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changed from mmtf to pdb files
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@thsa
thsa committed Jul 5, 2024
1 parent be34882 commit 7681bb7
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Showing 2 changed files with 108 additions and 68 deletions.
2 changes: 1 addition & 1 deletion src/main/java/org/openmolecules/fx/viewer3d/V3DScene.java
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ private void initializeDragAndDrop() {
} );
}

private void showMessage(String msg) {
public void showMessage(String msg) {
Alert alert = new Alert(Alert.AlertType.INFORMATION);
alert.setTitle("Information");
alert.setHeaderText(null);
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174 changes: 107 additions & 67 deletions src/main/java/org/openmolecules/fx/viewerapp/StartOptions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,13 @@

package org.openmolecules.fx.viewerapp;

import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.IDCodeParser;
import com.actelion.research.chem.Molecule3D;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.*;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile;
import com.actelion.research.chem.io.pdb.parser.PDBFileParser;
import com.actelion.research.chem.io.pdb.parser.StructureAssembler;
import com.actelion.research.util.Platform;
import javafx.scene.control.ChoiceDialog;
import javafx.scene.paint.Color;
import javafx.scene.shape.MeshView;
import org.openmolecules.chem.conf.gen.ConformerGenerator;
Expand All @@ -36,6 +37,10 @@
import org.openmolecules.fx.viewer3d.V3DScene;
import org.openmolecules.pdb.MMTFParser;

import java.io.File;
import java.util.List;
import java.util.Map;

public class StartOptions {
// home path used when loading pdb file from disk assuming OS is either Linux or MacOSX
private static final String HOME_PATH = Platform.isLinux() ? "~/" : "~/Documents/";
Expand Down Expand Up @@ -300,13 +305,13 @@ public class StartOptions {
private static final double SURFACE_SATURATION = 0.15; // must be less than 1.0 - SURFACE_BRIGHTNESS

private int mode;
private String pdbEntryCode,mmtfFile;
private String pdbEntryCode,pdbFile;
private boolean cropLigand;

public StartOptions(int mode, String pdbEntryCode, String mmtfFile, boolean cropLigand) {
public StartOptions(int mode, String pdbEntryCode, String pdbFile, boolean cropLigand) {
this.mode = mode;
this.pdbEntryCode = pdbEntryCode;
this.mmtfFile = mmtfFile;
this.pdbFile = pdbFile;
this.cropLigand = cropLigand;
}

Expand Down Expand Up @@ -345,70 +350,92 @@ else if (mode == 5)

private void loadPDBEntry(V3DScene scene) {
try {
Molecule3D[] mol = null;
if (mmtfFile != null)
mol = MMTFParser.getStructureFromFile(mmtfFile, pdbEntryCode, MMTFParser.MODE_SPLIT_CHAINS);
else if (!pdbEntryCode.isEmpty())
mol = MMTFParser.getStructureFromName(pdbEntryCode, MMTFParser.MODE_SPLIT_CHAINS);
PDBFileParser parser = new PDBFileParser();
PDBCoordEntryFile entryFile = (pdbFile != null) ?
parser.parse(new File(pdbFile))
: (!pdbEntryCode.isEmpty()) ? parser.getFromPDB(pdbEntryCode) : null;

if (entryFile == null) {
scene.showMessage("Unexpectedly didn't get PDB entry.");
return;
}

if (mol != null) {
// mMoleculePanel.setShowStructure(false);
MMTFParser.centerMolecules(mol);

V3DMolecule ligand = null;
int ligandIndex = -2; // will be -1, if we have more than one potential ligands
for (int i=0; i<mol.length; i++)
if (mol[i].getAllBonds() != 0 && mol[i].getAllAtoms() <= 100)
ligandIndex = (ligandIndex == -2) ? i : -1;

int largeMoleculeCount = 0;
for (int i=0; i<mol.length; i++)
if (mol[i].getAllBonds() != 0 && mol[i].getAllAtoms() > 100)
largeMoleculeCount++;

Color[] surfaceColor = new Color[largeMoleculeCount];
double inc = 2.0 * Math.PI / largeMoleculeCount;
double shift = 2.0 * Math.PI / 3.0;
for (int i=0; i<largeMoleculeCount; i++) {
double start = inc * i;
surfaceColor[i] = new Color(SURFACE_BRIGHTNESS + SURFACE_SATURATION * Math.sin(start),
SURFACE_BRIGHTNESS + SURFACE_SATURATION * Math.sin(start+shift),
SURFACE_BRIGHTNESS + SURFACE_SATURATION * Math.sin(start+2*shift), 1.0);
Map<String, List<Molecule3D>> map = entryFile.extractMols(false);
List<Molecule3D> ligands = map.get(StructureAssembler.LIGAND_GROUP);
if (ligands == null || ligands.isEmpty()) {
map = entryFile.extractMols(true);
ligands = map.get(StructureAssembler.LIGAND_GROUP);
if (ligands != null && !ligands.isEmpty())
scene.showMessage("Only covalent ligand(s) were found and disconnected from the protein structure.");
}

List<Molecule3D> proteins = map.get(StructureAssembler.PROTEIN_GROUP);
if (proteins == null || proteins.isEmpty()) {
scene.showMessage("No proteins found in file.");
return;
}

Molecule3D ligand = null;

if (ligands != null && !ligands.isEmpty()) {
int index = -1;
if (ligands.size() == 1) {
index = 0;
}
V3DRotatableGroup complex = new V3DRotatableGroup(pdbEntryCode);
System.out.println(pdbEntryCode);
scene.addGroup(complex);
int largeMoleculeIndex = 0;
int id = V3DMolecule.getNextID();
for (int i=0; i<mol.length; i++) {

