONECT   78   77
 
+CONECT   79   32   40   80
 
+CONECT   80   79  119
 
+CONECT   81   82
 
+CONECT   82   81   89  129
 
+CONECT   83   44   84
 
+CONECT   84   83  123  131
 
+CONECT   85   86
 
+CONECT   86   85   93  133
 
+CONECT   87   48   88
 
+CONECT   88   87  127  135
 
+CONECT   89   42   82   90
 
+CONECT   90   89   97  137
 
+CONECT   91   44   52   92
 
+CONECT   92   91  131  139
 
+CONECT   93   46   86   94
 
+CONECT   94   93  101  141
 
+CONECT   95   48   56   96
 
+CONECT   96   95  135  143
 
+CONECT   97   50   90   98
 
+CONECT   98   97  105  145
 
+CONECT   99   52   60  100
 
+CONECT  100   99  139  147
 
+CONECT  101   54   94  102
 
+CONECT  102  101  109  149
 
+CONECT  103   56   64  104
 
+CONECT  104  103  143  151
 
+CONECT  105   58   98  106
 
+CONECT  106  105  113  153
 
+CONECT  107   60   68  108
 
+CONECT  108  107  147  155
 
+CONECT  109   62  102  110
 
+CONECT  110  109  117  157
 
+CONECT  111   64   72  112
 
+CONECT  112  111  151  159
 
+CONECT  113   66  106  114
 
+CONECT  114  113
 
+CONECT  115   68   76  116
 
+CONECT  116  115  155
 
+CONECT  117   70  110  118
 
+CONECT  118  117
 
+CONECT  119   72   80  120
 
+CONECT  120  119  159
 
+CONECT  121  122
 
+CONECT  122  121  129  169
 
+CONECT  123   84  124
 
+CONECT  124  123  163  171
 
+CONECT  125  126
 
+CONECT  126  125  133  173
 
+CONECT  127   88  128
 
+CONECT  128  127  167  175
 
+CONECT  129   82  122  130
 
+CONECT  130  129  137  177
 
+CONECT  131   84   92  132
 
+CONECT  132  131  171  179
 
+CONECT  133   86  126  134
 
+CONECT  134  133  141  181
 
+CONECT  135   88   96  136
 
+CONECT  136  135  175  183
 
+CONECT  137   90  130  138
 
+CONECT  138  137  145  185
 
+CONECT  139   92  100  140
 
+CONECT  140  139  179  187
 
+CONECT  141   94  134  142
 
+CONECT  142  141  149  189
 
+CONECT  143   96  104  144
 
+CONECT  144  143  183  191
 
+CONECT  145   98  138  146
 
+CONECT  146  145  153  193
 
+CONECT  147  100  108  148
 
+CONECT  148  147  187  195
 
+CONECT  149  102  142  150
 
+CONECT  150  149  157  197
 
+CONECT  151  104  112  152
 
+CONECT  152  151  191  199
 
+CONECT  153  106  146  154
 
+CONECT  154  153
 
+CONECT  155  108  116  156
 
+CONECT  156  155  195
 
+CONECT  157  110  150  158
 
+CONECT  158  157
 
+CONECT  159  112  120  160
 
+CONECT  160  159  199
 
+CONECT  161  162
 
+CONECT  162  161  169
 
+CONECT  163  124  164
 
+CONECT  164  163
 
+CONECT  165  166
 
+CONECT  166  165  173
 
+CONECT  167  128  168
 
+CONECT  168  167
 
+CONECT  169  122  162  170
 
+CONECT  170  169  177
 
+CONECT  171  124  132  172
 
+CONECT  172  171
 
+CONECT  173  126  166  174
 
+CONECT  174  173  181
 
+CONECT  175  128  136  176
 
+CONECT  176  175
 
+CONECT  177  130  170  178
 
+CONECT  178  177  185
 
+CONECT  179  132  140  180
 
+CONECT  180  179
 
+CONECT  181  134  174  182
 
+CONECT  182  181  189
 
+CONECT  183  136  144  184
 
+CONECT  184  183
 
+CONECT  185  138  178  186
 
+CONECT  186  185  193
 
+CONECT  187  140  148  188
 
+CONECT  188  187
 
+CONECT  189  142  182  190
 
+CONECT  190  189  197
 
+CONECT  191  144  152  192
 
+CONECT  192  191
 
+CONECT  193  146  186  194
 
+CONECT  194  193
 
+CONECT  195  148  156  196
 
+CONECT  196  195
 
+CONECT  197  150  190  198
 
+CONECT  198  197
 
+CONECT  199  152  160  200
 
+CONECT  200  199
 
+END

+ 79 - 0
examples/models/molecules/lsd.pdb
Файл харах 

@@ -0,0 +1,79 @@
 
+HEADER    NONAME 23-Apr-10                                              NONE   1
 
+TITLE                                                                   NONE   2
 
+AUTHOR    Chemical Structure Services at http://cactus.nci.nih.gov      NONE   3
 
