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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $
* $Revision: 7273 $
*
* Copyright (C) 2007 Miguel, Bob, Jmol Development
*
* Contact: [email protected]
*
* 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 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.jvxl.readers;
import java.io.BufferedReader;
import org.jmol.util.Logger;
import javajs.util.P3;
import org.jmol.util.SimpleUnitCell;
// DSN6, MRC, and XPLOR readers
abstract class MapFileReader extends VolumeFileReader {
protected float dmin = Float.MAX_VALUE;
protected float dmax, dmean, drange;
MapFileReader(){}
@Override
void init2(SurfaceGenerator sg, BufferedReader br) {
init2MFR(sg, br);
}
protected void init2MFR(SurfaceGenerator sg, BufferedReader br) {
init2VFR(sg, br);
isAngstroms = true;
// undocumented; for debugging, I think
// adjustment = center;
// if (adjustment == null || Float.isNaN(adjustment.x))
// adjustment = new P3();
}
/*
* inputs:
*
a b c cell dimensions in angstroms
alpha beta gamma cell angles in degrees
nx number of columns (fastest changing in map)
ny number of rows
yz number of sections (slowest changing in map)
a0 offset of uc origin along a axis
b0 offset of uc origin along b axis
c0 offset of uc origin along c axis
na number of intervals along uc X -- a/na is unit vector
nb number of intervals along uc Y -- b/nb is unit vector
nc number of intervals along uc Z -- c/nc is unit vector
mapc axis corresp to cols (1,2,3 for X,Y,Z)
mapr axis corresp to rows (1,2,3 for X,Y,Z)
maps axis corresp to sections (1,2,3 for X,Y,Z)
originX, originY, originZ origin in X,Y,Z of unitCell (0,0,0)
*/
protected int mapc, mapr, maps;
protected int nx, ny, nz, mode;
protected int[] nxyzStart = new int[3];
protected int na, nb, nc;
protected float a, b, c, alpha, beta, gamma;
protected P3 origin = new P3();
//protected P3 adjustment = new P3();
protected P3[] vectors = new P3[3];
protected void getVectorsAndOrigin() {
Logger.info("grid parameters: nx,ny,nz: " + nx + "," + ny + "," + nz);
Logger.info("grid parameters: nxStart,nyStart,nzStart: " + nxyzStart[0]
+ "," + nxyzStart[1] + "," + nxyzStart[2]);
Logger.info("grid parameters: mx,my,mz: " + na + "," + nb + "," + nc);
Logger.info("grid parameters: a,b,c,alpha,beta,gamma: " + a + "," + b + ","
+ c + "," + alpha + "," + beta + "," + gamma);
Logger.info("grid parameters: mapc,mapr,maps: " + mapc + "," + mapr + ","
+ maps);
Logger.info("grid parameters: originX,Y,Z: " + origin);
SimpleUnitCell unitCell = SimpleUnitCell.newA( new float[] { a / na, b / nb, c / nc, alpha,
beta, gamma });
/*
Many thanks to Eric Martz for helping get this right.
Basically we have:
Three principal crystallographic axes: a, b, and c...
...also referred to as x, y, and z
...also referred to as directions 1, 2, and 3
...a mapping of "sheets" "rows" and "columns" of data
set in the file as
s1r1c1...s1r1c9.....
s1r2c1...s1r2c9.....
s2r1c1...s2r1c9.....
s2r2c1...s2r2c9.....
etc.
In Jmol, we always have x (our [0]) running slowest, so we
ultimately must make the following assignment:
MRC "maps" maps to .x or [0]
MRC "mapr" maps to .y or [1]
MRC "mapc" maps to .z or [2]
We really don't care if this is actually physical "x" "y" or "z".
In fact, for a hexagonal cell these will be combinations of xyz.
So it goes something like this:
scale the (a) vector by 1/mx and call that vector[0]
scale the (b) vector by 1/my and call that vector[1]
scale the (c) vector by 1/mz and call that vector[2]
Now map these vectors to Jmol volumetricVectors using
our x: volVector[0] = vector[maps - 1] (slow)
our y: volVector[1] = vector[mapr - 1]
our z: volVector[2] = vector[mapc - 1] (fast)
This is because our x is the slowest running variable.
