291 lines
13 KiB
C++
291 lines
13 KiB
C++
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/**************************************************************************************/
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/* */
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/* Visualization Library */
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/* http://visualizationlibrary.org */
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/* */
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/* Copyright (c) 2005-2020, Michele Bosi */
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/* All rights reserved. */
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/* */
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/* Redistribution and use in source and binary forms, with or without modification, */
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/* are permitted provided that the following conditions are met: */
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/* */
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/* - Redistributions of source code must retain the above copyright notice, this */
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/* list of conditions and the following disclaimer. */
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/* */
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/* - Redistributions in binary form must reproduce the above copyright notice, this */
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/* list of conditions and the following disclaimer in the documentation and/or */
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/* other materials provided with the distribution. */
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/* */
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/* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND */
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/* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED */
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/* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE */
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/* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR */
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/* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES */
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/* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; */
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/* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON */
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/* ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT */
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/* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS */
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/* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */
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/* */
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/**************************************************************************************/
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#ifndef Molecule_INCLUDE_ONCE
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#define Molecule_INCLUDE_ONCE
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#include <vlMolecule/link_config.hpp>
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#include <vlMolecule/Atom.hpp>
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#include <vlMolecule/Bond.hpp>
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#include <vlGraphics/Geometry.hpp>
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#include <vlGraphics/Actor.hpp>
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#include <vlGraphics/ActorTree.hpp>
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#include <vlGraphics/Text.hpp>
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#include <vlCore/String.hpp>
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#include <vlCore/KeyValues.hpp>
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namespace vl
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{
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//! Defines the main molecule styles.
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typedef enum
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{
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MS_AtomsOnly,
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MS_BallAndStick,
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MS_Sticks,
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MS_Wireframe,
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} EMoleculeStyle;
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/** The Molecule class is used to manage and render 3D molecular structures.
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* \sa
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* - \ref pagGuideMolecule "Molecule Visualization Tutorial"
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* - Atom
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* - Bond
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*
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* <img src="../pics/pagGuideMolecule.png">
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*/
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class VLMOLECULE_EXPORT Molecule: public Object
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{
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VL_INSTRUMENT_CLASS(vl::Molecule, Object)
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public:
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Molecule();
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~Molecule() { reset(); }
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Molecule(const Molecule& other): Object(other) { operator=(other); }
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Molecule& operator=(const Molecule& other);
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void reset();
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void setMoleculeName(const String& name) { mMoleculeName = name; }
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const String moleculeName() const { return mMoleculeName; }
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unsigned int id() const { return mId; }
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void setId(unsigned int id) { mId = id; }
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KeyValues* tags() { return mTags.get(); }
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const KeyValues* tags() const { return mTags.get(); }
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const std::vector< ref<Atom> >& atoms() const { return mAtoms; }
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std::vector< ref<Atom> >& atoms() { return mAtoms; }
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int atomCount() const { return (int)mAtoms.size(); }
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const Atom* atom(int index) const;
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Atom* atom(int index);
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void addAtom(Atom* atom);
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void eraseAtom(Atom*atom);
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void eraseAtom(int index);
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void eraseAllAtoms();
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const std::vector< ref<Bond> >& bonds() const { return mBonds; }
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std::vector< ref<Bond> >& bonds() { return mBonds; }
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int bondCount() const { return (int)mBonds.size(); }
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const Bond* bond(int index) const;
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Bond* bond(int index);
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const Bond* bond(Atom* a1, Atom* a2) const;
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Bond* bond(Atom* a1, Atom* a2);
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void addBond(Bond* bond);
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Bond* addBond(Atom* a1, Atom* a2);
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void eraseBond(Bond*bond);
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void eraseBond(int bond);
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void eraseBond(Atom* a1, Atom* a2);
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void eraseBond(int a1, int a2);
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void eraseAllBonds();
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void computeAtomAdjacency();
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void incidentBonds(std::vector<Bond*>& inc_bonds, Atom* atom);
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//! Returns the i-th cycle
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const std::vector< ref<Atom> >& cycle(int i) const { return mCycles[i]; }
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//! Returns the i-th cycle
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std::vector< ref<Atom> >& cycle(int i) { return mCycles[i]; }
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//! Returns the list of cycles
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const std::vector< std::vector< ref<Atom> > >& cycles() const { return mCycles; }
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//! Returns the list of cycles
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std::vector< std::vector< ref<Atom> > >& cycles() { return mCycles; }
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/** Generates the geometry representing the current molecule, atom and bond settings.