+REVDAT   1  23-Apr-10     0                                             NONE   4
 
+ATOM      1  C           0      -1.049   1.569  -0.186  0.00  0.00           C+0
 
+ATOM      2  C           0       1.717   0.715   0.155  0.00  0.00           C+0
 
+ATOM      3  C           0      -1.635  -2.212  -0.674  0.00  0.00           C+0
 
+ATOM      4  C           0      -4.657   0.896   0.691  0.00  0.00           C+0
 
+ATOM      5  C           0      -4.065  -2.519  -0.433  0.00  0.00           C+0
 
+ATOM      6  C           0      -2.792  -2.984  -0.745  0.00  0.00           C+0
 
+ATOM      7  C           0       4.762  -1.453  -0.659  0.00  0.00           C+0
 
+ATOM      8  C           0       3.241  -1.347   1.369  0.00  0.00           C+0
 
+ATOM      9  C           0      -0.294   3.762  -0.536  0.00  0.00           C+0
 
+ATOM     10  C           0       6.055  -0.727  -0.281  0.00  0.00           C+0
 
+ATOM     11  C           0       4.117  -0.699   2.443  0.00  0.00           C+0
 
+ATOM     12  H           0      -6.116  -0.586   0.423  0.00  0.00           H+0
 
+ATOM     13  O           0       3.348   0.665  -1.551  0.00  0.00           O+0
 
+ATOM     14  C           0      -2.243   1.917   0.716  0.00  0.00           C+0
 
+ATOM     15  C           0       1.270   2.005  -0.544  0.00  0.00           C+0
 
+ATOM     16  C           0       2.958   0.178  -0.511  0.00  0.00           C+0
 
+ATOM     17  C           0      -1.715  -0.898  -0.270  0.00  0.00           C+0
 
+ATOM     18  C           0      -3.338   0.903   0.522  0.00  0.00           C+0
 
+ATOM     19  C           0       0.596  -0.284   0.030  0.00  0.00           C+0
 
+ATOM     20  N           0       0.046   2.483   0.100  0.00  0.00           N+0
 
+ATOM     21  C           0      -0.654   0.118  -0.131  0.00  0.00           C+0
 
+ATOM     22  C           0      -4.182  -1.194  -0.016  0.00  0.00           C+0
 
+ATOM     23  N           0       3.634  -0.844   0.050  0.00  0.00           N+0
 
+ATOM     24  N           0      -5.176  -0.349   0.374  0.00  0.00           N+0
 
+ATOM     25  C           0      -3.008  -0.439   0.056  0.00  0.00           C+0
 
+ATOM     26  H           0      -1.370   1.771  -1.208  0.00  0.00           H+0
 
+ATOM     27  H           0      -0.679  -2.642  -0.934  0.00  0.00           H+0
 
+ATOM     28  H           0      -1.924   1.911   1.758  0.00  0.00           H+0
 
+ATOM     29  H           0      -2.616   2.907   0.457  0.00  0.00           H+0
 
+ATOM     30  H           0      -5.240   1.741   1.027  0.00  0.00           H+0
 
+ATOM     31  H           0      -4.930  -3.161  -0.511  0.00  0.00           H+0
 
+ATOM     32  H           0       0.816  -1.341   0.073  0.00  0.00           H+0
 
+ATOM     33  H           0      -2.694  -4.011  -1.065  0.00  0.00           H+0
 
+ATOM     34  H           0       1.919   0.915   1.207  0.00  0.00           H+0
 
+ATOM     35  H           0       2.050   2.761  -0.453  0.00  0.00           H+0
 
+ATOM     36  H           0       1.074   1.803  -1.597  0.00  0.00           H+0
 
+ATOM     37  H           0      -1.230   4.137  -0.122  0.00  0.00           H+0
 
+ATOM     38  H           0       0.501   4.484  -0.349  0.00  0.00           H+0
 
+ATOM     39  H           0      -0.405   3.615  -1.611  0.00  0.00           H+0
 
+ATOM     40  H           0       4.601  -1.373  -1.734  0.00  0.00           H+0
 
+ATOM     41  H           0       4.842  -2.504  -0.381  0.00  0.00           H+0
 
+ATOM     42  H           0       3.370  -2.429   1.399  0.00  0.00           H+0
 
+ATOM     43  H           0       2.196  -1.100   1.555  0.00  0.00           H+0
 
+ATOM     44  H           0       6.894  -1.180  -0.809  0.00  0.00           H+0
 
+ATOM     45  H           0       5.975   0.324  -0.559  0.00  0.00           H+0
 
+ATOM     46  H           0       6.215  -0.807   0.794  0.00  0.00           H+0
 
+ATOM     47  H           0       3.829  -1.077   3.424  0.00  0.00           H+0
 
+ATOM     48  H           0       5.163  -0.940   2.253  0.00  0.00           H+0
 
+ATOM     49  H           0       3.983   0.383   2.418  0.00  0.00           H+0
 
+CONECT    1   21   20   14   26                                         NONE  54
 
+CONECT    2   19   16   15   34                                         NONE  55
 
+CONECT    3   17    6   27    0                                         NONE  56
 
+CONECT    4   18   24   30    0                                         NONE  57
 
+CONECT    5   22    6   31    0                                         NONE  58
 
+CONECT    6    3    5   33    0                                         NONE  59
 
+CONECT    7   23   10   40   41                                         NONE  60
 
+CONECT    8   23   11   42   43                                         NONE  61
 
+CONECT    9   20   37   38   39                                         NONE  62
 
+CONECT   10    7   44   45   46                                         NONE  63
 
+CONECT   11    8   47   48   49                                         NONE  64
 
+CONECT   13   16    0    0    0                                         NONE  65
 
+CONECT   14   18    1   28   29                                         NONE  66
 
+CONECT   15   20    2   35   36                                         NONE  67
 
+CONECT   16    2   23   13    0                                         NONE  68
 
+CONECT   17   25   21    3    0                                         NONE  69
 
+CONECT   18   25   14    4    0                                         NONE  70
 
+CONECT   19   21    2   32    0                                         NONE  71
 
+CONECT   20    1   15    9    0                                         NONE  72
 
+CONECT   21   17    1   19    0                                         NONE  73
 
+CONECT   22   25   24    5    0                                         NONE  74
 
+CONECT   23   16    7    8    0                                         NONE  75
 
+CONECT   24   22    4   12    0                                         NONE  76
 
+CONECT   25   17   18   22    0                                         NONE  77
 
+END                                                                     NONE  78
 
+

+ 90 - 0
examples/models/molecules/lycopene.pdb
Файл харах 

@@ -0,0 +1,90 @@
 
+HEADER    PROTEIN                                 05-MAY-09   NONE
 
+TITLE     NULL                                                        
+COMPND    NULL                                                        
+SOURCE    NULL                                                        
+KEYWDS    NULL                                                        
+EXPDTA    NULL                                                        
+AUTHOR    Marvin                                                      
+REVDAT   1   05-MAY-09         0                                  
+HETATM    1  C   UNK     0      -1.075   0.818   0.485  0.00  0.00           C+0
 