*/
vectors[0] = P3.new3(1, 0, 0);
vectors[1] = P3.new3(0, 1, 0);
vectors[2] = P3.new3(0, 0, 1);
unitCell.toCartesian(vectors[0], false);
unitCell.toCartesian(vectors[1], false);
unitCell.toCartesian(vectors[2], false);
Logger.info("Jmol unit cell vectors:");
Logger.info(" a: " + vectors[0]);
Logger.info(" b: " + vectors[1]);
Logger.info(" c: " + vectors[2]);
voxelCounts[0] = nz; // slowest
voxelCounts[1] = ny;
voxelCounts[2] = nx; // fastest
volumetricVectors[0].setT(vectors[maps - 1]);
volumetricVectors[1].setT(vectors[mapr - 1]);
volumetricVectors[2].setT(vectors[mapc - 1]);
// only use nxyzStart if the origin is {0, 0, 0}
if (origin.x == 0 && origin.y == 0 && origin.z == 0) {
// older method -- wow! Beats me.....
int[] xyz2crs = new int[3];
xyz2crs[mapc - 1] = 0; // mapc = 2 ==> [1] = 0
xyz2crs[mapr - 1] = 1; // mapr = 1 ==> [0] = 1
xyz2crs[maps - 1] = 2; // maps = 3 ==> [2] = 2
int xIndex = xyz2crs[0]; // xIndex = 1
int yIndex = xyz2crs[1]; // yIndex = 0
int zIndex = xyz2crs[2]; // zIndex = 2
origin.scaleAdd2(nxyzStart[xIndex]/* + adjustment.x */, vectors[0], origin);
origin.scaleAdd2(nxyzStart[yIndex]/* + adjustment.y */, vectors[1], origin);
origin.scaleAdd2(nxyzStart[zIndex]/* + adjustment.z */, vectors[2], origin);
}
volumetricOrigin.setT(origin);
Logger.info("Jmol grid origin in Cartesian coordinates: " + origin);
Logger.info("Use isosurface OFFSET {x y z} if you want to shift it.\n");
/* example:
isosurface within 5 {_Fe} "1blu.ccp4";
reading isosurface data from C:/jmol-dev/workspace/Jmol/bobtest/1blu.ccp4
FileManager opening C:\jmol-dev\workspace\Jmol\bobtest\1blu.ccp4
data file type was determined to be MRC-
FileManager opening C:\jmol-dev\workspace\Jmol\bobtest\1blu.ccp4
MRC header: mode: 2
MRC header: dmin,dmax,dmean: -2.0043933,4.9972544,-0.0151823275
MRC header: ispg,nsymbt: 152,0
MRC header: rms: 0.46335652
MRC header: labels: 1
Created by MAPMAN V. 080625/7.8.5 at Tue Jan 19 08:04:40 2010 for A. Nonymous
MRC header: bytes read: 1024
cutoff set to (dmean + 2*rms) = 0.91153073
grid parameters: nx,ny,nz: 73,60,66
grid parameters: nxStart,nyStart,nzStart: -12,23,-32
grid parameters: mx,my,mz: 78,78,114
grid parameters: a,b,c,alpha,beta,gamma: 52.0,52.0,77.1875,90.0,90.0,120.0
grid parameters: mapc,mapr,maps: 2,1,3
grid parameters: originX,Y,Z: 0.0,0.0,0.0
Jmol unit cell vectors:
a: (0.6666667, 0.0, 0.0)
b: (-0.33333337, 0.57735026, 0.0)
c: (-2.9596254E-8, -5.1262216E-8, 0.6770833)
Jmol grid origin in Cartesian coordinates: (19.333334, -6.9282017, -21.666666)
Jmol origin in slow-to-fast system: (19.333334, -6.9282017, -21.666666)
*/
}
protected void setCutoffAutomatic() {
if (params.thePlane == null && params.cutoffAutomatic) {
params.cutoff = -1f;
Logger.info("MapReader: setting cutoff to default value of "
+ params.cutoff
+ (boundingBox == null ? " (no BOUNDBOX parameter)\n" : "\n"));
}
}
}