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* The actors, geometry, and transforms generated by this function can be found in actorTree() and transformTree().
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*/
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void prepareForRendering();
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//! The ActorTree node containing the Actor[s] representing the molecule.
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const ActorTree* actorTree() const { return mActorTree.get(); }
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//! The ActorTree node containing the Actor[s] representing the molecule.
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ActorTree* actorTree() { return mActorTree.get(); }
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//! Sets all the atoms' color to their CPK color.
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void setCPKAtomColors();
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//! Sets all the atoms' color to the specified color.
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void setAtomColors(const fvec4& color);
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//! Sets all the atoms' radii to their calculated atom radii
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void setCalculatedAtomRadii(float percentage=1.0f);
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//! Sets all the atoms' radii to their empirical atom radii
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void setEmpiricalAtomRadii(float percentage=1.0f);
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//! Sets all the atoms' radii to their covalent atom radii
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void setCovalentAtomRadii(float percentage=1.0f);
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//! Sets all the atoms' radii to their van der Waals atom radii
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void setVanDerWaalsAtomRadii(float percentage=1.0f);
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//! Sets all the atoms' radii to the specified one.
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void setAtomRadii(float radius);
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//! Sets all the bonds' radii to the specified one.
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void setBondRadii(float radius);
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void setAtomTypeVisible(EAtomType type, bool visible);
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//! The rendering style of the molecule
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void setMoleculeStyle(EMoleculeStyle style) { mMoleculeStyle = style; }
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//! The rendering style of the molecule
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EMoleculeStyle moleculeStyle() const { return mMoleculeStyle; }
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//! Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2)
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void setAtomDetail(int detail) { mAtomDetail = detail; }
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//! Geometrical detail used to render the atoms, usually between 0 and 3 (default is 2)
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int atomDetail() const { return mAtomDetail; }
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//! Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20)
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void setBondDetail(int detail) { mBondDetail = detail; }
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//! Geometrical detail used to render the bonds, usually between 5 and 50 (default is 20)
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int bondDetail() const { return mBondDetail; }
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float ringOffset() const { return mRingOffset; }
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void setRingOffset(float offset) { mRingOffset = offset; }
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void setAromaticBondsColor(const fvec4& color);
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void setAromaticRingColor(const fvec4& color) { mAromaticRingColor = color; }
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const fvec4& aromaticRingColor() const { return mAromaticRingColor; }
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float lineWidth() const { return mLineWidth; }
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bool smoothLines() const { return mSmoothLines; }
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void setLineWidth(float w) { mLineWidth = w; }
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void setSmoothLines(bool smooth) { mSmoothLines = smooth; }
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//! The transform tree used by the generated bonds, atoms and labels
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Transform* transformTree() { return mTransformTree.get(); }
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//! The transform tree used by the generated bonds, atoms and labels
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const Transform* transformTree() const { return mTransformTree.get(); }
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//! The text settings to be used to render the atom labels
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const Text* atomLabelTemplate() const { return mAtomLabelTemplate.get(); }
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//! The text settings to be used to render the atom labels
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Text* atomLabelTemplate() { return mAtomLabelTemplate.get(); }
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//! Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().
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void setShowAtomNames(bool show) { mShowAtomNames = show; }
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//! Globally defines whether the atom names should be rendered or not. See also Atom::setShowAtomName().
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bool showAtomNames() const{ return mShowAtomNames; }
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//! The Effect used to render the atom labels
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const Effect* atomLabelEffect() const { return mAtomLabelEffect.get(); }
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//! The Effect used to render the atom labels
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Effect* atomLabelEffect() { return mAtomLabelEffect.get(); }
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//! If enabled the atomToActorMap() and bondToActorMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
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void setMoleculeToActorMapEnabled(bool enabled) { mMoleculeToActorMapEnabled = enabled; }
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//! If enabled the atomToActorMap() and bondToActorMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
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bool isMoleculeToActorMapEnabled() const { return mMoleculeToActorMapEnabled; }
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//! If enabled the actorToAtomMap() and actorToBondMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
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void setActorToMoleculeMapEnabled(bool enabled) { mActorToMoleculeMapEnabled = enabled; }
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//! If enabled the actorToAtomMap() and actorToBondMap() maps will be compiled next time the molecule's geometry is regenerated (except for wireframe style).
