-
Notifications
You must be signed in to change notification settings - Fork 154
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Correct parsing and building of reaction SMARTS queries. Relatively s…
…imple adaption to existing parser.
- Loading branch information
Showing
5 changed files
with
164 additions
and
10 deletions.
There are no files selected for viewing
65 changes: 65 additions & 0 deletions
65
tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ReactionRole.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,65 @@ | ||
/* | ||
* Copyright (c) 2016 John May <jwmay@users.sf.net> | ||
* | ||
* Contact: cdk-devel@lists.sourceforge.net | ||
* | ||
* This program is free software; you can redistribute it and/or modify it | ||
* under the terms of the GNU Lesser General Public License as published by | ||
* the Free Software Foundation; either version 2.1 of the License, or (at | ||
* your option) any later version. All we ask is that proper credit is given | ||
* for our work, which includes - but is not limited to - adding the above | ||
* copyright notice to the beginning of your source code files, and to any | ||
* copyright notice that you may distribute with programs based on this work. | ||
* | ||
* This program 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 Lesser General Public | ||
* License for more details. | ||
* | ||
* You should have received a copy of the GNU Lesser General Public License | ||
* along with this program; if not, write to the Free Software | ||
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U | ||
*/ | ||
package org.openscience.cdk.isomorphism.matchers.smarts; | ||
|
||
import org.openscience.cdk.interfaces.IAtom; | ||
import org.openscience.cdk.interfaces.IChemObjectBuilder; | ||
|
||
/** | ||
* Matches atoms with a particular role in a reaction. | ||
*/ | ||
public class ReactionRole extends SMARTSAtom { | ||
|
||
public static final int ROLE_REACTANT = 0x1; | ||
public static final int ROLE_AGENT = 0x2; | ||
public static final int ROLE_PRODUCT = 0x4; | ||
public static final int ROLE_ANY = ROLE_REACTANT | ROLE_PRODUCT | ROLE_AGENT; | ||
|
||
private final int role; | ||
|
||
public final static ReactionRole RoleReactant = new ReactionRole(null, ROLE_REACTANT); | ||
public final static ReactionRole RoleAgent = new ReactionRole(null, ROLE_AGENT); | ||
public final static ReactionRole RoleProduct = new ReactionRole(null, ROLE_PRODUCT); | ||
|
||
public ReactionRole(IChemObjectBuilder builder, int role) { | ||
super(builder); | ||
this.role = role; | ||
} | ||
|
||
@Override | ||
public boolean matches(IAtom atom) { | ||
return true; // TODO | ||
} | ||
|
||
@Override | ||
public String toString() { | ||
StringBuilder sb = new StringBuilder(); | ||
if ((role & ROLE_REACTANT) != 0) | ||
sb.append("Reactant"); | ||
if ((role & ROLE_AGENT) != 0) | ||
sb.append("Agent"); | ||
if ((role & ROLE_PRODUCT) != 0) | ||
sb.append("Product"); | ||
return "ReactionRole(" + sb.toString() + ")"; | ||
} | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters