/* $RCSfile$ * $Author: hansonr $ * $Date: 2007-04-26 16:57:51 -0500 (Thu, 26 Apr 2007) $ * $Revision: 7502 $ * * Copyright (C) 2005 The Jmol Development Team * * Contact: jmol-developers@lists.sf.net * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ package org.jmol.util; import javajs.util.PT; public abstract class Edge implements SimpleEdge { /** * Extended Bond Definition Types * * Originally these were short 16-bit values * */ //.1 1111 1111 1100 0000 0000 //.0 9876 5432 1098 7654 3210 // //.. ...| |||| |||| |||| |||| render mask 0x01FFFF //.. ||.. CIP stereochemistry mask (unk) 3 << 18 0xC0000 //.. |... CIP stereochemistry Z 2 << 18 0x80000 //.. .|.. CIP stereochemistry E 1 << 18 0x40000 //.. ..|. new connection 1 << 17 0x20000 //.. ...| render as single 1 << 16 0x10000 //.. ...| .... PyMOL render single 2 << 15 0x18000 + covalent order //.. ...| |... PyMOL render multiple 3 << 15 0x18000 + covalent order //.. .... |... strut 1 << 15 0x08000 //.. ...| .nnm m... .... ...| atropisomer 0x10001 + (nnmm << 11) //.. .... .||| |... Hydrogen bond F << 11 0x03800 //.. .... .... .||| |||| |||| Covalent 0x003FF //.. .... .... .|.. Stereo 1 << 10 0x00400 //.. .... .... ..|. Aromatic 1 << 9 0x00200 //.. .... .... ...| Sulfur-Sulfur 1 << 8 0x00100 //.. .... .... .... |||. Partial n 7 << 5 0x00E00 //.. .... .... .... ...| |||| Partial m 0x0001F //.. .... .... .... .... .||| Covalent order 0x00007 //.0 0000 0000 0000 0001 0001 UNSPECIFIED //.0 0000 1111 1111 1111 1111 ANY //.0 0001 1111 1111 1111 1111 NULL public final static int BOND_RENDER_MASK = 0x1FFFF; public final static int BOND_RENDER_SINGLE = 0x10000; public final static int TYPE_ATROPISOMER = 0x10001; public final static int TYPE_ATROPISOMER_REV = 0x10002; // only used by SMILES, for ^^nm- private final static int ATROPISOMER_SHIFT = 11; // NOT IMPLEMENTED // public final static int BOND_CIP_STEREO_MASK = 0xC0000; // 3 << 18 // public final static int BOND_CIP_STEREO_UNK = 0xC0000; // 3 << 18 same as mask // public final static int BOND_CIP_STEREO_E = 0x80000; // 2 << 18 // public final static int BOND_CIP_STEREO_Z = 0x40000; // 1 << 18 // public final static int BOND_CIP_STEREO_SHIFT = 18; public final static int BOND_STEREO_MASK = 0x400; // 1 << 10 public final static int BOND_STEREO_NEAR = 0x401; // for JME reader and SMILES and XMLChemDraw reader public final static int BOND_STEREO_FAR = 0x411; // for JME reader and SMILES and XMLChemDraw reader public final static int BOND_STEREO_EITHER = 0x421; // for JME reader and SMILES and XMLChemDraw reader public final static int BOND_AROMATIC_MASK = 0x200; // 1 << 9 public final static int BOND_AROMATIC_SINGLE = 0x201; // same as single public final static int BOND_AROMATIC_DOUBLE = 0x202; // same as double public final static int BOND_AROMATIC = 0x203; // same as partial 2.1 public final static int BOND_SULFUR_MASK = 0x100; // 1 << 8; will be incremented public final static int BOND_PARTIAL_MASK = 0xE0; // 7 << 5; public final static int BOND_PARTIAL01 = 0x21; public final static int BOND_PARTIAL12 = 0x42; public final static int BOND_PARTIAL23 = 0x61; public final static int BOND_PARTIAL32 = 0x64; public final static int BOND_COVALENT_MASK = 0x3FF; // MUST be numerically correct in 0x7 if not partial public final static