Source of file Peptide.php

<?php

/**

 * Copyright 2018 University of Liverpool

 *

 * Licensed under the Apache License, Version 2.0 (the "License");

 * you may not use this file except in compliance with the License.

 * You may obtain a copy of the License at

 *

 * http://www.apache.org/licenses/LICENSE-2.0

 *

 * Unless required by applicable law or agreed to in writing, software

 * distributed under the License is distributed on an "AS IS" BASIS,

 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

 * See the License for the specific language governing permissions and

 * limitations under the License.

 */

namespace pgb_liv\php_ms\Core;

use pgb_liv\php_ms\Constant\ChemicalConstants;

use pgb_liv\php_ms\Constant\PhysicalConstants;

/**

 * A peptide object that encapsulates a modifiable sequence and provides additional properties

 *

 * @author Andrew Collins

 */

class Peptide implements ModifiableSequenceInterface

{

    use ModifiableSequenceTrait, ProteinTrait;

    const AMINO_ACID_X_MASS = 0;

    const AMINO_ACID_B_MASS = 0;

    const AMINO_ACID_Z_MASS = 0;

    /**

     *

     * @deprecated Use ChemicalConstants

     * @var float

     */

    const HYDROGEN_MASS = ChemicalConstants::HYDROGEN_MASS;

    /**

     *

     * @deprecated Use ChemicalConstants

     * @var float

     */

    const OXYGEN_MASS = ChemicalConstants::OXYGEN_MASS;

    /**

     *

     * @deprecated Use ChemicalConstants

     * @var float

     */

    const NITROGEN_MASS = ChemicalConstants::NITROGEN_MASS;

    /**

     *

     * @deprecated Use PhysicalConstants

     * @var float

     */

    const PROTON_MASS = PhysicalConstants::PROTON_MASS;

    /**

     *

     * @deprecated Use ChemicalConstants::HYDROGEN_MASS

     * @var float

     */

    const N_TERM_MASS = 1.007875;

    /**

     *

     * @deprecated Use ChemicalConstants::HYDROGEN_MASS+ChemicalConstants::OXYGEN_MASS

     * @var float

     */

    const C_TERM_MASS = 17.00278;

    private $missedCleavageCount;

    public function __construct($sequence = null)

    {

        if (! is_null($sequence)) {

            $this->setSequence($sequence);

        }

    }

    public function setMissedCleavageCount($count)

    {

        if (! is_int($count)) {

            throw new \InvalidArgumentException(

                'Argument 1 must be of type integer. Argument type is ' . gettype($count));

        }

        $this->missedCleavageCount = $count;

    }

    public function getMissedCleavageCount()

    {

        return $this->missedCleavageCount;

    }

    public function __clone()

    {

        // Create new instances of objects

        $oldMods = $this->modifications;

        $this->modifications = array();

        foreach ($oldMods as $modification) {

            $this->modifications[] = clone $modification;

        }

    }

    /**

     * Gets the molecular formula for this peptide string.

     *

     * @return string Molecular formula

     */

    public function getMolecularFormula()

    {

        $acids = str_split($this->getSequence(), 1);

        $frequency = array(

            'C' => 0,

            'H' => 0,

            'N' => 0,

            'O' => 0,

            'S' => 0

        );

        foreach ($acids as $acid) {

            $composition = AminoAcidComposition::getFormula($acid);

            $matches = array();

            preg_match_all('/([A-Z][a-z]?)([0-9]*)/', $composition, $matches, PREG_SET_ORDER);

            foreach ($matches as $match) {

                $chemical = $match[1];

                $count = $match[2];

                if (! isset($frequency[$chemical])) {

                    $frequency[$chemical] = 0;

                }

                $frequency[$chemical] += $count == '' ? 1 : $count;

            }

        }

        // Remove hydrogen and oxygen from C-TERM

        $frequency['H'] -= count($acids) - 1;

        $frequency['O'] -= count($acids) - 1;

        // Remove hydrogen from N-TERM.

        $frequency['H'] -= count($acids) - 1;

        $formula = '';

        foreach ($frequency as $chemical => $count) {

            if ($count == 0) {

                continue;

            }

            $formula .= $chemical;

            if ($count > 1) {

                $formula .= $count;

            }

        }

        return $formula;

    }

}