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filippis |
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package tools; |
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import java.sql.*; |
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import java.io.*; |
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import java.util.*; |
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import java.text.*; |
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/** |
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* Package: tools |
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* Class: PyMol |
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* Author: Ioannis Filippis, filippis@molgen.mpg.de |
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* Date: 20/03/2006 |
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* |
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* This class serves as a simple PyMol API. Most methods send PyMol commands |
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* to the PrintWriter taken by the constructor, while others return pymol |
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* selection strings. There is also the possibility to send the atomic |
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* coordinates of a specific model of a macromolecule directly from msdsd |
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* and load them on-the-fly. |
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* |
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* Notes: |
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* - This is not a full PyMol API. Existing methods wrap basic pymol commands |
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* in a simple, rather stupid way to facilitate contact graph visualization. |
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* |
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* Changelog: |
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* 20/03/06 first created by IF |
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*/ |
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public class PyMol { |
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// Out: the PrintWriter where PyMol commands are sent to |
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// attrs: a HashMap with keys the PyMol state variables allowed to be set |
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// by the set class. Values are integers (could be used in a "switch") |
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// DF: used to format decimal numbers so commands issued are readable |
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// objectNameQuotes: used to enable (disable) the use of double quotes for |
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// strings in PyMol commands (check list related methods) |
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private PrintWriter Out = null; |
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private HashMap<String, Integer> attrs = new HashMap<String, Integer>(); |
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private DecimalFormat DF = new DecimalFormat("#0.000"); |
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private boolean objectNameQuotes = true; |
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// constructor |
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public PyMol(PrintWriter out) { |
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this.Out = out; |
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attrs.put("sphere_transparency", new Integer(1)); |
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attrs.put("sphere_scale", new Integer(2)); |
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attrs.put("dash_gap", new Integer(3)); |
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attrs.put("dash_width", new Integer(4)); |
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attrs.put("transparancy", new Integer(5)); |
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} |
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/** |
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* sends the atom lines of a model (modelId) of a biological unit (assemblyId) of a protein |
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* (accessionCode) directly from msdsd. In this way, the structure is loaded wihout temporary |
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* pdb files. The structure object is named using the pattern accessionCode_assemblyId_modelId. |
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* |
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* Notes: |
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* - A connection file is needed to connect to msdsd |
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* - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used |
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* in the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol |
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* selections (all methods take care of that based on the boolean parameter msdsd) |
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* - There are two versions of sendAtomLines. One that takes the atomic coordinates from the |