+HETATM    2  C   UNK     0     -20.084  -9.817 -16.179  0.00  0.00           C+0
 
+HETATM    3  C   UNK     0      -0.713  -0.346   1.456  0.00  0.00           C+0
 
+HETATM    4  C   UNK     0     -19.685 -11.316 -16.318  0.00  0.00           C+0
 
+HETATM    5  C   UNK     0       1.324   0.571   4.582  0.00  0.00           C+0
 
+HETATM    6  C   UNK     0       2.150  -0.422   2.437  0.00  0.00           C+0
 
+HETATM    7  C   UNK     0     -21.966 -13.277 -16.664  0.00  0.00           C+0
 
+HETATM    8  C   UNK     0     -21.411 -13.321 -19.105  0.00  0.00           C+0
 
+HETATM    9  C   UNK     0     -20.930  -9.245 -13.860  0.00  0.00           C+0
 
+HETATM   10  C   UNK     0      -0.272   0.398  -1.881  0.00  0.00           C+0
 
+HETATM   11  C   UNK     0     -17.605  -7.104 -10.656  0.00  0.00           C+0
 
+HETATM   12  C   UNK     0      -3.688  -1.419  -5.187  0.00  0.00           C+0
 
+HETATM   13  C   UNK     0      -7.197  -3.296  -7.958  0.00  0.00           C+0
 
+HETATM   14  C   UNK     0     -14.089  -5.242  -7.881  0.00  0.00           C+0
 
+HETATM   15  C   UNK     0       1.029   0.084   3.233  0.00  0.00           C+0
 
+HETATM   16  C   UNK     0     -21.125 -12.803 -17.765  0.00  0.00           C+0
 
+HETATM   17  C   UNK     0      -1.350   0.342  -0.884  0.00  0.00           C+0
 
+HETATM   18  C   UNK     0     -19.823  -9.290 -14.825  0.00  0.00           C+0
 
+HETATM   19  C   UNK     0     -16.638  -7.337 -11.747  0.00  0.00           C+0
 
+HETATM   20  C   UNK     0      -4.573  -1.473  -4.006  0.00  0.00           C+0
 
+HETATM   21  C   UNK     0      -8.014  -3.326  -6.733  0.00  0.00           C+0
 
+HETATM   22  C   UNK     0     -13.187  -5.516  -9.012  0.00  0.00           C+0
 
+HETATM   23  C   UNK     0     -20.123 -11.908 -17.582  0.00  0.00           C+0
 
+HETATM   24  C   UNK     0      -0.240   0.124   2.758  0.00  0.00           C+0
 
+HETATM   25  C   UNK     0     -18.570  -8.892 -14.489  0.00  0.00           C+0
 
+HETATM   26  C   UNK     0      -2.571  -0.167  -1.186  0.00  0.00           C+0
 
+HETATM   27  C   UNK     0     -15.311  -7.135 -11.542  0.00  0.00           C+0
 
+HETATM   28  C   UNK     0      -5.784  -2.084  -4.084  0.00  0.00           C+0
 
+HETATM   29  C   UNK     0     -11.851  -5.294  -8.909  0.00  0.00           C+0
 
+HETATM   30  C   UNK     0      -9.256  -3.873  -6.736  0.00  0.00           C+0
 
+HETATM   31  C   UNK     0      -4.199  -0.885  -2.811  0.00  0.00           C+0
 
+HETATM   32  C   UNK     0     -17.065  -7.742 -12.999  0.00  0.00           C+0
 
+HETATM   33  C   UNK     0     -13.701  -5.957 -10.216  0.00  0.00           C+0
 
+HETATM   34  C   UNK     0      -7.540  -2.746  -5.572  0.00  0.00           C+0
 
+HETATM   35  C   UNK     0      -2.930  -0.738  -2.378  0.00  0.00           C+0
 
+HETATM   36  C   UNK     0     -18.165  -8.484 -13.246  0.00  0.00           C+0
 
+HETATM   37  C   UNK     0     -14.749  -6.793 -10.348  0.00  0.00           C+0
 
+HETATM   38  C   UNK     0      -6.252  -2.750  -5.177  0.00  0.00           C+0
 
+HETATM   39  C   UNK     0     -11.189  -4.811  -7.807  0.00  0.00           C+0
 
+HETATM   40  C   UNK     0      -9.894  -4.441  -7.811  0.00  0.00           C+0
 
+CONECT    1    3   17                                                       
+CONECT    2    4   18                                                       
+CONECT    3    1   24                                                       
+CONECT    4    2   23                                                       
+CONECT    5   15                                                            
+CONECT    6   15                                                            
+CONECT    7   16                                                            
+CONECT    8   16                                                            
+CONECT    9   18                                                            
+CONECT   10   17                                                            
+CONECT   11   19                                                            
+CONECT   12   20                                                            
+CONECT   13   21                                                            
+CONECT   14   22                                                            
+CONECT   15    5    6   24                                                  
+CONECT   16    7    8   23                                                  
+CONECT   17    1   10   26                                                  
+CONECT   18    2    9   25                                                  
+CONECT   19   11   27   32                                                  
+CONECT   20   12   28   31                                                  
+CONECT   21   13   30   34                                                  
+CONECT   22   14   29   33                                                  
+CONECT   23    4   16                                                       
+CONECT   24    3   15                                                       
+CONECT   25   18   36                                                       
+CONECT   26   17   35                                                       
+CONECT   27   19   37                                                       
+CONECT   28   20   38                                                       
+CONECT   29   22   39                                                       
+CONECT   30   21   40                                                       
+CONECT   31   20   35                                                       
+CONECT   32   19   36                                                       
+CONECT   33   22   37                                                       
+CONECT   34   21   38                                                       
+CONECT   35   26   31                                                       
+CONECT   36   25   32                                                       
+CONECT   37   27   33                                                       
+CONECT   38   28   34                                                       
+CONECT   39   29   40                                                       
+CONECT   40   30   39                                                       
+MASTER        0    0    0    0    0    0    0    0   40    0   78    0
 
