/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import java.awt.Color;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
*
* @author JimP
*
*/
public class JmolCommands extends StructureCommandsBase
{
private static final String CMD_COLOUR_BY_CHARGE = "select *;color white;select ASP,GLU;color red;"
+ "select LYS,ARG;color blue;select CYS;color yellow";
private static final String CMD_COLOUR_BY_CHAIN = "select *;color chain";
private static final String PIPE = "|";
private static final String HYPHEN = "-";
private static final String COLON = ":";
private static final String SLASH = "/";
/**
* {@inheritDoc}
*
* @return
*/
@Override
public int getModelStartNo()
{
return 1;
}
@Override
protected String getColourString(Color c)
{
return c == null ? null
: String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
c.getBlue());
}
/**
* Returns commands (one per colour key in the map) like
*
*
* select 2:A/1.1|3-27:B/1.1|9-12:A/2.1;color[173,0,82]
*
*/
@Override
public String[] colourBySequence(Map colourMap)
{
List colourCommands = buildColourCommands(colourMap);
return colourCommands.toArray(new String[colourCommands.size()]);
}
public String[] colourBySequence(StructureSelectionManager ssm,
String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
AlignmentViewPanel viewPanel)
{
// TODO refactor to call buildColoursMap() first...
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
AlignViewportI viewport = viewPanel.getAlignViewport();
HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();
List cset = new ArrayList<>();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
StringBuilder command = new StringBuilder(128);
List str = new ArrayList<>();
if (mapping == null || mapping.length < 1)
{
continue;
}
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
for (int sp, m = 0; m < mapping.length; m++)
{
if (mapping[m].getSequence() == sequence[pdbfnum][s]
&& (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
{
int lastPos = StructureMapping.UNASSIGNED_VALUE;
SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
if (Comparison.isGap(asp.getCharAt(r)))
{
continue;
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos == lastPos)
{
continue;
}
if (pos == StructureMapping.UNASSIGNED_VALUE)
{
// terminate current colour op
if (command.length() > 0
&& command.charAt(command.length() - 1) != ';')
{
command.append(";");
}
// reset lastPos
lastPos = StructureMapping.UNASSIGNED_VALUE;
continue;
}
lastPos = pos;
Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
finder);
/*
* shade hidden regions darker
*/
if (!cs.isVisible(r))
{
col = Color.GRAY;
}
String newSelcom = (mapping[m].getChain() != " "
? ":" + mapping[m].getChain()
: "") + "/" + (pdbfnum + 1) + ".1" + ";color"
+ getColourString(col);
if (command.length() > newSelcom.length() && command
.substring(command.length() - newSelcom.length())
.equals(newSelcom))
{
command = JmolCommands.condenseCommand(command, pos);
continue;
}
// TODO: deal with case when buffer is too large for Jmol to parse
// - execute command and flush
if (command.length() > 0
&& command.charAt(command.length() - 1) != ';')
{
command.append(";");
}
if (command.length() > 51200)
{
// add another chunk
str.add(command.toString());
command.setLength(0);
}
command.append("select " + pos);
command.append(newSelcom);
}
// break;
}
}
}
{
// add final chunk
str.add(command.toString());
command.setLength(0);
}
cset.addAll(str);
}
return cset.toArray(new String[cset.size()]);
}
public static StringBuilder condenseCommand(StringBuilder command,
int pos)
{
// work back to last 'select'
int p = command.length(), q = p;
do
{
p -= 6;
if (p < 1)
{
p = 0;
}
;
} while ((q = command.indexOf("select", p)) == -1 && p > 0);
StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
command = command.delete(0, q + 7);
String start;
if (command.indexOf("-") > -1)
{
start = command.substring(0, command.indexOf("-"));
}
else
{
start = command.substring(0, command.indexOf(":"));
}
sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
return sb;
}
@Override
public String colourByChain()
{
return CMD_COLOUR_BY_CHAIN;
}
@Override
public String colourByCharge()
{
return CMD_COLOUR_BY_CHARGE;
}
@Override
public String colourByResidues(Map colours)
{
StringBuilder cmd = new StringBuilder(128);
cmd.append("select *;color white;");
cmd.append(super.colourByResidues(colours));
return cmd.toString();
}
@Override
public String setBackgroundColour(Color col)
{
return "background " + getColourString(col);
}
@Override
public String focusView()
{
return "zoom 0";
}
@Override
public String showChains(List toShow)
{
StringBuilder atomSpec = new StringBuilder(128);
boolean first = true;
for (String chain : toShow)
{
String[] tokens = chain.split(":");
if (tokens.length == 2)
{
if (!first)
{
atomSpec.append(" or ");
}
first = false;
atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
}
}
String spec = atomSpec.toString();
String command = "select *;restrict " + spec + ";cartoon;center "
+ spec;
return command;
}
/**
* Returns a command to superpose atoms in {@code atomSpec} to those in
* {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
* For example
*
*
* compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
* ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
*
*
* where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
* time in seconds to animate the action. For this example, atoms in model 2
* are moved towards atoms in model 1.
