org.biojava.nbio.structure.io.mmcif.MMCIFFileTools Maven / Gradle / Ivy
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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.io.mmcif;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.List;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Element;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.GroupType;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.FileConvert;
import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
import org.biojava.nbio.structure.io.mmcif.model.Cell;
import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
import org.biojava.nbio.structure.xtal.CrystalCell;
import org.biojava.nbio.structure.xtal.SpaceGroup;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Some tools for mmCIF file writing.
*
* See http://www.iucr.org/__data/assets/pdf_file/0019/22618/cifguide.pdf
*
*
* @author duarte_j
*
*/
public class MMCIFFileTools {
private static final Logger logger = LoggerFactory.getLogger(MMCIFFileTools.class);
private static final String newline = System.getProperty("line.separator");
/**
* The character to be printed out in cases where a value is not assigned in mmCIF files
*/
public static final String MMCIF_MISSING_VALUE = "?";
/**
* The character to be printed out as a default value in mmCIF files, e.g. for the default alt_locs
*/
public static final String MMCIF_DEFAULT_VALUE = ".";
/**
* Produces a mmCIF loop header string for the given categoryName and className.
* className must be one of the beans in the {@link org.biojava.nbio.structure.io.mmcif.model} package
* @param categoryName
* @param className
* @return
* @throws ClassNotFoundException if the given className can not be found
*/
public static String toLoopMmCifHeaderString(String categoryName, String className) throws ClassNotFoundException {
StringBuilder str = new StringBuilder();
str.append(SimpleMMcifParser.LOOP_START+newline);
Class c = Class.forName(className);
for (Field f : c.getDeclaredFields()) {
str.append(categoryName+"."+f.getName()+newline);
}
return str.toString();
}
/**
* Converts a mmCIF bean (see {@link org.biojava.nbio.structure.io.mmcif.model} to
* a String representing it in mmCIF (single-record) format.
* @param categoryName
* @param o
* @return
*/
public static String toMMCIF(String categoryName, Object o) {
StringBuilder sb = new StringBuilder();
Class c = o.getClass();
int maxFieldNameLength = getMaxFieldNameLength(o);
for (Field f : c.getDeclaredFields()) {
f.setAccessible(true);
sb.append(categoryName+"."+f.getName());
int spacing = maxFieldNameLength - f.getName().length() + 3;
try {
Object obj = f.get(o);
String val;
if (obj==null) {
logger.debug("Field {} is null, will write it out as {}",f.getName(),MMCIF_MISSING_VALUE);
val = MMCIF_MISSING_VALUE;
} else {
val = (String) obj;
}
for (int i=0;i list) {
int[] sizes = getFieldSizes(list);
StringBuilder sb = new StringBuilder();
for (Object o:list) {
sb.append(toSingleLoopLineMmCifString(o, sizes));
}
sb.append(SimpleMMcifParser.COMMENT_CHAR+newline);
return sb.toString();
}
/**
* Given a mmCIF bean produces a String representing it in mmCIF loop format as a single record line
* @param a
* @param sizes the size of each of the fields
* @return
*/
private static String toSingleLoopLineMmCifString(Object a, int[] sizes) {
StringBuilder str = new StringBuilder();
Class c = a.getClass();
if (sizes.length!=c.getDeclaredFields().length)
throw new IllegalArgumentException("The given sizes of fields differ from the number of declared fields");
int i = -1;
for (Field f : c.getDeclaredFields()) {
i++;
f.setAccessible(true);
try {
Object obj = f.get(a);
String val;
if (obj==null) {
logger.debug("Field {} is null, will write it out as {}",f.getName(),MMCIF_MISSING_VALUE);
val = MMCIF_MISSING_VALUE;
} else {
val = (String) obj;
}
str.append(String.format("%-"+sizes[i]+"s ", addMmCifQuoting(val)));
} catch (IllegalAccessException e) {
logger.warn("Field {} is inaccessible", f.getName());
continue;
} catch (ClassCastException e) {
logger.warn("Could not cast value to String for field {}",f.getName());
continue;
}
}
str.append(newline);
return str.toString();
}
/**
* Adds quoting to a String according to the STAR format (mmCIF) rules
* @param val
* @return
*/
private static String addMmCifQuoting(String val) {
String newval;
if (val.contains("'")) {
// double quoting for strings containing single quotes (not strictly necessary but it's what the PDB usually does)
newval = "\""+val+"\"";
} else if (val.contains(" ")) {
// single quoting for stings containing spaces
newval = "'"+val+"'";
} else {
if (val.contains(" ") && val.contains("'")) {
// TODO deal with this case
logger.warn("Value contains both spaces and single quotes, won't format it: {}. CIF ouptut will likely be invalid.",val);
}
newval = val;
}
// TODO deal with all the other cases: e.g. multi-line quoting with ;;
return newval;
}
/**
* Converts a SpaceGroup object to a {@link Symmetry} object.