// millis = printDelay(millis);
// System.out.print("Creating V3DMolecule... ");

boolean isWater = (mol[i].getAllBonds() == 0);
boolean isLargeMolecule = (!isWater && mol[i].getAllAtoms() > 100);

V3DMolecule vm;
if (isWater)
vm = new V3DMolecule(mol[i], MoleculeArchitect.ConstructionMode.STICKS, MoleculeArchitect.HydrogenMode.ALL, id, V3DMolecule.MoleculeRole.SOLVENT,true);
else if (isLargeMolecule)
vm = new V3DMolecule(mol[i], MoleculeArchitect.ConstructionMode.WIRES, MoleculeArchitect.HYDROGEN_MODE_DEFAULT,
V3DMolecule.SurfaceMode.FILLED, SurfaceMesh.SURFACE_COLOR_DONORS_ACCEPTORS, surfaceColor[largeMoleculeIndex++], 0.5, V3DMolecule.getNextID(),V3DMolecule.MoleculeRole.MACROMOLECULE,true);
else
vm = new V3DMolecule(mol[i], MoleculeArchitect.ConstructionMode.BALL_AND_STICKS, MoleculeArchitect.HydrogenMode.ALL,id,V3DMolecule.MoleculeRole.LIGAND, true);
vm.setID(id);
if (i == ligandIndex)
ligand = vm;

// millis = printDelay(millis);
// System.out.print("adding molecule to scene... ");

scene.addMolecule(vm,complex);
// millis = printDelay(millis);
else {
String[] ligandName = new String[ligands.size()];
for (int i=0; i<ligands.size(); i++) {
String formula = new MolecularFormula(ligands.get(i)).getFormula();
ligandName[i] = (i + 1) + ": " + formula + "; " + (ligands.get(i).getName() == null ? "Unnamed" : ligands.get(i).getName());
}

ChoiceDialog<String> dialog = new ChoiceDialog<>(ligandName[0], ligandName);
dialog.titleProperty().set("Select one of multiple ligands:");
dialog.showAndWait();
String name = dialog.getSelectedItem();
if (name != null)
index = Integer.parseInt(name.substring(0, name.indexOf(':')))-1;
}

if (ligand != null && cropLigand) {
scene.crop(ligand, 10.0);
if ((index != -1))
ligand = ligands.get(index);
}

// mMoleculePanel.setShowStructure(false);
// MMTFParser.centerMolecules(mol);

Color[] surfaceColor = new Color[proteins.size()];
double inc = 2.0 * Math.PI / proteins.size();
double shift = 2.0 * Math.PI / 3.0;
for (int i=0; i<proteins.size(); i++) {
double start = inc * i;
surfaceColor[i] = new Color(SURFACE_BRIGHTNESS + SURFACE_SATURATION * Math.sin(start),
SURFACE_BRIGHTNESS + SURFACE_SATURATION * Math.sin(start+shift),
SURFACE_BRIGHTNESS + SURFACE_SATURATION * Math.sin(start+2*shift), 1.0);
}

V3DRotatableGroup complex = new V3DRotatableGroup(pdbEntryCode);
System.out.println(pdbEntryCode);
scene.addGroup(complex);

for (int i=0; i<proteins.size(); i++) {
V3DMolecule vm = new V3DMolecule(proteins.get(i), MoleculeArchitect.ConstructionMode.WIRES, MoleculeArchitect.HYDROGEN_MODE_DEFAULT,
V3DMolecule.SurfaceMode.FILLED, SurfaceMesh.SURFACE_COLOR_DONORS_ACCEPTORS, surfaceColor[i], 0.5, V3DMolecule.getNextID(), V3DMolecule.MoleculeRole.MACROMOLECULE, true);
scene.addMolecule(vm, complex);
}

List<Molecule3D> solvents = map.get(StructureAssembler.SOLVENT_GROUP);
for (Molecule3D mol : solvents) {
V3DMolecule vm = new V3DMolecule(mol, MoleculeArchitect.ConstructionMode.STICKS, MoleculeArchitect.HydrogenMode.ALL, V3DMolecule.getNextID(), V3DMolecule.MoleculeRole.SOLVENT,true);
scene.addMolecule(vm, complex);
}

if (ligand != null) {
V3DMolecule vm = new V3DMolecule(ligand, MoleculeArchitect.ConstructionMode.BALL_AND_STICKS, MoleculeArchitect.HydrogenMode.ALL,V3DMolecule.getNextID(),V3DMolecule.MoleculeRole.LIGAND, true);
scene.addMolecule(vm, complex);

if (cropLigand) {
scene.crop(vm, 10.0);
scene.optimizeView();
}
}
Expand All @@ -417,6 +444,19 @@ else if (isLargeMolecule)
}
}

private Map<String, List<Molecule3D>> addProteinAndLigand(PDBCoordEntryFile entryFile, V3DScene scene) {
Map<String, List<Molecule3D>> map = entryFile.extractMols(false);
List<Molecule3D> ligands = map.get(StructureAssembler.LIGAND_GROUP);
if (ligands == null || ligands.isEmpty()) {
map = entryFile.extractMols(true);
ligands = map.get(StructureAssembler.LIGAND_GROUP);
if (ligands != null && !ligands.isEmpty())
scene.showMessage("Only covalent ligand(s) were found and disconnected from the protein structure.");
}

return map;
}

private void testMolecules(V3DScene scene) {
for (int i = 0; i < TEST_POSITIONS_13.length; i++) {
double[] coord = TEST_POSITIONS_13[i];
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