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bool isActorToMoleculeMapEnabled() const { return mActorToMoleculeMapEnabled; }
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//! Maps an Atom to it's corresponding Actor
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const std::map< ref<Atom>, ref<Actor> >& atomToActorMap() const { return mAtomToActorMap; }
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//! Maps an Actor to it's corresponding Atom
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const std::map< ref<Actor>, ref<Atom> >& actorToAtomMap() const { return mActorToAtomMap; }
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//! Maps a Bond to it's corresponding Actor
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const std::map< ref<Bond>, ref<Actor> >& bondToActorMap() const { return mBondToActorMap; }
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//! Maps an Actor to it's corresponding Bond
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const std::map< ref<Actor>, ref<Bond> >& actorToBondMap() const { return mActorToBondMap; }
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//! Maps an Atom to it's corresponding Actor
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std::map< ref<Atom>, ref<Actor> >& atomToActorMap() { return mAtomToActorMap; }
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//! Maps an Actor to it's corresponding Atom
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std::map< ref<Actor>, ref<Atom> >& actorToAtomMap() { return mActorToAtomMap; }
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//! Maps a Bond to it's corresponding Actor
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std::map< ref<Bond>, ref<Actor> >& bondToActorMap() { return mBondToActorMap; }
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//! Maps an Actor to it's corresponding Bond
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std::map< ref<Actor>, ref<Bond> >& actorToBondMap() { return mActorToBondMap; }
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protected:
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void prepareAtomInsert(int bonus=100)
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{
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if (atoms().size() == atoms().capacity())
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atoms().reserve(atoms().size() + bonus);
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}
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void prepareBondInsert(int bonus=100)
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{
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if (bonds().size() == bonds().capacity())
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bonds().reserve(bonds().size() + bonus);
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}
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void wireframeStyle();
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void atomsStyle();
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void ballAndStickStyle();
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void sticksStyle();
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void generateRings();
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void generateAtomLabels();
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void generateAtomLabel(const Atom* atom, Transform* tr);
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protected:
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fvec4 mAromaticRingColor;
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ref<ActorTree> mActorTree;
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ref<Transform> mTransformTree;
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std::vector< ref<Atom> > mAtoms;
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std::vector< ref<Bond> > mBonds;
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std::vector< std::vector< ref<Atom> > > mCycles;
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std::map< ref<Atom>, ref<Actor> > mAtomToActorMap;
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std::map< ref<Actor>, ref<Atom> > mActorToAtomMap;
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std::map< ref<Bond>, ref<Actor> > mBondToActorMap;
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std::map< ref<Actor>, ref<Bond> > mActorToBondMap;
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String mMoleculeName;
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ref<KeyValues> mTags;
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ref<Text> mAtomLabelTemplate;
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ref<Effect> mAtomLabelEffect;
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unsigned int mId;
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EMoleculeStyle mMoleculeStyle;
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int mAtomDetail;
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int mBondDetail;
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float mRingOffset;
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float mLineWidth;
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bool mSmoothLines;
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bool mShowAtomNames;
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bool mMoleculeToActorMapEnabled;
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bool mActorToMoleculeMapEnabled;
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};
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//! Loads a Tripos MOL2 file.
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//! The Molecule tags will contain the following key/value pairs:
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//! - \p "MultiMol2Index": the index (0-based) of the structure in a multi MOL2 file.
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//! - \p "FilePath": the full path of the file that contained the structure.
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VLMOLECULE_EXPORT bool loadMOL2(const String& path, std::vector< ref<Molecule> >& structures);
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//! Loads a Tripos MOL2 file.
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//! The Molecule tags will contain the following key/value pairs:
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//! - \p "MultiMol2Index": the index (0-based) of the structure in a multi MOL2 file.
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//! - \p "FilePath": the full path of the file that contained the structure.
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VLMOLECULE_EXPORT bool loadMOL2(VirtualFile* vfile, std::vector< ref<Molecule> >& structures);
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}
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#endif
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