/*
* 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 MCview;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.util.Comparison;
import java.awt.Color;
import java.util.List;
import java.util.Vector;
public class PDBChain
{
public static final String RESNUM_FEATURE = "RESNUM";
private static final String IEASTATUS = "IEA:jalview";
public String id;
public Vector bonds = new Vector<>();
public Vector atoms = new Vector<>();
public Vector residues = new Vector<>();
public int offset;
/**
* sequence is the sequence extracted by the chain parsing code
*/
public SequenceI sequence;
/**
* shadow is the sequence created by any other parsing processes (e.g. Jmol,
* RNAview)
*/
public SequenceI shadow = null;
public boolean isNa = false;
public boolean isVisible = true;
public int pdbstart = 0;
public int pdbend = 0;
public int seqstart = 0;
public int seqend = 0;
public String pdbid = "";
public PDBChain(String thePdbid, String theId)
{
this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
this.id = theId;
}
/**
* character used to write newlines
*/
protected String newline = System.getProperty("line.separator");
public Mapping shadowMap;
public void setNewlineString(String nl)
{
newline = nl;
}
public String getNewlineString()
{
return newline;
}
public String print()
{
StringBuilder tmp = new StringBuilder(256);
for (Bond b : bonds)
{
tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
.append(" ").append(offset).append(newline);
}
return tmp.toString();
}
/**
* Annotate the residues with their corresponding positions in s1 using the
* alignment in as NOTE: This clears all atom.alignmentMapping values on the
* structure.
*
* @param as
* @param s1
*/
public void makeExactMapping(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
// first clear out any old alignmentMapping values:
for (Atom atom : atoms)
{
atom.alignmentMapping = -1;
}
// and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')
{
alignpos++;
}
if (as.astr2.charAt(i) != '-')
{
pdbpos++;
}
boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
as.astr2.charAt(i), false);
if (sameResidue)
{
if (pdbpos >= residues.size())
{
continue;
}
Residue res = residues.elementAt(pdbpos);
for (Atom atom : res.atoms)
{
atom.alignmentMapping = alignpos;
}
}
}
}
/**
* Annotate the residues with their corresponding positions in s1 using the
* alignment in as NOTE: This clears all atom.alignmentMapping values on the
* structure.
*
* @param as
* @param s1
*/
public void makeExactMapping(StructureMapping mapping, SequenceI s1)
{
// first clear out any old alignmentMapping values:
for (Atom atom : atoms)
{
atom.alignmentMapping = -1;
}
SequenceI ds = s1;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
int pdboffset = 0;
for (Residue res : residues)
{
// res.number isn't set correctly for discontinuous/mismapped residues
int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
char strchar = sequence.getCharAt(pdboffset++);
if (seqpos == StructureMapping.UNASSIGNED_VALUE)
{
continue;
}
char seqchar = ds.getCharAt(seqpos - ds.getStart());
boolean sameResidue = Comparison.isSameResidue(
seqchar, strchar, false);
if (sameResidue)
{
for (Atom atom : res.atoms)
{
atom.alignmentMapping = seqpos - 1;
}
}
}
}
/**
* Copies over the RESNUM seqfeatures from the internal chain sequence to the
* mapped sequence
*
* @param seq
* @param status
* The Status of the transferred annotation
*/
public void transferRESNUMFeatures(SequenceI seq,
String status)
{
SequenceI sq = seq;
while (sq != null && sq.getDatasetSequence() != null)
{
sq = sq.getDatasetSequence();
if (sq == sequence)
{
return;
}
}
/*
* Remove any existing features for this chain if they exist ?
* SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
* totfeat=seqsfeatures.length; // Remove any features for this exact chain
* ? for (int i=0; i features = sequence.getSequenceFeatures();
for (SequenceFeature feature : features)
{
if (feature.getFeatureGroup() != null
&& feature.getFeatureGroup().equals(pdbid))
{
int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
.elementAt(0).alignmentMapping;
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
feature.getFeatureGroup(), feature.getScore());
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0)
? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
{
sq.addSequenceFeature(tx);
}
}
}
}
/**
* Traverses the list of residues and constructs bonds where CA-to-CA atoms or
* P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of
* residues contain a P not a CA.