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* partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster), |
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* while the other uses the merged table (really slow - should be avoided) |
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* - In general, the method is slow. The use of temporary files should be preferred. Have a look |
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* at Msdsd2Pdb class. |
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*/ |
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public void sendAtomLines(String accessionCode, int assemblyId, int modelId, int atomDataTblNum, String connFile) { |
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String query = "SELECT CONCAT("+ |
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"RPAD(\"ATOM\", 6, \" \"), "+ |
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"LPAD(serial, 5, \" \"), "+ |
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"\" \", "+ |
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"LPAD(chem_atom_name, 4, \" \"), "+ |
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"IF(alt_code IS NULL, \" \", alt_code), "+ |
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"code_3_letter, "+ |
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"\" \", "+ |
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"IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+ |
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"LPAD(residue_serial, 4, \" \"), "+ |
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"IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+ |
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"REPEAT(\" \", 3), "+ |
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"LPAD(x, 8, \" \"), "+ |
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"LPAD(y, 8, \" \"), "+ |
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"LPAD(z, 8, \" \"), "+ |
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"LPAD(occupancy, 6, \" \"), "+ |
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"REPEAT(\" \", 6), "+ |
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"REPEAT(\" \", 6), "+ |
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"RPAD(chain_code, 4, \" \") "+ |
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") AS atom_lines FROM msdsd.atom_data_"+atomDataTblNum+" WHERE "+ |
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"(assembly_id = "+assemblyId+") AND "+ |
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"(model_id = "+modelId+") AND "+ |
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"((alt_code = \"A\") OR (alt_code IS NULL)) AND "+ |
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"(pdb_group = \"A\") "+ |
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"ORDER BY chain_code, residue_serial, serial;"; |
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mySQLConnect SQLC = new mySQLConnect(); |
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SQLC.readConnectionFile(connFile); |
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Connection conn = SQLC.openConnection(); |
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Statement S; |
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ResultSet R; |
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Out.print("cmd.read_pdbstr(\"\"\""); |
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try { |
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S = conn.createStatement(); |
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R = S.executeQuery(query); |
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while (R.next()) { |
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Out.println(R.getString(1)+"\\"); |
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} |
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R.close(); |
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S.close(); |
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} // end try |
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catch (SQLException E) { |
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System.out.println("SQLException: " + E.getMessage()); |
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System.out.println("SQLState: " + E.getSQLState()); |
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System.out.println("VendorError: " + E.getErrorCode()); |
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} // end catch |
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SQLC.closeConnection(conn); |
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Out.println("END\"\"\", \""+accessionCode+"_"+assemblyId+"_"+modelId+"\")"); |
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} |
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/** |
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* sends the atom lines of a model (modelId) of a biological unit (assemblyId) of a protein |
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* (accessionCode) directly from msdsd. In this way, the structure is loaded wihout temporary |
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* pdb files. The structure object is named using the pattern accessionCode_assemblyId_modelId. |
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* |
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* Notes: |
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* - A connection file is needed to connect to msdsd |
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* - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used |
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* in the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol |
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* selections (all methods take care of that based on the boolean parameter msdsd) |
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* - There are two versions of sendAtomLines. One that takes the atomic coordinates from the |
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* partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster), |
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* while the other uses the merged table (really slow - should be avoided) |
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* - In general, the method is slow. The use of temporary files should be preferred. Have a look |
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* at Msdsd2Pdb class. |
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*/ |
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public void sendAtomLines(String accessionCode, int assemblyId, int modelId, String connFile) { |
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String query = "SELECT CONCAT("+ |
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"RPAD(\"ATOM\", 6, \" \"), "+ |
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"LPAD(serial, 5, \" \"), "+ |
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"\" \", "+ |
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"LPAD(chem_atom_name, 4, \" \"), "+ |
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"IF(alt_code IS NULL, \" \", alt_code), "+ |
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"code_3_letter, "+ |
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"\" \", "+ |
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"IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+ |
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"LPAD(residue_serial, 4, \" \"), "+ |
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"IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+ |
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"REPEAT(\" \", 3), "+ |
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"LPAD(x, 8, \" \"), "+ |
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"LPAD(y, 8, \" \"), "+ |
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"LPAD(z, 8, \" \"), "+ |
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"LPAD(occupancy, 6, \" \"), "+ |
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"REPEAT(\" \", 6), "+ |
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"REPEAT(\" \", 6), "+ |
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"RPAD(chain_code, 4, \" \") "+ |
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") AS atom_lines FROM msdsd.atom_data WHERE "+ |
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"(assembly_id = "+assemblyId+") AND "+ |
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"(model_id = "+modelId+") AND "+ |
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"((alt_code = \"A\") OR (alt_code IS NULL)) AND "+ |
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"(pdb_group = \"A\") "+ |
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"ORDER BY chain_code, residue_serial, serial;"; |
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mySQLConnect SQLC = new mySQLConnect(); |
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SQLC.readConnectionFile(connFile); |
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Connection conn = SQLC.openConnection(); |
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Statement S; |
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ResultSet R; |
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Out.print("cmd.read_pdbstr(\"\"\""); |
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try { |
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S = conn.createStatement(); |
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R = S.executeQuery(query); |
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while (R.next()) { |
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Out.println(R.getString(1)+"\\"); |
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} |
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R.close(); |
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S.close(); |
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} // end try |
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catch (SQLException E) { |
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System.out.println("SQLException: " + E.getMessage()); |
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System.out.println("SQLState: " + E.getSQLState()); |
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System.out.println("VendorError: " + E.getErrorCode()); |
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} // end catch |
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SQLC.closeConnection(conn); |
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Out.println("END\"\"\", \""+accessionCode+"_"+assemblyId+"_"+modelId+"\")"); |
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} |
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/** |
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* loads a pdb file |
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* |
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* Notes: |
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* - There are two versions. One of them loads the pdb file specified by its name and the directory path, while |
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* the other just uses the filename. |
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* - Pdb file is expected to have the extension ".pdb". |
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* - The structure object is named using the accession code (extension ".pdb" is trimmed) |
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*/ |
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public String loadPDB(String pdbFileName, String pdbDir) { |
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Out.println("cmd.load(\""+pdbDir+"/"+pdbFileName+"\", \""+pdbFileName.substring(0, pdbFileName.length()-4)+"\", 1)"); |
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return (pdbFileName.substring(0, pdbFileName.length()-4)); |
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} |
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/** |
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* loads a pdb file |
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* |
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* Notes: |
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* - There are two versions. One of them loads the pdb file specified by its name and the directory path, while |
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* the other just uses the filename. |
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* - Pdb file is expected to have the extension ".pdb". |
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* - The structure object is named using the accession code (extension ".pdb" is trimmed) |
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*/ |
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public String loadPDB(String pdbFileName) { |
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Out.println("cmd.load(\""+pdbFileName+"\", \""+pdbFileName.substring(0, pdbFileName.length()-4)+"\", 1)"); |
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return (pdbFileName.substring(0, pdbFileName.length()-4)); |
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} |
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/** |
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* adds a node as a sphere centered on the Ca of a residue |
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* |
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* Notes: |
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* - The node object is named n.cid.num (e.g. n.A.15 is the 15th residue-node in chain A) |
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* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
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* segi is used instead of chain |
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*/ |
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public String addNode(String cid, int num, boolean msdsd) { |
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String nodeName = "n."+cid+"."+num; |
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String nodeSel = selectNode(cid, num, msdsd, true); |
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Out.println("cmd.create(\""+nodeName+"\", \""+nodeSel+"\""); |
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Out.println("cmd.show(\"sphere\", \""+nodeName+"\""); |
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return nodeName; |
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} |
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/** |
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* adds an edge as a distance object between the Ca's of 2 residues |
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* |
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* Notes: |
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* - The edge object is named e.i_cid.i_num.j_cid.j_num (e.g. e.A.1.B.10 is the edge |
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* between the 1st residue-node in chain A and the 10th residue in chain B) |
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* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
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* segi is used instead of chain |
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*/ |
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public String addEdge(String i_cid, int i_num, String j_cid, int j_num, boolean msdsd) { |
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String edgeName = "e."+i_cid+"."+i_num+"."+j_cid+"."+j_num; |
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String iNodeSel = selectNode(i_cid, i_num, msdsd, true); |