+END

+ 133 - 0
examples/models/molecules/nacl.pdb
Файл харах 

@@ -0,0 +1,133 @@
 
+HEADER    MOLECULE
 
+COMPND    SODIUM CHLORIDE BIG CRYSTAL
 
+AUTHOR    A. W. MAVERICK
 
+ATOM      1 CL     UNK   1      -5.640  -2.820  -4.230  1.00  0.00 
+ATOM      2 NA     UNK   1      -5.640  -2.820  -1.410  1.00  0.00 
+ATOM      3 CL     UNK   1      -5.640  -2.820   1.410  1.00  0.00 
+ATOM      4 NA     UNK   1      -5.640  -2.820   4.230  1.00  0.00 
+ATOM      5 NA     UNK   1      -5.640   0.000  -4.230  1.00  0.00 
+ATOM      6 CL     UNK   1      -5.640   0.000  -1.410  1.00  0.00 
+ATOM      7 NA     UNK   1      -5.640   0.000   1.410  1.00  0.00 
+ATOM      8 CL     UNK   1      -5.640   0.000   4.230  1.00  0.00 
+ATOM      9 CL     UNK   1      -5.640   2.820  -4.230  1.00  0.00 
+ATOM     10 NA     UNK   1      -5.640   2.820  -1.410  1.00  0.00 
+ATOM     11 CL     UNK   1      -5.640   2.820   1.410  1.00  0.00 
+ATOM     12 NA     UNK   1      -5.640   2.820   4.230  1.00  0.00 
+ATOM     13 NA     UNK   1      -2.820  -2.820  -4.230  1.00  0.00 
+ATOM     14 CL     UNK   1      -2.820  -2.820  -1.410  1.00  0.00 
+ATOM     15 NA     UNK   1      -2.820  -2.820   1.410  1.00  0.00 
+ATOM     16 CL     UNK   1      -2.820  -2.820   4.230  1.00  0.00 
+ATOM     17 CL     UNK   1      -2.820   0.000  -4.230  1.00  0.00 
+ATOM     18 NA     UNK   1      -2.820   0.000  -1.410  1.00  0.00 
+ATOM     19 CL     UNK   1      -2.820   0.000   1.410  1.00  0.00 
+ATOM     20 NA     UNK   1      -2.820   0.000   4.230  1.00  0.00 
+ATOM     21 NA     UNK   1      -2.820   2.820  -4.230  1.00  0.00 
+ATOM     22 CL     UNK   1      -2.820   2.820  -1.410  1.00  0.00 
+ATOM     23 NA     UNK   1      -2.820   2.820   1.410  1.00  0.00 
+ATOM     24 CL     UNK   1      -2.820   2.820   4.230  1.00  0.00 
+ATOM     25 CL     UNK   1       0.000  -2.820  -4.230  1.00  0.00 
+ATOM     26 NA     UNK   1       0.000  -2.820  -1.410  1.00  0.00 
+ATOM     27 CL     UNK   1       0.000  -2.820   1.410  1.00  0.00 
+ATOM     28 NA     UNK   1       0.000  -2.820   4.230  1.00  0.00 
+ATOM     29 NA     UNK   1       0.000   0.000  -4.230  1.00  0.00 
+ATOM     30 CL     UNK   1       0.000   0.000  -1.410  1.00  0.00 
+ATOM     31 NA     UNK   1       0.000   0.000   1.410  1.00  0.00 
+ATOM     32 CL     UNK   1       0.000   0.000   4.230  1.00  0.00 
+ATOM     33 CL     UNK   1       0.000   2.820  -4.230  1.00  0.00 
+ATOM     34 NA     UNK   1       0.000   2.820  -1.410  1.00  0.00 
+ATOM     35 CL     UNK   1       0.000   2.820   1.410  1.00  0.00 
+ATOM     36 NA     UNK   1       0.000   2.820   4.230  1.00  0.00 
+ATOM     37 NA     UNK   1       2.820  -2.820  -4.230  1.00  0.00 
+ATOM     38 CL     UNK   1       2.820  -2.820  -1.410  1.00  0.00 
+ATOM     39 NA     UNK   1       2.820  -2.820   1.410  1.00  0.00 
+ATOM     40 CL     UNK   1       2.820  -2.820   4.230  1.00  0.00 
+ATOM     41 CL     UNK   1       2.820   0.000  -4.230  1.00  0.00 
+ATOM     42 NA     UNK   1       2.820   0.000  -1.410  1.00  0.00 
+ATOM     43 CL     UNK   1       2.820   0.000   1.410  1.00  0.00 
+ATOM     44 NA     UNK   1       2.820   0.000   4.230  1.00  0.00 
+ATOM     45 NA     UNK   1       2.820   2.820  -4.230  1.00  0.00 
+ATOM     46 CL     UNK   1       2.820   2.820  -1.410  1.00  0.00 
+ATOM     47 NA     UNK   1       2.820   2.820   1.410  1.00  0.00 
+ATOM     48 CL     UNK   1       2.820   2.820   4.230  1.00  0.00 
+ATOM     49 CL     UNK   1       5.640  -2.820  -4.230  1.00  0.00 
+ATOM     50 NA     UNK   1       5.640  -2.820  -1.410  1.00  0.00 
+ATOM     51 CL     UNK   1       5.640  -2.820   1.410  1.00  0.00 
+ATOM     52 NA     UNK   1       5.640  -2.820   4.230  1.00  0.00 
+ATOM     53 NA     UNK   1       5.640   0.000  -4.230  1.00  0.00 
+ATOM     54 CL     UNK   1       5.640   0.000  -1.410  1.00  0.00 
+ATOM     55 NA     UNK   1       5.640   0.000   1.410  1.00  0.00 
+ATOM     56 CL     UNK   1       5.640   0.000   4.230  1.00  0.00 
+ATOM     57 CL     UNK   1       5.640   2.820  -4.230  1.00  0.00 
+ATOM     58 NA     UNK   1       5.640   2.820  -1.410  1.00  0.00 
+ATOM     59 CL     UNK   1       5.640   2.820   1.410  1.00  0.00 
+ATOM     60 NA     UNK   1       5.640   2.820   4.230  1.00  0.00 
+CONECT    1    2    5   13
 