*
* The two atomspecs should each be for one model only, but may have more than
* one chain. The number of atoms specified should be the same for both
* models, though if not, Jmol may make a 'best effort' at superposition.
*
* @see https://chemapps.stolaf.edu/jmol/docs/#compare
*/
@Override
public String superposeStructures(AtomSpecModel refAtoms,
AtomSpecModel atomSpec)
{
StringBuilder sb = new StringBuilder(64);
int refModel = refAtoms.getModels().iterator().next();
int model2 = atomSpec.getModels().iterator().next();
sb.append(String.format("compare {%d.1} {%d.1}", model2, refModel));
sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
/*
* command examples don't include modelspec with atoms, getAtomSpec does;
* it works, so leave it as it is for simplicity
*/
sb.append(getAtomSpec(atomSpec, true)).append("}{");
sb.append(getAtomSpec(refAtoms, true)).append("}");
sb.append(" ROTATE TRANSLATE ");
sb.append(getCommandSeparator());
/*
* show residues used for superposition as ribbon
*/
sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
.append("cartoons");
return sb.toString();
}
@Override
public String openCommandFile(String path)
{
/*
* https://chemapps.stolaf.edu/jmol/docs/#script
* not currently used in Jalview
*/
return "script " + path;
}
@Override
public String saveSession(String filepath)
{
/*
* https://chemapps.stolaf.edu/jmol/docs/#write
* not currently used in Jalview
*/
return "write \"" + filepath + "\"";
}
@Override
protected String getColourCommand(String atomSpec, Color colour)
{
StringBuilder sb = new StringBuilder(atomSpec.length()+20);
sb.append("select ").append(atomSpec).append(getCommandSeparator())
.append("color").append(getColourString(colour));
return sb.toString();
}
@Override
protected String getResidueSpec(String residue)
{
return residue;
}
/**
* Generates a Jmol atomspec string like
*
*
* 2-5:A/1.1,8:A/1.1,5-10:B/2.1
*
*
* Parameter {@code alphaOnly} is not used here - this restriction is made by
* a separate clause in the {@code compare} (superposition) command.
*/
@Override
public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
{
StringBuilder sb = new StringBuilder(128);
boolean first = true;
for (int modelNo : model.getModels())
{
for (String chain : model.getChains(modelNo))
{
for (int[] range : model.getRanges(modelNo, chain))
{
if (!first)
{
sb.append(PIPE);
}
first = false;
if (range[0] == range[1])
{
sb.append(range[0]);
}
else
{
sb.append(range[0]).append(HYPHEN).append(range[1]);
}
sb.append(COLON).append(chain.trim()).append(SLASH);
sb.append(String.valueOf(modelNo)).append(".1");
}
}
}
return sb.toString();
}
@Override
public String showBackbone()
{
return "select *; cartoons off; backbone";
}
}