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String jNodeSel = selectNode(j_cid, j_num, msdsd, true); |
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Out.println("cmd.distance(\""+edgeName+"\", \""+iNodeSel+"\", \""+jNodeSel+"\""); |
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Out.println("cmd.hide(\"labels\")"); |
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return edgeName; |
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} |
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/** |
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* adds an edge as a sausage Compiled Graphic Object (cgo) between the Ca's of 2 residues |
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* |
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* Notes: |
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* - The edge object is named e.i_cid.i_num.j_cid.j_num (e.g. e.A.1.B.10 is the edge |
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* between the 1st residue-node in chain A and the 10th residue in chain B) |
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* - If the graph is directed, then only half of the user-formatted sausage will be |
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* drawn towards the target node and the rest will be drawn as a thin sausage. |
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* - rgb(color) and half_rgb(half_color) define the color of the two parts of the edge (if directed). |
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* There are two versions of addCgoEdge, one with string (color) and one with array of doubles |
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* (rgb) parameters. |
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* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
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* segi is used instead of chain. |
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*/ |
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public String addCgoEdge(String i_cid, int i_num, String j_cid, int j_num, double[] rgb, double dashGap, double dashLength, double dashRadius, boolean directed, double[] half_rgb, boolean msdsd) { |
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String edgeName = "e."+i_cid+"."+i_num+"."+j_cid+"."+j_num; |
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String iNodeSel = selectNode(i_cid, i_num, msdsd, true); |
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String jNodeSel = selectNode(j_cid, j_num, msdsd, true); |
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Out.println("edge name="+edgeName+", i_node="+iNodeSel+", j_node="+jNodeSel+", r="+rgb[0]+", g="+rgb[1]+", b="+rgb[2]+", dg="+dashGap+", dl="+dashLength+", dr="+dashRadius+", dir="+(directed?1:0)+", dir_r="+half_rgb[0]+", dir_g="+half_rgb[1]+", dir_b="+half_rgb[2]+""); |
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return edgeName; |
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} |
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/** |
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* adds an edge as a sausage Compiled Graphic Object (cgo) between the Ca's of 2 residues |
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* |
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* Notes: |
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* - The edge object is named e.i_cid.i_num.j_cid.j_num (e.g. e.A.1.B.10 is the edge |
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* between the 1st residue-node in chain A and the 10th residue in chain B) |
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* - If the graph is directed, then only half of the user-formatted sausage will be |
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* drawn towards the target node and the rest will be drawn as a thin sausage. |
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* - rgb(color) and half_rgb(half_color) define the color of the two parts of the edge (if directed). |
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* There are two versions of addCgoEdge, one with string (color) and one with array of doubles |
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* (rgb) parameters. |
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* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
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* segi is used instead of chain. |
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* - Have a look at the /project/StruPPi/PyMolAll/pymol/scripts/ioannis/graph.py with the |
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* implementation of the edge command |
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*/ |
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public String addCgoEdge(String i_cid, int i_num, String j_cid, int j_num, String color, double dashGap, double dashLength, double dashRadius, boolean directed, String half_color, boolean msdsd) { |
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|
|
String edgeName = "e."+i_cid+"."+i_num+"."+j_cid+"."+j_num; |
| 322 |
|
|
String iNodeSel = selectNode(i_cid, i_num, msdsd, true); |
| 323 |
|
|
String jNodeSel = selectNode(j_cid, j_num, msdsd, true); |
| 324 |
|
|
|
| 325 |
|
|