int BOND_COVALENT_SINGLE = 1; // and in 0xE0 if partial public final static int BOND_COVALENT_DOUBLE = 2; public final static int BOND_COVALENT_TRIPLE = 3; public final static int BOND_COVALENT_QUADRUPLE = 4; public final static int BOND_COVALENT_QUINTUPLE = 5; public final static int BOND_COVALENT_sextuple = 6; public final static int BOND_ORDER_UNSPECIFIED = 0x11; public final static int BOND_ORDER_ANY = 0x0FFFF; public final static int BOND_ORDER_NULL = 0x1FFFF; public static final int BOND_STRUT = 0x08000; public final static int BOND_PYMOL_NOMULT = 0x10000; public static final int BOND_PYMOL_MULT = 0x18000; public final static int BOND_NEW = 0x20000; public final static int BOND_HBOND_SHIFT = 11; public final static int BOND_HYDROGEN_MASK = 0xF << 11; public final static int BOND_H_REGULAR = 1 << 11; public final static int BOND_H_CALC_MASK = 0xE << 11; // excludes regular public final static int BOND_H_CALC = 2 << 11; public final static int BOND_H_PLUS_2 = 3 << 11; public final static int BOND_H_PLUS_3 = 4 << 11; public final static int BOND_H_PLUS_4 = 5 << 11; public final static int BOND_H_PLUS_5 = 6 << 11; public final static int BOND_H_MINUS_3 = 7 << 11; public final static int BOND_H_MINUS_4 = 8 << 11; public final static int BOND_H_NUCLEOTIDE = 9 << 11; private final static int[] argbsHbondType = { 0xFFFF69B4, // 0 unused - pink 0xFFFFFF00, // 1 regular yellow 0xFFFFFF00, // 2 calc -- unspecified; yellow 0xFFFFFFFF, // 3 +2 white 0xFFFF00FF, // 4 +3 magenta 0xFFFF0000, // 5 +4 red 0xFFFFA500, // 6 +5 orange 0xFF00FFFF, // 7 -3 cyan 0xFF00FF00, // 8 -4 green 0xFFFF8080, // 9 nucleotide }; public int index = -1; public int order; abstract public int getAtomIndex1(); abstract public int getAtomIndex2(); @Override abstract public int getCovalentOrder(); @Override abstract public boolean isCovalent(); abstract public boolean isPartial(); abstract public boolean isHydrogen(); public static int getArgbHbondType(int order) { int argbIndex = ((order & BOND_HYDROGEN_MASK) >> BOND_HBOND_SHIFT); return argbsHbondType[argbIndex]; } /** * used for formatting labels and in the connect PARTIAL command * * @param order * @return a string representation to preserve float n.m */ public final static String getBondOrderNumberFromOrder(int order) { order &= BOND_RENDER_MASK; switch (order) { case BOND_ORDER_NULL: case BOND_ORDER_ANY: return "0"; // I don't think this is possible case BOND_STEREO_NEAR: case BOND_STEREO_FAR: return "1"; default: if (isOrderH(order) || isAtropism(order) || (order & BOND_SULFUR_MASK) != 0) return "1"; if ((order & BOND_PARTIAL_MASK) != 0) return (order >> 5) + "." + (order & 0x1F); return EnumBondOrder.getNumberFromCode(order); } } public final static String getCmlBondOrder(int order) { String sname = getBondOrderNameFromOrder(order); switch (sname.charAt(0)) { case 's': case 'd': case 't': return "" + sname.toUpperCase().charAt(0); case 'a': if (sname.indexOf("Double") >= 0) return "D"; else if (sname.indexOf("Single") >= 0) return "S"; return "aromatic"; case 'p': if (sname.indexOf(" ") >= 0) return sname.substring(sname.indexOf(" ") + 1); return "partial12"; } return null; } public final static String getBondOrderNameFromOrder(int order) { order &= BOND_RENDER_MASK; switch (order) { case BOND_ORDER_ANY: case BOND_ORDER_NULL: return ""; case BOND_STEREO_NEAR: return "near"; case BOND_STEREO_FAR: return "far"; case BOND_STRUT: return EnumBondOrder.STRUT.name; case BOND_COVALENT_SINGLE: return EnumBondOrder.SINGLE.name; case BOND_COVALENT_DOUBLE: return EnumBondOrder.DOUBLE.name; } if ((order & BOND_PARTIAL_MASK) != 0) return "partial " + getBondOrderNumberFromOrder(order); if (isOrderH(order)) return EnumBondOrder.H_REGULAR.name; if ((order & TYPE_ATROPISOMER) == TYPE_ATROPISOMER) { int code = getAtropismCode(order); return "atropisomer_" + (code / 4) + (code % 4); } if ((order & BOND_SULFUR_MASK) != 0) return EnumBondOrder.SINGLE.name; return EnumBondOrder.getNameFromCode(order); } public static int getAtropismOrder(int nn, int mm) { return getAtropismOrder12(((nn) << 2) + mm); } public static int getAtropismOrder12(int nnmm) { return ((nnmm << ATROPISOMER_SHIFT) | TYPE_ATROPISOMER); } private static int getAtropismCode(int order) { return (order >> (ATROPISOMER_SHIFT)) & 0xF; } public static Node getAtropismNode(int order, Node a1, boolean isFirst) { int i1 = (order >> (ATROPISOMER_SHIFT + (isFirst ? 0 : 2))) & 3; return (Node) a1.getEdges()[i1 - 1].getOtherNode(a1); } public static boolean isAtropism(int order) { return (order & TYPE_ATROPISOMER) == TYPE_ATROPISOMER; } public static boolean isOrderH(int order) { return (order & BOND_HYDROGEN_MASK) != 0 && (order & TYPE_ATROPISOMER) == 0; } public final static int getPartialBondDotted(int order) { return (order & 0x1F); } public final static int getPartialBondOrder(int order) { return ((order & BOND_RENDER_MASK) >> 5); } protected final static int getCovalentBondOrder(int order) { if ((order & BOND_STEREO_MASK) != 0) return 1; if ((order & BOND_COVALENT_MASK) == 0) return 0; order &= BOND_RENDER_MASK; if ((order & BOND_PARTIAL_MASK) != 0) return getPartialBondOrder(order); if ((order & BOND_SULFUR_MASK) != 0) order &= ~BOND_SULFUR_MASK; if ((order & 0xF8) != 0) // "ANY" order = 1; return order & 7; } public final static int getBondOrderFromFloat(float fOrder) { switch ((int) (fOrder * 10)) { case 10: return BOND_COVALENT_SINGLE; case 5: case -10: return BOND_PARTIAL01; case 15: return BOND_AROMATIC; case -15: return BOND_PARTIAL12; case 20: return BOND_COVALENT_DOUBLE; case 25: return BOND_PARTIAL23; case -25: return BOND_PARTIAL32; case 30: return BOND_COVALENT_TRIPLE; case 40: return BOND_COVALENT_QUADRUPLE; } return BOND_ORDER_NULL; } /** * Encode name such as 1 2 3 2.1 3.1 single double triple atropisomer_12 or * "partial 1.3" * * @param s * @return encoded form of bond */ public static int getBondOrderFromString(String s) { if (s.indexOf(' ') < 0) { if (s.indexOf(".") >= 0) { s = "partial " + s; } else { if (PT.isOneOf(s, ";1;2;3;4;5;6;")) { return s.charAt(0) - '0'; } // single double triple... int order = EnumBondOrder.getCodeFromName(s); if (order != BOND_ORDER_NULL || !s.toLowerCase().startsWith("atropisomer_") || s.length() != 14) return order; try { // atropoisomer_12 or atropisomer_21 stereochemistry order = getAtropismOrder(Integer.parseInt(s.substring(12, 13)), Integer.parseInt(s.substring(13, 14))); } catch (NumberFormatException e) { // BOND_ORDER_NULL } return order; } } if (s.toLowerCase().indexOf("partial ") != 0) return BOND_ORDER_NULL; s = s.substring(8).trim(); return getPartialBondOrderFromFloatEncodedInt(getFloatEncodedInt(s)); } /** * reads standard n.m double-as-integer (n*1000000 + m) * and returns partial bond order as (n % 7) << 5 + (m % 0x1F) * * @param bondOrderInteger * @return partial bond order encoded as an integer */ public static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger) { return (((bondOrderInteger / 1000000) % 7) << 5) + ((bondOrderInteger % 1000000) & 0x1F); } /** * Encodes a string such as "2.10" as an integer instead of a double so as to * distinguish "2.1" from "2.10". * * For n.m, returns n * 1000000 + m. * * 2147483647 is maxvalue, so this allows an encoding of up to * n = 2147 and m = 999999 * * Used in Jmol for model numbers and partial bond orders. * * @param strDecimal * @return double encoded as an integer */ public static int getFloatEncodedInt(String strDecimal) { int pt = strDecimal.indexOf("."); if (pt < 1 || strDecimal.charAt(0) == '-' || strDecimal.endsWith(".") || strDecimal.contains(".0")) return Integer.MAX_VALUE; int i = 0; int j = 0; if (pt > 0) { try { i = Integer.parseInt(strDecimal.substring(0, pt)); if (i < 0) i = -i; } catch (NumberFormatException e) { i = -1; } } if (pt < strDecimal.length() - 1) try { j = Integer.parseInt(strDecimal.substring(pt + 1)); } catch (NumberFormatException e) { // not a problem } i = i * 1000000 + j; return (i < 0 || i > Integer.MAX_VALUE ? Integer.MAX_VALUE : i); } @Override public int getBondType() { return order & BOND_RENDER_MASK; } private enum EnumBondOrder { SINGLE(BOND_COVALENT_SINGLE,"1","single"), DOUBLE(BOND_COVALENT_DOUBLE,"2","double"), TRIPLE(BOND_COVALENT_TRIPLE,"3","triple"), QUADRUPLE(BOND_COVALENT_QUADRUPLE,"4","quadruple"), QUINTUPLE(BOND_COVALENT_QUINTUPLE,"5","quintuple"), sextuple(BOND_COVALENT_sextuple,"6","sextuple"), AROMATIC(BOND_AROMATIC,"1.5","aromatic"), STRUT(BOND_STRUT,"1","struts"), H_REGULAR(BOND_H_REGULAR,"1","hbond"), PARTIAL01(BOND_PARTIAL01,"0.5","partial"), PARTIAL12(BOND_PARTIAL12,"1.5","partialDouble"), PARTIAL23(BOND_PARTIAL23,"2.5","partialTriple"), PARTIAL32(BOND_PARTIAL32,"2.5","partialTriple2"), AROMATIC_SINGLE(BOND_AROMATIC_SINGLE,"1","aromaticSingle"), AROMATIC_DOUBLE(BOND_AROMATIC_DOUBLE,"2","aromaticDouble"), ATROPISOMER(TYPE_ATROPISOMER, "1", "atropisomer"), UNSPECIFIED(BOND_ORDER_UNSPECIFIED,"1","unspecified"); private int code; protected String number; protected String name; /** * @j2sIgnoreSuperConstructor * @param code * @param number * @param name */ private EnumBondOrder(int code, String number, String name) { this.code = code; this.number = number; this.name = name; } protected static int getCodeFromName(String name) { for (EnumBondOrder item : values()) if (item.name.equalsIgnoreCase(name)) return item.code; return BOND_ORDER_NULL; } protected static String getNameFromCode(int code) { for (EnumBondOrder item: values()) if (item.code == code) return item.name; return "?"; } protected static String getNumberFromCode(int code) { for (EnumBondOrder item: values()) if (item.code == code) return item.number; return "?"; } } /** * @param c */ public void setCIPChirality(int c) { // default is no action } /** * @param doCalculate * @return CIP chirality label */ public String getCIPChirality(boolean doCalculate) { return ""; } }