+CONECT    2    1    3    6   14
 
+CONECT    3    2    4    7   15
 
+CONECT    4    3    8   16
 
+CONECT    5    1    6    9   17
 
+CONECT    6    2    5    7   10   18
 
+CONECT    7    3    6    8   11   19
 
+CONECT    8    4    7   12   20
 
+CONECT    9    5   10   21
 
+CONECT   10    6    9   11   22
 
+CONECT   11    7   10   12   23
 
+CONECT   12    8   11   24
 
+CONECT   13    1   14   17   25
 
+CONECT   14    2   13   15   18   26
 
+CONECT   15    3   14   16   19   27
 
+CONECT   16    4   15   20   28
 
+CONECT   17    5   13   18   21   29
 
+CONECT   18    6   14   17   19
 
+CONECT   18   22   30
 
+CONECT   19    7   15   18   20
 
+CONECT   19   23   31
 
+CONECT   20    8   16   19   24   32
 
+CONECT   21    9   17   22   33
 
+CONECT   22   10   18   21   23   34
 
+CONECT   23   11   19   22   24   35
 
+CONECT   24   12   20   23   36
 
+CONECT   25   13   26   29   37
 
+CONECT   26   14   25   27   30   38
 
+CONECT   27   15   26   28   31   39
 
+CONECT   28   16   27   32   40
 
+CONECT   29   17   25   30   33   41
 
+CONECT   30   18   26   29   31
 
+CONECT   30   34   42
 
+CONECT   31   19   27   30   32
 
+CONECT   31   35   43
 
+CONECT   32   20   28   31   36   44
 
+CONECT   33   21   29   34   45
 
+CONECT   34   22   30   33   35   46
 
+CONECT   35   23   31   34   36   47
 
+CONECT   36   24   32   35   48
 
+CONECT   37   25   38   41   49
 
+CONECT   38   26   37   39   42   50
 
+CONECT   39   27   38   40   43   51
 
+CONECT   40   28   39   44   52
 
+CONECT   41   29   37   42   45   53
 
+CONECT   42   30   38   41   43
 
+CONECT   42   46   54
 
+CONECT   43   31   39   42   44
 
+CONECT   43   47   55
 
+CONECT   44   32   40   43   48   56
 
+CONECT   45   33   41   46   57
 
+CONECT   46   34   42   45   47   58
 
+CONECT   47   35   43   46   48   59
 
+CONECT   48   36   44   47   60
 
+CONECT   49   37   50   53
 
+CONECT   50   38   49   51   54
 
+CONECT   51   39   50   52   55
 
+CONECT   52   40   51   56
 
+CONECT   53   41   49   54   57
 
+CONECT   54   42   50   53   55
 
+CONECT   54   58
 
+CONECT   55   43   51   54   56
 
+CONECT   55   59
 
+CONECT   56   44   52   55   60
 
+CONECT   57   45   53   58
 
+CONECT   58   46   54   57   59
 
+CONECT   59   47   55   58   60
 
+CONECT   60   48   56   59
 
+MASTER        0    0    0    0    0    0    0    0   60    0   60    0
 
+END

+ 62 - 0
examples/models/molecules/nicotine.pdb
Файл харах 

@@ -0,0 +1,62 @@
 
+HEADER    PROTEIN                                 25-AUG-08   NONE
 
+TITLE     NULL                                                        
+COMPND    MOLECULE: 184                                               
+SOURCE    NULL                                                        
+KEYWDS    NULL                                                        
+EXPDTA    NULL                                                        
+AUTHOR    Marvin                                                      
+REVDAT   1   25-AUG-08         0                                  
+HETATM    1  N   UNK     0       2.066  -2.269   0.129  0.00  0.00           N+0
 
+HETATM    2  N   UNK     0      -0.352   1.181  -0.413  0.00  0.00           N+0
 
+HETATM    3  C   UNK     0       2.542  -0.987   0.731  0.00  0.00           C+0
 
+HETATM    4  C   UNK     0       2.489  -1.212   2.267  0.00  0.00           C+0
 
+HETATM    5  C   UNK     0       1.783  -2.566   2.444  0.00  0.00           C+0
 
+HETATM    6  C   UNK     0       2.170  -3.317   1.164  0.00  0.00           C+0
 
+HETATM    7  C   UNK     0       1.723   0.195   0.320  0.00  0.00           C+0
 