Out.println("edge name="+edgeName+", i_node="+iNodeSel+", j_node="+jNodeSel+", color="+color+", dg="+dashGap+", dl="+dashLength+", dr="+dashRadius+", dir="+(directed?1:0)+", dir_color="+color+""); |
| 326 |
|
|
|
| 327 |
|
|
return edgeName; |
| 328 |
|
|
|
| 329 |
|
|
} |
| 330 |
|
|
|
| 331 |
|
|
/** |
| 332 |
|
|
* deletes an object or selection |
| 333 |
|
|
*/ |
| 334 |
|
|
public void delete(String objectName) { |
| 335 |
|
|
|
| 336 |
|
|
Out.println("cmd.delete("+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 337 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 338 |
|
|
|
| 339 |
|
|
} |
| 340 |
|
|
|
| 341 |
|
|
/** |
| 342 |
|
|
* deletes a node |
| 343 |
|
|
*/ |
| 344 |
|
|
public void delNode(String cid, int num) { |
| 345 |
|
|
|
| 346 |
|
|
String nodeName = "\"n."+cid+"."+num+"\""; |
| 347 |
|
|
Out.println("cmd.delete("+nodeName+")"); |
| 348 |
|
|
|
| 349 |
|
|
} |
| 350 |
|
|
|
| 351 |
|
|
/** |
| 352 |
|
|
* deletes an edge |
| 353 |
|
|
*/ |
| 354 |
|
|
public void delEdge(String i_cid, int i_num, String j_cid, int j_num) { |
| 355 |
|
|
|
| 356 |
|
|
String edgeName = "\"e."+i_cid+"."+i_num+"."+j_cid+"."+j_num+"\""; |
| 357 |
|
|
Out.println("cmd.delete("+edgeName+")"); |
| 358 |
|
|
|
| 359 |
|
|
} |
| 360 |
|
|
|
| 361 |
|
|
/** |
| 362 |
|
|
* turns on atom/bond representation specified by what for an object or selection |
| 363 |
|
|
*/ |
| 364 |
|
|
public void showWhat(String what, String objectName) { |
| 365 |
|
|
|
| 366 |
|
|
Out.println("cmd.show(\""+what+"\", "+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 367 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 368 |
|
|
|
| 369 |
|
|
} |
| 370 |
|
|
|
| 371 |
|
|
/** |
| 372 |
|
|
* turns on atom/bond representation for all bonds for an object or selection |
| 373 |
|
|
*/ |
| 374 |
|
|
public void show(String objectName) { |
| 375 |
|
|
|
| 376 |
|
|
Out.println("cmd.show(\"everything\", "+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 377 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 378 |
|
|
|
| 379 |
|
|
} |
| 380 |
|
|
|
| 381 |
|
|
|
| 382 |
|
|
/** |
| 383 |
|
|
* turns on node representation |
| 384 |
|
|
*/ |
| 385 |
|
|
public void showNode(String cid, int num) { |
| 386 |
|
|
|
| 387 |
|
|
String nodeName = "n."+cid+"."+num; |
| 388 |
|
|
Out.println("cmd.show(\"sphere\", \""+nodeName+"\")"); |
| 389 |
|
|
|
| 390 |
|
|
} |
| 391 |
|
|
|
| 392 |
|
|
/** |
| 393 |
|
|
* turns on edge representation |
| 394 |
|
|
*/ |
| 395 |
|
|
public void showEdge(String i_cid, int i_num, String j_cid, int j_num) { |
| 396 |
|
|
|
| 397 |
|
|
String edgeName = "e."+i_cid+"."+i_num+"."+j_cid+"."+j_num; |
| 398 |
|
|
Out.println("cmd.show(\"everything\", \""+edgeName+"\""); |
| 399 |
|
|
|
| 400 |
|
|
} |
| 401 |
|
|
|
| 402 |
|
|
/** |
| 403 |
|
|
* turns off atom/bond representation specified by what for an object or selection |
| 404 |
|
|
*/ |
| 405 |
|
|
public void hideWhat(String what, String objectName) { |
| 406 |
|
|
|
| 407 |
|
|
Out.println("cmd.hide(\""+what+"\", "+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 408 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 409 |
|
|
|
| 410 |
|
|
} |
| 411 |
|
|
|
| 412 |
|
|
/** |
| 413 |
|
|
* turns off atom/bond representation for all bonds for an object or selection |
| 414 |
|
|
*/ |
| 415 |
|
|
public void hide(String objectName) { |
| 416 |
|
|
|
| 417 |
|
|
Out.println("cmd.hide(\"everything\", "+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 418 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 419 |
|
|
|
| 420 |
|
|
} |
| 421 |
|
|
|
| 422 |
|
|
/** |
| 423 |
|
|
* turns off node representation |
| 424 |
|
|
*/ |
| 425 |
|
|
public void hideNode(String cid, int num) { |
| 426 |
|
|
|
| 427 |
|
|
String nodeName = "n."+cid+"."+num; |
| 428 |
|
|
Out.println("cmd.hide(\"everything\", \""+nodeName+"\")"); |
| 429 |
|
|
|
| 430 |
|
|
} |
| 431 |
|
|
|
| 432 |
|
|
/** |
| 433 |
|
|
* turns off edge representation |
| 434 |
|
|
*/ |
| 435 |
|
|
public void hideEdge(String i_cid, int i_num, String j_cid, int j_num) { |
| 436 |
|
|
|
| 437 |
|
|
String edgeName = "e."+i_cid+"."+i_num+"."+j_cid+"."+j_num; |
| 438 |
|
|
Out.println("cmd.hide(\"everything\", \""+edgeName+"\")"); |
| 439 |
|
|
|
| 440 |
|
|
} |
| 441 |
|
|
|
| 442 |
|
|
/** |
| 443 |
|
|
* creates a named neighbourhood selection using all atoms within distCutOff Angstrom from |
| 444 |
|
|
* all atoms of the specified residue |
| 445 |
|
|
* |
| 446 |
|
|
* Notes: |
| 447 |
|
|
* - The neighbourhood selection is named n.cid.num.N (e.g. n.A.1.N is the neighbourhood of |
| 448 |
|
|
* the 1st residue-node in chain A) |
| 449 |
|
|
* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
| 450 |
|
|
* segi is used instead of chain. |
| 451 |
|
|
*/ |
| 452 |
|
|
public void selNbrPml(String cid, int num, double distCutOff, boolean msdsd) { |
| 453 |
|
|
|
| 454 |
|
|
String nodeNbrName = "n."+cid+"."+num+".N"; |
| 455 |
|
|
String nodeSel = selectNode(cid, num, msdsd, false); |
| 456 |
|
|
|
| 457 |
|
|
Out.println("cmd.select(\""+nodeNbrName+"\", \""+nodeSel + " around "+DF.format(distCutOff)+"\")"); |
| 458 |
|
|
|
| 459 |
|
|
} |
| 460 |
|
|
|
| 461 |
|
|
/** |
| 462 |
|
|
* creates a selection called name using the atom selection of the papameter selection |
| 463 |
|
|
* |
| 464 |
|
|
* Notes: |