*/
public void makeCaBondList()
{
boolean na = false;
int numNa = 0;
for (int i = 0; i < (residues.size() - 1); i++)
{
Residue tmpres = residues.elementAt(i);
Residue tmpres2 = residues.elementAt(i + 1);
Atom at1 = tmpres.findAtom("CA");
Atom at2 = tmpres2.findAtom("CA");
na = false;
if ((at1 == null) && (at2 == null))
{
na = true;
at1 = tmpres.findAtom("P");
at2 = tmpres2.findAtom("P");
}
if ((at1 != null) && (at2 != null))
{
if (at1.chain.equals(at2.chain))
{
if (na)
{
numNa++;
}
makeBond(at1, at2);
}
}
else
{
System.out.println("not found " + i);
}
}
/*
* If > 99% 'P', flag as nucleotide; note the count doesn't include the last
* residue
*/
if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
{
isNa = true;
}
}
/**
* Construct a bond from atom1 to atom2 and add it to the list of bonds for
* this chain
*
* @param at1
* @param at2
*/
public void makeBond(Atom at1, Atom at2)
{
bonds.addElement(new Bond(at1, at2));
}
/**
* Traverses the list of atoms and
*
* - constructs a list of Residues, each containing all the atoms that share
* the same residue number
* - adds a RESNUM sequence feature for each position
* - creates the sequence string
* - determines if nucleotide
* - saves the residue number of the first atom as 'offset'
* - adds temp factor annotation if the flag is set to do so
*
*
* @param visibleChainAnnotation
*/
public void makeResidueList(boolean visibleChainAnnotation)
{
int count = 0;
Object symbol;
boolean deoxyn = false;
boolean nucleotide = false;
StringBuilder seq = new StringBuilder(256);
Vector resFeatures = new Vector<>();
Vector resAnnotation = new Vector<>();
int iSize = atoms.size() - 1;
int resNumber = -1;
char insCode = ' ';
for (int i = 0; i <= iSize; i++)
{
Atom tmp = atoms.elementAt(i);
resNumber = tmp.resNumber;
insCode = tmp.insCode;
int res = resNumber;
char ins = insCode;
if (i == 0)
{
offset = resNumber;
}
Vector resAtoms = new Vector<>();
// Add atoms to a vector while the residue number
// remains the same as the first atom's resNumber (res)
while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
{
resAtoms.add(atoms.elementAt(i));
i++;
if (i < atoms.size())
{
resNumber = atoms.elementAt(i).resNumber;
insCode = atoms.elementAt(i).insCode;
}
else
{
resNumber++;
}
}
// We need this to keep in step with the outer for i = loop
i--;
// Add inserted residues as features to the base residue
Atom currAtom = resAtoms.get(0);
if (currAtom.insCode != ' ' && !residues.isEmpty()
&& residues.lastElement().atoms
.get(0).resNumber == currAtom.resNumber)
{
String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+ pdbid + id;
SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
+ count - 1, offset + count - 1, "PDB_INS");
resFeatures.addElement(sf);
residues.lastElement().atoms.addAll(resAtoms);
}
else
{
// Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
String desc = tmpat.resName
+ ":" + tmpat.resNumIns + " " + pdbid + id;
SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
if ((symbol = ResidueProperties.getAA3Hash()
.get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
// use the aaIndex rather than call 'toLower' - which would take a bit
// more time.