+HETATM    8  C   UNK     0       2.616  -2.630  -1.204  0.00  0.00           C+0
 
+HETATM    9  C   UNK     0       2.288   1.493   0.336  0.00  0.00           C+0
 
+HETATM   10  C   UNK     0       0.364   0.083  -0.061  0.00  0.00           C+0
 
+HETATM   11  C   UNK     0       1.521   2.611  -0.035  0.00  0.00           C+0
 
+HETATM   12  C   UNK     0       0.180   2.427  -0.411  0.00  0.00           C+0
 
+HETATM   13  H   UNK     0       3.587  -0.824   0.438  0.00  0.00           H+0
 
+HETATM   14  H   UNK     0       3.506  -1.278   2.666  0.00  0.00           H+0
 
+HETATM   15  H   UNK     0       1.958  -0.426   2.811  0.00  0.00           H+0
 
+HETATM   16  H   UNK     0       2.114  -3.088   3.347  0.00  0.00           H+0
 
+HETATM   17  H   UNK     0       0.697  -2.426   2.484  0.00  0.00           H+0
 
+HETATM   18  H   UNK     0       3.194  -3.699   1.242  0.00  0.00           H+0
 
+HETATM   19  H   UNK     0       1.485  -4.144   0.969  0.00  0.00           H+0
 
+HETATM   20  H   UNK     0       3.695  -2.803  -1.157  0.00  0.00           H+0
 
+HETATM   21  H   UNK     0       2.421  -1.821  -1.910  0.00  0.00           H+0
 
+HETATM   22  H   UNK     0       2.131  -3.532  -1.581  0.00  0.00           H+0
 
+HETATM   23  H   UNK     0       3.263   1.631   0.620  0.00  0.00           H+0
 
+HETATM   24  H   UNK     0      -0.106  -0.822  -0.076  0.00  0.00           H+0
 
+HETATM   25  H   UNK     0       1.934   3.546  -0.026  0.00  0.00           H+0
 
+HETATM   26  H   UNK     0      -0.402   3.223  -0.680  0.00  0.00           H+0
 
+CONECT    1    3    6    8                                                  
+CONECT    2   10   12                                                       
+CONECT    3    1    4    7   13                                             
+CONECT    4    3    5   14   15                                             
+CONECT    5    4    6   16   17                                             
+CONECT    6    1    5   18   19                                             
+CONECT    7    3    9   10                                                  
+CONECT    8    1   20   21   22                                             
+CONECT    9    7   11   23                                                  
+CONECT   10    2    7   24                                                  
+CONECT   11    9   12   25                                                  
+CONECT   12    2   11   26                                                  
+CONECT   13    3                                                            
+CONECT   14    4                                                            
+CONECT   15    4                                                            
+CONECT   16    5                                                            
+CONECT   17    5                                                            
+CONECT   18    6                                                            
+CONECT   19    6                                                            
+CONECT   20    8                                                            
+CONECT   21    8                                                            
+CONECT   22    8                                                            
+CONECT   23    9                                                            
+CONECT   24   10                                                            
+CONECT   25   11                                                            
+CONECT   26   12                                                            
+MASTER        0    0    0    0    0    0    0    0   26    0   54    0
 