| 465 |
|
|
* - If pink is false, the selection display is disabled (pink stuff go away!!!!) |
| 466 |
|
|
*/ |
| 467 |
|
|
public void selPml(String name, String selection, boolean pink) { |
| 468 |
|
|
|
| 469 |
|
|
Out.println("cmd.select(\""+name+"\", \""+selection+"\")"); |
| 470 |
|
|
if (!pink) { Out.println("cmd.disable(\""+name+"\")"); }; |
| 471 |
|
|
|
| 472 |
|
|
} |
| 473 |
|
|
|
| 474 |
|
|
/** |
| 475 |
|
|
* returns an atom selection string for a node |
| 476 |
|
|
* |
| 477 |
|
|
* Notes: |
| 478 |
|
|
* - The CA boolean is used to denote whether the Ca atom should be only selected |
| 479 |
|
|
* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
| 480 |
|
|
* segi is used instead of chain. |
| 481 |
|
|
*/ |
| 482 |
|
|
public String selectNode(String cid, int num, boolean msdsd, boolean CA) { |
| 483 |
|
|
|
| 484 |
|
|
return "("+(msdsd?"segi ":"chain ")+(cid.equals("")?"\"\"":cid)+" and resi "+num+(CA?" and name CA":"")+")"; |
| 485 |
|
|
|
| 486 |
|
|
} |
| 487 |
|
|
|
| 488 |
|
|
/** |
| 489 |
|
|
* returns an atom selection string for a chain |
| 490 |
|
|
* |
| 491 |
|
|
* Notes: |
| 492 |
|
|
* - The msdsd boolean is used to denote whether msdsd is the source of the structure. In that case, |
| 493 |
|
|
* segi is used instead of chain. |
| 494 |
|
|
*/ |
| 495 |
|
|
public String selectChain(String cid, boolean msdsd) { |
| 496 |
|
|
|
| 497 |
|
|
return "("+(msdsd?"segi ":"chain ")+(cid.equals("")?"\"\"":cid)+")"; |
| 498 |
|
|
|
| 499 |
|
|
} |
| 500 |
|
|
|
| 501 |
|
|
/** |
| 502 |
|
|
* changes one of the PyMol state variable (attribute) for a specific object or selection |
| 503 |
|
|
* and sets it equal to the provided value. |
| 504 |
|
|
* |
| 505 |
|
|
* Notes: |
| 506 |
|
|
* - If the state variable is not defined in the attrs hashMap, then set returns -1 else 0. |
| 507 |
|
|
*/ |
| 508 |
|
|
public int set(String attribute, double value, String objectName) { |
| 509 |
|
|
|
| 510 |
|
|
Integer key = null; |
| 511 |
|
|
key = attrs.get(attribute); |
| 512 |
|
|
|
| 513 |
|
|
if (key == null) { return -1; } |
| 514 |
|
|
|
| 515 |
|
|
Out.println("cmd.set(\""+attribute+"\", "+DF.format(value)+", "+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 516 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 517 |
|
|
|
| 518 |
|
|
return 0; |
| 519 |
|
|
|
| 520 |
|
|
} |
| 521 |
|
|
|
| 522 |
|
|
/** |
| 523 |
|
|
* sets the color for a node |
| 524 |
|
|
*/ |
| 525 |
|
|
public void setNodeColor(String color, String nodeName) { |
| 526 |
|
|
|
| 527 |
|
|
Out.println("cmd.set(\"sphere_color\", \""+color+"\", "+(objectNameQuotes?"\""+nodeName+"\"":nodeName)+")"); |
| 528 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 529 |
|
|
|
| 530 |
|
|
} |
| 531 |
|
|
|
| 532 |
|
|
/** |
| 533 |
|
|
* sets the color for an object or selection |
| 534 |
|
|
*/ |
| 535 |
|
|
public void setColor(String color, String objectName) { |
| 536 |
|
|
|
| 537 |
|
|
Out.println("cmd.color(\""+color+"\", "+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 538 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 539 |
|
|
|
| 540 |
|
|
} |
| 541 |
|
|
|
| 542 |
|
|
/** |
| 543 |
|
|
* define a new color or rather color name based on an existing color |
| 544 |
|
|
*/ |
| 545 |
|
|
public void createColor(String colorName, String color) { |
| 546 |
|
|
|
| 547 |
|
|
Out.println("cmd.set_color(\""+colorName+"\", cmd.get_color_tuple(cmd.get_color_index(\""+color+"\")))"); |
| 548 |
|
|
|
| 549 |
|
|
} |
| 550 |
|
|
|
| 551 |
|
|
/** |
| 552 |
|
|
* define a new color providing the RGB array of doubles |
| 553 |
|
|
*/ |
| 554 |
|
|
public void createColor(String colorName, double[] rgb) { |
| 555 |
|
|
|
| 556 |
|
|
Out.println("cmd.set_color(\""+colorName+"\", ["+DF.format(rgb[0])+", "+DF.format(rgb[1])+", "+DF.format(rgb[2])+"])"); |
| 557 |
|
|
|
| 558 |
|
|
} |
| 559 |
|
|
|
| 560 |
|
|
/** |
| 561 |
|
|
* create/initialize a list |
| 562 |
|
|
*/ |
| 563 |
|
|
public void initList(String listName) { |
| 564 |
|
|
|
| 565 |
|
|
Out.println(listName+" = []"); |
| 566 |
|
|
|
| 567 |
|
|
} |
| 568 |
|
|
|
| 569 |
|
|
/** |
| 570 |
|
|
* append objects to a list |
| 571 |
|
|
*/ |
| 572 |
|
|
public void appendList(String listName, String value) { |
| 573 |
|
|
|
| 574 |
|
|
Out.println(listName+".append(\""+value+"\")"); |
| 575 |
|
|
|
| 576 |
|
|
} |
| 577 |
|
|
|
| 578 |
|
|
/** |
| 579 |
|
|
* iterate through list objects |
| 580 |
|
|
* |
| 581 |
|
|
* Notes: |
| 582 |
|
|
* - item is the name of the variable containing the object |
| 583 |
|
|
* - This is the only method that "print" instead of "println". |
| 584 |
|
|
* In this way, a method can be executed at each iteration e.g. |
| 585 |
|
|
* PyMol pml = new PyMol(out); |
| 586 |
|
|
* ... |
| 587 |
|
|
* pml.iterateList("edges", "edge"); |
| 588 |
|
|
* pml.setColor("red", "edge"); |
| 589 |
|
|
* - In the previous example, the "edge" parameter in the setColor command |
| 590 |
|
|
* is the name of tha variable holding the actual object. Therefore, it must |
| 591 |
|
|
* be evaluated and so not quoted. This is why this method disables the use |
| 592 |
|
|
* of quotes. setColor, after streaming the command, will reset the objectNameQuotes |
| 593 |
|
|
* again back to true. |
| 594 |
|
|
*/ |
| 595 |
|
|