deoxyn = nucname.length() == 2
&& ResidueProperties.aaIndex[nucname
.charAt(0)] == ResidueProperties.aaIndex['D'];
if (tmpat.name.equalsIgnoreCase("CA")
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
char r = ResidueProperties.getSingleCharacterCode(
ResidueProperties.getCanonicalAminoAcid(tmpat.resName));
seq.append(r == '0' ? 'X' : r);
// System.err.println("PDBReader:Null aa3Hash for " +
// tmpat.resName);
}
else
{
// nucleotide flag
nucleotide = true;
seq.append(nucname.charAt((deoxyn ? 1 : 0)));
}
}
else
{
if (nucleotide)
{
System.err.println(
"Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
}
seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
count++;
}
}
if (id.length() < 1)
{
id = " ";
}
isNa = nucleotide;
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
// resNumber-offset
// ~=
// seq.size()
// Add normalised feature scores to RESNUM indicating start/end of sequence
// sf.setScore(offset+count);
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
if (StructureImportSettings.isShowSeqFeatures())
{
iSize = resFeatures.size();
for (int i = 0; i < iSize; i++)
{
sequence.addSequenceFeature(resFeatures.elementAt(i));
resFeatures.setElementAt(null, i);
}
}
if (visibleChainAnnotation)
{
Annotation[] annots = new Annotation[resAnnotation.size()];
float max = 0f;
float min = 0f;
iSize = annots.length;
for (int i = 0; i < iSize; i++)
{
annots[i] = resAnnotation.elementAt(i);
max = Math.max(max, annots[i].value);
min = Math.min(min, annots[i].value);
resAnnotation.setElementAt(null, i);
}
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
"Temperature Factor", "Temperature Factor for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
}
/**
* Colour start/end of bonds by charge
*
* - ASP and GLU red
* - LYS and ARG blue
* - CYS yellow
* - others light gray
*
*/
public void setChargeColours()
{
for (Bond b : bonds)
{
if (b.at1 != null && b.at2 != null)
{
b.startCol = getChargeColour(b.at1.resName);
b.endCol = getChargeColour(b.at2.resName);
}
else
{
b.startCol = Color.gray;
b.endCol = Color.gray;
}
}
}
public static Color getChargeColour(String resName)
{
Color result = Color.lightGray;
if ("ASP".equals(resName) || "GLU".equals(resName))
{
result = Color.red;
}
else if ("LYS".equals(resName) || "ARG".equals(resName))
{
result = Color.blue;
}
else if ("CYS".equals(resName))
{
result = Color.yellow;
}
return result;
}
/**
* Sets the start/end colours of bonds to those of the start/end atoms
* according to the specified colour scheme. Note: currently only works for
* peptide residues.
*
* @param cs
*/
public void setChainColours(ColourSchemeI cs)
{
int index;
for (Bond b : bonds)
{
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
null, null, 0f);
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
null, null, 0f);
} catch (Exception e)
{
b.startCol = Color.gray;
b.endCol = Color.gray;
}
}
}
public void setChainColours(Color col)
{
for (Bond b : bonds)
{
b.startCol = col;
b.endCol = col;
}
}
/**
* copy any sequence annotation onto the sequence mapped using the provided
* StructureMapping
*
* @param mapping
* - positional mapping between destination sequence and pdb resnum
* @param sqmpping
* - mapping between destination sequence and local chain
*/
public void transferResidueAnnotation(StructureMapping mapping,
jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
if (sqmpping == null)
{
// SIFTS mappings are recorded in the StructureMapping object...
sqmpping = mapping.getSeqToPdbMapping();
}
if (sq != null)
{
while (dsq.getDatasetSequence() != null)
{
dsq = dsq.getDatasetSequence();
}
// any annotation will be transferred onto the dataset sequence
if (shadow != null && shadow.getAnnotation() != null)
{
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
List transfer = sq
.getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(sequence, shadowMap);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
}
else
{
continue;
}
}
}
else
{
if (sequence != null && sequence.getAnnotation() != null)
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
List transfer = dsq
.getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
// mapping.transfer(ana);
}
else
{
continue;
}
}
}
}
if (false)
{
// Useful for debugging mappings - adds annotation for mapped position
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
for (int i = sq.getStart(), j = sq
.getEnd(), k = 0; i <= j; i++, k++)
{
int prn = mapping.getPDBResNum(k + 1);
an[k] = new Annotation(prn);
if (min == -1)
{
min = k;
max = k;
}
else
{
if (min > k)
{
min = k;
}
else if (max < k)
{
max = k;
}
}
}
sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
"PDB Residue Numbering for " + this.pdbid + ":" + this.id,
an, min, max, AlignmentAnnotation.LINE_GRAPH));
}
}
}
}