+END

+ 150 - 0
examples/models/molecules/ybco.pdb
Файл харах 

@@ -0,0 +1,150 @@
 
+HEADER    MOLECULE
 
+COMPND    "123" YBa2Cu3O7 SUPERCONDUCTOR
 
+AUTHOR    A. W. MAVERICK
 
+ATOM      1  Y     UNK   1       0.000  -4.290   0.000  1.00  0.00 
+ATOM      2 BA     UNK   1       0.000  -0.602   0.000  1.00  0.00 
+ATOM      3 BA     UNK   1       0.000   3.703   0.000  1.00  0.00 
+ATOM      4 CU     UNK   1      -1.912  -5.976   1.943  1.00  0.00 
+ATOM      5 CU     UNK   1      -1.912  -5.976  -1.943  1.00  0.00 
+ATOM      6 CU     UNK   1       1.911  -5.976   1.943  1.00  0.00 
+ATOM      7 CU     UNK   1       1.911  -5.976  -1.943  1.00  0.00 
+ATOM      8 CU     UNK   1      -1.912  -2.603   1.943  1.00  0.00 
+ATOM      9 CU     UNK   1      -1.912  -2.603  -1.943  1.00  0.00 
+ATOM     10 CU     UNK   1       1.911  -2.603   1.943  1.00  0.00 
+ATOM     11 CU     UNK   1       1.911  -2.603  -1.943  1.00  0.00 
+ATOM     12 CU     UNK   1      -1.912   1.551   1.943  1.00  0.00 
+ATOM     13 CU     UNK   1      -1.912   1.551  -1.943  1.00  0.00 
+ATOM     14 CU     UNK   1       1.911   1.551   1.943  1.00  0.00 
+ATOM     15 CU     UNK   1       1.911   1.551  -1.943  1.00  0.00 
+ATOM     16 CU     UNK   1      -1.912   5.704   1.943  1.00  0.00 
+ATOM     17 CU     UNK   1      -1.912   5.704  -1.943  1.00  0.00 
+ATOM     18 CU     UNK   1       1.911   5.704   1.943  1.00  0.00 
+ATOM     19 CU     UNK   1       1.911   5.704  -1.943  1.00  0.00 
+ATOM     20  O     UNK   1      -3.823  -5.723   1.943  1.00  0.00 
+ATOM     21  O     UNK   1      -3.823  -5.723  -1.943  1.00  0.00 
+ATOM     22  O     UNK   1       0.000  -5.723   1.943  1.00  0.00 
+ATOM     23  O     UNK   1       0.000  -5.723  -1.943  1.00  0.00 
+ATOM     24  O     UNK   1       3.823  -5.723   1.943  1.00  0.00 
+ATOM     25  O     UNK   1       3.823  -5.723  -1.943  1.00  0.00 
+ATOM     26  O     UNK   1      -1.912  -5.704   3.886  1.00  0.00 
+ATOM     27  O     UNK   1      -1.912  -5.704   0.000  1.00  0.00 
+ATOM     28  O     UNK   1      -1.912  -5.704  -3.886  1.00  0.00 
+ATOM     29  O     UNK   1       1.911  -5.704   3.886  1.00  0.00 
+ATOM     30  O     UNK   1       1.911  -5.704   0.000  1.00  0.00 
+ATOM     31  O     UNK   1       1.911  -5.704  -3.886  1.00  0.00 
+ATOM     32  O     UNK   1      -1.912  -2.875   3.886  1.00  0.00 
+ATOM     33  O     UNK   1      -1.912  -2.875   0.000  1.00  0.00 
+ATOM     34  O     UNK   1      -1.912  -2.875  -3.886  1.00  0.00 
+ATOM     35  O     UNK   1       1.911  -2.875   3.886  1.00  0.00 
+ATOM     36  O     UNK   1       1.911  -2.875   0.000  1.00  0.00 
+ATOM     37  O     UNK   1       1.911  -2.875  -3.886  1.00  0.00 
+ATOM     38  O     UNK   1      -3.823  -2.857   1.943  1.00  0.00 
+ATOM     39  O     UNK   1      -3.823  -2.857  -1.943  1.00  0.00 
+ATOM     40  O     UNK   1       0.000  -2.857   1.943  1.00  0.00 
+ATOM     41  O     UNK   1       0.000  -2.857  -1.943  1.00  0.00 
+ATOM     42  O     UNK   1       3.823  -2.857   1.943  1.00  0.00 
+ATOM     43  O     UNK   1       3.823  -2.857  -1.943  1.00  0.00 
+ATOM     44  O     UNK   1      -1.912  -0.300   1.943  1.00  0.00 
+ATOM     45  O     UNK   1      -1.912  -0.300  -1.943  1.00  0.00 
+ATOM     46  O     UNK   1       1.911  -0.300   1.943  1.00  0.00 
+ATOM     47  O     UNK   1       1.911  -0.300  -1.943  1.00  0.00 
+ATOM     48  O     UNK   1      -1.912   1.551   3.886  1.00  0.00 
+ATOM     49  O     UNK   1      -1.912   1.551   0.000  1.00  0.00 
+ATOM     50  O     UNK   1      -1.912   1.551  -3.886  1.00  0.00 
+ATOM     51  O     UNK   1       1.911   1.551   3.886  1.00  0.00 
+ATOM     52  O     UNK   1       1.911   1.551   0.000  1.00  0.00 
+ATOM     53  O     UNK   1       1.911   1.551  -3.886  1.00  0.00 
+ATOM     54  O     UNK   1      -1.912   3.401   1.943  1.00  0.00 
+ATOM     55  O     UNK   1      -1.912   3.401  -1.943  1.00  0.00 
+ATOM     56  O     UNK   1       1.911   3.401   1.943  1.00  0.00 
+ATOM     57  O     UNK   1       1.911   3.401  -1.943  1.00  0.00 
+ATOM     58  O     UNK   1      -3.823   5.958   1.943  1.00  0.00 
+ATOM     59  O     UNK   1      -3.823   5.958  -1.943  1.00  0.00 
+ATOM     60  O     UNK   1       0.000   5.958   1.943  1.00  0.00 
+ATOM     61  O     UNK   1       0.000   5.958  -1.943  1.00  0.00 
+ATOM     62  O     UNK   1       3.823   5.958   1.943  1.00  0.00 
+ATOM     63  O     UNK   1       3.823   5.958  -1.943  1.00  0.00 
+ATOM     64  O     UNK   1      -1.912   5.976   3.886  1.00  0.00 
+ATOM     65  O     UNK   1      -1.912   5.976   0.000  1.00  0.00 
+ATOM     66  O     UNK   1      -1.912   5.976  -3.886  1.00  0.00 
+ATOM     67  O     UNK   1       1.911   5.976   3.886  1.00  0.00 
+ATOM     68  O     UNK   1       1.911   5.976   0.000  1.00  0.00 
+ATOM     69  O     UNK   1       1.911   5.976  -3.886  1.00  0.00 
+CONECT    1   22   23   27   30
 