* @param sg
* @return
*/
public static Symmetry convertSpaceGroupToSymmetry(SpaceGroup sg) {
Symmetry sym = new Symmetry();
sym.setSpace_group_name_H_M(sg.getShortSymbol());
// TODO do we need to fill any of the other values?
return sym;
}
/**
* Converts a CrystalCell object to a {@link Cell} object.
* @param c
* @return
*/
public static Cell convertCrystalCellToCell(CrystalCell c) {
Cell cell = new Cell();
cell.setLength_a(String.format("%.3f",c.getA()));
cell.setLength_b(String.format("%.3f",c.getB()));
cell.setLength_c(String.format("%.3f",c.getC()));
cell.setAngle_alpha(String.format("%.3f",c.getAlpha()));
cell.setAngle_beta(String.format("%.3f",c.getBeta()));
cell.setAngle_gamma(String.format("%.3f",c.getGamma()));
return cell;
}
/**
* Converts an Atom object to an {@link AtomSite} object.
* @param a
* @param model
* @param chainId
* @param internalChainId
* @return
*/
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId) {
return convertAtomToAtomSite(a, model, chainId, internalChainId, a.getPDBserial());
}
/**
* Converts an Atom object to an {@link AtomSite} object.
* @param a
* @param model
* @param chainId
* @param internalChainId
* @param atomId the atom id to be written to AtomSite
* @return
*/
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId, int atomId) {
/*
ATOM 7 C CD . GLU A 1 24 ? -10.109 15.374 38.853 1.00 50.05 ? ? ? ? ? ? 24 GLU A CD 1
ATOM 8 O OE1 . GLU A 1 24 ? -9.659 14.764 37.849 1.00 49.80 ? ? ? ? ? ? 24 GLU A OE1 1
ATOM 9 O OE2 . GLU A 1 24 ? -11.259 15.171 39.310 1.00 50.51 ? ? ? ? ? ? 24 GLU A OE2 1
ATOM 10 N N . LEU A 1 25 ? -5.907 18.743 37.412 1.00 41.55 ? ? ? ? ? ? 25 LEU A N 1
ATOM 11 C CA . LEU A 1 25 ? -5.168 19.939 37.026 1.00 37.55 ? ? ? ? ? ? 25 LEU A CA 1
*/
Group g = a.getGroup();
String record ;
if ( g.getType().equals(GroupType.HETATM) ) {
record = "HETATM";
} else {
record = "ATOM";
}
String entityId = "0";
String labelSeqId = Integer.toString(g.getResidueNumber().getSeqNum());
if (g.getChain()!=null && g.getChain().getEntityInfo()!=null) {
entityId = Integer.toString(g.getChain().getEntityInfo().getMolId());
labelSeqId = Integer.toString(g.getChain().getEntityInfo().getAlignedResIndex(g, g.getChain()));
}
Character altLoc = a.getAltLoc() ;
String altLocStr = altLoc.toString();
if (altLoc==null || altLoc == ' ') {
altLocStr = MMCIF_DEFAULT_VALUE;
}
Element e = a.getElement();
String eString = e.toString().toUpperCase();
if ( e.equals(Element.R)) {
eString = "X";
}
String insCode = MMCIF_MISSING_VALUE;
if (g.getResidueNumber().getInsCode()!=null ) {
insCode = Integer.toString(g.getResidueNumber().getInsCode());
}
AtomSite atomSite = new AtomSite();
atomSite.setGroup_PDB(record);
atomSite.setId(Integer.toString(atomId));
atomSite.setType_symbol(eString);
atomSite.setLabel_atom_id(a.getName());
atomSite.setLabel_alt_id(altLocStr);
atomSite.setLabel_comp_id(g.getPDBName());
atomSite.setLabel_asym_id(internalChainId);
atomSite.setLabel_entity_id(entityId);
atomSite.setLabel_seq_id(labelSeqId);
atomSite.setPdbx_PDB_ins_code(insCode);