public void iterateList(String listName, String item) { |
| 596 |
|
|
|
| 597 |
|
|
Out.print("for "+item+" in "+listName+":"); |
| 598 |
|
|
setObjectNameQuotes(false); |
| 599 |
|
|
|
| 600 |
|
|
} |
| 601 |
|
|
|
| 602 |
|
|
/** |
| 603 |
|
|
* opens a log file |
| 604 |
|
|
* |
| 605 |
|
|
* Notes: |
| 606 |
|
|
* - There are two versions. One of them opens the log file specified by its name and the directory path, while |
| 607 |
|
|
* the other just uses the filename. |
| 608 |
|
|
*/ |
| 609 |
|
|
public void openLog(String fileName, String dir) { |
| 610 |
|
|
|
| 611 |
|
|
Out.println("log_open "+dir+"/"+fileName+".pml"); |
| 612 |
|
|
|
| 613 |
|
|
} |
| 614 |
|
|
|
| 615 |
|
|
/** |
| 616 |
|
|
* opens a log file |
| 617 |
|
|
* |
| 618 |
|
|
* Notes: |
| 619 |
|
|
* - There are two versions. One of them opens the log file specified by its name and the directory path, while |
| 620 |
|
|
* the other just uses the filename. |
| 621 |
|
|
*/ |
| 622 |
|
|
public void openLog(String fileName) { |
| 623 |
|
|
|
| 624 |
|
|
Out.println("log_open "+fileName+".pml"); |
| 625 |
|
|
|
| 626 |
|
|
} |
| 627 |
|
|
|
| 628 |
|
|
/** |
| 629 |
|
|
* closes the last opened log file |
| 630 |
|
|
*/ |
| 631 |
|
|
public void closeLog() { |
| 632 |
|
|
|
| 633 |
|
|
Out.println("log_close"); |
| 634 |
|
|
|
| 635 |
|
|
} |
| 636 |
|
|
|
| 637 |
|
|
/** |
| 638 |
|
|
* writes a png format image file of the current frame |
| 639 |
|
|
* |
| 640 |
|
|
* Notes: |
| 641 |
|
|
* - rayTraced defines whether the image will be ray-traced or not |
| 642 |
|
|
* - There are two versions. One of them saves the image file as specified by its name and the directory path, |
| 643 |
|
|
* while the other just uses the filename. |
| 644 |
|
|
*/ |
| 645 |
|
|
public void saveImage(String imageName, String dir, boolean rayTraced) { |
| 646 |
|
|
|
| 647 |
|
|
if (rayTraced) { Out.println("ray"); } |
| 648 |
|
|
Out.println("png "+dir+"/"+imageName+".png"); |
| 649 |
|
|
|
| 650 |
|
|
} |
| 651 |
|
|
|
| 652 |
|
|
/** |
| 653 |
|
|
* writes a png format image file of the current frame |
| 654 |
|
|
* |
| 655 |
|
|
* Notes: |
| 656 |
|
|
* - rayTraced defines whether the image will be ray-traced or not |
| 657 |
|
|
* - There are two versions. One of them saves the image file as specified by its name and the directory path, |
| 658 |
|
|
* while the other just uses the filename. |
| 659 |
|
|
*/ |
| 660 |
|
|
public void saveImage(String imageName, boolean rayTraced) { |
| 661 |
|
|
|
| 662 |
|
|
if (rayTraced) { Out.println("ray"); } |
| 663 |
|
|
Out.println("png "+imageName+".png"); |
| 664 |
|
|
|
| 665 |
|
|
} |
| 666 |
|
|
|
| 667 |
|
|
/** |
| 668 |
|
|
* sources a pymol command script |
| 669 |
|
|
* |
| 670 |
|
|
* Notes: |
| 671 |
|
|
* - There are two versions. One of them runs the file specified by its name and the directory path, |
| 672 |
|
|
* while the other just uses the filename. |
| 673 |
|
|
*/ |
| 674 |
|
|
public void runScript(String fileName, String dir) { |
| 675 |
|
|
|
| 676 |
|
|
Out.println("@"+dir+"/"+fileName+".pml"); |
| 677 |
|
|
|
| 678 |
|
|
} |
| 679 |
|
|
|
| 680 |
|
|
/** |
| 681 |
|
|
* sources a pymol command script |
| 682 |
|
|
* |
| 683 |
|
|
* Notes: |
| 684 |
|
|
* - There are two versions. One of them runs the file specified by its name and the directory path, |
| 685 |
|
|
* while the other just uses the filename. |
| 686 |
|
|
*/ |
| 687 |
|
|
public void runScript(String fileName) { |
| 688 |
|
|
|
| 689 |
|
|
Out.println("@"+fileName+".pml"); |
| 690 |
|
|
|
| 691 |
|
|
} |
| 692 |
|
|
|
| 693 |
|
|
/** |
| 694 |
|
|
* zooms on an object or selection |
| 695 |
|
|
*/ |
| 696 |
|
|
public void zoom(String objectName) { |
| 697 |
|
|
|
| 698 |
|
|
Out.println("cmd.zoom("+(objectNameQuotes?"\""+objectName+"\"":objectName)+")"); |
| 699 |
|
|
if (!objectNameQuotes) { setObjectNameQuotes(true); } |
| 700 |
|
|
|
| 701 |
|
|
} |
| 702 |
|
|
|
| 703 |
|
|
/** |
| 704 |
|
|
* sets the background color |
| 705 |
|
|
*/ |
| 706 |
|
|
public void background(String color) { |
| 707 |
|
|
|
| 708 |
|
|
Out.println("cmd.bg_color(\""+color+"\")"); |
| 709 |
|
|
|
| 710 |
|
|
} |
| 711 |
|
|
|
| 712 |
|
|
/** |
| 713 |
|
|
* some initialization commands for structure visualization |
| 714 |
|
|
* |
| 715 |
|
|
* Notes: |
| 716 |
|
|
* - These are defined according to Ioannis' preferences |
| 717 |
|
|
*/ |
| 718 |
|
|
public void init() { |
| 719 |
|
|
|
| 720 |
|
|
Out.println("cmd.set(\"depth_cue\", 0)"); |
| 721 |
|
|
Out.println("cmd.set(\"ray_trace_fog\", 0)"); |
| 722 |
|
|
Out.println("cmd.hide()"); |
| 723 |
|
|
Out.println("cmd.show(\"cartoon\")"); |
| 724 |
|
|
Out.println("cmd.cartoon(\"automatic\")"); |
| 725 |
|
|
Out.println("cmd.set(\"cartoon_flat_sheets\", 0)"); |
| 726 |
|
|
Out.println("cmd.set(\"cartoon_fancy_helices\", 1)"); |
| 727 |
|
|
Out.println("cmd.hide(\"spheres\", \"hetatm\")"); |
| 728 |
|
|
|
| 729 |
|
|
} |
| 730 |
|
|
|
| 731 |
|
|
/** |
| 732 |
|
|
* enables (disables) the use of double quotes for strings in PyMol commands |
| 733 |
|
|
* |
| 734 |
|
|
* Notes: |
| 735 |
|
|
* - check list related methods |
| 736 |
|
|
*/ |
| 737 |
|
|
private void setObjectNameQuotes(boolean value) { |
| 738 |
|
|
|
| 739 |
|
|
this.objectNameQuotes = value; |
| 740 |
|
|
|
| 741 |
|
|
} |
| 742 |
|
|
|
| 743 |
|
|
} |