+CONECT    1   33   36   40   41
 
+CONECT    4   20   22   26   27
 
+CONECT    5   21   23   27   28
 
+CONECT    6   22   24   29   30
 
+CONECT    7   23   25   30   31
 
+CONECT    8   32   33   38   40
 
+CONECT    8   44
 
+CONECT    9   33   34   39   41
 
+CONECT    9   45
 
+CONECT   10   35   36   40   42
 
+CONECT   10   46
 
+CONECT   11   36   37   41   43
 
+CONECT   11   47
 
+CONECT   12   44   48   49   54
 
+CONECT   13   45   49   50   55
 
+CONECT   14   46   51   52   56
 
+CONECT   15   47   52   53   57
 
+CONECT   16   54   58   60   64
 
+CONECT   16   65
 
+CONECT   17   55   59   61   65
 
+CONECT   17   66
 
+CONECT   18   56   60   62   67
 
+CONECT   18   68
 
+CONECT   19   57   61   63   68
 
+CONECT   19   69
 
+CONECT   20    4
 
+CONECT   21    5
 
+CONECT   22    1    4    6
 
+CONECT   23    1    5    7
 
+CONECT   24    6
 
+CONECT   25    7
 
+CONECT   26    4
 
+CONECT   27    1    4    5
 
+CONECT   28    5
 
+CONECT   29    6
 
+CONECT   30    1    6    7
 
+CONECT   31    7
 
+CONECT   32    8
 
+CONECT   33    1    8    9
 
+CONECT   34    9
 
+CONECT   35   10
 
+CONECT   36    1   10   11
 
+CONECT   37   11
 
+CONECT   38    8
 
+CONECT   39    9
 
+CONECT   40    1    8   10
 
+CONECT   41    1    9   11
 
+CONECT   42   10
 
+CONECT   43   11
 
+CONECT   44    8   12
 
+CONECT   45    9   13
 
+CONECT   46   10   14
 
+CONECT   47   11   15
 
+CONECT   48   12
 
+CONECT   49   12   13
 
+CONECT   50   13
 
+CONECT   51   14
 
+CONECT   52   14   15
 
+CONECT   53   15
 
+CONECT   54   12   16
 
+CONECT   55   13   17
 
+CONECT   56   14   18
 
+CONECT   57   15   19
 
+CONECT   58   16
 
+CONECT   59   17
 
+CONECT   60   16   18
 
+CONECT   61   17   19
 
+CONECT   62   18
 
+CONECT   63   19
 
+CONECT   64   16
 
+CONECT   65   16   17
 
+CONECT   66   17
 
+CONECT   67   18
 
+CONECT   68   18   19
 
+CONECT   69   19
 
+MASTER        0    0    0    0    0    0    0    0   69    0   69    0
 
+END