atomSite.setCartn_x(FileConvert.d3.format(a.getX()));
atomSite.setCartn_y(FileConvert.d3.format(a.getY()));
atomSite.setCartn_z(FileConvert.d3.format(a.getZ()));
atomSite.setOccupancy(FileConvert.d2.format(a.getOccupancy()));
atomSite.setB_iso_or_equiv(FileConvert.d2.format(a.getTempFactor()));
atomSite.setAuth_seq_id(Integer.toString(g.getResidueNumber().getSeqNum()));
atomSite.setAuth_comp_id(g.getPDBName());
atomSite.setAuth_asym_id(chainId);
atomSite.setAuth_atom_id(a.getName());
atomSite.setPdbx_PDB_model_num(Integer.toString(model));
return atomSite;
}
/**
* Converts a Group into a List of {@link AtomSite} objects
* @param g
* @param model
* @param chainId
* @param internalChainId
* @return
*/
private static List convertGroupToAtomSites(Group g, int model, String chainId, String internalChainId) {
List list = new ArrayList();
int groupsize = g.size();
for ( int atompos = 0 ; atompos < groupsize; atompos++) {
Atom a = null ;
a = g.getAtom(atompos);
if ( a == null)
continue ;
list.add(convertAtomToAtomSite(a, model, chainId, internalChainId));
}
if ( g.hasAltLoc()){
for (Group alt : g.getAltLocs() ) {
list.addAll(convertGroupToAtomSites(alt, model, chainId, internalChainId));
}
}
return list;
}
/**
* Converts a Chain into a List of {@link AtomSite} objects
* @param c
* @param model
* @param chainId
* @param internalChainId
* @return
*/
public static List convertChainToAtomSites(Chain c, int model, String chainId, String internalChainId) {
List list = new ArrayList();
if (c.getEntityInfo()==null) {
logger.warn("No Compound (entity) found for chain {}: entity_id will be set to 0, label_seq_id will be the same as auth_seq_id", c.getChainID());
}
for ( int h=0; h convertStructureToAtomSites(Structure s) {
List list = new ArrayList();
for (int m=0;m list) {
if (list.isEmpty()) throw new IllegalArgumentException("List of beans is empty!");
int[] sizes = new int [list.get(0).getClass().getDeclaredFields().length];
for (Object a:list) {
Class c = a.getClass();
int i = -1;
for (Field f : c.getDeclaredFields()) {
i++;
f.setAccessible(true);
try {
Object obj = f.get(a);
int length;
if (obj==null) {
length = MMCIF_MISSING_VALUE.length();
} else {
String val = (String) obj;
length = addMmCifQuoting(val).length();
}
if (length>sizes[i]) sizes[i] = length;
} catch (IllegalAccessException e) {
logger.warn("Field {} is inaccessible", f.getName());
continue;
} catch (ClassCastException e) {
logger.warn("Could not cast value to String for field {}",f.getName());
continue;
}
}
}
return sizes;
}
/**
* Finds the max length of the field strings corresponding to the given mmCIF bean.
* Useful for producing mmCIF single-record data that is aligned for all values.
* @param a
* @return
* @see #toMMCIF(String, Object)
*/
private static int getMaxFieldNameLength(Object a) {
int size = 0;
Class c = a.getClass();
for (Field f : c.getDeclaredFields()) {
f.setAccessible(true);
if (f.getName().length() > size) {
size = f.getName().length();
}
}
return size;
}
}
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